Dept. of Crop Sciences Thu, 18 Jan 2018 12:18:42 GMT 2018-01-18T12:18:42Z Herbicide safeners: upregulating detoxification mechanisms for selective weed management in grain sorghum (Sorghum bicolor L. Moench) Herbicide safeners: upregulating detoxification mechanisms for selective weed management in grain sorghum (Sorghum bicolor L. Moench) Goodrich, Loren Victoria Grain sorghum (Sorghum bicolor L. Moench) is one of the world’s most important crops based on area sown and production. Sorghum utilizes C4 photosynthesis and is one of the most efficient crops for water usage and solar energy conversion. It is grown for human consumption, animal feed, and fuel worldwide. Originating in the northeast Sahel region of Africa, the wide range of sorghum cultivation can be attributed to its tolerance to both high heat and drought conditions. It is the third largest cereal grain grown in the United States with acreage in the U.S. increasing over 20% from 2014. Controlling weeds selectively is one of the most significant challenges when producing grain sorghum. Growers are restricted to preemergence (PRE) and post emergence (POST) herbicides that typically target broadleaf weeds, but options for controlling grasses are limited. Due to the high potential of gene flow from sorghum to wild and weedy relatives, the use of transgenes to confer herbicide selectivity in grain sorghum is limited. In order to achieve herbicide selectivity, seed-applied herbicide safeners are frequently used with herbicides that normally cause injury in unsafened grain sorghum. The use of herbicide safeners increases the range of herbicides that can be used in grain sorghum to achieve weed control. A current seed safener marketed for sorghum is fluxofenim (Concep® III; Syngenta Crop Protection, LLC.), which was first introduced in 1979. Fluxofenim is typically applied as a seed treatment to avoid safening weedy Sorghum relatives. Safeners confer protection to cereal crops by inducing herbicide detoxification and defense systems. This includes massive increases in the expression and activity of glutathione S-transferases (GSTs) and cytochrome P450s, although the precise molecular mechanism of action and signaling pathways remain unknown. Chapter 1 of this thesis includes a literature review of grain sorghum as a model crop, common PRE herbicides used in grain sorghum with a specific focus on very-long-chain fatty acid (VLCFA)-inhibiting herbicides, a section on the history and use of herbicide safeners in cereals, and safener-mediated herbicide metabolism in plants. Chapter 2 covers a genome-wide association study conducted to identify key molecular-genetic factors involved in the safener-induced detoxification pathway. Diverse sorghum inbred lines (761) were evaluated for their responses to seed-applied safener and PRE herbicide applications. Data analysis revealed that the molecular marker most significantly associated with safener-induced response was located on chromosome 9, where a single nucleotide polymorphism (SNP) was located within a phi-class SbGST gene and about 15 kb from a different phi-class SbGST. Transcript levels of these two candidate SbGSTs were quantified in etiolated shoot tissues using quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) and gene-specific primers designed from each SbGST coding region. Basal and safener-induced expression of these SbGSTs was examined in three sorghum genotypes at 4, 8, and 12 hrs after treatment (HAT) to quantify safener induction of these genes relative to three stably expressed reference genes: GTPB, SAND, and EIF4a. Results indicated expression of each SbGST gene increased within 12 hr following safener treatment but differed by specific gene and genotype, suggesting these SbGSTs play a functional role in the safening response from herbicides. Chapter 3 provides applied information on the use of fluxofenim as herbicide safener for hybrid grain sorghum when used with the PRE herbicide pyroxasulfone (Zidua®), a VLCFA inhibitor. A greenhouse study was first conducted to understand how pyroxasulfone affects grain sorghum emergence and seedling growth under controlled conditions, and to determine the efficacy of fluxofenim in protecting sorghum seedlings from pyroxasulfone. Using the data from the greenhouse, a field study was designed to evaluate the protective ability of seed-applied fluxofenim from pyroxasulfone at single and split application times. Weed control, crop injury, stand count, and yield data were assessed to compare the effects of pyroxasulfone to S-metolachlor (Dual Magnum®; a different VLCFA inhibitor) applied PRE in grain sorghum, with or without fluxofenim. Results indicated that pyroxasulfone provides greater weed control compared to S-metolachlor. However, as weed control increases, crop injury also increases regardless of safener. This finding demonstrates that a herbicide safener tailored towards enhancing the ability of grain sorghum to metabolize pyroxasulfone is needed for future use of this product under field conditions. Chapter 4 summarizes the discussion and conclusions from Chapters 2 and 3 and identifies current limitations and future research goals for utilizing seed-applied safeners in grain sorghum. Herbicide safeners; Grain sorghum; Pyroxasulfone; S-metolachlor; Glutathione S-transferase; Phi-class GSTs Thu, 27 Apr 2017 00:00:00 GMT 2017-04-27T00:00:00Z Goodrich, Loren Victoria Soil quality in long-term corn and soybean rotations Soil quality in long-term corn and soybean rotations Hoss, Mollie Jo Although soil quality is significant for crop productivity, input efficiency, and environmental stewardship, the effect of cropping systems on soil quality has not been examined very thoroughly for most cropping systems in the Midwest. Thus the advantages and disadvantages associated with standard agricultural practices, especially crop rotation, from the soil quality standpoint are either unknown or incomplete in most instances. The objective of this study was to evaluate soil properties under three common Illinois crop rotations more than ten years after establishment. Continuous corn (CCC), corn-soybean (CS), and corn-corn-soybean (CCS) rotations were arranged in a randomized complete block design (RCBD), with three or four replications at six University of Illinois Crop Sciences research centers, at Urbana, Monmouth, Perry, Dixon Springs, DeKalb, and Brownstown, with all phases present each year. We measured soil bulk density (BD), water aggregate stability (WAS), cation exchange capacity (CEC), soil organic matter (SOM), and plant-essential nutrients at the depths of 0-15, 15-30, 30-60, and 60-90 cm. Univariate and multivariate statistical analyses were conducted, including stepwise selection and canonical discriminant analysis (CDA). These approaches helped to clearly separate and identify locations, reflecting the different soil types and environments at each site. Crop rotations had little to no discernible effect on any of the soil properties evaluated. Soil quality; Soil health; Corn; Soybeans; Crop rotation; Mollisol; Alfisol; Illinois; Soil; Macronutrients; Micronutrients; Soil organic matter; Nitrogen Tue, 25 Apr 2017 00:00:00 GMT 2017-04-25T00:00:00Z Hoss, Mollie Jo Impact of arbuscular mycorrhizal fungi on crop and weed growth: potential implications for integrated weed managment Impact of arbuscular mycorrhizal fungi on crop and weed growth: potential implications for integrated weed managment Li, Meng With the growing problem of herbicide-resistant weeds, efficient and environmentally friendly non-chemical weed control approaches are needed to develop multi-tactic integrated weed management (IWM) programs. Using soil microbes for weed suppression has been considered as one of the non-chemical approaches, owing to the microbial potential for reducing weed growth and influencing weed community dynamics. However, successful use of soil microbes as classical biocontrol agents, which rely on importing control agents in the introduced environment, has been rare in agricultural fields. This is because agricultural practices can strongly change the soil and environmental properties in a way that reduce the population density of an introduced agent and result in an insufficient level of weed control. Therefore, conservation biocontrol approaches based on manipulating the population of residential enemies of target species that are well adapted to local environments, may hold more promise. In this study, I investigated whether arbuscular mycorrhizal fungi (AMF), a group of widely distributed soil fungi, can have suppressive effects on weeds under field conditions varying in soil management practices, and thereby contribute to IWM in agricultural systems. AMF form symbiotic associations with more than 80% of land plants, and can strongly influence plant growth through impacts on nutrient and water uptake, stress tolerance, and pathogen defense. AMF can negatively influence the growth of some weeds, including many non-host weeds and some host weeds. Non-host weeds, which are resistant to the colonization of AMF, tend to have negative responses when interacting with AMF, based on several mechanisms. AMF can also inflict costs on host weeds when external nutrients, particular phosphorus (P), are abundant, or when the host weed is physically near a host crop species. Based on these facts, I hypothesized that AMF have the potential to contribute to weed control through direct and indirect pathways: directly suppress non-host weeds by influencing their root development, and indirectly suppress some host weeds mediated by competitive effects exerted by strong neighboring host crops. In this study, I used three quantitative and experimental approaches to test these hypotheses. First, a systematic meta-analysis was conducted to identify patterns in crop and weed responses to AMF from an intensive survey of published data. The effects of crop and weed host status (strong and weak AMF hosts are divided in this study by a 10% root length colonization threshold), AMF diversity (single vs. mixed), and soil nitrogen (N) and P fertility management on plant mycorrhizal growth responses (MGR) was quantified. Results from meta-analysis supported the first hypothesis demonstrating that AMF had a significantly negative impact on the growth of weak host weeds. In addition, in the presence of N and P fertilizers, strong host crops had a stronger positive response to AMF than strong host weeds, which supported the second hypothesis. Second, a field experiment was carried out to test whether the suppressive effects of AMF on weed growth were consistent under field conditions when soil properties were manipulated by tillage and cover crop treatments. Five weed species were planted within combinations of two tillage and cover crop treatments at two locations: Illinois (IL) and Minnesota (MN). Structural equation modeling approach was used to quantify the direct and indirect impact of AMF, soil inorganic N, and soil physical properties on weed growth. Results showed that although AMF colonization rate showed slightly negative effects on the growth of some weed species, the relationships were not significant under field conditions. In addition, the relative importance of AMF on weed growth was weaker than that of soil properties. Third, I investigated whether managing the community structure of AMF can enhance their potential for weed control. A two-year field experiment was conducted in IL, and five weed species were planted in a maize field. The experimental design was the same as the second study. AMF community DNA in weed and maize roots was extracted and sequenced. Multivariate analyses were carried out to identify AMF species that have selective effects on the growth of maize and weed species as well as quantify the relative importance of plant identity, tillage, and cover cropping in influencing AMF community structure. The results demonstrated that several AMF taxa could suppress the growth of specific weeds without influencing the growth of maize. Tillage and cover cropping made significant contributions to AMF community structure, but their effect sizes were small, indicating a limited possibility of using tillage and cover cropping to manage AMF communities. Approaches to weed management based on direct augmentation (e.g., inoculation with particular AMF strains) of the weed-suppressing AMF taxa may hold more promise. Overall, the results from three studies demonstrated that AMF have direct or indirect impacts on weed growth based on weed identity, host status, and environmental context. Although the effect of the AMF community as a whole on weed growth may be not significant under field conditions, increasing the abundance of potential weed-suppressive AMF species in the AMF community through direct augmentation (e.g., inoculation with particular AMF strains) may help to improve the control potential of AMF on specific weed species. Additional research supporting improved weed control by AMF, and the incorporation of other biological, physical, and chemical control methods will be necessary to make AMF a viable part of the IWM toolkit. Arbuscular mycorrhizal fungi; Integrated weed management; Crop; Weed; Tillage; Cover crop; Meta-analysis; Community strucuture Tue, 18 Apr 2017 00:00:00 GMT 2017-04-18T00:00:00Z Li, Meng Production factors to improve edamame emergence and crop competitiveness with weeds Production factors to improve edamame emergence and crop competitiveness with weeds Crawford, Laura Elizabeth There is a lack of information on edamame production in the United States, despite growing consumer demand. Edamame is typically managed similarly to grain soybean, but edamame differs in several key characteristics, including larger seed size in edamame. Seed size can affect emergence patterns and competitive ability. The available literature indicates edamame typically has low crop emergence and that there are relatively few weed management options for edamame. Little research has been done on the low crop emergence in edamame, but some have indicated that edamame is frequently planted too deep. There has been a successful push to get more herbicides labelled for use in edamame, but producers need complementing management tactics as herbicide resistance becomes more widespread. Integrated weed management plans can include several complementing weed management tactics, including cover crops and crop interference. Research was conducted near Urbana, Illinois to examine the roles of planting depth, cover crops, and crop interference in emergence and weed management in edamame production systems. Seed were separated into small and large size classes in the planting depth and interference trials to evaluate the relationships between seed size and planting depth and between seed size and crop interference. Seed size did not affect total emergence, but smaller seed reached 50% emergence 0.7 days faster than large seed. Planting at 5 cm reduced total emergence by 19% and resulted in a 1.5 day delay in reaching 50% emergence relative to planting at 1 or 2 cm. These results indicate edamame should be planted shallower than is recommended for grain soybean. Results from the study on the use of cover crops in edamame indicate a fall-seeded rye cover crop terminated 6-8 weeks before edamame planting is the best cover crop residue system for suppressing weeds without suppressing the crop. The rye treatment terminated 6-8 weeks before edamame planting resulted in the same crop emergence but 19% lower weed emergence and 93% less weed biomass than the bare soil treatment. Results on the varying degrees of crop interference indicate that larger seeds within a cultivar can influence edamame’s ability to tolerate weed interference and that edamame’s weed suppressive ability can be affected by cultivar choice. Larger seed had 15 and 13% higher tolerance in terms of crop area and biomass, respectively, at 8 weeks after emergence. Compared to other cultivars, White Lion had 53% lower weed suppressive ability in terms of weed biomass at 8 weeks after emergence. These results improve understanding of crop emergence and integrated weed management plans in edamame production. Edamame; Planting depth; Cover crops; Seed size Tue, 18 Apr 2017 00:00:00 GMT 2017-04-18T00:00:00Z Crawford, Laura Elizabeth The critical seed-filling period duration is dependent on soybean planting date and cultivar maturity selection: implications for crop management The critical seed-filling period duration is dependent on soybean planting date and cultivar maturity selection: implications for crop management Vossenkemper, Jacob P Historically, planting soybean in early when compared to late May in the midwestern United States was not found to contribute to increasing soybean [Glycine max (L.) Merr.] yields. However, decades of genetic improvement concurrent with crop management research has resulted in a clear consensus among midwestern university researchers that soybean yield potential is increased when the crop is planted in late April and early May. These findings have encouraged earlier planting, but raise questions about how planting date might interact with other management factors. In 58 on-farm trials in Illinois and Indiana in 2011 and 2012, our objective was to examine if soybean seed treatments (fungicide + insecticide + rhizobia inoculant) and cultivar maturity selection interact with planting date. We found that using seed treatments increased yield, by an average of 80.7 kg ha-1, but did not interact with planting date. However, cultivar maturity selection did interact with planting date. Full-maturity cultivars yielded 182 kg ha-1 more when planted in late April vs. mid- to late May, but planting date had no effect on the yield of the short-maturity cultivars. Using small plot trials conducted at 12 site-years in Iowa, and in the northern half of Illinois in the 2012, 2013 and 2014 growing seasons, we examined the interaction between cultivar maturity selection and planting date more closely. Our objectives were to investigate how planting date and cultivar maturity selection influenced the critical seed-filling period duration, and to examine if planting in early May vs early June shifted the range in maturity group that produced close to maximum yields toward fuller-maturity cultivars. The seed-filling period duration was highly related to yield. Simple linear correlations coefficients ranged from r = 0.31 to r = 0.78 when the seed-filing period was expressed as accumulated incoming solar radiation and accumulated modified growing degree days. Planting date and cultivar maturity interacted to effect the duration of the seed-filling period. At the early May planting date, the seed-filling period for the full-maturity cultivars was 11.4 and 4.6 days longer than the short- and mid-maturity cultivars. For the early June planting date, however, cultivar maturity only had small effects on the seed-filling period duration. A slightly fuller range in maturity group was required for near maximum yields (within 67 kg ha-1 of maximum yield) at the early May vs. early June planting date, but even at the early planting date the fullest-maturity cultivars did not yield more than the mid-maturity cultivars, despite accumulating 32 MJ m–2 more incoming solar radiation over a 4.6 day longer seed-filling period. A lower seed-filling rate, perhaps related to lower late-season night temperatures for the full-maturity cultivars meant that the longer seed-filling period did not result in higher yields. To investigate more closely how late-season air temperatures may interact with cultivar maturity. We used 92 total site-years of variety trials in northern and central, IL conducted by the University of Illinois Variety Testing program to examine if site-years with warm air temperatures during the seed-filling period would result in full-maturity cultivars yielding more than mid-maturity cultivars. We also were interested to see if site-years with cool air temperatures during the seed-filling period would result in full-maturity cultivars yielding less than mid-maturity cultivars. In northern, IL, when mean daily air temperatures were warm during the seed-filling period, the full-maturity cultivar class (3.1 to 3.5) produced 232 and 167 kg ha-1 more grain than the 2.3 to 2.6 and 2.7 to 3.0 mid-maturity cultivar classes. In northern, IL, full- and mid-maturity cultivars generally had similar yields when air temperatures were cool during the seed-filling period. In central, IL, the 3.5 to 3.8 mid-maturity cultivar class produced 59 kg ha-1 more grain on average, than the 3.9 to 4.4 full-maturity cultivar class, and warm or cool air temperatures during the seed-filling period changed that very little. In northern, IL, full-maturity cultivars may have higher yield potentials than mid-maturity cultivars, but that yield potential may only materialize if air temperatures during the seed-filling period are warmer than normal. Soybean; Planting date; Cultivar maturity; Seed-filling period; Air temperatures; Seed-filling rate; On-farm research; Reproductive growth duration; Crop management Thu, 13 Apr 2017 00:00:00 GMT 2017-04-13T00:00:00Z Vossenkemper, Jacob P Breeding for increased protein concentration, sudden death syndrome resistance, and soybean cyst nematode resistance in soybean Breeding for increased protein concentration, sudden death syndrome resistance, and soybean cyst nematode resistance in soybean Brzostowski, Lillian Frances Soybean (Glycine max (L.) Merr.) is one of the most important agronomic crops in the USA and worldwide with dynamic uses in food, industry, and feed. Development of improved soybean cultivars is critical to provide the resources necessary for a growing world population. Approximately 83 million acres/33.5 million hectares of soybean were harvested in 2016 in the USA, and Illinois is one of the top soybean producing states. For the past several decades, soybean breeders have sought to protect and improve the economic value of soybean through genetic improvement of seed composition and disease resistance traits. In order for a gene to be effectively incorporated into a breeding program, it must maintain its desired effect across many genetic backgrounds without a negative effect on agronomic traits such as yield. The objective of this dissertation was to identify genetic regions that can be used in breeding programs to successfully increase protein concentration, sudden death syndrome (SDS) resistance, and soybean cyst nematode (SCN) resistance. Soybean; Soybean protein; Sudden death syndrome; Soybean cyst nematode Fri, 07 Apr 2017 00:00:00 GMT 2017-04-07T00:00:00Z Brzostowski, Lillian Frances Development of prairie cordgrass (spartina pectinata link) as a dedicated bioenergy crop Development of prairie cordgrass (spartina pectinata link) as a dedicated bioenergy crop Guo, Jia Development of perennial-grass bioenergy crops relies on investigating the genetic resources, understanding the physiology, and optimizing the agronomic practices related to biomass production. As one of the dominant native grass species (Poaceae), prairie cordgrass (Spartina pectinata Link) showed potential as a dedicated bioenergy crop on marginal land. However, prairie cordgrass biomass-production research has been limited to several local varieties or cultivars. To further investigate its genetic resources, natural prairie cordgrass populations collected from the Midwest to east coast of U.S. were planted and evaluated in an experimental nursery at Urbana, IL. The 4-year field study of 42 prairie cordgrass natural populations revealed extensive variations in biomass yield and phenotypic traits associated with biomass yield among these populations. A survey of molecular variation of 96 natural populations identified significant population structures and potential gene pools within the species. ‘Savoy’ prairie cordgrass, a cultivar developed from a natural Central Illinois prairie cordgrass population, was evaluated for biomass yield and feedstock quality in response to seeding rate, row spacing, and nitrogen fertilization. Based on the results of four years’ evaluation, ‘Savoy’ prairie cordgrass can be successfully established in 76-cm rows spacing with a seeding rate of 162 PLS m-2; after establishment, the recommended N application rate is 6 kg N ha-1 per dry Mg of biomass removed from prairie cordgrass harvested after a killing frost. To compare the growth development of dormant prairie cordgrass and switchgrass (Panicum virgatum L.), two locally adapted prairie cordgrass populations, ‘IL102’ and ‘PCG109’, were subjected to ambient photoperiods in a temperature-controlled greenhouse. The results indicated prairie cordgrass has a more synchronized dormancy-breaking pattern than switchgrass. Prairie cordgrass; Biomass; Variation; Population; Morphological; Photoperiod Tue, 28 Mar 2017 00:00:00 GMT 2017-03-28T00:00:00Z Guo, Jia Molecular characterization of signaling mechanisms in flowering transition in arabidopsis and association mapping of temperature response in floral development within glycine soja Molecular characterization of signaling mechanisms in flowering transition in arabidopsis and association mapping of temperature response in floral development within glycine soja Sedivy, Eric James Flowering is a major developmental event that occurs in the life cycle of all angiosperms. It is a finely tuned and highly elaborate set of mechanisms that combines internal and external stimuli to facilitate the transition from vegetative to reproductive growth. The timing of flowering has a significant impact on the fitness and reproductive efficacy of plants. To better understand floral control we address two major gaps in our knowledge. First, much of the molecular and biochemical mechanisms behind FLOWERING LOCUS T (FT), a flowering inducer, and TERMINAL FLOWER 1 (TFL1), a flowering repressor, are still largely unknown. Second, there is limited information about the mechanisms of flowering control in economically important crop species. In this study, we aim to further understand floral regulation using two approaches. 1) We will explore the role of inositol polyphosphate 5-phosphatase13 (5PTase13) in floral regulation mediated by TFL1 and FT. 2) We will take a broader view of floral regulation by examining the genome-wide effects of temperature response in flowering and maturity of Glycine Soja, the wild progenitor of cultivated soybean In the first approach Yeast Two-Hybrid assay reveals 5PTase13, an inositol polyphosphate 5-phosphatase involved in phospholipid signaling, interacts with TFL1 at a key functional residue. Both overexpressed TFL1 and mutant tfl1-1 are revealed to have increased sensitivity to root gravitropism similar to 5PTase13. While 5ptase single and double mutants do not exhibit a flowering phenotype, mutations in 5ptase13-1 and its homologs 5ptase14-1 and 5ptase12-1 significantly reduce the late flowering phenotype of overexpressed TFL1. Moreover, the 5PTases mitigate the late and early flowering phenotypes of ft-1 mutants and overexpressed FT respectively. Mutations in PHOSPHOLIPASE C2 (PLC2) an enzyme upstream of 5PTase13 in the phospholipid signaling pathway, is observed to enhance the early flowering phenotype of tfl1-1 mutants, whereas overexpression of PLC2 mitigates the early and late flowering phenotypes of tfl1-1 mutants and overexpressed TFL1 respectively. Fluorescent microscopy reveals that TFL1, FT and 5PTase13 localize in the nucleus and associate with the endoplasmic reticulum (ER). Bimolecular complementation experiments in Nicotiana tabacum and Arabidopsis further support our in vitro results, demonstrating that TFL1 and 5PTase13, and FT and 5PTase13 physically interact in both the nucleus and ER of live cells. Furthermore it is revealed the major sperm protein (MSP) domain within 5PTase13 is necessary and sufficient for TFL1 interaction. Similarly, changing the TFL1 histidine-88 residue to a tyrosine inhibits 5PTase13 interaction, whereas changing the residue to phenylalanine has very little impact on 5PTase13 association. We observed that transiently expressed 5PTase13 in N. tabacum and Arabidopsis shifted localization from the ER to the nucleus upon application of the vesicle trafficking inhibitor, brefeldin A. Moreover, 5PTase13 experiences a similar relocation to the nucleus when co-infiltrated with TFL1. We propose that in addition to the well-documented actions in lipid signaling, 5PTase13 also plays an important role in floral regulation through interaction with TFL1. In the second approach we observe two panels of 96 (P1) and 192 (P2) Glycine soja accessions grown at 20°C and 30°C to examine soybean ambient temperature response. Measured traits include R1 flowering, R5 seed-filling, R7-pod maturity, height, lodging, branching, vining, pod number, trifoliate number, bud number, and internode length. Using genotypic information from the SoySNP50K, both STRUCTURE and principle component analysis revealed that accessions clustered into three subpopulations that were correlated with their geographic origins. In general, plants grown at 30°C exhibited accelerated R1 flowering, and increased branching, height, and vining compared to 20°C, with accession maturity group having a large effect on accession phenotype across all traits. The G. soja accessions that were both most and least sensitive to temperature originated from Northeast China, Russia, Japan, and South Korea. A genome wide association study was conducted using the relative mean difference between 20°C and 30°C as a measure of temperature response. In P1, 592 and 188 SNPs were observed to be significant at an fdr of 0.20 and 0.05, respectively, across 13 traits. In P2, 1371 and 324 SNPs were observed to be significant at an fdr of 0.20, and 0.05, respectively, across 11 traits. 1778 and 837 genes were identified nearby these significant SNPs in P1 and P2 respectively, with 31 of those genes being previously characterized in plant temperature response. Notable examples are HEAT SHOCK PROTEIN 90, HEAT SHOCK FACTOR A4A, and HEAT SHOCK FACTOR A1A. Given the limited information on soybean temperature regulation, these candidates may set the framework for what genes are involved in soybean ambient temperature response. Wild soybean; Soybean; Genome-wide association studies (GWAS); Flowering; Temperature response; TERMINAL FLOWER 1 (TFL1); Inositol polyphosphate 5-phosphatase13 (5PTASE13) Tue, 18 Apr 2017 00:00:00 GMT 2017-04-18T00:00:00Z Sedivy, Eric James Transcriptomic study of evolution and gene expression in diploid and allotetraploid glycine subgenus glycine Transcriptomic study of evolution and gene expression in diploid and allotetraploid glycine subgenus glycine Belaffif, Mohammad Bahrelfi The genus Glycine is divided into two subgenera, subgenus Soja and subgenus Glycine. One of the member species of subgenus Soja, soybean (Glycine max) is an important crop plant that has been extensively studied. Unlike soybean, the perennial wild relatives in subgenus Glycine are less well known even though they possess both an interesting evolutionary history of speciation and polyploidization, and a possible potential as a source of diversity to expand the current soybean gene pool. Most studies on the member species of subgenus Glycine have focused on either their taxonomic aspects or the history of polyploidization within this subgenus. In this thesis we try to expand the scope of the studies in the member species of the subgenus Glycine by looking at the evolution and expression of their genes. We first look at the evolutionary forces that drive the speciation between soybean and its perennial wild relatives. We leveraged the use of de novo transcriptome assembly to gain access to the transcriptome of the perennial wild relatives of soybean. Using 2,430 orthologous genes shared between soybean and the perennial wild Glycine we perform test to detect signature of selection acting on the protein coding sequence. We found five genes that show signatures of selection in this study. One of the genes that we found, Glyma02g00320 showed positive selection in the soybean lineage. Along with several nucleotide variants, we also found a 24-base-pair sequence deleted in the 5’-region containing the putative signal peptide. Glyma02g00320 encodes for a BolA4-like protein, a protein with known conservation across the three different domains of life, Archaea, Bacteria, and Eukaryote. In silico prediction on the subcellular localization of soybean BolA4-like protein suggested a dual targeting nature between chloroplast and mitochondria. A similar BolA protein in Arabidopsis thaliana has been implicated in the mediation of redox homeostasis. Changes in distribution of this BolA4-like protein due to the 24-base-pair deletion in the soybean lineage would likely make this protein differently distributed in soybean compared to its perennial wild relatives. Whether the predicted changes does have effect on soybean redox homeostasis compared to wild perennial Glycine is still an open question that merits further investigation. We also look at the changes in gene expression on an allotetraploid species and its diploid progenitors species in the subgenus Glycine following exposure to high light stress. We compared the overall expression of homeologous gene pairs (duplicated genes due to whole genome duplication) with the expression of its homologous genes in its diploid progenitors. We observed that a majority of the genes observed showed equal level of expression between the allotetraploid Glycine and its diploid progenitors, with only a small fraction of the genes observed showing unequal expression levels. We also found that the homeologous gene pairs in allotetraploid Glycine displayed differential pattern of homeolog expression bias after exposure to high light stress across hundreds of genes. The extent of the observed differential pattern of homeolog expression bias across hundreds of genes suggests a regulatory mechanism that acts on a group of genes, one possible example mechanism involving the maintenance of DNA methylation level of said genes. The promoters of soybean orthologs of the genes showing differential pattern of homeolog expression bias were enriched for two distinct, non-overlapping subsets of known cis-regulatory motifs related to light and / or hormone response. Taken together, this would suggest that expression sub-functionalization achieved through differential pattern of homeolog expression bias may have an important role in the increase adaptability of allotetraploid species to a wider range of environmental conditions. Glycine; Soybean; Evolution; Transcriptome; Genome expression bias; Sub-functionalization; Positive selection; Gene expression Tue, 28 Feb 2017 00:00:00 GMT 2017-02-28T00:00:00Z Belaffif, Mohammad Bahrelfi A sorghum NAC gene is associated with variation in vascular development, biomass properties, and yield potential A sorghum NAC gene is associated with variation in vascular development, biomass properties, and yield potential Xia, Jingnu Sorghum bicolor is an important cereal, forage and energy crop adapted to semiarid areas. Primary goals for crop breeding include maximizing sugar and grain yield while maintaining the rigidity and strength of the stalk. Vascular architecture influences not only stalk strength and rigidity, but also water, nutrient and sugar transport, which ultimately determine grain yield. The building blocks of the vascular system are secondary cell walls, which make up the majority of plant biomass. Understanding the gene regulatory network underlying secondary cell wall synthesis can improve the understanding of vascular development and yield and ultimately benefit future cereal breeding. This thesis describes the mapping of the Dry Midrib (D) locus in sorghum, which controls a phenotypic difference between juicy green (dd) and dry white (DD) vascular tissue. The first chapter describes fine-mapping and GWAS using green/white midrib color as the mapping phenotype. Near isogenic lines (NILs) were created, and flanking markers and genotyping-by-sequencing (GBS) were applied to BC3 and BC2F2 individuals to reduce the region of interest to a 38 kb interval containing 4 candidate genes. One of these genes is a NAC gene containing a stop codon mutation in the mutant (dd) allele. A preliminary analysis of transcriptome differences in midrib tissue of dd and DD NILs is also described. The second chapter compares differential gene expression analysis in midrib and stalk tissue of dd and DD NILs. A glycosyl hydrolase gene is differentially expressed between dd and DD NILs in midrib, stalk, and midrib + stalk analyses. Gene ontology analysis in all three sets showed significant enrichment of hydrolase activities on O-glycosal compounds and glycosal bonds in genes differentially-expressed between dd and DD. Overall, these results provide valuable hints to fine-tune sorghum breeding in the future. Sorghum; NAC genes Fri, 28 Apr 2017 00:00:00 GMT 2017-04-28T00:00:00Z Xia, Jingnu