Many soybean [Glycine max (L.) Merrill] cultivars have narrow leaflet shape but it is not known if all of these lines derive this trait from the ln gene or another locus. This project was conducted to determine the inheritance of the narrow leaflet trait in several soybean genotypes and wild [Glycine soja Sieb. et Zucc.] accessions, and also to determine the allelism of the genes for this trait in the selected lines. The parents, F1, F2 and F2:3 generations were grown at Kentland Research Farm near Blacksburg, VA or in the greenhouse. The F2 and F2:3 generations (where available) were observed for segregation in leaflet shape. The populations were scored as having either broad or narrow leaflets using visual classification and leaf measurements when necessary. 'Camp' was crossed with broad leaflet parent 'Essex' to study the inheritance of the narrow leaflet trait in Camp. Observation of the F2 and F2:3 generations lead to the conclusion that a single recessive gene controls leaflet shape in Camp. Narrow leaf parents 'SRF 400' and Camp were crossed with lines having the ln gene (T41, S56, and D64-4731). None of the crosses among Camp, T41, SRF 400, S56 and D64-4731 segregated for leaflet shape in the F2 generation leading to the conclusion that they all have the ln allele at the same locus controlling lanceolate leaflet shape. T313, a line containing a gene for narrow rugose leaflets (lnr), was crossed with Camp to study allelism between the lnr and ln genes. Segregation for leaflet shape was observed in the F2 and F2:3 generations allowing the conclusion that the lnr gene controlling the narrow rugose leaflet trait in T313 is at a locus independent from the ln gene. A deficiency of narrow rugose plants was observed in all of the populations with T313 as a parent, and was theorized as being caused by selection against lnr gametes. After adjustment for the lnr deficiency, the F2 data appeared to fit a 9 broad : 3 narrow : 4 narrow rugose ratio. Three G. soja lines were crossed to broad and narrow leaflet parents and the F2 generations were examined to determine the inheritance of the very narrow leaf phenotype. The results indicate that there are one or two recessive genes controlling narrow leaflet shape in the G. soja accessions, which are not allelic to the ln gene. Since these populations were not advanced to the F3 generation, definite conclusions cannot be drawn about the genetics of the very narrow leaf phenotype. / Master of Science

The understanding of plant defense response in plant-pathogen interaction provides useful information to combat the disease. Soybean cyst nematode (SCN), Heterodera glycines, and charcoal rot causing fungus, Macrophomina phaseolina, are major pathogens of soybean, Glycine max, and infestation with SCN has found to aggravate the fungal disease severity. The gene expression analysis in resistant and susceptible interactions between H. glycines and G. max has identified some candidate resistance genes and signaling pathways but they are yet to be fully characterized. This dissertation aims to characterize one such gene, Conserved Oligomeric Golgi (COG) complex. The COG complex is important in structural and functional integrity of Golgi complex among eukaryotes, but very little is understood about its role in plants. This study demonstrated a defensive role of the COG complex in G. max against H. glycines. The transgenic plants for overexpression of COG genes, which were originally susceptible to the pathogen, showed reduced parasitism. In contrast, the RNA interference (RNAi) in originally resistant soybean lines showed a marked increase in parasitism. Further, these COG genes were found to be inducible by harpin elicitor molecules. In another study, the already proven resistance genes (NDR1, NPR1, EDS1 and TGA2) against H. glycines were investigated against the fungal pathogen. The transgenic plants for overexpression of these genes showed reduced disease severity, while the RNAi resulted increased severity compared to control lines. In addition, the H. glycines parasitism study and the candidate gene expression analysis in M. Phaseolina susceptible and moderately resistant G. max indicate that there are some cross communications between the defense processes of G. max to H. glycines and M. phaseolina.

No description available.

This research was conducted to analyze the genetics of soybean mosaic virus (SMV) resistance in soybean [Glycine max (L.) Merr.] and to determine allelic relationships of SMV resistance genes and their interactions with SMV strain groups. In the first part of this study, the inheritance of SMV resistance in OX670 and 'Harosoy' was studied to determine the source and identity of the resistance gene/genes in OX670. Other researchers reported that OX670 possesses a single gene at a locus independent of Rsv1 and assigned the gene symbol Rsv2. Rsv2 was presumably derived from the cultivar 'Raiden'. However, later work showed that Raiden contains a single resistance gene at the Rsv1 locus, raising the possibility that the resistance gene in OX670 was not from Raiden. Harosoy and its derivatives make up much of the remaining pedigree of OX670. Results from crosses of OX670 with susceptible cultivars indicate that it contains two independent genes for SMV resistance. One is allelic to the Rsv1 locus, expresses resistance to SMV-G1 and G7 and is derived from Raiden. The other is allelic to the Rsv3 locus, expresses resistance to SMV-G7 but susceptibility to SMV-G1 and is derived from Harosoy. Therefore the Rsv2 locus does not appear to exist in OX670 or its ancestors. The presence of Rsv1 and Rsv3 makes OX670 resistant to all SMV strains from G1 through G7. The second study was conducted to investigate the inheritance and allelomorphic relationships of resistance gene(s) in 'Tousan 140' and 'Hourei', which were reported to carry single independent resistance genes when inoculated with the Japanese SMV strain C. Both of these lines exhibit resistance to strains SMV-G1 through G7. This inheritance study shows that Tousan 140 and Hourei each possess two resistance genes. One of the genes in Hourei confers resistance to SMV-G1 and G7 strains; the other gene confers susceptibility to SMV-G1 but resistance to SMV-G7. Allelism tests indicate that one of the genes in both Hourei and Tousan 140 is allelic to Rsv1, and the other is allelic to Rsv3. The two genes in Tousan 140 were separated into individual lines, R1 and R2. R1, most probably containing Rsv1, exhibited resistance to SMV-G1 through G3 but was susceptible to SMV-G5 through G7. Line R2, most likely possesses Rsv3 gene, was susceptible to SMV-G1 through G3 but resistant to SMV-G5 through G7. Therefore, presence of these two genes makes Tousan 140 resistant to SMV-G1 through G7. The objective of the third study was to investigate inheritance and allelomorphic relationships of SMV resistance in PI88788. PI88788 exhibits resistance to SMV-G1 through G7. Genetic analysis of our data reveals that SMV resistance in PI88788 is conferred by a single gene at a locus tentatively labeled 'Rsv4'. Expression of this gene in the homozygous state decreased accumulation rate and prevented vascular movement of SMV. In the heterozygous state vascular movement of the SMV was delayed but not prevented. / Ph. D.

Commercially available leaf area index (LAI) meters are tools that can be used in making insect management decisions. However, proper technique must be determined for LAI estimation, and accuracy must be validated for the meters. Full-season soybean require LAI values of at least 3.5 to 4.0 by early to mid-reproductive developmental stages to achieve maximum yield potential, but the relationship between double-crop soybean LAI and yield is unknown. This research (1) evaluated minimum plot size requirements for mechanically defoliated soybean experiments using the LAI-2000 Plant Canopy Analyzer, (2) compared LAI estimates among LAI-2000 detector types which respond to different wavelengths of light, (3) compared LAI-2000 estimates with directly determined LAI values for 0, 33, 66, and 100% mechanical defoliation levels, (4) used linear and non-linear models to describe the response of full-season and double-crop soybean yields to reductions in LAI through mechanical defoliation, and (5) evaluated the response of double-crop soybean yields to reductions in LAI through insect defoliation. The minimum plot size for obtaining accurate LAI estimates of defoliated canopies in soybean with 91 cm row centers is four rows by 2 m, with an additional 1 m at the ends of the two middle rows also defoliated. The wide-blue detector, which is found in newer LAI-2000 units and responds to wavelengths of light from 360 to 460 nm, gave higher LAI estimates than the narrow-blue detector, which responds to light from 400 to 490 nm. The unit with the narrow-blue detector gave estimates equal to directly determined LAI in two of three years for 0, 33, and 66% defoliation levels, while the units with the wide-blue detectors gave estimates higher than directly determined LAI in the two years that they were studied, except for a few accurate 33% defoliation estimates. Therefore, the LAI-2000 usually provides reasonable estimates of LAI. Yield decreased linearly with LAI when LAI values were below 3.5 to 4.0 by developmental stages R4 to R5 in both full-season and double-crop soybean. Usually, there was no relationship between yield and LAI at LAI values greater than 4.0. There was an average yield reduction of 820 ± 262 kg ha⁻¹ for each unit decrease in LAI below the critical 3.5 to 4.0 level; maximum yields ranged from 1909 to 3797 kg ha⁻¹. Insect defoliators did not defoliate double-crop soybean plots to LAI levels less than 4.0, and there was no yield difference between insect-defoliated and control plots. Therefore, double-crop soybean that maintains LAI values above the 3.5 to 4.0 critical level during mid-reproductive developmental stages is capable of tolerating defoliating pest / Ph. D.

Phytic acid, also known as myo-inositol hexakisphosphate or Ins(1,2,3,4,5,6)P6, is the major storage form of phosphorus in plant seeds. Phytic acid is poorly digested by non-ruminant animals such as swine and poultry, and it chelates mineral cations including calcium, iron, zinc, and potassium, classifying it as an anti-nutrient. The excretion of unutilized phytic acid in manure translates to an excess amount of phosphorus runoff that can lead to eutrophication of lakes and ponds. Understanding the phytic acid biosynthetic pathway will allow for the development of low phytic acid (lpa) soybeans by the down-regulation of specific genes. The goal of this research was to elucidate the pathway(s) for phytic acid biosynthesis in soybean (Glycine max). We have isolated several myo-inositol phosphate kinase genes in soybean as possible candidates for steps in the biosynthetic pathway. We have characterized the genes for four myo-inositol(1,3,4)P3 5/6-kinases (GmItpk1-4), one myo-inositol(1,4,5)P3 6/3/5-kinase (GmIpk2), and one myo-inositol(1,3,4,5,6)P5 2-kinase (GmIpk1). We have examined expression in developing seeds and other tissues by Northern blot analysis and quantitative RT-PCR. We have expressed all six genes as tagged fusion proteins in E. coli, and verified enzyme activity on the proposed substrates. For each enzyme, we have conducted biochemical characterization to determine enzyme kinetics and substrate specificities. We have verified in vivo activity of GmIpk2 and GmIpk1 by complementing yeast mutants in the respective genes. Our studies indicate the likelihood that three of the genes may be involved in phytic acid biosynthesis: GmItpk3, GmIpk2 and GmIpk1. For future work, to more fully understand the contribution of each kinase gene to phytic acid biosynthesis, an RNA interference approach will be employed. The gene sequences identified in this study will be used to construct silencing vectors for use in future transformation of soybean embryogenic cultures to determine the effects of down-regulation on myo-inositol phosphate profiles. / Ph. D.

The growing consumer demand for edamame (vegetable soybean, Glycine max (L.) Merr.) in the U.S. has led to current research efforts to increase the production of this nutritious vegetable in the country. This specialty crop has been suggested as an economically attractive alternative to tobacco production, which has decreased in the Mid-Atlantic and Southeast areas. Thus, breeding programs led by Virginia Tech and University of Arkansas have been working on the development of edamame cultivars that meet both agronomical and consumer expectations for production and sales in the U.S. In two consecutive years, selected genotypes were tested in the field and by consumers, in order to identify breeding lines that could potentially be released and succeed in the U.S. market. Twenty genotypes were grown in Virginia and Arkansas in 2018 and, among them, ten were selected to be grown in Virginia, Missouri and Mississippi in 2019. Then, sensory evaluation and consumer studies (surveys) were conducted to identify desired/valuable characteristics of edamame and support breeding selection criteria. Participants of the sensory panels were adult volunteers not allergic to soy. Both years, overall acceptability was significantly different among edamame genotypes (p < 0.05) and higher scores were positively associated with 'salty' and 'sweet', but negatively associated with 'bitter', 'sour', 'sulfury/rotten egg' flavor attributes. The a* color coordinate (CIELAB) and green intensity index were significant predictors of appearance liking (p < 0.05) and consumers were willing to pay more for dark green than light green edamame beans. The outcomes of our web-based survey suggested consumers have a positive attitude towards domestically produced edamame and have a higher intention to buy fresh products and edamame in the pods. Additionally, price, availability, and familiarity with the vegetable brand, respectively, seemed to be the most important factors consumers consider in their decision-making process to purchase edamame. These important findings will continue to provide guidance for further research on edamame and can be used to prepare key messages to stakeholders at all stages of the agriculture and food (edamame) systems for the purpose of promoting a sustainable domestic production of this specialty crop in the U.S. / Doctor of Philosophy / The agriculture and food systems have been challenged to develop more nutritious foods and adopt more sustainable practices in order to properly feed our growing global population and improve food security. In this context, foods with sensory characteristics (appearance, aroma, taste, texture) that consumers appreciate have higher chances to succeed in the market, which may reduce food waste. Over the years, several fruit and vegetable crops for U.S. production had their nutritional value, overall quality, and/or agronomic characteristics improved through breeding techniques. In the last decade, edamame (vegetable soybean) has gained attention from plant breeders and food producers due to its increasing consumption and sales in the country. Edamame is a protein-rich legume traditionally consumed in Asia; it has been suggested as a high-value crop for production in the Mid-Atlantic and Southeast areas, where tobacco production has decreased significantly. Thus, researchers across the country have been working to develop high-quality edamame seeds that can grow well in the U.S. and can succeed in the domestic market. In 2018, Virginia Tech and University of Arkansas breeding programs selected twenty edamame seeds to be grown in Virginia and Arkansas; then, in 2019, ten of these seeds were grown in Virginia, Missouri, and Mississippi. In sequence, sensory evaluation and consumer studies were performed to support breeding decisions and identify consumers preferences. Overall, edamame described as 'salty' or 'sweet' was preferred over edamame described as 'bitter' or 'sour' and differences in consumer acceptability helped breeders to identify seeds with higher sensory quality. Greener color of edamame beans was associated with more likeable appearance and consumers showed willingness to pay higher price for darker green edamame beans. Our study suggested consumers have a preference for fresh products, for edamame in the pods, and tend to value domestically grown edamame over imported products. Price, availability, and familiarity with the vegetable brand were suggested as the major factors that consumers ponder when purchasing edamame. Our findings will support future research on edamame and can be used to prepare key messages for the purpose of promoting a sustainable production of this nutritious vegetable in the U.S.

As the global population rises, the demand for food increases which underscores a need for improvement in food security. Disease pressures are a major concern surrounding sustainable agriculture. Static crop populations, containing little to no genetic diversity, are vulnerable to diverse pathogen populations. Wild relatives of crop plants are a reservoir for new disease resistance traits that can be introgressed into cultivated crops. The identification of novel disease resistance is of paramount importance because pathogen co-evolution is not only defeating current resistance genes (R genes) but chemical controls as well. Phytophthora sojae (P. sojae), the causal agent of Phytophthora root and stem rot disease, reduces soybean harvests worldwide. We developed an approach to screen for new R genes that recognize core effectors from P. sojae. We expect R genes identified by these screens to be durable because P. sojae requires core effectors for virulence. We utilized effector-based screening to probe Glycine soja germplasm with core RXLR effectors from P. sojae to search for novel R genes. We developed segregating populations from crosses of P. sojae resistant G. soja germplasm with susceptible G. max cultivar Williams to determine inheritance of potential R genes in germplasm that responded to core effectors. We are using marker assisted breeding to map disease resistance traits in recombinant inbred (RI) lines. To better understand pathosystems, we examined host resistance and susceptibility using bioinformatics. We analyzed the interaction between Arabidopsis thaliana ecotype Col-0 and Hyaloperonospora arabidopsidis isolate Emwa1 using a publicly available RNA time-course experiment. We describe a new algorithm to sort genes into time-point specific clusters using activation and repression parameters. Gene ontology annotations were used to identify defense genes with unique expression profiles, and A. thaliana null mutants for these genes were significantly more susceptible to Emwa1 than wild-type. We plan to use these tools to rapidly identify and guide introgression of durable disease resistance into crop species. / Ph. D.

Palmer amaranth (Amaranthus palmeri) and common ragweed (Ambrosia artemisiifolia) are two of the most troublesome weeds in soybean. Both weeds possess widespread resistance to glyphosate and acetolactate synthase (ALS) inhibiting herbicides resulting in the use of protoporphyrinogen oxidase- (PPO) inhibitors to control these biotypes, although PPO-resistant biotypes are increasing. New soybean herbicide-resistant trait technologies enable novel herbicide combinations. Combinations of two herbicide sites-of-action (SOA) improved control 19 to 25% and 14 to 19% of Palmer amaranth and common ragweed, respectively, versus using one SOA (mesotrione, dicamba, 2,4-D, or glufosinate alone). Seed production of 5 to 10 cm Palmer amaranth and common ragweed was reduced greater than 76% by fomesafen, auxin (dicamba and 2,4-D), or glufosinate containing treatments. Some weeds survived and set seed even when treated at the proper size. As weed size increased from 10 to 30 cm, control diminished and fecundity increased, underscoring the importance of proper herbicide application timing. Effective preemergence herbicides reduced the number of weeds present at the postemergence application compared to no treatment, reducing the likelihood of herbicide resistance development. Dicamba, 2,4-D, or glufosinate applied alone or auxin + glufosinate combinations reduced Palmer amaranth seed production greater than 95% when applied at first visible female inflorescence; this first report, in addition to previous reports on individual herbicides, indicates this application timing may be useful for soil seed bank management. This research informs mitigation of herbicide resistance spread and development. / Master of Science in Life Sciences / Over 30 million hectares of soybeans were harvested in 2019 in the United States, totaling over $31 billion in value. Two of the most troublesome weeds in soybean, Palmer amaranth (Amaranthus palmeri) and common ragweed (Ambrosia artemisiifolia) can cause even greater yield reductions in soybean, up to 79 to 95%, respectively. Frequent, exclusive, and repeated use of a single herbicide has led to multiple herbicide-resistance in both of these weeds. Co-applying two effective herbicides reduces the likelihood of resistance development. New soybean varieties have been genetically modified for resistance to herbicides that were previously unusable, allowing new herbicide combinations. Research was established to investigate these herbicide options to control and reduce seed production of Palmer amaranth and common ragweed with the overarching goal of mitigating herbicide resistance, particularly resistance to protoporphyrinogen oxidase (PPO) inhibiting herbicides, which are a critical part of herbicide options in soybean production. Preemergence herbicides are vital tools in herbicide programs, reducing the number of weeds present at a postemergence application and thereby reducing the risk of herbicide resistance development to the postemergence herbicide. PPO herbicides (flumioxazin, sulfentrazone, or fomesafen) applied preemergence reduced Palmer amaranth and common ragweed density at the postemergence application 82 to 89% and 53 to 94%, respectively. The preemergence herbicide used did not affect control four weeks after the postemergence herbicides were applied. Postemergence herbicides were applied targeting three weed heights: 5 to 10 cm (ideal), 10 to 20 cm, and 20 to 30 cm. Control decreased as weed height increased and larger weeds had greater biomass and seed production, underscoring the importance of proper herbicide application timing. The single site-of-action treatments dicamba, 2,4-D, glufosinate, or fomesafen resulted in greater than 85 and 92% morality of 5 to 10 cm Palmer amaranth and common ragweed, respectively. Palmer amaranth and common ragweed control improved by 19 to 25% and 14 to 19%, respectively, when using two herbicide sites-of-action increased versus using one SOA (mesotrione, dicamba, 2,4-D, or glufosinate alone). The use of two herbicide sites of action resulted in maximum biomass reductions, depending on weed height, of 57 to 96% and 73 to 85% for Palmer amaranth and common ragweed, respectively. Dicamba, 2,4-D, glufosinate alone and in combination with fomesafen reduced seed production (relative to the nontreated) of 5 to 10 cm Palmer amaranth and common ragweed greater than 98 and 76%, respectively. Dicamba, 2,4-D, and glufosinate applied alone or auxin (dicamba and 2,4-D) and glufosinate combinations reduced Palmer amaranth seed production greater than 95% when applied at first visible female inflorescence. This indicates that these herbicides may be useful in soil weed seed bank management. This research reinforces the utility of PPO herbicides for preemergence control and their efficacy postemergence when combined with another effective herbicide, a practice known to reduce herbicide resistance development. This research also reinforces the potential for dicamba, 2,4-D, or glufosinate to reduce weed seed production when applied at a delayed timing. Future research should investigate the progeny of these weeds treated with herbicides at a delayed timing to evaluate the potential for this practice to reduce herbicide resistance development.

Soybean mosaic virus (SMV) is the major virus disease reported all over the world in soybean crop. This disease causes reduction in the yield and quality of soybean crop. Three independent genes Rsv1, Rsv3, and Rsv4, were found to provide host resistance in soybean. Rsv1 confers resistance to all but most virulant strains of SMV. Rsv1 has been mapped to soybean molecular linkage group (MLG) F by using molecular markers. The purpose of this study is to investigate the location of Rsv3 gene on soybean map using molecular markers. The Rsv3 gene of soybean confers resistance to the most vurulent strains (G5-G7) of SMV. In order to map the gene, an F2 population was constructed from a cross between L29, an Rsv3 isoline of 'Williams', and 'Lee 68', a susceptible cultivar. Rsv3 genotypes of 183 F2 plants were determined by inoculating F2:3 progeny with the G7 strain of SMV. A preliminary survey of two parental lines, near isogenic lines (NILs), and bulk segregants with 136 restriction fragment length polymorphism (RFLP) markers yielded 36 markers showing variation between the two parents. These polymorphic RFLP markers unable to provided any indication of linkage to Rsv3. As an alternative strategy, amplified fragment length polymorphic (AFLP) marker analysis of the two parental lines, NILs and bulk segregants was performed using 64 primer combinations. Initial breakthrough came in the form of AFLP primer combination of Eco+AAC/Mse+CTG exhibited polymorphism between NILs, bulk segregants, and two parental lines. This AFLP marker was isolated and cloned to convert it into a RFLP clone to further investigate the linkage to Rsv3 by F2 segregation analysis. A mapping population constructed by crossing Glycine max x Glycine soja employed in determining the location AFLP-derived RFLP clone on soybean linkage map. This population has densely mapped molecular marker data that enabled determining the location of AFLP-derived RFLP clone ACR1 on soybean molecular linkage group (MLG) B2 between the markers pA516 and pA519. This finding, made it easy to establish the linkage of markers pA519, pA516, and pA593 in L29 x Lee 68 population by F2 segregation analysis. The closest marker linked pA519, was 0.9 cM away from Rsv3. In another study Rsv4 is reported to be mapped to MLG D1b of soybean. Results of this study are useful in marker-based selection (MAS), pyramiding viral resistance genes and in cloning the Rsv3 gene. / Master of Science