Browsing by Author "Shea, Zachary"
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- Determining Genetic Markers and Seed Compositions Related to High Test Weight in Glycine maxShea, Zachary; Singer, William M.; Rosso, Luciana; Song, Qijian; Zhang, Bo (MDPI, 2023-08-19)Test weight, one of the primary indicators of soybean seed quality, is measured as the amount of soybean seeds in kilograms that can fit into one hectoliter. The price that growers receive for their soybean is dependent on test weight. Over the past 50 years, growers have observed a decreasing trend in test weight. Therefore, it is imperative to understand better the relationship between soybean test weight and other traits to enable breeders to select parental lines with high test weights in breeding programs to ensure the grower’s profitability. The objectives of the study were to identify genetic markers associated with high test weight in soybean and to determine the correlation between high test weight and five important seed composition traits (protein, oil, sucrose, raffinose, and stachyose content). Maturity group IV and V germplasms from the USDA soybean germplasm collection were grown in Blacksburg and Warsaw in Virginia from 2019 to 2021 and were measured for all of the above traits. Results show that test weight values ranged from 62–77 kg/hL over the three years. Multiple single-nucleotide polymorphisms (SNPs) significantly associated with high test weight were found on chromosome (Chr.) 15 along with a couple on chromosome 14, and 11 candidate genes were found near these SNPs. Test weight was found to be significantly negatively correlated with oil content, inconsistently correlated with protein content in all environments, and negatively correlated but not significantly with all three sugars except for raffinose in Blacksburg 2019. We concluded that the genes that underlie test weight might be on chromosome 15, and the validated associated SNPs might be used to assist breeding selection of test weight. Breeders should pay special attention to test weight while selecting for high oil content in soybean due to their negative correlation.
- Enhancing Seed Quality and Application of Soybean through High Test Weigh and Low Trypsin InhibitorsShea, Zachary (Virginia Tech, 2023-02-09)Soybean is an integral oilseed crop that is used all over the world. Despite this, soybean has been experiencing a decrease in seed quality seen by the decreasing trend in test weight, and is limited in its uses due to the antinutritional factor, trypsin inhibitor (TI). This project first worked to identify single nucleotide polymorphisms (SNPs) associated with high test weight through a genome-wide association study (GWAS) as well as determine the relationship between important seed composition traits and test weight. Additionally, it focused on identifying and knocking out KTI genes specifically expressed in soybean seed tissue through CRISPR/Cas9. Lastly, this project investigated further use of soybean in aquaculture by evaluating the performance of Rainbow trout fed diets with low-TI, 'VT Barrack' soy meal. Nine SNPs on chromosome 15 were found to be significantly associated with high test weight as and eight potential gene candidates were identified. Test weight was found to be significantly, and negatively related to seed oil content and had inconsistent correlations with protein and sugar content. The KTI genes KTI1, Glyma01g095000, and KTI3, Glyma08g341500, were found to be only expressed in seed tissues and multiple KTI knock-out soybean plants with decreased seed TI content and activity were developed. Lastly, we found that our low-TI soymeal could replace 30% of fish meal in aquafeeds with no negative effects on trout growth and health.
- Evaluate the guide RNA effectiveness via Agrobacterium-mediated transient assays in Nicotiana benthamianaWang, Zhibo; Shea, Zachary; Li, Qi; Wang, Kunru; Mills, Kerri; Zhang, Bo; Zhao, Bingyu (Frontiers, 2023-02-20)CRISPR/Cas9-based genome editing system is a powerful tool for plant genetic improvement. However, the variable efficiency of guide RNA(s) (gRNA) represents a key limiting factor that hampers the broad application of the CRISPR/Cas9 system in crop improvement. Here, we employed the Agrobacterium-mediated transient assays to evaluate the effectiveness of gRNAs for editing genes in Nicotiana benthamiana and soybean. We designed a facile screening system based on indels that can be introduced by CRISPR/Cas9-mediated gene editing. A gRNA binding sequence (23 nucleotides) was inserted into the open reading frame of yellow fluorescent protein (YFP) gene (gRNA-YFP), which disrupted the YFP reading frame and results in no fluorescent signal when it was expressed in plant cells. Transiently co-expression of Cas9 and a gRNA targeting the gRNA-YFP gene in plant cells could restore the YFP reading frame and recover the YFP signals. We evaluated five gRNAs targeting Nicotiana benthamiana and soybean genes and confirmed the reliability of the gRNA screening system. The effective gRNAs targeting NbEDS1, NbWRKY70, GmKTI1, and GmKTI3 had been used to generate transgenic plants and resulted in expected mutations on each gene. While a gRNA targeting NbNDR1 was confirmed to be ineffective in transient assays. This gRNA indeed failed to trigger target gene mutations in stable transgenic plants. Thus, this new transient assay system can be used to validate the effectiveness of gRNAs before generating stable transgenic plants.
- Genome-Wide Association Study and Genomic Selection for Proteinogenic Methionine in Soybean SeedsSinger, William; Shea, Zachary; Yu, Dajun; Huang, Haibo; Mian, M.A. Rouf; Shang, Chao; Rosso, Maria L.; Song, Qijan J.; Zhang, Bo (Frontiers, 2022-04-25)Soybean [Glycine max (L.) Merr.] seeds have an amino acid profile that provides excellent viability as a food and feed protein source. However, low concentrations of an essential amino acid, methionine, limit the nutritional utility of soybean protein. The objectives of this study were to identify genomic associations and evaluate the potential for genomic selection (GS) for methionine content in soybean seeds. We performed a genome-wide association study (GWAS) that utilized 311 soybean accessions from maturity groups IV and V grown in three locations in 2018 and 2019. A total of 35,570 single nucleotide polymorphisms (SNPs) were used to identify genomic associations with proteinogenic methionine content that was quantified by high-performance liquid chromatography (HPLC). Across four environments, 23 novel SNPs were identified as being associated with methionine content. The strongest associations were found on chromosomes 3 (ss715586112, ss715586120, ss715586126, ss715586203, and ss715586204), 8 (ss715599541 and ss715599547) and 16 (ss715625009). Several gene models were recognized within proximity to these SNPs, such as a leucine-rich repeat protein kinase and a serine/threonine protein kinase. Identification of these linked SNPs should help soybean breeders to improve protein quality in soybean seeds. GS was evaluated using k-fold cross validation within each environment with two SNP sets, the complete 35,570 set and a subset of 248 SNPs determined to be associated with methionine through GWAS. Average prediction accuracy (r2) was highest using the SNP subset ranging from 0.45 to 0.62, which was a significant improvement from the complete set accuracy that ranged from 0.03 to 0.27. This indicated that GS utilizing a significant subset of SNPs may be a viable tool for soybean breeders seeking to improve methionine content.
- A Review of Bioactive Compound Effects from Primary Legume Protein Sources in Human and Animal HealthShea, Zachary; Ogando do Granja, Matheus; Fletcher, Elizabeth B.; Zheng, Yaojie; Bewick, Patrick; Wang, Zhibo; Singer, William M.; Zhang, Bo (MDPI, 2024-05-01)The global demand for sustainable and nutritious food sources has catalyzed interest in legumes, known for their rich repertoire of health-promoting compounds. This review delves into the diverse array of bioactive peptides, protein subunits, isoflavones, antinutritional factors, and saponins found in the primary legume protein sources—soybeans, peas, chickpeas, and mung beans. The current state of research on these compounds is critically evaluated, with an emphasis on the potential health benefits, ranging from antioxidant and anticancer properties to the management of chronic diseases such as diabetes and hypertension. The extensively studied soybean is highlighted and the relatively unexplored potential of other legumes is also included, pointing to a significant, underutilized resource for developing health-enhancing foods. The review advocates for future interdisciplinary research to further unravel the mechanisms of action of these bioactive compounds and to explore their synergistic effects. The ultimate goal is to leverage the full spectrum of benefits offered by legumes, not only to advance human health but also to contribute to the sustainability of food systems. By providing a comprehensive overview of the nutraceutical potential of legumes, this manuscript sets a foundation for future investigations aimed at optimizing the use of legumes in the global pursuit of health and nutritional security.
- Soybean Production, Versatility, and ImprovementShea, Zachary; Singer, William Monte; Zhang, Bo (IntechOpen, 2020)Soybean is one of the most widely planted and used legumes in the world due to its valuable seed composition. The many significant agronomic practices that are utilized in soybean production are highlighted with an emphasis on those used during the pregrowing season and growing season. The various pests of soybeans and the pest management strategies used to control them are described with special attention to insects, weeds, bacteria, fungi, and nematodes. The multitude of soybean uses for livestock and human consumption, and its industrial uses are discussed in this chapter. Additionally, the conventional breeding and genetic engineering attempts to improve soybean protein, oil, and sucrose content as well as eliminate the antinutritional factors, such as trypsin inhibitors, raffinose, stachyose, and phytate, are examined. In this chapter, the various management practices, uses, and breeding efforts of soybean will be discussed.