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Plant genetic resources in India: management and utilization

Plant genetic resources (PGR) are the foundation of agriculture as well as food and nutritional security. The ICAR-NBPGR is the nodal institution at national level for management of PGR in India under the umbrella of Indian Council of Agricultural Research (ICAR), New Delhi. India being one of the gene-rich countries faces a unique challenge of protecting its natural heritage while evolving mutually beneficial strategies for germplasm exchange with other countries. The Bureaus activities include PGR exploration, collection, exchange, characterization, evaluation, conservation and documentation. It also has the responsibility to carry out quarantine of all imported PGR including transgenics meant for research purposes. The multifarious activities are carried out from ICAR-NBPGR headquarters and its 10 regional stations located in different agro-climatic zones of India. It has linkages with international organizations of the Consultative Group on International Agricultural Research (CGIAR) and national crop-based institutes to accomplish its mandated activities. NBPGR collects and acquires germplasm from various sources, conserves it in the Genebank, characterizes and evaluates it for different traits and provides ready material for breeders to develop varieties for farmers. ICAR-NBPGR encompasses the National Genebank Network and at present, the National Genebank conserves more than 0.40 million accessions. NBPGR works in service-mode for effective utilization of PGR in crop improvement programmes which depends mainly on its systematic characterization and evaluation, and identification of potentially useful germplasm. NBPGR is responsible for identifying trait-specific pre-adapted climate resilient genotypes, promising material with disease resistance and quality traits which the breeders use for various crop improvement programmes. The system has contributed immensely towards safeguarding the indigenous and introducing useful exotic PGR for enhancing the agricultural production. Presently, our focus is on characterization of ex situ conserved germplasm and detailed evaluation of prioritized crops for enhanced utilization; assessment of impact of on-farm conservation practices on genetic diversity; genome-wide association mapping for identification of novel genes and alleles for enhanced utilization of PGR; identification and deployment of germplasm/landraces using climate analog data; validation of trait-specific introduced germplasm for enhanced utilization. Key words: plant genetic resources; gene banks; wild relatives; biotic and abiotic stresses; marker-assisted selection.

Introduction
Plant genetic resources (PGR) are one of essential components of agro-biodiversity and defined as the genetic material of plants having value as a resource for present and future generations. PGR hold the key to the very foundation of agriculture as well as food and nutritional security for the world. Agricultural biodiversity, agri-or agro-biodiversity (a subset of biodiversity) is defined as 'all crops and livestocks, their wild relatives, and all interacting species of pollinators, symbionts, pests, parasites, predators and competitors' (Qualset et al., 1995). Indian subcontinent has a rich and varied heritage of biodiversity, encompassing a wide spectrum of habitats from tropical rainforests to alpine vegetation and from temperate forests to coastal wetlands. It is one of the eight centres of origin (Vavilov, 1951) and is one of the 12 mega gene centres of the world. It possesses 11.9 % of world flora, and about 33 % of the country's recorded flora are endemic to the region and are concentrated mainly in the North-East, Western Ghats, North West Himalayas and the Andaman and Nicobar islands. Of the 49,219 higher plant species, 5,725 are endemic and belong to 141 genera under 47 families (Nayar, 1980). Of these 3,500 are found in the Himalayas and adjoining regions and 1,600 in the Western Ghats alone (Arora, 1991). The concept of biodiversity hotspots was originated by Dr. Norman Myers in two articles in "The Environmentalist" (1988), revised after thorough analysis by Myers and others in "Hotspots: Earth's biologically Richest and Most Endangered Terrestrial Ecoregions". The hotspots idea was also promoted by Russell Mittermeier in the popular book "Hotspots revisited". Around the world, 34 biodiversity hotspots exists as of today. These sites support nearly 60 % of the world's plant, bird, mammal, reptile, and amphibian species, with a very high share of endemic species (Myers et al., 2000).
From centuries, tribal or traditional farming communities have continuously adapted and shapened the dimensions of rich genetic material available with them. These resources or traditional varieties or landrace populations often bear specific traits -early or late maturing, adaptability to a particular soil type, uses and usually have local names which has enabled them to survive so long under various biotic and abiotic stresses in the centers of diversity along with wild progenitors of crop plants, wild and weedy relatives. Besides these resources, potential domesticates (also called wild economic species) are involved in the PGR spectrum; they are those wild species, which are not yet domesticated but are extensively used. Some of them grow widely, though genetically and culturally in a near wild state. With richness of plant genetic resources, the tribal regions have therefore been identified as "Hot Spots" of agri-biodiversty. However, they are different from the biodiversity hot-spots (as per definition of Myers et al., 2000) which include all entire endemic biodiversity as a priority for defining hot-spots of a region.
During the process of crop evolution crops originated in its centre of origin have changed from the wild progenitors in morphological, physiological and agronomic traits to newer types through selection for desired traits. In this whole process, agriculture (broadly the process of rearing plants and animals, wild or tamed), cultivation (physical activities which are relevant to and associated with agriculture) and domestication (process of genetic shift in domesticated population to adapt them to better/changed or artificial environment, created by cultivation conditions) have shapened them for appropriate PGR. PGRs are exchanged and searched continuously for specific traits to improve crops in terms of yield and nutritional value, and their interdependence plays a very important role in international collection and exchange of germplasm. Every nation is concerned with acquisition of diverse and superior germplasm for conservation and utilization.
Over the years, India has developed sound and scientific management regimes for ex situ conservation and access to its genetic resources (Dhillon, Saxena, 2003). Groups of institutions, scientific societies, non-governmental organizations are Plant genetic resources in India: management and utilization addressing the task with ICAR-NBPGR, New Delhi, as the nodal agency for its coordination. It aims at efficient management of plant genetic resources by providing convenience of access to the various crop improvement programmes. It also encompasses the National Genebank Network. At present, the genebank holds more than 4.4 lakhs accessions. The Cryobank Facility in the National Genebank has accessions of varied germplasm of orthodox, intermediate and recalcitrant seed species and also of pollen samples. The in vitro genebank conserves various priority crops which are maintained under short-to medium-term storage periods. These include tuberous and bulbous crops, tropical fruits species, spices and industrial crops, medicinal and aromatic plants species.
Centre of origin and diversity of crop plants are concepts relating to the patterns of distribution and build-up in regions and habitats, consequent to use and domestication by man in areas representing independent agricultural systems and separated by major geographical barriers. Various terms have been used to designate these 'geobotanical' diversity patterns in crop plants viz. primary and secondary centres of diversity, gene centres, cradles/subcradles of agriculture, megacentres, regions (Vavilov, 1926;Zhukovsky, 1968), non-centres, micro centres (Harlan, 1975), cradles of angiosperm diversity (Takhtajan, 1969). However, within centres of diversity, geobotanical patterns of variation, add a practical connotation to the use of these concepts in PGR. The significant point, as stated above is that centres of diversity are the consequence of continuing processes of evolution and domestication, and hence subject to change. The concept of 'ecological passports' in different sites where different crops show parallelism in characters by Vavilov, form the basis for understanding the diversity within the crop species, and in relation to the crop genepool (Harlan, de Wet, 1971).

PGR conservation
The National Bureau of Plant Genetic Resources (ICAR-NBPGR) was established by the Indian Council of Agricultural Research (ICAR) in 1976 with its headquarters at New Delhi. The chronology of events leading to the present day ICAR-NBPGR dates back to 1905 when Botany Division was established under the then Imperial Agricultural Research Institute. ICAR-NBPGR has been given the mandate to act as a nodal institute at the national level for acquisition and management of indigenous and exotic PGR for agriculture, and to carry out related research and human resources development for sustainable growth of agriculture. The Bureau is also vested with the authority to issue Import Permit and Phytosanitary Certificate and conduct quarantine checks in seed material and vegetative propagules (including transgenic material) introduced from abroad or exported for research purposes. Besides having a 40 ha experimental farm at Issapur village (about 45 km west of Pusa Campus), the Bureau has a strong national network comprising Regional Stations/Base Centers and ICAR Institutes/SAUs that provide access to representative agro-ecological situations in the country.
The major components of the National Genebank include the seed genebank, field genebank, cryo-bank and the in vitro genebank. The focus of seed genebank of NGB is long term conservation of orthodox seeds. The basic parameters that are assessed for conservation are: (i) Uniqueness of the accession. Redundancy is a major issue in all genebanks and best efforts are made to avoid duplication of accessions. (ii) Seed quality. The global genebank standards recommends a minimum of 2000 seeds in self-pollinated crops and 4000 seeds in cross pollinated crops. In wild germplasm accessions, the minimum number has been relaxed to 500 seeds. (iii) Seed viability. A minimum viability of 85 % is essential for seed samples. However in those cases where the Indian Minimum Seed Certification Standards have approved a lower level of standard germination, the viability requirements are accordingly modified in gene bank also. (iv) Seed health. Pest free conservation is a priority at NGB.
There is a strong collaboration between the Division of Germplasm Conservation and Division of Plant Quarantine, wherein all accessions are tested for any form of pest infestation prior to their processing. (v) Availability of passport information. The utilization of the conserved accessions can be facilitated only if all relevant passport information is available in the database. Hence, only those accessions having basic information on parameters like biological status, collection details if acquired through exploration, pedigree details if it's a breeding line/ genetic stock or cultivar and any other unique trait if applicable, is accepted for long term conservation.
The qualified accessions are then subjected to drying, which is the most crucial step in genebank processing. A walk-indrying chamber functioning at 15 % RH and 15 °C is used for the drying purpose. For species with hard seed coats and which require longer drying duration are shifted to batch dryers, after preliminary drying in chamber. The standard moisture testing method used in gene banks is the hot-air oven method and the procedure recommended for each crop by the International Seed Testing Association is duly followed. Once the desired moisture is achieved (as mentioned below), the seeds are packed in aluminum foil packets. They have the advantage that they can be resealed and also occupy less space than other containers.
Conservation of genetic resources is carried out through two types of collections: (a) Collection of seed samples for long term conservation, which is known as base collection. Base collections are main tained at -18 to -20 °C, to ensure seed viability for maximum possible time period. The moisture content of seed to be stored as base collections should be between 3 and 7 % depending on the species. (b) Collection of seed samples for immediate use, termed as active collection. Active collection are maintained in conditions that ensure at least 65 % viability for 10-20 years. The moisture content of seeds to be stored as active collections should be between 3 and 8 % for seeds having poor storability and between 7 and 11 % for seeds having good storability, depending on the temperature used for storage. These collections are conserved in different types of storage facilities. Depending on the duration of storage, three basic types of storages are recognized: (a) Short term storage. The period for short term storage of seeds is from one year upto 18 months. It requires a cool 309 генетические ресурсы и биоколлекции / genetics resources and biocollections and dry atmosphere (20-22 °C and 45-50 % RH) where the seeds can be conveniently stored for one to two years without much loss in their viability. (b) Medium term storage. The active collection, which are generally larger than those meant for base collection are conserved in the medium term storage. The accessions are for regular distribution and therefore the time period for storage is not more than 5 yrs. The active collections are stored at temperatures ranging from 0-10 °C and relative humidity of 20-30 %. (c) Long term storage. This is the storage facility for base collection, where the seeds that meet all the above mentioned criteria for NGB conservation are maintained at -18 to -20 °C.
The ex situ genebank at NBPGR comprises 12 long term modules holding the base collection. The active collections are distributed in 22 medium term modules maintained at 4 °C for storing germplasm at active sites. The genebank is currently being upgraded with new infrastructure and all efforts are being made to bring the NGB to global standards.

Crop wild relatives
Crop wild relatives (CWR) are wild taxa closely related to crop plants, including wild progenitors and/or wild forms of crops. Maxted et al. (2006) defined a CWR as a wild plant taxon that has an indirect use derived from its close genetic relationship to a crop. The closer the species related, the more the possibility/practicality to get their traits incorporated. They form an important source of useful traits such as agronomic, quality, biotic and abiotic stresses, which are identified as critical component for food security and environmental sustainability in the 21st century. CWRs are often associated with disturbed habitats and neither these habitats are offered adequate protection by ecosystem conservation agencies (Maxted, Kell, 2009) nor their diversity properly conserved ex situ. CWR diversity, like that for many species, is at a declining stage; which is associated with the loss of genetic diversity (Hopkins, Maxted, 2010). This necessitates the need to establish CWR inventories which is also an indispensable tool for exploration, surveys and collection of CWR. Therefore, the need for novel genes for developing climate resilient varieties, increasing pressure on wild species populations and habitats and the present meagre ex situ collections, all accentuate the importance of locating and collecting germplasm of wild relatives. Arora and Nayar (1984) reported the occurrence of over 320 wild relatives of crops (51 cereals and millets; 31 grain legumes; 12 oilseeds; 24 fibre plants; 27 spices and condiments; 109 of fruits, 54 of vegetables and 27 of others) in India. The NHCP of ICAR-NBPGR serves as a nodal point for confirming the botanical identity of crop wild relative's taxa. With the identification of diversity-rich spots, availability of location details of intended taxa, India is moving forward in the systematic collecting of CWR from diverse habitats for conservation and sustainable use. Only one third of shortlisted taxa have been assembled by ICAR-NBPGR; among them more than half the taxa with <10 accessions. Analysis of gaps in collection in a scientific manner (keeping in view the conserved material, actual variability/diversity present in habitats, best utilization of GIS tools) through a mission-mode approach is currently being employed the way. In addition, detailed studies on habitat ecology, floral biology and breeding system, crossability (with crop), seed dormancy and storage behaviour of species would enable their meaningful conservation and sustainable utilization. Crossability studies aids in realization of gene-pool concept in crops, and knowing the closer relatives (even from different genera). Ensuring correct taxonomic identity, safe conservation and supply of germplasm to crop-based institutes would strengthen the pre-breeding/base-broadening/ gene-pyramiding activities through designing suitable long term multi-parental breeding programmes. All these indicate the need for trained expertise in classical subjects like taxonomy and cytogenetics, with long-term commitment. Also it is imperative to undertake studies on assessing the gene flow between wild (progenitors and naturally crossable relatives) and cultivated taxa in the wake of concerns of biosafety. All taxonomic related species may not have an equal potential as a gene donor to crops (Maxted et al., 2007). Prioritization of CWRs for management preferably on genetic relationship is important for optimization of resources. Economic importance of the crop, crossability relationship, threat and rarity of the taxa and habitat, conservation status in the genebank are the other criteria for prioritization.
Conservation of niche-specific taxa needs attention as they are often rare and endemic. Predicted extinction of species is more likely to affect RET taxa. Various steps involved in the effective management of CWRs such as development of an inventory, prioritization of CWRs taxa and habitats, ecogeographic and genetic analysis of CWRs, threat analysis and genetic erosion assessment of individual CWRs taxa, gap analysis and fixing conservation targets, development of ex situ/in situ strategies, leading to conservation and finally utilization and sustainable availability for crop improvement (Maxted et al., 2007) are all important in the Indian context also. Constituting specialized group in the country devoted to these aspects of CWRs may be a feasible option.
The above studies would facilitate a national-level mapping of CWR distribution after incorporating additional information from eco-geographic studies, which will help in the identification of CWR hotspots, which can be matched with existing protected area network in the country, thereby areas and taxa demanding conservation can be identified (Maxted et al., 2011). Strong networking among all the stakeholders working on characterization, evaluation and conservation is the need of the hour, as it is difficult for a single institute to collect, conserve and evaluate all the target species due to paucity of land, resources and expertise.

PGR characterization and evaluation
The utilization of PGR in crop improvement programs rests on identification of promising accessions. The collected or introduced germplasm is characterized and evaluated to assess its potential, by recording data on agronomic traits such as yield, quality, and tolerance to biotic and abiotic stresses. The germplasm is also evaluated for new traits using molecular tools to identify the genes to develop new varieties as per requirement of the farmers. Approximately 10,000 accessions are characterized/evaluated every year at ICAR-NBPGR and its regional stations. Till date, more than 2.35 lakhs accessions of different agri-horticultural crops have been characterized and evaluated and passport data is available.
Plant genetic resources in India: management and utilization Core sets have been developed to facilitate the enhanced utilization of germplasm. Genetic diversity in large collection has been determined using morphological and DNA fingerprinting markers. Mega programme on characterization and evaluation under the National Initiative for Climate Resilient Agriculture (NICRA) executed in collaboration with SAUs for 21,822 accessions of wheat and 18,775 accessions of chickpea. Generation, validation and utilization of genomic resources is one of the major objective of ICAR-NBPGR. These resources are utilized for value addition to the plant germplasm resources harboured in the genebank and for generating molecular profiles varieties of agri-horticultural crops. The advent of next generation sequencing with improved chemistries and lower input costs have resulted in high throughput data that could be mined for generating SSR and SNP markers.

Application of genomic tools for PGR utilization and pre-breeding
One of the major objectives of ICAR-NBPGR is to supply germplasm, collected indigenously or from exotic sources, to the breeders and other researchers in the country. These germplasm accessions have helped to develop improved varieties in various national programmes. Till date more than 5 lakh samples were supplied for utilization to various stakeholders for use in crop improvement programmes. Ever-increasing significance of conservation and utilization of PGR on one hand and advancements in computer technology for digitization and management of data on the other have catapulted PGR Informatics into limelight.
Genomics has provided various technologies including se quencing and re-sequencing platforms, availability of genome sequences as references, high-throughput genotyping platforms, SNP arrays, genome editing tools, etc. These technologies are shortly described here.
Genome sequencing. The inexpensive sequencing and resequencing technologies are the major driving forces behind increased number of assembled plant genomes of different crops including wild relatives. A single reference genome does not represent the total diversity within a species, hence, resequencing of cultivars, landraces and wild accessions is required to harness the total genetic variation and to identify the superior alleles for the target traits. Genome information availability has generated many next-generation sequencing-based platforms for allele mining and candidate genes identification. Next generation sequencing and whole-genome resequencing is required for discovery, validation, and assessment of diagnostic markers in different crops and it provides genome-wide markers. The draft genome sequences are now available in a number of crops through different genome sequencing consortia for rice International Rice Genome Sequencing Project (IRGSP 2005), pigeonpea (Varshney et al., 2014), chickpea (Varshney et al., 2018), wheat International Wheat Genome Sequencing Consortium (IWGSC 2018), etc.
The genome sequencing using NGS has resulted in large collections of functional markers which enhance gene assisted breeding, reducing the possibility of losing the desirable trait variation due to recombination. Sequencing and resequencing of populations developed in crossing programs or of natural population (germplasm) along with high-throughput phenotyping helps in identification and linking of variations in gene sequences to their phenotypes. Kim et al. (2016) reported the whole-genome resequencing of the 137 rice mini core collection, potentially representing 25,604 rice germplasms in the Korean genebank of the Rural Development Administration (RDA) based on the Nipponbare reference genome, and resequencing data yielded more than 15 million SNPs and 1.3 million INDELs. Further study of this rice mini core with phylogenetic and population analysis using 2,046,529 highquality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that the SNPs capture evolutionary signatures present in rice subpopulations. Similarly, a population structure analysis of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) was carried out based on the 201,817 SNPs obtained from sequencing, divided accessions in nine subpopulations . However, hierarchical clustering and principal component analysis showed intermingle of spring type accessions with semi-winter types pointing out towards frequent hybridization between spring and semi-winter ecotypes in China.
Sequence-based markers associated with rare elite alleles facilitate positional cloning and prebreeding. In case of PGR including landraces and wild relatives, screening of collection to be used for genomic analysis can be done based on passport data (collection site, specific traits, etc.) in combination with evaluation data. Sequencing based approaches provide opportunity to identify novel variations for a large number of genes through genotype-phenotype associations. Resequencing of large number of genotypes helps in determining process of origin, domestication, population structure and identifies lines with deleterious mutations in the genomes that can be eliminated to minimize the genetic load in the crop species as observed in case of maize (Bevan et al., 2017). NGS technologies together with precise phenotyping have been used for identification of marker trait associations in several crops, for example, rare wheat haplotypes effective against abiotic or biotic stresses were developed through introgression of useful and novel stress and quality traits' alleles to lines derived from crosses of exotics with CIMMYT's best elite germplasm under CIMMYT's Seeds of Discovery (SeeD) initiative . Singh et al. (2018) used next-generation sequencing, together with multi-environment phenotyping to study the contribution of exotic genomes to 984 three-waycrossderived (exotic/elite1//elite2) pre-breeding lines (PBLs) for accelerating grain yield gains using exotic wheat genetic resources.
Molecular markers and genetic maps. Recent developments in genome sequencing and or resequencing has resulted in development of large number of molecular markers in different crops. Availability of molecular markers linked to specific traits enhances pre-breeding efficiency and effectiveness through marker assisted selection (MAS). Molecular markers that are linked to the genes of a desired trait known as diagnostic markers can be indirectly used for selection of target traits (Xu, Crouch, 2008). A major earlier success for crop breeding using genomic markers was the marker-assisted introgression of the ethylene response factor, known as Submergence 1A (Sub1A) gene, for submergence tolerance into high-yielding commercial rice varieties which acts by limiting shoot elongation during the inundation period (Bailey-Serres  Riar et al. (2012) used polymorphic D-genomespecific SSR markers for analysing the cosegregation of the 5DS anchored markers (Xcfd18, Xcfd78, Xfd81 and Xcfd189) with the rust resistance in an F 2 population, and mapped the leaf rust resistance gene (LrAC, a novel homoeoallele of an orthologue Lr57) on the short arm of wheat chromosome 5D. Vikal et al. (2014) used SSR markers for pyramiding of candidate genes for xa8, the resistance gene against Bacterial blight disease in elite rice varieties. Ellur et al. (2016) incorporated a novel Bacterial blight resistance gene Xa38 in variety PB1121 from donor parent PR114-Xa38 using a modified markerassisted backcross breeding (MABB) scheme.
Genomics has provided powerful approaches to understand interaction between many genes and complex signalling pathways in case of polygenic traits like resistance to abiotic and biotic stresses. In rice breeding, high-density genome maps are being effectively used in background selection integrated with foreground selection of bacterial blight resistance (xa13 and Xa21 genes), amylose content (waxy gene) and fertility restorer gene in order to identify superior lines with maximum recovery of Basmati rice genome along with the quality traits and minimum non-targeted genomic introgressions of the donor chromosomes (Gopalakrishnan et al., 2008). Quantitative trait loci (QTL) analysis of the genome linked to quantitative phenotypic traits, has yielded climate goverened QTL in diverse crop species (Scheben et al., 2016). Rodrigues et al. (2017) determined protein content and genetic divergence of twenty-nine soybean genotypes using 39 microsatellite markers from QTL regions of the trait grain protein content for plant breeding purposes. The pairs of genotypes with greater genetic distances and protein contents were selected to produce populations with higher means and genetic variances and greater gains with selection.
Genome wide association studies (GWAS) could overcome several constraints of conventional linkage mapping and provide a powerful complementary strategy for dissecting complex traits. GWAS make use of past recombinations in diverse association panels to identify genes linked to phenotypic traits at higher resolution than QTL analysis. GWAS has become a powerful tool for QTL mapping in plants because a broad range of genetic resources may be accessed for marker trait association without any limitation on marker availability. Different approaches used for GWAS include: (a) SNP marker arrays or SNP chips approach. Discovery and tagging of new genes using GWAS or QTL analysis have now become much easier. The availability of high-density SNP marker arrays has opened a way for cost effective GWAS using natural populations. Wang et al. (2017) developed a high-throughput NJAU 355K SoySNP array and conducted GWAS in 367 soybean accessions (including 105 wild and 262 cultivated) across multiple environments and reported a strong linkage disequilibrium region on chromosome 20 significantly correlated with seed weight. Zhao et al. (2019) carried out meta-analysis GWAS using 775 tomato accessions (including wild accessions) and 2,316,117 SNPs from three GWAS panels and discovered 305 significant associations for the contents of sugars, acids, amino acids, and flavor related volatiles. (b) Genotyping by sequencing (GBS) approach. As the cost of sequencing is continuously declining, GBS also known as next generation genotyping method, is becoming more common for discovering novel plant SNPs and used them for GWAS studies (Arruda et al., 2016). Kim et al. (2016) reported the whole-genome resequencing of 137 rice mini core collection and conducted genome wide association studies on four agriculturally important traits including 'grain pericarp colour', 'amylose content', 'protein content', and 'panicle number' and identify some novel alleles. Similarly, Arora et al. (2017) genetically characterized 177 A. tauschii accessions using GBS to study the variation for grain size using genome-wide association study. Genomic selection. Genomics assisted breeding approach known as genomic selection (GS) is a better approach which simultaneously uses large genotypic data (genome wide) (exceeding phenotypic data), phenotypic data and modelling using statistical tools to predict the genomic estimated breeding values (GEBVs) for each individual (Meuwissen et al., 2001;Crossa et al., 2017). In genomic se lection, a statistical model is generated using a representative population of the breeding population known as training population. This model is subsequently used to calculate the allelic effects of all marker loci, i. e. genomic assisted breeding values without having phenotypic data and these values can be used for preselection of trait-specific genotypes (Heffner et al., 2011). Xu et al. (2012) and Spindel et al. (2016) highlighted that coupling of genome wide data with genomic selection offered great specificity and predictability which can be used to accelerate prebreeding. Using GS, complex traits can be improved rapidly through generation of reliable phenotypes by shortening the selection cycle. GS application in pasture grass Lolium perenne resulted in four-year reduction in the breeding cycle (Lin et al., 2016). In genomic selections, genomic estimated and true breeding values were found to be closely correlated, even for polygenic traits with low heritability (Jia, Jannink, 2012). GS can facilitate selection of complex traits, e. g., grain yield (Saint  and tolerance to abiotic and biotic stress. In genomic selection, genetic diversity specific to the population or family (species) of interest is captured through markers developed through GBS which minimized the ascertainment bias. GS is superior in respect of fixing all the genetic variation and to select individuals with higher Genomic Breeding Value (GEBV) without any phenotyping. In case of polyploid species, polysomic inheritance and possibility of double reduction requires specific consideration while using for genomic selection.
Genome editing. Recent advancements in genomics have also made feasible the editing of genomes and their use in crop improvement programs. Pre-breeding involves genetic transformation through recombination and genome editing (GE) tools provide an alternative. To replace conventional genetic engineering, a number of genome editing technologies have been developed during last two decades including antisense, RNA interference (RNAi), virus-induced gene silencing (VIGS), oligonucleotide directed mutagenesis (ODM), zinc finger nuclease (ZFN), transcription activator-like effects nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) (Sauer et al., 2015). These genome editing technologies can accelerate pre-breeding programs through beneficial knockout mutations, Plant genetic resources in India: management and utilization e. g. identification of genes for disease resistance or suppressing of unwanted traits linked with desired traits in wild species, as products of these technologies are not considered a genetically modified organism (GMO) (Huang et al., 2016). Most of these genome editing tools except RNAi, act by inserting, removing or replacing specific regions of genome with the help of specific nucleases known as "molecular scissors" (Esvelt, Wang, 2014).
GE approaches can be used to modify genes with defined quantitative trait nucleotides (QTNs) that cause a sizeable phenotypic effect. Further, GE tools can be used for broadening the allele pool through generating targeted variations useful for genomic selection . Using GE tools, desired traits can be physically linked to ensure their co-segregation known as "trait stacking" (Urnov et al., 2010). For example, ZFN-assisted gene targeting helped insertion of heritably insert herbicide-resistant genes (SuRA/SuRB and PAT) in the Z. mays genome (Shukla et al., 2009). Zhang et al. (2016) recently used CRISPR/Cas9 system for production of homozygous transgene free wheat mutants. Jenko et al. (2015) showed that GE and GS, both can be combined and referred as the promotion of alleles by genome editing (PAGE) which also has a great potential for pre-breeding. Recently, Gupta (2019) reviewed the latest modification of CRISPR/Cas9 system, a base editing technology applicable to DNA as well as RNA, has revolutionized GE and demonstrated in several crops including rice, maize, wheat, etc. will be highly useful for base broadening to be used for genomic selection and relating phenotypes to genes through mutant development, particularly in primitive landraces and wild species and will provide a new direction to pre-breeding programmes.

PGR Informatics
PGR Informatics is the management (creation, storage, retrieval and presentation) and analyses (discovery, exploration and extraction) of diverse information (facts, figures, statistics, knowledge and news). PGR Informatics has assumed significance because of the following factors: (i) increased awareness about PGRFA, (ii) various international agreements (CBD, GPA, ITPGRFA) coming into force, (iii) availability of information in text, images, maps, videos, etc., (iv) technologies to record, link and archive such diverse types of information, (v) growing power (and falling costs) of computers and internet to facilitate access and retrieval. Fundamental merit of an organized digital information system is that it provides fair and just opportunity for all to access. On-line portals, as a consequence of PGR Informatics, enable non-exclusive access to PGR information to a large number of users involved in overlapping research areas on PGR management. Typically information is collected on details of multitude of passport data including taxonomy, biogeography, and ethnobotany of the germplasm acquisitions (domestic collections and exotic introductions), their seed health, multiplication for supply and conservation, regeneration, experimental data on characterization and evaluation leading to utilization. In addition to field data, it also includes biochemical and genomic data as well as publications. Once the information is digitized and stored, computer technologies allow management and analysis irrespective of the scale and types of data leading to better visualization and predictions.
The need for countries to develop, maintain and exchange information "from all publicly available sources, relevant to conservation and sustainable use of biological diversity" including "results of technical, scientific and socio-economic research" has been recognized in the Convention on Biological Diversity (CBD, Articles 7d, 17), and the Global Plan of Action (GPA, priority activities 17 and 18). Information of this nature is imperative for planning and implementing activities; sustainable use and sharing of benefits accrued from its use. Global assessment indicates that many of the world's PGR are insufficiently and poorly documented. The passport information and characterization and evaluation data on genebank accessions conserved in genebanks are either lacking or poorly recorded or scattered at different places, such as passport data sheets, reports of collection and exploration missions, crop catalogues, published articles, etc. In addition, there exist informal or non-coded knowledge held by traditional farmers and indigenous people.

Recent advances in PGR Informatics in India
NBPGR has been striving to establish PGR information set up since 2002 (Archak, Agrawal, 2012). Development of mobile apps in PGR Informatics facilitates enhanced access to PGR information which in turn could lead to enhanced utilization. NBPGR has developed two mobile apps "Genebank" and "PGR Map". Both the apps are first of their kind for any genebank in the world. The apps have been developed for both Android and iOS. No other ICAR app is available for iPhone. Licenses were purchased and the apps have been hosted on Google Play and App Store.
Genebank app provides a dashboard view of indigenous collections (state-wise), exotic collections (country-wise), addition of accessions to genebank, etc. The app also helps generate routine genebank reports. The app uses databases live on the backend and hence always gives updated information.
PGR Map app offers three benefits: "What's around me" helps user to obtain quickly the accessions that have been collected and conserved in the genebank from a particular location in India where the user is located at the moment; "Search the map" helps user to list the accessions that have been collected and conserved in the genebank from any selected location in India; "Search for species" helps user to map the collection sites of a crop species.

Perspectives
All countries are interdependent for their PGR requirements and cannot acquire and conserve resources to satisfy all their needs. There is a need to collaborate at local, regional and international levels for the acquisition and conservation of the germplasm. It is also imperative to obey the quarantine and biosafety rules for the safe movement of germplasm. Priority collection trips are required to identify areas which are not sufficiently covered so far and a repeated visits are required to be made in areas that showed diversity in the past. New tools of geographical information system (GIS) and remote sensing need to be deployed to supplement the existing ground data in PGR programmes to exploit agro-biodiversity particularly in difficult/inaccessible areas.
There is a need to adopt complementary conservation strategies involving both in situ and ex situ approaches. For in situ conservation due attention is required to be given to genetically rich hotspots including tribal belts and to strengthen and expand the network of germplasm conservation by including all the stakeholders, including the communities. Characterization and evaluation are essential to promote the utilization of materials. These tasks require substantial inputs and a decentralized evaluation network. There is a need to modify the descriptors for evaluation accordingly, and make the search for the desired characteristics in the database as quick and efficient as possible. The core collection concept is more structured and efficient approach to identify limited sets of diverse germplasm and utilise the same more effectively. Pre-breeding is needed to incorporate new kinds of pest resistance, to bring in new levels of productivity and stability of performance, and to provide quality traits for food and feed products. Awareness generation of the people at various levels (policy makers, scientific, administration, farmers, etc.) about the value of PGR wealth, its protection and conservation is essential. In addition the interface among different stakeholders is likely to bring out new useful PGR management alternatives.


provenance: AgriculturalAndFoodSciences,2019-2020-Agricultural And Food Sciences-2020.jsonl.gz.gz

text:
Hand-held mechanical device improves thinning efficiency of peach trees

The objective of this study was to evaluate the effect of mechanical-manual thinning (MmT) at different developmental stages in the thinning efficiency and productive performance of ‘Sensação’ peach trees. The experiment was performed during the 2013 and 2014 growing seasons, in a commercial orchard located in Morro Redondo (RS), Brazil. Plant material consisted of 7-year-old peach trees grafted on Capdeboscq rootstock and trained as an open-vase system. The experiment was arranged as a randomized block design, with five three-trees replications. In order to reduce the effect of personal experience, the treatments and measurements were applied by the same person in a set of replications throughout the experiment. Treatments consisted of: control I [without thinning (WT)]; control II [hand thinning (HT) 40 days after full bloom (40 DAFB)]; MmT at full bloom (FB): 50% of open flowers; MmT at the end of bloom (EB): 80-100% of open flowers; MmT at petal fall (PF); and MmT at the green fruit (GF) stage (fruit with ~1 cm of diameter). The MmT was performed using a hand-held portable device. The parameters assessed were: percentage of thinning, fruit set, thinning time, work economy, production per tree, fruit mass, estimated yield and fruit size distribution. The use of the MmT at the stages tested reduces thinning time of ‘Sensação’ peach trees, resulting in labor saving, as well as increases the percentage of fruit in category (CAT) 1. The MmT when performed at GF results in a higher percentage of thinning. The treatment MmT at FB increases the average fruit mass.

Introduction
Stone fruit usually shows profuse flowering and fruit set, resulting in excessive fruit load that trees cannot support, producing fruit of low commercial value (Costa et al., 2005). In this sense, the thinning of flowers and fruit is one of the standard practices used by growers aiming to adjust crop load in order to increase fruit size and quality, reduce alternate bearing, and improve selling price (Byers et al., 2003). Thinning in peach trees are generally performed manually and although it is a practice that results in several benefits, is delicate and requires high labor input in a short window of time, increasing production costs (Costa and Vizzotto, 2000). The cost of thinning in peach trees represents around one third of the total costs with hand labor in a season and could take up to 150 h man -1 ha -1 , depending on tree vigor, age, size, flowering abundance, and cultivar (Lichou et al., 1997;Taheri et al., 2012). Satisfactory results from thinning are directly related with the precocity this is performed (Miller et al., 2011). According to Byers et al. (2003), thinning during flowering can increase the yield and fruit size from 7 to 30% when compared with HT performed between 40 and 50 DAFB. Due to the high costs and low availability of hand labor currently observed in orchards around the world, several alternative studies have been carried out with mechanical and chemical thinning. The main objective of these studies were to reduce the time required for hand thinning or even replace its need (McArtney et al., 2012). Mechanical thinning is a technique of physical action that immediately causes visible effects, allowing the reproducibility of execution, thus it is less variable and more predictable than chemical thinning. The first mechanical thinning experiments used inertial trunk shakers (Powell et al., 1975), but they often caused uneven or excessive fruit thinning. Mechanical methods for flower and fruit thinning use flexible wires, rubber straps or strings that are moved over and through the trees in a tractor platform known as "Darwin String Thinner". These kinds of equipment usually transfer less energy to the tree than trunk shakers. Martin et al. (2010) and Schupp et al. (2008) tested a tractor string equipment for thinning after flowering which reduced up to 91 % and 63% the crop load of the trees, respectively, relative to HT, whereas when a follow-up hand thinning was performed, crop load was reduced up to 81% and 54 %, respectively. However, fruit diameter did not differ among treatments with this method. Tractor platforms for thinning show better results in orchards previously designed for mechanization, where the objective is building a fruiting wall (Baugher et al., 2010;Schupp and Baugher, 2011;Hehnen et al., 2012). Tractor-driven platforms are usually expansive, reason why they are little used by small growers. An alternative strategy for mechanical thinning is the use of hand-held portable equipment, which uses batteries as energy source, thus allowing more work flexibility.
Due to its manual characteristic, they allow thinning regardless training system and are more accessible to small growers. These equipment are currently being widely used, mainly in Europe. Martin et al. (2010) in Murcia, Spain, evaluated different hand-held thinning equipment. They observed that, in general, all devices tested reduced the time necessary for thinning from 46 to 90% and the harvest load 38%, while fruit size increased 47% in comparison to trees not thinned. In the same study, no differences among treatments were found for production per tree. Glozer and Hasey (2006) reported that the use of a hand-held thinning equipment reduced time needed for thinning from 30 to 41%. Considering the reduced availability and high costs of hand labor, the lack of peach orchards designed for mechanization, and the scarcity of information about mechanical thinning in Brazil, studies about this subject are of major importance as means to improve the development peach industry. The objective of this study was, therefore, to evaluate the effect of mechanical-manual thinning at different developmental stages in the thinning efficiency and productive performance of 'Sensação' peach trees.

Percentage of thinning, thinning time, time for follow-up hand thinning, and labor saving
The greatest percentage of thinning was found with MmT at GF, differing of the other treatments in both growing seasons (2013 and 2014). In the growing season of 2013, all treatments showed differences relative to HT, while in 2014 only the MmT at GF showed significant differences compared to HT (Table 1). In the growing season of 2013, the MmT at GF needed more thinning time relative to the other MmT treatments. On the other hand, in 2014 no differences were found among MmT treatments. However, all of them significantly reduced the time necessary for thinning relative to HT. The time necessary for follow-up HT (s tree -1 ) did not differ among MmT treatments in both growing seasons (Table 1). Considering the total thinning time per tree, the MmT at EB required the lowest time, not differing of MmT at PF and FB (Table 1). Relative to HT, the total thinning time per tree was lower in all MmT treatments. In the growing season of 2014, the results were similar to the previous season, except that the total thinning time per tree did not differ among MmT treatments ( Table 1). The parameter labor saving (%), did not differ among MmT treatments in both growing seasons. However, all MmT treatments significantly reduced the labor needed for thinning relative to HT (Table 1).

Fruit set and number of fruit removed on follow-up hand thinning
In the growing season of 2013, the lowest fruit set was observed in the MmT at GF, while in 2014 no differences were observed between the MmT treatments. When each MmT treatment was compared to control I (WT), all of them showed lower fruit set in both growing seasons (Table 2). Regarding the number of fruit removed in the follow-up HT, significant differences were not observed between the MmT treatments in 2013. On the other hand, in 2014, the MmT at PF and GF resulted in the lowest number of fruit removed, differing only of MmT at FB ( Table 2).

Number of fruit per tree, fruit mass, production per tree, and estimated yield
In 2013, the MmT at GF showed the lowest final number of fruit per tree, differing of the other MmT treatments, while in 2014 it differed only of MmT at FB ( Table 2). The lowest average fruit mass (g), considering the MmT treatments, was observed with MmT at GF in both growing seasons, but in 2014 it differed only of MmT at FB. Compared to control I (WT) fruit from all MmT treatments showed greater mass, in both seasons. Regarding the comparison with control II, in 2013 all treatments, but MmT at GF, showed greater fruit mass, while in 2014 this result was observed only with MmT at FB (Table 2). Regarding the production per tree, the comparison among the MmT showed similar behavior of average fruit mass in 2013, where the MmT at GF showed the lowest value. In 2014, the MmT at FB was responsible for the greater production per tree (Table 2). In comparison to control I (WT), only the MmT at GF was different in 2013, showing lower production per tree and in 2014, besides this treatment, the MmT at PF also showed lower production per tree than control I (WT). Considering the comparison of MmT with control II (HT) in 2013, significant differences were not found. However, in 2014, the MmT at FB and PF obtained greater production per tree compared to control II (HT) ( Table 2). Production per tree of trees treated with these MmT was increased 15.75 kg and 6.76 kg, respectively, relative to control II (HT). The estimated yield (ton ha -1 ), showed similar behavior as production per tree.

Fruit size distribution according to categories
The parameter percentage of fruit according the fruit size category (CAT) showed significant interaction with treatment (Table 3). Considering the treatments in each CAT in 2013, it was observed that control I (WT) showed the greater percentage of fruit in CAT 4 while in the CAT 3 no differences were found among treatments. On the other hand, all treatments showed greater fruit in CAT 1 and 2 than control I (WT). Considering the factor category within the treatment control I (WT), the greatest percentage of fruit was found in CAT 4, while the opposite was observed for the other treatments, i.e., the greater percentage of fruit were classified as CAT 1 (Table 3). Regarding the growing season of 2014, considering the levels of treatment in the CAT 4, the greatest percentage of fruit was observed in control I (WT), while in CAT 3 and 2 significant differences were not found.  In CAT 1, the treatments MmT at FB and EB showed greater percentage of fruit than control I (WT) and MmT at GF. Regarding the categories within each treatment level, in control I (WT) the greatest percentage of fruit was observed in CAT 4, which did not differ of CAT 3. For the other treatments the percentage of fruit in CAT 1 was greater than the other categories, except the MmT at GF, where the percentage of fruit in CAT 1 was superior only to CAT 3 and 4 (Table 3).

Discussion
Overall, our results show that the percentage of thinning was increased by MmT treatments relative to standard HT, and more markedly when performed at GF stage. On the contrary, thinning time was reduced by MmT. Similar results were found in studies with 'Cresthaven' (Marini, 2002) and 'Carson' (Martin-Gorriz et al., 2010;Martin-Gorriz et al., 2011) peaches, where the mechanical and mechanicalmanual thinning of flowers and fruit resulted in an economy of time of 88% and 54%, respectively, compared to HT. The parameter time necessary for follow-up HT (s tree -1 ) did not differ among MmT treatments in both growing seasons (Table 1). MmT treatments reduced approximately 50% the labor needed for thinning, similarly as observed by Martin-Gorriz et al. (2012) in a study with the cultivar 'Carson', using a mechanical-manual device specific for fruit thinning. Using this device, they needed from 120 to 198 seconds per tree, while for HT 1500 to 1962 seconds per tree were necessary. The economy of time provided by the mechanical device ranged from 87 to 93%, allowing the thinning of an average of 23 trees h -1 . According to the same authors, when performing the follow-up HT after mechanical thinning, an average of 318 to 668 seconds per tree was necessary. Compared to HT a reduction of 46 to 82% was observed. The authors emphasize that the results were positive because the reduction in the costs relative to HT and the possibility of performing the thinning of fruit, timing when freezing events are reduced in the region where the study was performed. The final outcome of mechanical thinning is removing fruit without reducing yield to non-economic levels, or similar to standard HT. In our study, MmT at GF reduced the yield relative to HT and the other MmT treatments, but in 2014 it was similar to standard HT. Similarly, Martin-Gorriz et al. (2011) in a study with the peach cultivar 'Carson' testing three equipment for MmT of flowers and fruit, reported that they did not affect yield and did not differ among them, as well as in comparison with HT. In our study, the only exception was the control I (without thinning) which resulted in greater yield than the other treatments in 2013, but only to MmT at PF and GF in 2014. This result is likely due the greater crop density, i.e., greater number of fruit (Table 2), as observed by Martin-Gorriz et al. (2012) in 'Carson' peach trees. By definition, successful thinning reduces crop load and increases fruit size (Martin-Gorriz et al., 2012). Similar results were found in our study were crop load was reduced and fruit size (mass) increased, without negatively affecting production per tree and estimated yield, relative to control I (WT). In fact, when the MmT was performed at FB and EB, despite reducing crop load relative to control I (WT), production per tree and estimated yield were similar to control I (WT) and significantly greater than control II (HT), without negatively affecting fruit size, showing that early thinning increases the potential to achieve high yields with good fruit size. The early thinning (at bloom or soon after pollination) results in larger fruit, indicating that peach fruit growth is source-limited during the early periods of development (Costa and Vizzotto, 2000), which explains the greater fruit mass of fruit from trees of MmT at FB. Overall, all MmT treatments and HT showed a greater proportion of fruit on CAT 1, which is extremely important because this is one of the main factors determining the final price of the fruit paid by industry and fresh market (Martin et al., 2010).

Plant material
The experiment was performed during the growing seasons of 2013 and 2014, in a commercial orchard localized in the municipality of Morro Redondo (RS), Brazil (31°39'55,09''S, 52°34'51,30''W Greenwich and altitude of 245 m). According to the Köppen climatic classification, the region shows a Cfa climate: humid subtropical, average annual precipitation of 1582 mm, annual average temperature of 18.4 °C, annual relative humidity of 78 %, and an average accumulation of 550 chilling hours (bellow 7.2 °C) (Diniz et al., 2003). The soil of the experimental field is a Ultisol. Plant material consisted of 7-year-old peach trees of cultivar Sensação, grafted onto 'Capdeboscq' rootstock. Trees were trained as an open-vase system, and spaced 5 m between rows and 1.5 within the row, resulting in a planting density of 1333 trees ha -1 . Cultural practices during the experiment were similar among treatments and consisted on fertilization based on soil analysis, pest and disease treatments as needed, and weed control.

Experimental design and treatments
The experiment was arranged as a randomized block design, with five replications, each one composed of three trees, where the central one was used for data collection leaving one in each side as border. The trees were selected by uniformity of size and grouped in blocks based on trunk diameter, measured at 20 cm from the ground. The six treatments tested were: 1) Control I [without thinning (WT)]; 2) Control II [(hand thinning (HT) at 40 days after full bloom (DAFF)]; 3) mechanical-manual thinning (MmT) at full bloom (FB; 50% of flowers at anthesis); 4) MmT at end of bloom (EB; 80-100% of flowers at anthesis; T5) MmT at petal fall (PF) and; 6) MmT of green fruit (GF; with 1 cm of diameter). In all MmT treatments, HT was performed at 40 DAPF to remove remaining unwanted fruit. Since the effect of personal experience may have a great effect on the thinning results, all treatments were applied by two students properly trained. By the time of first treatment (MmT at FB) a group of replications was set for each student: student one worked on replications 1 and 2 and student two on replications 3, 4, and 5. This scheme was kept until throughout the experiment. The MmT was performed using a hand-held portable device (Carpa Electro total control ® -REF 30I31), which consists on a rotary spindle (20 cm long) with flexible rubber rings. This spindle is connected to a 1.8 m long cable that is connected to four portable batteries, enabling amplitude and work mobility. The total device weight is 3.79 kg. Working speed to apply the treatments was 5350 rpm (revolutions per minute).

Measurements
In both growing seasons, thinning treatments were performed in whole trees. In order to determine the percentage of thinning (%) and fruit set (%), the number of flowers (at FB) and fruit was counted in six mixed shoots (25-60 cm long) selected per tree, before and after thinning. The percentage of thinning was calculated using the following formula: [100 -(nº of flowers or fruit after thinning/nº of flowers or fruit before thinning x 100)]. After the natural fruit drop (~40 DAFB), all remaining fruit in the selected shoots were counted to obtain the fruit set (%), according the relationship (nº fruit x 100) / (nº flowers). After that, standard HT was performed in control II (standard HT) and in MmT treatments to remove the excess of fruit in some portions of the tree and adjust the distance between then when necessary (follow-up HT). Standard HT and follow-up HT were performed at 40 DAFB by the two students and scheme previously described, leaving 10 to 15cm between fruit according to shoot vigor. Full bloom occurred in 28 July 2013 and 25 July 2014. The time spent to perform each treatment was recorded with a digital chronometer and expressed as seconds (s) per tree -1 From the time for MmT and time for follow-up HT, the total working time (s tree -1 ) was calculated. The economy of work (%), was determined from the reduction of time necessary for thinning provided by the MmT + follow-up HT relative to standard HT. The final fruit number per tree (nº tree -1 ) was determined by counting the number of fruit in each experimental unit before harvest. Fruit were harvested in 13 November 2013 (109 DAFB) and 10 November 2014 (108 DAFB). For each experimental unit (tree), 50 fruit were randomly sampled. These fruit were then weighed with a digital scale to determine average fruit mass (g), by the relationship fruit mass/fruit number (sample). From this parameter the production per tree (kg tree -1 ) was calculated, by multiplying the average fruit mass and fruit number per tree. The estimated yield (ton ha -1 ) was obtained by the relationship between production per tree and number of trees per ha (1333). Fruit size distribution was determined using classification rings according to commercial standards and then classified in the following categories (CAT): CAT IV) 45 < 55 mm, CAT III) 55 < 60 mm, CAT II) 60 < 65 mm, CAT I) > 65 mm, and expressed as the percentage of fruit (%) in each CAT.

Statistical analysis
The statistical analysis were performed using the R software (R Core Team, 2017). The data were analyzed separately for each season (2013 and 2014) regarding the normality by Shapiro-Wilk's test, the homogeneity of variances by Hartley's test and, the independence of residues by graphical analysis. Data expressed as percentage or counts were transformed by arcsin [square root (n + 1)] and square root (n + 1), respectively. Then, the data were submitted to analysis of variance (ANOVA) by F test (p ≤ 0,05), and when significant differences were found, the effects of MmT were compared by Waller-Duncan's test (p  0,05), and the comparison with the control I and II (WT and standard HT, respectively) performed by Dunnett's test (p0,05).

Conclusions
Our results show that the use of a mechanical-manual device at different developmental stages improves thinning efficiency of 'Sensação' peach trees, reducing approximately 50% of labor needed compared to standard hand-thinning. Fruit set is reduced and the percentage of thinning is increased by the mechanical-manual thinning at different developmental stages, without negatively affecting production per tree and estimated yield. The greatest percentage of thinning is obtained when the mechanicalmanual treatment is performed at the green fruit stage. Fruit mass is not reduced by any of the MmT compared to hand thinning, while is consistently increased when MmT is performed at full bloom. The percentage of fruit classified as category I is increased when MmT is performed between full bloom and petal fall, as well as traditional hand-thinning.


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Performance of Boro rice cv. BRRI dhan28 as Influenced by Different Plant Establishment Methods and Weeding Regimes

: At present time food safety is a precedence issues in Bangladesh. It is essential to increase the production level of rice to address this mission. Suitable plant establishment method is necessary to get higher yield. Indifferent of the method of establishment, weeds are a prime barrier to rice production. Enormity of weed infestation, types of weed species and types of associated crop causes yield loss of rice. The study was undertaken to evaluate the yield performance of Boro rice cv. BRRI dhan28 under different plant establishment methods and weeding regimes The experiment was conducted at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh during December 2017 to June 2018. It was a two factor experiment that comprehended three plant establishment methods viz. sprouted seeds in line, sprouted seeds in broadcasting and transplanting of seedlings in line; five weeding regimes viz. no weeding, one hand weeding at 20 Day after planting (DAP), two hand weeding at 20 and 40 DAP, three hand weeding at 20, 40 and 60 DAP, and application of herbicide. The experiment was observed in a randomized complete block design with three replications.Yield contributing characters and yield of Boro rice were exerted significantly by plant establishment methods and the highest results were recorded in transplanting of seedlings in line method in which the number of total tiller hill -1 (6.39), number of effective tiller hill -1 (5.93), grains panicle -1 (99.28), 1000 grain weight (24.16 g) and grain yield (4.19 t ha -1 ). And the lowest results were found in sprouted seeds in broadcasting method. Considering weeding regimes, the highest number of total tillers hill -1 (6.03), effective tillers hill -1 (5.28), grains panicle -1 (101.4), grain yield (4.12 t ha -1 ) and straw yield (5.74 t ha -1 ) were recorded with application of herbicide method. Contrariwise, no weeding showed the lowest values. In interaction effect, maximum grain yield (4.48 t ha -1 ) was obtained in transplanting of seedlings in line method with application of herbicide and Sprouted seeds in broadcasting method with no weeding was performed the lowest grain yield (2.86 t ha -1 ). In the overall results the growers can be recommended to cultivate Boro rice cv. BRRI dhan28 in transplanting of seedlings in line method with application of herbicide at different Agro-ecological zones of Bangladesh. controlled t ha -1 (6.84t ha in transplanting of seedlings in line method with application of herbicide. the yield (2.86 ha was in sprouted seeds in line method with no weeding. transplanted seedling with compared to in in line transplanting of seedlings in line with hand weeding.

I. Introduction
Rice (Oryza sativa L.) is the most important semi-aquatic annual grass plants under Gramineae family. About 135 million people of Bangladesh consume rice as their staple food. Bangladesh as an agro-based developing country is striving hard for its rapid development of economy. The economic development of this country is mainly depended on agriculture. The contribution of this sector in GDP is 14.32% (BBS, 2017). This sector plays significant impact on poverty alleviation, human resource development and food security. In Bangladesh, rice is main food crop and about 84.67% of cropped area is used for rice production with annual production of 34.42 million tons (BBS, 2017). However, the area and production of Boro rice in the country were 4.14 million hectares and 15.89 million tons gradually in 2016-2017(BBS, 2017. For the last few years, the production in agricultural sector was startling and the most momentous role was played by rice. So, it is necessary to accept further steps to increase the production level of rice. Transplanting is the most common and elaborative plant establishment technique in irrigated situation across Bangladesh. But in dry condition and deep water culture direct-seeded practice is widely used . Pre-germinated seedlings are used to transfer the wet field from seedbed. It requires less seed and enables the crop to be planted right time in the field as nurseries raised in advanced. It is an effective method to control weeds and other intercultural operations. The seedlings are shown at the time of transplanting are able to compete with weeds that propagated. That's why weed infestation is generally much lower in transplanted rice compare to direct-seeded rice which increase crop yield. Mechanical power or manual labor is used to transplant rice seedling in the main field. It is troublesome and cost intensive practice because considerable amount of labor that is required to transplant (Islam et al., 2016). However, compare to direct-seeded rice the growth duration of transplanted rice is somewhat longer because of the stress procured by transplantation. In Boro season, a large amount of seedlings are damaged due to dense fog and cold weather and the availability of seedlings become shortage. Farmers are now switching over to direct seedling method under puddle conditions as wet seeding reduces the amount of labor needed for growing rice crop. Wet seeding also helps to harvest earlier by 8-10 days than transplanted rice. It can eliminate the operations such as nursery bed preparation, care of seedling, pulling, transporting and transplanting to the main filed (Chandrapala, 2009 andSreelatha, 2011). However, in direct-seeded rice crop weed infestation becomes higher which reduce yield. So, to get maximum yield by avoiding weed infestation appropriate plant establishment method should be selected.
In rice cultivation weed creates serious yield reduction problems. Weed infestation is an innate phenomenon in rice field. Improperly controlled weeds compete for soil nutrition with more rapidly in growth and cause reduction of yield and grain quality. A large number of noxious weed species are grown in rice field as the climatic condition of Bangladesh is favorable for weeds. Weed acts as a barrier for rice plants that compete for nutrients, space, water, air and light (Miah et al., 1990). Each kilogram weed infestation reduce approximately 0.75 kg yield in rice crop. In rice production weeds are major biotic constraints (Yeasmin and Ye 2008) and weed management is a serious challenge for farmers and researcher as well (Anwer et al., 2011). Weed management requires a large number of labors which increase the production cost. From the economic point of view lower cost of weeding is preferable. Choosing the suitable weeding regime depends on weed flora, weed dynamics, weed intensity, time of weeding and soil moisture. The cost of production of rice can be reduced by adopting of alternative methods of weed control which includes mechanical, biological and chemical weed control in combination with manual weeding. Herbicides and mechanical weeding are the alternative to hand weeding. However, herbicides are getting popularity at present time because it saves labor and regarded as cost effective. In controlling weeds numerous pre-emergence herbicides are used together with hand weeding . So, the selection of the effective weeding regime plays an important role to get higher yield by reducing the weed infestation.
Choosing a suitable plant establishment method and weed management practice is an imperative for rice production in a sustainable way. Hence, the present study was undertaken to find out the yield performance of Boro rice cv. BRRI dhan28 under different plant establishment methods and weeding regimes.

II. Materials and Methods
The experiment was carried out at the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh during the period in December 2017 to June 2018. The experiment consisted three plant establishment method viz Sprouted seeds in line, Sprouted seeds in broadcast, Transplanting of seedlings in line; five weeding regimes viz. no weeding, one hand weeding at 20 DAP, two hand weeding at 20 and 40 DAP, three hand weeding at 20, 40 and 60 DAP, and application of herbicide (Sathi 10WP @ 185 g ha -1 ). The experiment was placed in a randomized complete block design (RCBD) with three replications. Thus total numbers of unit plot was 45. The space between blocks and between unit plots was 1.0 m and 0.75 m. The size of the unit plot was 10m 2 (4.0 x 2.5 m). Seeds of BRRI dhan28 were collected in the Agronomy Field Laboratory, Bangladesh Agricultural University, Mymensingh. After soaking in water for 48 hours the sprouted seeds were sown in 30 plots for direct seeding, 15 plots of them were placed with sprouted seeds in line and 15 plots of them were sprouted seeds in broadcast. Sprouted seeds were sown in 25 cm individual lines successively and for the broadcast, sprouted seeds were randomly broadcasted on 12 December 2017. For transplanting of seedlings in line method, seedlings were raised on nursery bed. Sprouted seeds were broadcasted on prepared nursery bed on 12 December 2017. Fourteen five days old seedlings were then transplanted on 27 January 2018 with 25 cm × 15 cm spacing at two seedlings per hill -1 . Weeding was done as per experimental treatments. In case of no weeding treatment, weeds were allowed to grow in the plots in sowing to harvesting of the crop. Others intercultural operations were done for ensuring and maintaining the normal growth of the crop. Harvesting was done when 90% of grains turned yellow. The plants in one square meter area in the centre of the plot were harvested at ground level. The direct seeded plots were mature earlier than the transplanted plots. The direct seeded mature plots were harvested on 25 May, 2018. And the transplanted plots were harvest on 5 June, 2018. The crop was then separately threshed, grain and straws were sun dried thoroughly and weights were recorded. Prior to the harvest, five hills were randomly selected in each unit plot to collect data on yield components. While it was completed to collect the data then the grains and straws in five sampling hill were added to the total grain and straw yield. All the recorded data were compiled

III. Results and Discussion
Effect of plant establishment method: Plant establishment methods affected significantly to yield contributing characters and yield of Boro rice cv. BRRI dhan28 (Table 1). Tallest plant (85.26 cm) was obtained in transplanting of seedling in line method and shortest plant (76.62 cm) was recorded in sprouted seeds in broadcasting method. Maximum spacing and more availability of nutrients ensure highest growth in transplanted rice crop. Chandrapala (2009) and Mahapatra et al. (1985) found the similar results. The highest number of total tiller hill -1 (6.39) was obtained in transplanting of seedlings in line method and the lowest tiller hill -1 (4.58) was found in sprouted seeds in broadcasting method. Biswas and Salokhe (2005) reported similar results. The highest number of effective tillers hill -1 (5.93) was found in transplanting of seedlings in line method and lowest number of effective tillers hill -1 (3.74) was found with sprouted seeds in broadcasting method. It may be the fact that transplanting method provides enough nutrients, lights and air which helped in producing maximum effective tillers hill -1 . The findings of Mridha et al. (1991) were same. Highest number of non-effective tillers hill -1 (0.85) was found in sprouted seeds in broadcasting method and lowest number of non-effective tillers hill -1 (0.46) was found in transplanting of seedlings in line method.  found the highest number of non-effective tillers hill -1 in direct seeded method in rice. Numerically the longest panicle (21.62 cm) was obtained in transplanting of seedlings in line method and shortest panicle (21.20 cm) was obtained in sprouted seeds in broadcasting method. Goel and Verma (2000) found longest panicle length in the transplanting. Transplanting of seedling in line method showed highest number of grains panicle -1 (99.28) and lowest grains panicle -1 (96.97) was in sprouted seeds in broadcasting method. Reddy and Ghosh (1987) were reported the same observations who stated that transplanting method produced highest number of grains panicle -1 . Transplanting of seedling in line method showed lowest number of sterile spikelet panicle -1 (11.65) and the highest (11.78) was in sprouted seeds in broadcasting method.  reported similar result. The highest weight of 1000 grain (24.16 g) was observed in transplanting of seedlings in line method and the lowest weight of 1000-grain (23.23 g) was observed in sprouted seeds in broadcast method. Xiang et al. (1999) found higher 1000-grains weight in transplanting seedlings than sprouted seeds. It was found that the highest grain yield (4.19 t ha -1 ) and straw yield (6.19 t ha -1 ) were obtained in transplanting of seedling in line method and the lowest grain yield (3.33 t ha -1 ) and straw yield (4.15 t ha -1 ) were obtained in sprouted seeds in broadcasting method. Roy et al. (1990) and Chowdhury et al. (1993) reported same observations and stated that yield depends on some contributing characters. Highest harvest index (44.51 %) was produced by sprouted seeds in broadcasting method and lowest harvest index (40.36%) was found in transplanting of seedlings in line method. Sarkar et al. (2003) reported highest harvest index in direct seeded crops than the nursery seedlings.

Effect of weeding:
Yield components and yield of Boro rice cv. BRRI dhan28 were significantly affected by weeding regimes ( Table 2). The tallest plant (81.77 cm) was obtained in application of herbicide and the shortest plant height (79.33 cm) was obtained in no weeding. The highest number of total tillers hill -1 (6.03) was obtained in application of herbicide and no weeding showed the lowest number of total tillers hill -1 (4.38). Competition between rice plants and weeds for nutrients and water was lowest in case of application of herbicide compared to no weeding. It may be the fact that favored rice plants to produce more tillers reported by Walia et al. (2009). The highest number of effective tillers hill -1 (5.28) was obtained in application of herbicide and the lowest number of effective tillers hill -1 (3.83) was recorded in no weeding. Lowest competition between rice plants and weeds in case of herbicide application might have resulted in highest number of effective tillers hill -1 . Smith (1981) was supported this results. The highest number of non-effective tillers hill -1 (0.76) was obtained in no weeding and the lowest number of non-effective tillers hill -1 (0.55) was obtained in application of herbicide. Similar observations were also made by Singh and Ghosh (2007). Lowest number of non-effective tillers hill -1 found where there were highest weed competition. The longest panicle (21.80 cm) was obtained in application of herbicide. The shortest panicle (21.14 cm) was obtained in no weeding. These results are in conformity with the findings of Sharma et al., (1994). The highest number of grains panicle -1 (101.4) was recorded in application of herbicide and the lowest number of grains panicle -1 (90.84) was showed by no weeding. Less competition among rice plants and weeds might have encouraged the distribution of assimilates towards grains resulting in highest number of grains panicle -1 . This observation was similar to Mukhupadhyay and Ghosh (1981). The highest number of sterile spikelets panicle -1 (13.45) was obtained in no weeding and the lowest number of sterile spikelets panicle -1 (11.15) was obtained in application of herbicide. The highest number of sterile spikelets in no weeding might be due to severe competition between weeds and rice plants. Sreelatha (2011) reported that less weed competition resulted in lowest sterility in rice. The highest weight of 1000-grain (23.69 g) was obtained in In a column, figures having dissimilar letter (s) differ significantly as per DMRT **=Significant at 1% level of probability NS=Not significant LSD = Least Significant Difference DAP = Day after planting

Interaction effect between plant establishment method and weeding regimes:
The interaction effect of plant establishment method and weeding exposed significant influence on yield components and yield of Boro rice cv. BRRI dhan28 ( Table 3). Transplanting of seedling in line method with application of herbicide produced the tallest plant (87.20 cm) and the shortest plant (72.33cm) was obtained in sprouted seeds in broadcasting method with no weeding. Lowest crop-weed competition ensures favorable environment for crop growth. The results are in accordance with the findings of Ahmed et al. (2012). The highest number of total tillers hill -1 (7.70) was enumerated in transplanting of seedling in line method with application of herbicide. Elsewhere the lowest number of total tillers hill -1 (3.70) was found in sprouted seeds in broadcasting method with no weeding. Similar observation was reported by Subramanian et al. (2006). The highest number of effective tillers hill -1 (7.70) was listed in transplanting of seedling in line method with application of herbicide. Besides the lowest number of effective tillers hill -1 (3.27) was found in sprouted seeds in broadcasting method with no weeding. Hugar et al. (2009) and Sinha and Talati (2006) also opined similarly. It was found that the highest non-effective tillers hill -1 (1.13) was obtained in sprouted seeds in broadcasting method with no weeding and the lowest number of non effective tillers hill -1 (0.26) was obtained in transplanting of seedling in line method with application of herbicide. The longest panicle (22.31cm) was obtained in transplanting of seedlings in line method with application of herbicide. The shortest panicle (20.74 cm) was obtained in sprouted seeds in line method with no weeding. Paul (1999) found the longest panicle in transplanted of seedlings with weed management practice compared to the clonally propagated tillers. It was observed that numerically the highest number of grains panicle -1 (105.5) was computed in transplanting of seedlings in line method with application of herbicide and sprouted of seeds in line method with no weeding showed the lowest number of grains panicle -1 (94.15). Dwivedi et al. (1996) found highest total grains panicle -1 in transplanting of seedling in weed controlled condition. Xiang et al. (1999) found the similar result. The highest number of sterile spikelet panicle -1 (13.73) was obtained in sprouted seeds in line method with no weeding and the lowest number of sterile spikelet panicle -1 (10.03) was obtained in transplanting of seedlings in line method with application of herbicide. Nagalakshmi 2002 recorded lowest sterile spikelet in transplanted seedlings in weed maintained condition. The highest weight of 1000-grain was observed (24.54 g) in transplanting of seedlings in line method with application of herbicide and the lowest 1000-grain weight (22.66g) was obtained in sprouted of seeds in broadcasting method with no weeding. Rahman (1992) found highest 1000-grains weight in the combination of transplanted of seedling and controlled weed practice. The highest grain yield (4.48 t ha -1 ) and straw yield (6.84t ha -1 ) were counted in transplanting of seedlings in line method with application of herbicide. As opposed to the lowest grain yield (2.86 t ha -1 ) was counted in sprouted seeds in line method with no weeding.  reported that the grain yield of the line transplanted of seedling in rice with weeding increased compared to others conventional methods. Chandrapala (2009) also reported similar results. The highest harvest index (47.20 %) was obtained in sprouted of seeds in line with application of herbicide and the lowest harvest index (39.34%) was obtained in transplanting of seedlings in line method with three hand weeding. Sreenivas (1992) also reported similar observations. Where, W 0 = No weeding W 1 = One hand weeding at 20 DAP W 2 = Two hand weeding at 20 and 40 DAP W 3 = Three hand weeding at 20, 40 and 60 DAP W 4 = Application of herbicide (Sathi 10WP @ 185 g ha -1 )

IV. Conclusions
Results of the experiment concluded that the best performance was showed in transplanting of seedlings in line method with application of herbicide among the others for cultivation of Boro rice cv. BRRI dhan28. It was recorded the highest grain yield. Therefore, our results suggest that BRRI dhan28 in transplanting of seedlings in line method with application of herbicide may be recommended to get higher yield.