222 results on '"Henry T Nguyen"'
Search Results
2. Prospects for developing allergen‐depleted food crops
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Vadthya Lokya, Sejal Parmar, Arun K. Pandey, Hari K. Sudini, Dongxin Huai, Peggy Ozias‐Akins, Christine H. Foyer, Chogozie Victor Nwosu, Barbara Karpinska, Alison Baker, Pei Xu, Boshou Liao, Reyazul Rouf Mir, Xiaoping Chen, Baozhu Guo, Henry T. Nguyen, Rakesh Kumar, Sandeep K. Bera, Prashant Singam, Anirudh Kumar, Rajeev K. Varshney, and Manish K. Pandey
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio‐molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentially life‐threatening consequences. The relentless working lifestyles of the modern era often incorporate poor eating habits that include readymade prepackaged and processed foods, which contain additives such as peanuts, tree nuts, wheat, and soy‐based products, rather than traditional home cooking. Of the predominant allergenic foods (soybean, wheat, fish, peanut, shellfish, tree nuts, eggs, and milk), peanuts (Arachis hypogaea) are the best characterized source of allergens, followed by tree nuts (Juglans regia, Prunus amygdalus, Corylus avellana, Carya illinoinensis, Anacardium occidentale, Pistacia vera, Bertholletia excels), wheat (Triticum aestivum), soybeans (Glycine max), and kidney beans (Phaseolus vulgaris). The prevalence of food allergies has risen significantly in recent years including chance of accidental exposure to such foods. In contrast, the standards of detection, diagnosis, and cure have not kept pace and unfortunately are often suboptimal. In this review, we mainly focus on the prevalence of allergies associated with peanut, tree nuts, wheat, soybean, and kidney bean, highlighting their physiological properties and functions as well as considering research directions for tailoring allergen gene expression. In particular, we discuss how recent advances in molecular breeding, genetic engineering, and genome editing can be used to develop potential low allergen food crops that protect consumer health.
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- 2023
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3. Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed
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William M. Singer, Yi‐Chen Lee, Zachary Shea, Caio Canella Vieira, Dongho Lee, Xiaoying Li, Mia Cunicelli, Shaila S. Kadam, Mohammad Aamir Waseem Khan, Grover Shannon, M. A. Rouf Mian, Henry T. Nguyen, and Bo Zhang
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract Soybean [Glycine max (L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end‐uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and amino acids, oil and fatty acids, carbohydrates, and specific food‐grade considerations; discusses the application of advanced breeding technology such as CRISPR/Cas9 in creating seed composition variations; and provides future directions and breeding recommendations regarding soybean seed composition traits.
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- 2023
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4. Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans
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Tri D. Vuong, Liliana Florez‐Palacios, Leandro Mozzoni, Michael Clubb, Chuck Quigley, Qijian Song, Shaila Kadam, Yuxuan Yuan, Ting Fung Chan, Mohamed Abdur Rouf Mian, and Henry T. Nguyen
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract Breeding for increased protein without a reduction in oil content in soybeans [Glycine max (L.) Merr.] is a challenge for soybean breeders but an expected goal. Many efforts have been made to develop new soybean varieties with high yield in combination with desirable protein and/or oil traits. An elite line, R05‐1415, was reported to be high yielding, high protein, and low oil. Several significant quantitative trait loci (QTL) for protein and oil were reported in this line, but many of them were unstable across environments or genetic backgrounds. Thus, a new study under multiple field environments using the Infinium BARCSoySNP6K BeadChips was conducted to detect and confirm stable genomic loci for these traits. Genetic analyses consistently detected a single major genomic locus conveying these two traits with remarkably high phenotypic variation explained (R2), varying between 24.2% and 43.5%. This new genomic locus is located between 25.0 and 26.7 Mb, distant from the previously reported QTL and did not overlap with other commonly reported QTL and the recently cloned gene Glyma.20G085100. Homolog analysis indicated that this QTL did not result from the paracentric chromosome inversion with an adjacent genomic fragment that harbors the reported QTL. The pleiotropic effect of this QTL could be a challenge for improving protein and oil simultaneously; however, a further study of four candidate genes with significant expressions in the seed developmental stages coupled with haplotype analysis may be able to pinpoint causative genes. The functionality and roles of these genes can be determined and characterized, which lay a solid foundation for the improvement of protein and oil content in soybeans.
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- 2023
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5. Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research
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Vanika Garg, Aamir W. Khan, Kevin Fengler, Victor Llaca, Yuxuan Yuan, Tri D. Vuong, Charlotte Harris, Ting‐Fung Chan, Hon Ming Lam, Rajeev K. Varshney, and Henry T. Nguyen
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract Complete, gapless telomere‐to‐telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orientation of genes. Using complementary genomics technologies and assembly algorithms, we developed highly contiguous, nearly gapless, genome assemblies for two economically important soybean [Glycine max (L.) Merr] cultivars (Williams 82 and Lee). The centromeres were distinctly annotated on all the chromosomes of both assemblies. We further found that the canonical telomeric repeats were present at the telomeres of all chromosomes of both Williams 82 and Lee genomes. A total of 10 chromosomes in Williams 82 and eight in Lee were entirely reconstructed in single contigs without any gap. Using the combination of ab initio prediction, protein homology, and transcriptome evidence, we identified 58,287 and 56,725 protein‐coding genes in Williams 82 and Lee, respectively. The genome assemblies and annotations will serve as a valuable resource for studying soybean genomics and genetics and accelerating soybean improvement.
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- 2023
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6. Diversity of fatty acid biosynthesis genes across the soybean pangenome
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Mark C. Derbyshire, Jacob Marsh, Soodeh Tirnaz, Henry T. Nguyen, Jacqueline Batley, Philipp E. Bayer, and David Edwards
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract Soybean (Glycine max) is a major crop that contributes more than half of global oilseed production. Much research has been directed towards improvement of the fatty acid profile of soybean seeds through marker assisted breeding. Recently published soybean pangenomes, based on thousands of soybean lines, provide an opportunity to identify new alleles that may be involved in fatty acid biosynthesis. In this study, we identify fatty acid biosynthesis genes in soybean pangenomes based on sequence identity with known genes and examine their sequence diversity across diverse soybean collections. We find three possible instances of a gene missing in wild soybean, including FAD8 and FAD2‐2D, which may be involved in oleic and linoleic acid desaturation, respectively, although we recommend follow‐up research to verify the absence of these genes. More than half of the 53 fatty acid biosynthesis genes identified contained missense variants, including one linked with a previously identified QTL for oil quality. These variants were present in multiple studies based on either short read mappings or alignment of reference grade genomes. Missense variants were found in previously characterized genes including FAD2‐1A and FAD2‐1B, both of which are involved in desaturation of oleic acid, as well as uncharacterized candidate fatty acid biosynthesis genes. We find that the frequency of missense alleles in fatty acid biosynthesis genes has been reduced significantly more than the global average frequency of missense mutations during domestication, and missense variation in some genes is near absent in modern cultivars. This could be due to the selection for fatty acid profiles in seed, though future work should be conducted towards understanding the phenotypic impacts of these variants.
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- 2023
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7. Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits
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Rahul Chandnani, Tongfei Qin, Heng Ye, Haifei Hu, Karim Panjvani, Mutsutomo Tokizawa, Javier Mora Macias, Alma Armenta Medina, Karine Bernardino, Pierre-Luc Pradier, Pankaj Banik, Ashlyn Mooney, Jurandir V. Magalhaes, Henry T. Nguyen, and Leon V. Kochian
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 ,Botany ,QK1-989 - Abstract
Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.
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- 2023
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8. Genome‐wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments
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Habtamu Ayalew, William Schapaugh, Tri Vuong, and Henry T. Nguyen
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Plant culture ,SB1-1110 ,Genetics ,QH426-470 - Abstract
Abstract Improving seed yield is one of the main targets of soybean [Glycine max (L.) Merr.] breeding. Identification of loci that influence productivity and understanding their genetic mechanism will help marker‐assisted trait introgression. The present study evaluated a diverse panel of 541 soybean genotypes consisting of three maturity groups (MGs III–V) in four environments in Kansas, U.S. Data on seed yield, seed weight, shattering resistance, days to maturity, and plant height showed significant genotype, environmental, and genotype × environment interaction variations. Seed yield and shattering had moderate broad‐sense heritability (90%). The SoySNP50K iSelect BeadChip dataset was used to identify significantly associated loci via genome‐wide association studies (GWAS). A total of 19 single‐nucleotide polymorphisms (SNPs) were significantly associated with seed yield. Particularly, two stable seed yield quantitative trait loci (QTL) on chromosomes 9 and 17 were consistently detected in at least three out of four environments. Candidate gene analysis surrounding seed yield QTL on chromosome 9 showed that Glyma.09G048900, an oxygen binding protein, was the closest to the QTL peak. Similarly, Glyma.17G090200 and Glyma.17G090400 were within 20‐kb region of the seed yield QTL on chromosome 17. The candidate genes warrant further analysis to determine their functional mechanisms and develop markers for seed yield improvement.
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- 2022
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9. Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development
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Muhammad Khuram Razzaq, Reena Rani, Guangnan Xing, Yufei Xu, Ghulam Raza, Muqadas Aleem, Shahid Iqbal, Muhammad Arif, Zahid Mukhtar, Henry T. Nguyen, Rajeev K. Varshney, Kadambot H. M. Siddique, and Junyi Gai
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Hsp40/J-protein family ,Glycine max (L.) Merr. ,J-protein characterization ,growth period ,seed development ,Genetics ,QH426-470 - Abstract
The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we divided the 111 potential soybean J-proteins into 12 main clades (I–XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality.
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- 2023
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10. Registration of ‘S17‐2243C’: A non‐genetically modified maturity group IV soybean cultivar with high yield and elevated oil concentration
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Pengyin Chen, J. Grover Shannon, Dongho Lee, Matheus Ogando do Granja, Caio Canella Vieira, Yi‐Chen Lee, Md Liakat Ali, Emanuel Ferrari do Nascimento, Andrew Scaboo, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Henry T. Nguyen, Zenglu Li, Melissa Goellner Mitchum, Ben Averitt, Jason P. Bond, Clinton G. Meinhardt, Mariola Usovsky, Shuxian Li, James R. Smith, Anne M. Gillen, Alemu Mengistu, Bo Zhang, Leandro Angel Mozzoni, and David Moseley
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resistance ,Root-knot nematode ,genotypes ,Genetics ,Agronomy and Crop Science ,diseases - Abstract
'S17-2243C' (Reg. no. CV-557, PI 700003) is a semi-determinate, maturity group IV (relative maturity 4.9), non-genetically modified (non-GM) soybean [Glycine max (L.) Merr.] cultivar developed and released by the University of Missouri-Fisher Delta Research, Extension, and Education Center. S17-2243C was developed to meet the growing demands for new non-GM soybean cultivars with high yield and elevated seed oil content. S17-2243C is resistant to stem canker and charcoal rot and has tolerance to salinity conditions. Seed of S17-2243C has averaged 232 g kg(-1) of oil concentration on a dry weight basis, which was significantly higher than all check cultivars in the 2020 USDA Uniform Soybean Tests, Southern States. S17-2243C was tested against high-yielding private and public soybean cultivars from 2018 to 2021 in 80 locations across 12 states, including Alabama, Arkansas, Illinois, Kentucky, Louisiana, Mississippi, Missouri, North Carolina, Ohio, South Carolina, Tennessee, and Virginia. With high yield potential, broad adaptability, early maturity, elevated seed oil content, and non-GM traits, S17-2243C is an excellent cultivar choice for soybean growers adopting alternative growing systems and benefiting from premium prices offered for non-GM soybean products. Missouri Soybean Merchandising Council [6066-21220-014-000D]; USDA-ARS Project; [301] Published version Missouri Soybean Merchandising Council, Grant/Award Number: 301; USDA-ARS Project, Grant/Award Number: 6066-21220-014-000D Public domain – authored by a U.S. government employee
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- 2023
11. Registration of ‘S16‐11644C’: A maturity group IV soybean cultivar with high‐yielding performance and broad disease resistance
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Pengyin Chen, J. Grover Shannon, Dongho Lee, Matheus Ogando do Granja, Md Liakat Ali, Caio Canella Vieira, Yi‐Chen Lee, Emanuel Ferrari do Nascimento, Andrew Scaboo, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Henry T. Nguyen, Zenglu Li, Melissa Goellner Mitchum, Ben Averitt, Jason P. Bond, Clinton G. Meinhardt, Mariola Usovsky, Shuxian Li, James R. Smith, Anne M. Gillen, Alemu Mengistu, Bo Zhang, Leandro Angel Mozzoni, Robert T. Robbins, and David Moseley
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Genetics ,Agronomy and Crop Science - Published
- 2022
12. Registration of ‘S15‐10434C’ soybean cultivar with high yield, resistance to multiple diseases, and wide adaptation
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Pengyin Chen, M. L. Ali, Grover Shannon, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Caio Canella Vieira, Dongho Lee, Andrew Scaboo, Mariola Usovsky, Henry T. Nguyen, Melissa G. Mitchum, Zenglu Li, Jason Bond, Clinton Meinhardt, Shuxian Li, Alemu Mengistu, Robert T. Robbins, Leandro A. Mozzoni, Bo Zhang, James R. Smith, and Blair Buckley
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Genetics ,Agronomy and Crop Science - Published
- 2022
13. Registration of ‘S16‐5540GT’ soybean cultivar with high yield, resistance to multiple diseases, elevated protein content, and wide adaptation
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Pengyin Chen, Md Liakat Ali, J. Grover Shannon, Caio Canella Vieira, Dongho Lee, Melissa Crisel, Scotty Smothers, Michael Clubb, Stewart Selves, Andrew Scaboo, Mariola Usovsky, Henry T. Nguyen, Melissa G. Mitchum, Zenglu Li, Jason P. Bond, Clinton G. Meinhardt, Shuxian Li, Alemu Mengistu, Robert T. Robbins, Leandro A. Mozzoni, Bo Zhang, James R. Smith, and J. Blair Buckley
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Genetics ,Agronomy and Crop Science - Published
- 2022
14. Registration of ‘S13‐3851C’ soybean as a high‐yielding conventional cultivar with high oil content and broad disease resistance and adaptation
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S. Selves, C. Meinhardt, Alemu Mengistu, M. Crisel, Pengyin Chen, M. L. Ali, Jason P. Bond, C. C. Vieira, Henry T. Nguyen, Z. Li, S. Smothers, Andrew Scaboo, Shuxian Li, Melissa G. Mitchum, Robert T. Robbins, D. Lee, Mariola Usovsky, M. Clubb, and Grover Shannon
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Horticulture ,Oil content ,Genetics ,Cultivar ,Plant disease resistance ,Adaptation ,Biology ,Agronomy and Crop Science - Published
- 2021
15. Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed
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Mallory A Cullen, Oussama Badad, Zhou Zhou, Mohamed G Embaby, Amer AbuGhazaleh, Henry T. Nguyen, Abdelhalim El Baz, Khalid Meksem, Tri D. Vuong, Dounya Knizia, Shiming Liu, and Naoufal Lakhssassi
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chemistry.chemical_classification ,food.ingredient ,fungi ,food and beverages ,Fatty acid ,General Medicine ,Biology ,Soybean oil ,Palmitic acid ,chemistry.chemical_compound ,Oleic acid ,food ,chemistry ,Thioesterase ,Biochemistry ,Genetics ,Gene family ,lipids (amino acids, peptides, and proteins) ,Agronomy and Crop Science ,Gene ,Acyl group ,Biotechnology - Abstract
Soybean acyl-ACP thioesterase gene family have been characterized; GmFATA1A mutants were discovered to confer high oleic acid, while GmFATB mutants presented low palmitic and high oleic acid seed content. Soybean oil stability and quality are primarily determined by the relative proportions of saturated versus unsaturated fatty acids. Commodity soybean typically contains 11% palmitic acid, as the primary saturated fatty acids. Reducing palmitic acid content is the principal approach to minimize the levels of saturated fatty acids in soybean. Though high palmitic acid enhances oxidative stability of soybean oil, it is negatively correlated with oil and oleic acid content and can cause coronary heart diseases for humans. For plants, acyl–acyl carrier protein (ACP) thioesterases (TEs) are a group of enzymes to hydrolyze acyl group and release free fatty acid from plastid. Among them, GmFATB1A has become the main target to genetically reduce the palmitic acid content in soybean. However, the role of members in soybean acyl-ACP thioesterase gene family is largely unknown. In this study, we characterized two classes of TEs, GmFATA, and GmFATB in soybean. We also denominated two GmFATA members and discovered six additional members that belong to GmFATB gene family through phylogenetic, syntenic, and in silico analysis. Using TILLING-by-Sequencing+, we identified an allelic series of mutations in five soybean acyl-ACP thioesterase genes, including GmFATA1A, GmFATB1A, GmFATB1B, GmFATB2A, and GmFATB2B. Additionally, we discovered mutations at GmFATA1A to confer high oleic acid (up to 34.5%) content, while mutations at GmFATB presented low palmitic acid (as low as 5.6%) and high oleic acid (up to 36.5%) phenotypes. The obtained soybean mutants with altered fatty acid content can be used in soybean breeding program for improving soybean oil composition traits.
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- 2021
16. Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305
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Z. Li, François Belzile, Tri D. Vuong, C. Meinhardt, Henry T. Nguyen, Gunvant Patil, J. G. Shannon, Robert T. Robbins, Humira Sonah, Ki-Seung Kim, and Mariola Usovsky
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Germplasm ,Genetics ,education.field_of_study ,Population ,Haplotype ,food and beverages ,General Medicine ,Quantitative trait locus ,Biology ,Genetic analysis ,Inbred strain ,Copy-number variation ,education ,Agronomy and Crop Science ,Genotyping ,Biotechnology - Abstract
Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes concurrently present in a single soybean accession, which has not been reported earlier. An exotic soybean [Glycine max (L.) Merr.] accession, PI 567305, was reported to be highly resistant to three important nematode species, soybean cyst (SCN), root-knot (RKN), and reniform (RN) nematodes. However, genetic basis controlling broad-spectrum resistance in this germplasm has not been investigated. We report results of genetic analysis to identify genomic loci conferring resistance to these nematode species. A bi-parental population consisting of 242 F8-derived recombinant inbred lines (RILs) was developed from a cross of a nematode susceptible cultivar, Magellan, and resistant accession, PI 567305. The RILs were phenotyped for nematode resistance to three SCN HG types. They were genotyped using the Infinium SoySNP6K BeadChips and genotype-by-sequencing (GBS) methods in an attempt to evaluate the cost-effectiveness and efficiency of these two genotyping platforms. Genetic analysis confirmed the major QTL on chromosomes (Chrs) 10 and 18 with broad-spectrum resistance to the three nematodes present in this germplasm. Haplotype and copy number variation analyses of SCN resistance QTL indicated that PI 567305 has a different haplotype, which is associated with likely a unique SCN resistance mechanism different from Peking- or PI 88788-type resistance. The evaluations of both Infinium Beadchip- and GBS-based genotyping technologies provided comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping and for other genomic studies in soybeans.
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- 2021
17. Differentially reset transcriptomes and genome bias response orchestrate wheat response to phosphate deficiency
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Ruonan Wang, Yinglong Chen, Gazaldeep Kaur, Xiaoba Wu, Henry T. Nguyen, Renfang Shen, Ajay Kumar Pandey, and Ping Lan
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Gene Expression Regulation, Plant ,Physiology ,Gene Expression Profiling ,Genetics ,Phosphorus ,Cell Biology ,Plant Science ,General Medicine ,Transcriptome ,Plant Roots ,Triticum ,Phosphates ,Transcription Factors - Abstract
Phosphorus (P) is an essential macronutrient for all organisms. Phosphate (Pi) deficiency reduces grain yield and quality in wheat. Understanding how wheat responds to Pi deficiency at the global transcriptional level remains limited. We revisited the available RNA-seq transcriptome from Pi-starved wheat roots and shoots subjected to Pi starvation. Genome-wide transcriptome resetting was observed under Pi starvation, with a total of 917 and 2338 genes being differentially expressed in roots and shoots, respectively. Chromosomal distribution analysis of the gene triplets and differentially expressed genes (DEGs) revealed that the D genome displayed genome induction bias and, specifically, the chromosome 2D might be a key contributor to Pi-limiting triggered gene expression response. Alterations in multiple metabolic pathways pertaining to secondary metabolites, transcription factors and Pi uptake-related genes were evidenced. This study provides genomic insight and the dynamic landscape of the transcriptional changes contributing to the hexaploid wheat during Pi starvation. The outcomes of this study and the follow-up experiments have the potential to assist the development of Pi-efficient wheat cultivars.
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- 2022
18. OsGERLP: A novel aluminum tolerance rice gene isolated from a local cultivar in Indonesia
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Dewi Indriyani Roslim, Miftahudin Miftahudin, Rizky Dwi Satrio, Eka Indah Umaiyah, Henry T. Nguyen, Alex Hartana, Yohana C. Sulistyaningsih, Ahmad Zulkifli, Miftahul Huda Fendiyanto, J. Perry Gustafson, Suharsono Suharsono, and Tatik Chikmawati
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0106 biological sciences ,0301 basic medicine ,clone (Java method) ,Candidate gene ,Physiology ,Transgene ,Plant Science ,Biology ,Molecular cloning ,Plant Roots ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Tobacco ,Gene expression ,Genetics ,Gene silencing ,Cultivar ,Gene ,Plant Proteins ,food and beverages ,Oryza ,Plants, Genetically Modified ,030104 developmental biology ,Indonesia ,Aluminum ,010606 plant biology & botany - Abstract
There is a decrease in the land available for rice cultivation due to the rapid conversion to urban uses. Subsequently, acid soil could be an alternative land cultivating rice, but will require the use of aluminum (Al)-tolerant rice varieties. This Al tolerance trait is genetically controlled, and there is a need to discover more genes needed to develop Al-tolerant rice. Therefore, the objective of this study was to clone and characterize a novel Al tolerance gene isolated from a local cultivar of Indonesian rice. The gene cloning was conducted based on the rye/rice microsynteny relationship. In addition, the root growth and gene expression analyses were performed to verify the role of the gene on Al tolerance in gene-silenced rice and in overexpressed transgenic tobacco. The results showed an Al tolerance candidate gene, OsGERLP, was successfully cloned from rice cv. Hawara Bunar, with its gene encoding a protein similar to a bacterial ribosomal L32 protein. Additionally, the analysis showed that low gene expression caused the gene-silenced rice to be sensitive to Al, while high expression induced the Al tolerance in transgenic tobacco. Furthermore, it was discovered that the gene expression level in both plants was in line with the lower expression of the OsFRDL4 gene in the silenced rice and the high expression of the MATE gene in transgenic tobacco also with the higher citrate secretion from transgenic tobacco roots. In conclusion, the OsGERLP gene could act as a regulator for other Al tolerance genes, with the potential to develop Al-tolerant rice varieties.
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- 2021
19. ‘S13‐1955C’: A high‐yielding conventional soybean with high oil content, multiple disease resistance, and broad adaptation
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Grover Shannon, Melissa G. Mitchum, Pengyin Chen, S. Smothers, Shuxian Li, S. Selves, Robert T. Robbins, Andrew Scaboo, M. Crisel, D. Lee, Mariola Usovsky, M. L. Ali, Jason P. Bond, Alemu Mengistu, C. Meinhardt, M. Clubb, C. C. Vieira, Henry T. Nguyen, and Z. Li
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Agronomy ,Oil content ,Genetics ,Adaptation ,Plant disease resistance ,Biology ,Agronomy and Crop Science - Published
- 2021
20. Registration of ‘S13‐2743C’ as a conventional soybean cultivar with high oil content, broad disease resistance, and high yield potential
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C. C. Vieira, Shuxian Li, M. Clubb, Robert T. Robbins, S. Selves, S. Smothers, Z. Li, M. Crisel, Andrew Scaboo, James R. Smith, Jason P. Bond, Mariola Klepadlo, C. Meinhardt, Melissa G. Mitchum, Pengyin Chen, M. L. Ali, Grover Shannon, Henry T. Nguyen, Anne M. Gillen, and Alemu Mengistu
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Horticulture ,Yield (engineering) ,Oil content ,Genetics ,Cultivar ,Biology ,Plant disease resistance ,Agronomy and Crop Science - Published
- 2021
21. Correction to: Breeding for disease resistance in soybean: a global perspective
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Feng Lin, Sushil Satish Chhapekar, Caio Canella Vieira, Marcos Paulo Da Silva, Alejandro Rojas, Dongho Lee, Nianxi Liu, Esteban Mariano Pardo, Yi-Chen Lee, Zhimin Dong, Jose Baldin Pinheiro, Leonardo Daniel Ploper, John Rupe, Pengyin Chen, Dechun Wang, and Henry T. Nguyen
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Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Published
- 2022
22. Genetic characterization of qSCN10 from an exotic soybean accession PI 567516C reveals a novel source conferring broad-spectrum resistance to soybean cyst nematode
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Mariola Usovsky, Jinrong Wan, Yun Lian, Lijuan Zhou, Li Song, Henry T. Nguyen, Tri D. Vuong, and Heng Ye
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Genetic Markers ,0106 biological sciences ,Candidate gene ,Genetic Linkage ,Quantitative Trait Loci ,Soybean cyst nematode ,Locus (genetics) ,Quantitative trait locus ,01 natural sciences ,Chromosomes, Plant ,Genetics ,Animals ,Tylenchoidea ,Gene ,Phylogeny ,Disease Resistance ,Plant Diseases ,biology ,Heterodera ,fungi ,Haplotype ,Chromosome Mapping ,food and beverages ,General Medicine ,biology.organism_classification ,Plant Breeding ,Nematode ,Soybeans ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
The qSCN10 locus with broad-spectrum SCN resistance was fine-mapped to a 379-kb region on chromosome 10 in soybean accession PI 567516C. Candidate genes and potential application benefits of this locus were discussed. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pests of soybean, causing significant yield losses worldwide every year. Genetic resistance has been the major strategy to control this pest. However, the overuse of the same genetic resistance derived primarily from PI 88788 has led to the genetic shifts in nematode populations and resulted in the reduced effectiveness in soybean resistance to SCN. Therefore, novel genetic resistance resources, especially those with broad-spectrum resistance, are needed to develop new resistant cultivars to cope with the genetic shifts in nematode populations. In this study, a quantitative trait locus (QTL) qSCN10 previously identified from a soybean landrace PI 567516C was confirmed to confer resistance to multiple SCN HG Types. This QTL was further fine-mapped to a 379-kb region. There are 51 genes in this region. Four of them are defense-related and were regulated by SCN infection, suggesting their potential role in mediating resistance to SCN. The phylogenetic and haplotype analyses of qSCN10 as well as other information indicate that this locus is different from other reported resistance QTL or genes. There was no yield drag or other unfavorable traits associated with this QTL when near-isogenic lines with and without qSCN10 were tested in a SCN-free field. Therefore, our study not only provides further insight into the genetic basis of soybean resistance to SCN, but also identifies a novel genetic resistance resource for breeding soybean for durable, broad-spectrum resistance to this pest.
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- 2021
23. Mapping QTL controlling soybean seed sucrose and oligosaccharides in a single family of soybean nested association mapping (SoyNAM) population
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Patrick Obia Ongom, Tri D. Vuong, Mohammad Wali Salari, Katy M. Rainey, Henry T. Nguyen, and Rima Thapa
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Genetics ,education.field_of_study ,Sucrose ,Population ,Plant Science ,Quantitative trait locus ,Biology ,chemistry.chemical_compound ,chemistry ,Nested association mapping ,education ,Agronomy and Crop Science ,Single family - Published
- 2020
24. Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C
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Tri D. Vuong, Gunvant Patil, Henry T. Nguyen, Mariola Usovsky, Lijuan Zhou, Jinrong Wan, and Heng Ye
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0106 biological sciences ,Candidate gene ,Quantitative Trait Loci ,Population ,Soybean cyst nematode ,Locus (genetics) ,Quantitative trait locus ,01 natural sciences ,Chromosomes, Plant ,Gene Expression Regulation, Plant ,Genetics ,Animals ,Tylenchoidea ,Allele ,education ,Gene ,Disease Resistance ,Plant Diseases ,Plant Proteins ,education.field_of_study ,Polymorphism, Genetic ,biology ,Haplotype ,Chromosome Mapping ,food and beverages ,General Medicine ,biology.organism_classification ,Phenotype ,Soybeans ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
The qSCN18 QTL from PI 56756C was confirmed and fine-mapped to improve soybean resistance to the SCN population HG Type 2.5.7 using near-isogenic lines carrying recombination crossovers within the QTL region. The QTL underlying resistance was fine-mapped to a 166-Kbp region on chromosome 18, and the candidate genes were selected based on genomic analyses. Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) is the most devastating pathogen of soybean. Understanding the genetic basis of SCN resistance is crucial for managing this parasite in the field. Two major loci, rhg1 and Rhg4, were previously characterized as valuable resources for SCN resistance. However, their continuous use has caused shifts in the virulence of SCN populations, which can overcome the resistance conferred by these two major loci. Reduced effectiveness became a major concern in the soybean industry due to continuous use of rhg1 for decades. Thus, it is imperative to identify sources of SCN resistance for durable SCN management. A novel QTL qSCN18 was identified in PI567516C. To fine-map qSCN18 and identify resistance genes, a large backcross population was developed. Nineteen near-isogenic lines (NILs) carrying recombination crossovers within the QTL region were identified. The first phase of fine-mapping narrowed the QTL region to 549-Kbp, whereas the second phase confined the region to 166-Kbp containing 23 genes. Two flanking markers, MK-1 and MK-6, were developed and validated to detect the presence of the qSCN18 resistance allele. Haplotype analysis clustered the fine-mapped qSCN18 region from PI 567516C with the cqSCN-007 locus previously mapped in the wild soybean accession PI 468916. The NILs were developed to further characterize the causal gene(s) harbored in this QTL. This study also confirmed the previously identified qSCN18. The results will facilitate marker-assisted selection (MAS) introducing the qSCN18 locus from PI 567516C into high-yielding soybean cultivars with durable resistance to SCN.
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- 2020
25. Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement
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Chad E. Niederhuth, Himabindu Kudapa, Vikas K. Singh, Gaurav Agarwal, Manish K. Pandey, Abirami Ramalingam, Henry T. Nguyen, Gunvant Patil, Rajeev K. Varshney, Vanika Garg, Divya Choudhary, Ramanjulu Sunkar, Baozhu Guo, and Pallavi Sinha
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Crops, Agricultural ,Epigenomics ,0106 biological sciences ,0301 basic medicine ,Plant Development ,Computational biology ,01 natural sciences ,DNA sequencing ,Histones ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genetics ,Epigenetics ,Phenotypic plasticity ,biology ,General Medicine ,Methylation ,DNA Methylation ,Plants ,Chromatin ,Histone Code ,Plant Breeding ,030104 developmental biology ,Histone ,DNA methylation ,biology.protein ,sense organs ,Protein Processing, Post-Translational ,010606 plant biology & botany - Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
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- 2020
26. Breeding for disease resistance in soybean: a global perspective
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Feng Lin, Sushil Satish Chhapekar, Caio Canella Vieira, Marcos Paulo Da Silva, Alejandro Rojas, Dongho Lee, Nianxi Liu, Esteban Mariano Pardo, Yi-Chen Lee, Zhimin Dong, Jose Baldin Pinheiro, Leonardo Daniel Ploper, John Rupe, Pengyin Chen, Dechun Wang, and Henry T. Nguyen
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Genetics ,NEMATOIDES PARASITOS DE PLANTAS ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Abstract
Key message This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Abstract Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
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- 2022
27. Registration of ‘S14‐9017GT’ soybean cultivar with high yield, resistance to multiple diseases, and high seed oil content
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C. C. Vieira, Jason P. Bond, Pengyin Chen, Andrew Scaboo, Z. Li, M. Clubb, Mariola Usovsky, S. Smothers, M. L. Ali, Henry T. Nguyen, C. Meinhardt, Melissa G. Mitchum, Alemu Mengistu, M. Crisel, Shuxian Li, Robert T. Robbins, Grover Shannon, and S. Selves
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Horticulture ,Yield (engineering) ,Resistance (ecology) ,Oil content ,Genetics ,Cultivar ,Biology ,Agronomy and Crop Science - Published
- 2020
28. Registration of ‘S14‐15138GT’ soybean as a high‐yielding RR1/STS cultivar with broad disease resistance and adaptation
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Melissa G. Mitchum, Andrew Scaboo, Mariola Usovsky, Shuxian Li, Grover Shannon, C. Meinhardt, D. Lee, Robert T. Robbins, M. L. Ali, C. C. Vieira, M. Clubb, M. Crisel, Pengyin Chen, Alemu Mengistu, Jason P. Bond, S. Smothers, Z. Li, James R. Smith, Henry T. Nguyen, and S. Selves
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Horticulture ,Genetics ,Cultivar ,Adaptation ,Biology ,Plant disease resistance ,Agronomy and Crop Science - Published
- 2020
29. Registration of ‘S14‐15146GT’ soybean, a high‐yielding RR1 cultivar with high oil content and broad disease resistance and adaptation
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Andrew Scaboo, C. Meinhardt, S. Smothers, Stewart Selves, Grover Shannon, Jason P. Bond, C. C. Vieira, Pengyin Chen, Melissa G. Mitchum, Zenglu Li, Alemu Mengistu, Mariola Klepadlo, Henry T. Nguyen, Melissa Crisel, Md. Liakat Ali, M. Clubb, Shuxian Li, and Robert T. Robbins
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Horticulture ,Oil content ,Genetics ,Cultivar ,Adaptation ,Plant disease resistance ,Biology ,Agronomy and Crop Science - Published
- 2020
30. Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean
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Tri D. Vuong, Babu Valliyodan, Glen L. Hartman, Henry T. Nguyen, and Michelle L. Pawlowski
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0106 biological sciences ,Candidate gene ,Genotype ,Quantitative Trait Loci ,Drought tolerance ,Plant disease resistance ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Crop ,Mycorrhizae ,Genetics ,Colonization ,Cultivar ,Symbiosis ,Phylogeny ,Genetic association ,Whole Genome Sequencing ,fungi ,food and beverages ,General Medicine ,Phenotype ,Soybeans ,Agronomy and Crop Science ,Genome-Wide Association Study ,010606 plant biology & botany ,Biotechnology - Abstract
A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with colonization of soybean by an arbuscular mycorrhizal fungus (Rhizophagus intraradices). Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist their host plants by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified in crops, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal of our study was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean genotypes inoculated with Rhizophagus intraradices were microscopically evaluated for root colonization using a modified gridline intersect method. Root colonization differed significantly (P
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- 2019
31. Impacts of genomic research on soybean improvement in East Asia
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Fuk-Ling Wong, Bingjun Jiang, Akito Kaga, Guohong Zhang, Tianfu Han, Zhili Wang, Gyuhwa Chung, Henry T. Nguyen, Man-Wah Li, and Hon-Ming Lam
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0106 biological sciences ,Germplasm ,food.ingredient ,Review ,Biology ,01 natural sciences ,Agricultural economics ,Soybean oil ,03 medical and health sciences ,food ,Genetics ,East Asia ,China ,Domestication ,030304 developmental biology ,0303 health sciences ,Food security ,Asia, Eastern ,business.industry ,fungi ,food and beverages ,Genomics ,General Medicine ,Plants, Genetically Modified ,Plant Breeding ,Phenotype ,Agriculture ,Soybeans ,Far East ,business ,Agronomy and Crop Science ,Genome, Plant ,010606 plant biology & botany ,Biotechnology - Abstract
It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea.
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- 2019
32. The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content
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Hamid Mazouz, Teresa Register, My Abdelmajid Kassem, Tri D. Vuong, Dounya Knizia, Henry T. Nguyen, Mariola Usovsky, Naoufal Lakhssassi, Earl Williams, Khalid Meksem, Qijian Song, Nacer Bellaloui, Frances Betts, Jiazheng Yuan, and Alemu Mengistu
- Subjects
Candidate gene ,Population ,SNP ,Single-nucleotide polymorphism ,Genome-wide association study ,Plant Science ,Quantitative trait locus ,Biology ,Article ,genistein ,chemistry.chemical_compound ,Genetic linkage ,Williams 82 ,soybean ,education ,Ecology, Evolution, Behavior and Systematics ,Genetic association ,Genetics ,education.field_of_study ,Ecology ,Botany ,food and beverages ,RIL ,Glycitein ,linkage map ,chemistry ,QK1-989 ,Forrest ,daidzein ,glycitein ,isoflavone - Abstract
Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306), map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020), identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. And among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents.
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- 2021
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33. Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs
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Silvia F. Zanini, Philipp E. Bayer, Rachel Wells, Rod J. Snowdon, Jacqueline Batley, Rajeev K. Varshney, Henry T. Nguyen, David Edwards, and Agnieszka A. Golicz
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Genetics ,Hordeum ,Oryza ,Plant Science ,Genomics ,Sequence Analysis, DNA ,Soybeans ,Agronomy and Crop Science ,Genome, Plant ,Triticum - Abstract
Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.
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- 2021
34. Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL
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Maxime de Ronne, Parthasarathy Santhanam, Benjamin Cinget, Caroline Labbé, Amandine Lebreton, Heng Ye, Tri D. Vuong, Haifei Hu, Babu Valliyodan, David Edwards, Henry T. Nguyen, François Belzile, and Richard Bélanger
- Subjects
Phytophthora ,Plant Breeding ,Quantitative Trait Loci ,Genetics ,Plant Science ,Soybeans ,Agronomy and Crop Science ,Disease Resistance ,Genome-Wide Association Study ,Plant Diseases - Abstract
In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome-wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a diverse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight; (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes; and (c) exhaustive genotyping through whole-genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single-nucleotide polymorphism (SNP) including Glyma.15G217100, which encodes a major latex protein (MLP)-like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant (R) allele compared with those carrying the susceptible (S) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.
- Published
- 2021
35. Neutralization of Natural Killer Cell Associated Cytokines Improves Vascular Function and Reduces Blood Pressure in Placental Ischemic Rats
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Geilda A. Tardo, Jan M. Williams, Henry T. Nguyen, Denise C. Cornelius, Tyler Johnson, Andrea K Brown, Shani Siddiq, Chelsea Giachelli, Madison T. Crosby, and Olivia K. Travis
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Blood pressure ,medicine.anatomical_structure ,Chemistry ,Immunology ,Genetics ,medicine ,Vascular function ,Molecular Biology ,Biochemistry ,Neutralization ,Biotechnology ,Natural killer cell - Published
- 2021
36. Registration of ‘S11‐20124C’ Soybean with High Yield Potential, Multiple Nematode Resistance, and Salt Tolerance
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Grover Shannon, Henry T. Nguyen, Pengyin Chen, Andrew Scaboo, C. Meinhardt, Robert T. Robbins, Melissa G. Mitchum, C. C. Vieira, M. Crisel, S. Selves, Z. Li, S. Smothers, M. L. Ali, M. Clubb, and Jason P. Bond
- Subjects
chemistry.chemical_classification ,Nematode ,Yield (engineering) ,biology ,Resistance (ecology) ,Agronomy ,chemistry ,Genetics ,Salt (chemistry) ,biology.organism_classification ,Agronomy and Crop Science - Published
- 2019
37. A reference-grade wild soybean genome
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Ailin Liu, Christine H. Foyer, Steven B. Cannon, Man-Wah Li, Takanari Tanabata, Chen Lu, Babu Valliyodan, Deng Tianquan, Linfeng Yang, Ai-Si Fu, Suk Wah Tong, Ting-Fung Chan, Gyuhwa Chung, Hon-Ming Lam, Ming Sin Ng, Zhili Wang, Fuk Ling Wong, Jun-Xian He, Tin Hang Wong, Alden King-Yung Leung, Min Xie, Sachiko Isobe, Zhixia Xiao, He Lijuan, Claire Yik Lok Chung, Qiong Ding, Kejing Fan, Xinpeng Qi, Henry T. Nguyen, and Xin Wang
- Subjects
0301 basic medicine ,Germplasm ,DNA Copy Number Variations ,Genotype ,Science ,Quantitative Trait Loci ,General Physics and Astronomy ,Sequence assembly ,Locus (genetics) ,02 engineering and technology ,Biology ,Genome ,Translocation, Genetic ,Article ,General Biochemistry, Genetics and Molecular Biology ,Domestication ,03 medical and health sciences ,Copy-number variation ,lcsh:Science ,Gene ,Genome size ,Plant Proteins ,Genetics ,Multidisciplinary ,Contig ,fungi ,food and beverages ,Molecular Sequence Annotation ,Genomics ,General Chemistry ,021001 nanoscience & nanotechnology ,Biological Evolution ,Plant Breeding ,030104 developmental biology ,lcsh:Q ,Soybeans ,Peptides ,0210 nano-technology ,Genome, Plant - Abstract
Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs., Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.
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- 2019
38. Whole‐genome re‐sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad‐based resistance to soybean cyst nematode
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Sondus S. Kahil, Khalid Meksem, Jinrong Wan, Adrian O. Stec, Zhou Zhou, Li Song, Robert M. Stupar, Babu Valliyodan, Vincent Colantonio, Henry T. Nguyen, Naoufal Lakhssassi, J Hollis Rice, Tri D. Vuong, Mariola Klepadlo, Tarek Hewezi, Sarbottam Piya, and Gunvant Patil
- Subjects
0106 biological sciences ,0301 basic medicine ,DNA Copy Number Variations ,broad‐based resistance ,Soybean cyst nematode ,Locus (genetics) ,Plant Science ,Plant disease resistance ,01 natural sciences ,Genome ,03 medical and health sciences ,Animals ,Tylenchoidea ,Copy-number variation ,soybean ,Promoter Regions, Genetic ,Gene ,Research Articles ,Disease Resistance ,Plant Diseases ,Genetics ,Base Sequence ,biology ,Haplotype ,copy number variation ,biology.organism_classification ,rhg1 ,Protein Structure, Tertiary ,SCN ,030104 developmental biology ,Haplotypes ,nervous system ,Genetic Loci ,haplotype analysis ,Epistasis ,Female ,Soybeans ,sense organs ,Agronomy and Crop Science ,Genome, Plant ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Summary Soybean cyst nematode (SCN) is the most devastating plant‐parasitic nematode. Most commercial soybean varieties with SCN resistance are derived from PI88788. Resistance derived from PI88788 is breaking down due to narrow genetic background and SCN population shift. PI88788 requires mainly the rhg1‐b locus, while ‘Peking’ requires rhg1‐a and Rhg4 for SCN resistance. In the present study, whole genome re‐sequencing of 106 soybean lines was used to define the Rhg haplotypes and investigate their responses to the SCN HG‐Types. The analysis showed a comprehensive profile of SNPs and copy number variations (CNV) at these loci. CNV of rhg1 (GmSNAP18) only contributed towards resistance in lines derived from PI88788 and ‘Cloud’. At least 5.6 copies of the PI88788‐type rhg1 were required to confer SCN resistance, regardless of the Rhg4 (GmSHMT08) haplotype. However, when the GmSNAP18 copies dropped below 5.6, a ‘Peking’‐type GmSHMT08 haplotype was required to ensure SCN resistance. This points to a novel mechanism of epistasis between GmSNAP18 and GmSHMT08 involving minimum requirements for copy number. The presence of more Rhg4 copies confers resistance to multiple SCN races. Moreover, transcript abundance of the GmSHMT08 in root tissue correlates with more copies of the Rhg4 locus, reinforcing SCN resistance. Finally, haplotype analysis of the GmSHMT08 and GmSNAP18 promoters inferred additional levels of the resistance mechanism. This is the first report revealing the genetic basis of broad‐based resistance to SCN and providing new insight into epistasis, haplotype‐compatibility, CNV, promoter variation and its impact on broad‐based disease resistance in plants.
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- 2019
39. Molecular characterization of genomic regions for resistance to Pythium ultimum var. ultimum in the soybean cultivar Magellan
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Mariola Klepadlo, Tri D. Vuong, Anne E. Dorrance, Henry T. Nguyen, and Christine Susan Balk
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0106 biological sciences ,0301 basic medicine ,Candidate gene ,Genetic Linkage ,Quantitative Trait Loci ,Population ,Pythium ,Biology ,Plant disease resistance ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,01 natural sciences ,03 medical and health sciences ,Genetics ,education ,Disease Resistance ,Plant Diseases ,Pythium ultimum var. ultimum ,education.field_of_study ,Chromosome Mapping ,food and beverages ,General Medicine ,biology.organism_classification ,SNP genotyping ,Pythium ultimum ,Phenotype ,030104 developmental biology ,Soybeans ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Two novel QTL for resistance to Pythium ultimum var. ultimum were identified in soybean using an Illumina SNP Chip and whole genome re-sequencing. Pythium ultimum var. ultimum is one of numerous Pythium spp. that causes severe pre- and post-emergence damping-off of seedlings and root rot of soybean [Glycine max (L.) Merr.]. The objective of this research was to identify quantitative trait loci (QTL) for resistance to P. ultimum var. ultimum in a recombinant inbred line population derived from a cross of 'Magellan' (moderately resistant) and PI 438489B (susceptible). Two different mapping approaches were utilized: the universal soybean linkage panel (USLP 1.0) and the bin map constructed from whole genome re-sequencing (WGRS) technology. Two genomic regions associated with variation in three disease-related parameters were detected using both approaches, with the bin map providing higher resolution. Using WGRS, the first QTL were mapped within a 350-kbp region on Chr. 6 and explained 7.5-13.5% of the phenotypic variance. The second QTL were positioned in a 260-kbp confidence interval on Chr. 8 and explained 6.3-16.8% of the phenotypic variation. Candidate genes potentially associated with disease resistance were proposed. High-resolution genetic linkage maps with a number of significant SNP markers could benefit marker-assisted breeding and dissection of the molecular mechanisms underlying soybean resistance to Pythium damping-off in 'Magellan.' Additionally, the outputs of this study may encourage more screening of diverse soybean germplasm and utilization of genome-wide association studies to understand the genetic basis of quantitative disease resistance.
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- 2018
40. Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes
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Tarek Hewezi, Khalid Meksem, Tri D. Vuong, Henry T. Nguyen, Sarbottam Piya, Naoufal Lakhssassi, Robert T. Robbins, Robert M. Stupar, Gunvant Patil, and Mariola Usovsky
- Subjects
0106 biological sciences ,0301 basic medicine ,DNA Copy Number Variations ,Soybean cyst nematode ,Locus (genetics) ,Plant Science ,QH426-470 ,Quantitative trait locus ,01 natural sciences ,SB1-1110 ,03 medical and health sciences ,Genetics ,Animals ,Tylenchoidea ,Rotylenchulus reniformis ,Gene ,Disease Resistance ,Plant Diseases ,biology ,Cysts ,Heterodera ,Plant culture ,food and beverages ,biology.organism_classification ,030104 developmental biology ,Nematode ,Epistasis ,Soybeans ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Reniform nematode (RN, Rotylenchulus reniformis Linford & Oliveira) has emerged as one of the most important plant parasitic nematodes of soybean [Glycine max (L.) Merr.]. Planting resistant varieties is the most effective strategy for nematode management. The objective of this study was to identify quantitative trait loci (QTL) for RN resistance in an exotic soybean line, PI 438489B, using two linkage maps constructed from the Universal Soybean Linkage Panel (USLP 1.0) and next‐generation whole‐genome resequencing (WGRS) technology. Two QTL controlling RN resistance were identified—the soybean cyst nematode (SCN, Heterodera glycines) resistance gene GmSNAP18 at the rhg1 locus and its paralog GmSNAP11. Strong association between resistant phenotype and haplotypes of the GmSNAP11 and GmSNAP18 was observed. The results indicated that GmSNAP11 possibly could have epistatic effect on GmSNAP18, or vice versa, with the presence of a significant correlation in RN resistance of rhg1‐a GmSNAP18 vs. rhg1‐b GmSNAP18. Most importantly, our preliminary data suggested that GmSNAP18 and GmSNAP11 proteins physically interact in planta, suggesting that they belong to the same pathway for resistance. Unlike GmSNAP18, no indication of GmSNAP11 copy number variation was found. Moreover, gene‐based single nucleotide polymorphism (SNP) markers were developed for rapid detection of RN or SCN resistance at these loci. Our analysis substantiates synergic interaction between GmSNAP11 and GmSNAP18 genes and confirms their roles in RN as well as SCN resistance. These results could contribute to a better understanding of evolution and subfunctionalization of genes conferring resistance to multiple nematode species and provide a framework for further investigations.
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- 2021
41. Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
- Author
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Tri D. Vuong, Jacqueline Batley, David Edwards, Haifei Hu, Jacob I. Marsh, Babu Valliyodan, Henry T. Nguyen, Rajeev K. Varshney, Gunvant Patil, Hon-Ming Lam, Philipp E. Bayer, Qijian Song, and Yuxuan Yuan
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0106 biological sciences ,0301 basic medicine ,Germplasm ,Population ,Plant Science ,Biology ,01 natural sciences ,Domestication ,03 medical and health sciences ,Genetics ,Plant breeding ,education ,United States Department of Agriculture ,Allele frequency ,Gene ,2. Zero hunger ,education.field_of_study ,Genetic diversity ,food and beverages ,Fabaceae ,15. Life on land ,United States ,Plant Breeding ,030104 developmental biology ,Soybeans ,Agronomy and Crop Science ,Genome, Plant ,010606 plant biology & botany ,Reference genome - Abstract
The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.
- Published
- 2021
42. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing
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David Edwards, Sam Reddy, Philipp E. Bayer, Theresa A. Musket, Trupti Joshi, Allen Sessions, Babu Valliyodan, Anne V. Brown, Tri D. Vuong, Ruth Wagner, Rex T. Nelson, Manish Roorkiwal, Rajeev K. Varshney, Juexin Wang, Paul I. Otyama, Xiaolei Wu, Dong Xu, Steven B. Cannon, Pradeep Marri, Gunvant Patil, Xin Liu, Yang Liu, Henry T. Nguyen, Qijian Song, and David Grant
- Subjects
Crops, Agricultural ,0106 biological sciences ,Germplasm ,Statistics and Probability ,Data Descriptor ,Linkage disequilibrium ,Genotype ,Science ,Library and Information Sciences ,Polymorphism, Single Nucleotide ,01 natural sciences ,Plant breeding ,Linkage Disequilibrium ,Education ,03 medical and health sciences ,Genetic variation ,Selection, Genetic ,Domestication ,030304 developmental biology ,Genetics ,0303 health sciences ,Genetic diversity ,Geography ,biology ,food and beverages ,Fabaceae ,biology.organism_classification ,Computer Science Applications ,Genetic structure ,Soybeans ,Glycine soja ,Statistics, Probability and Uncertainty ,Plant sciences ,Genome, Plant ,010606 plant biology & botany ,Information Systems - Abstract
We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions., Measurement(s) genetic variation • SNP • Linkage Disequilibrium Technology Type(s) DNA sequencing • bioinformatics analysis • computational phylogenetic analysis Sample Characteristic - Organism Glycine soja • Glycine max Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13568552
- Published
- 2021
- Full Text
- View/download PDF
43. Qualification of Soybean Responses to Flooding Stress Using UAV-Based Imagery and Deep Learning
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Jing Zhou, Pengyin Chen, Jianfeng Zhou, Henry T. Nguyen, Liakat Ali, Huawei Mou, and Heng Ye
- Subjects
0106 biological sciences ,Canopy ,Multispectral image ,QH426-470 ,01 natural sciences ,Normalized Difference Vegetation Index ,SB1-1110 ,Genetics ,Cultivar ,Remote sensing ,business.industry ,Deep learning ,fungi ,Flooding (psychology) ,Botany ,Plant culture ,food and beverages ,04 agricultural and veterinary sciences ,Above ground ,QK1-989 ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Environmental science ,Artificial intelligence ,business ,Agronomy and Crop Science ,Research Article ,010606 plant biology & botany ,Field conditions - Abstract
Soybean is sensitive to flooding stress that may result in poor seed quality and significant yield reduction. Soybean production under flooding could be sustained by developing flood-tolerant cultivars through breeding programs. Conventionally, soybean tolerance to flooding in field conditions is evaluated by visually rating the shoot injury/damage due to flooding stress, which is labor-intensive and subjective to human error. Recent developments of field high-throughput phenotyping technology have shown great potential in measuring crop traits and detecting crop responses to abiotic and biotic stresses. The goal of this study was to investigate the potential in estimating flood-induced soybean injuries using UAV-based image features collected at different flight heights. The flooding injury score (FIS) of 724 soybean breeding plots was taken visually by breeders when soybean showed obvious injury symptoms. Aerial images were taken on the same day using a five-band multispectral and an infrared (IR) thermal camera at 20, 50, and 80 m above ground. Five image features, i.e., canopy temperature, normalized difference vegetation index, canopy area, width, and length, were extracted from the images at three flight heights. A deep learning model was used to classify the soybean breeding plots to five FIS ratings based on the extracted image features. Results show that the image features were significantly different at three flight heights. The best classification performance was obtained by the model developed using image features at 20 m with 0.9 for the five-level FIS. The results indicate that the proposed method is very promising in estimating FIS for soybean breeding.
- Published
- 2021
44. Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions
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Henry T. Nguyen, Jinrong Wan, Guozheng Zhang, Heng Ye, Huatao Chen, Yi Dai, Zhenzhi Pan, Lin Chen, and Li Song
- Subjects
0106 biological sciences ,0301 basic medicine ,lcsh:QH426-470 ,Datasets as Topic ,RNA-Seq ,Biology ,drought response ,Genes, Plant ,01 natural sciences ,Plant Roots ,Article ,Transcriptome ,03 medical and health sciences ,Exon ,alternative splicing ,Stress, Physiological ,Gene expression ,Genetics ,Protein Isoforms ,soybean ,Gene ,Genetics (clinical) ,Plant Proteins ,Abiotic stress ,Gene Expression Profiling ,Alternative splicing ,fungi ,food and beverages ,root ,Droughts ,Plant Leaves ,lcsh:Genetics ,030104 developmental biology ,Gene Ontology ,RNA, Plant ,RNA splicing ,Soybeans ,transcriptome ,010606 plant biology & botany - Abstract
Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate drought responses in soybean remains poorly understood. In this study, we performed a genome-wide analysis of AS events in soybean (Glycine max) roots grown under various drought conditions using the high-throughput RNA-sequencing method, identifying 385, 989, 1429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Among them, alternative 3&prime, splice sites and skipped exons were the major types of AS. Overall, 2120 genes that experienced significant AS regulation were identified from these drought-treated root samples. Gene Ontology term analysis indicated that the AS regulation of binding activity has vital roles in the drought response of soybean root. Notably, the genes encoding splicing regulatory factors in the spliceosome pathway and mRNA surveillance pathway were enriched according to the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Splicing regulatory factor-related genes in soybean root also responded to drought stress and were alternatively spliced under drought conditions. Taken together, our data suggest that drought-responsive AS acts as a direct or indirect mode to regulate drought response of soybean roots. With further in-depth research of the function and mechanism of AS in the process of abiotic stress, these results will provide a new strategy for enhancing stress tolerance of plants.
- Published
- 2020
- Full Text
- View/download PDF
45. Identification and characterization of novel QTL conferring internal detoxification of aluminium in soybean
- Author
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Heng Ye, Lijuan Zhao, Tri D. Vuong, Yan Li, Henry T. Nguyen, Qijian Song, Yang Li, Li Song, and J. Grover Shannon
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Population ,Quantitative Trait Loci ,Plant Science ,Quantitative trait locus ,Biology ,Root tip ,01 natural sciences ,03 medical and health sciences ,Allele ,education ,Phylogeny ,Genetics ,education.field_of_study ,Phylogenetic tree ,Abiotic stress ,Chromosome Mapping ,Phenotype ,Plant Breeding ,030104 developmental biology ,Number ratio ,Soybeans ,010606 plant biology & botany ,Aluminum - Abstract
Aluminium (Al) toxicity inhibits soybean root growth, leading to insufficient water and nutrient uptake. Two soybean lines (‘Magellan’ and PI 567731) were identified differing in Al tolerance, as determined by primary root length ratio, total root length ratio, and root tip number ratio under Al stress. Serious root necrosis was observed in PI 567731, but not in Magellan under Al stress. An F8 recombinant inbred line population derived from a cross between Magellan and PI 567731 was used to map the quantitative trait loci (QTL) for Al tolerance. Three QTL on chromosomes 3, 13, and 20, with tolerant alleles from Magellan, were identified. qAl_Gm13 and qAl_Gm20 explained large phenotypic variations (13–27%) and helped maintain root elongation and initiation under Al stress. In addition, qAl_Gm13 and qAl_Gm20 were confirmed in near-isogenic backgrounds and were identified to epistatically regulate Al tolerance via internal detoxification instead of Al3+ exclusion. Phylogenetic and pedigree analysis identified the tolerant alleles of both loci derived from the US ancestral line, A.K.[FC30761], originally from China. Our results provide novel genetic resources for breeding Al-tolerant soybean and suggest that internal detoxification contributes to soybean tolerance to excessive soil Al.
- Published
- 2020
46. Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes
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Gaurav Agarwal, Rupesh Deshmukh, Shuai Zeng, Nitika Rana, Gunvant Patil, Trupti Joshi, Yang Liu, Henry T. Nguyen, Humira Sonah, and Rajeev K. Varshney
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Protein domain ,Plant Science ,Computational biology ,Biology ,01 natural sciences ,Genome ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genetics ,Gene ,Phylogeny ,Plant Proteins ,Gene Expression Profiling ,Transporter ,Cell Biology ,General Medicine ,Transmembrane protein ,Transmembrane domain ,030104 developmental biology ,Membrane protein ,Soybeans ,Genome, Plant ,010606 plant biology & botany - Abstract
Transporters, a class of membrane proteins that facilitate exchange of solutes including diverse molecules and ions across the cellular membrane, are vital component for the survival of all organisms. Understanding plant transporters is important to get insight of the basic cellular processes, physiology, and molecular mechanisms including nutrient uptake, signaling, response to external stress, and many more. In this regard, extensive analysis of transporters predicted in soybean and other plant species was performed. In addition, an integrated database for soybean transporter protein, SoyTD, was developed that will facilitate the identification, classification, and extensive characterization of transporter proteins by integrating expression, gene ontology, conserved domain and motifs, gene structure organization, and chromosomal distribution features. A comprehensive analysis was performed to identify highly confident transporters by integrating various prediction tools. Initially, 7541 transmembrane (TM) proteins were predicted in the soybean genome; out of these, 3306 non-redundant transporter genes carrying two or more transmembrane domains were selected for further analysis. The identified transporter genes were classified according to a standard transporter classification (TC) system. Comparative analysis of transporter genes among 47 plant genomes provided insights into expansion and duplication of transporter genes in land plants. The whole genome resequencing (WGRS) and tissue-specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profile associated with transporter(s) of interest. Overall, SoyTD provides a comprehensive interface to study genetic and molecular function of soybean transporters. SoyTD is publicly available at http://artemis.cyverse.org/soykb_dev/SoyTD/.
- Published
- 2020
47. Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population
- Author
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Silvas J. Prince, Tri D. Vuong, Xiaolei Wu, Yonghe Bai, Fang Lu, Siva P. Kumpatla, Babu Valliyodan, J. Grover Shannon, and Henry T. Nguyen
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,quantitative trait loci (QTL) ,molecular markers ,Population ,Introgression ,Single-nucleotide polymorphism ,Plant Science ,Biology ,Quantitative trait locus ,lcsh:Plant culture ,01 natural sciences ,03 medical and health sciences ,single nucleotide polymorphism ,lcsh:SB1-1110 ,Allele ,education ,inter-specific genetic population ,Original Research ,Genetics ,education.field_of_study ,food and beverages ,biology.organism_classification ,KASP assay ,030104 developmental biology ,soybean (Glycine max) ,Seedling ,Glycine soja ,010606 plant biology & botany ,shoot and root architecture - Abstract
Wild soybean species (Glycine soja Siebold & Zucc.) comprise a unique resource to widen the genetic base of cultivated soybean [Glycine max (L.) Merr.] for various agronomic traits. An inter-specific mapping population derived from a cross of cultivar Williams 82 and PI 483460B, a wild soybean accession, was utilized for genetic characterization of root architecture traits. The objectives of this study were to identify and characterize quantitative trait loci (QTL) for seedling shoot and root architecture traits, as well as to determine additive/epistatic interaction effects of identified QTLs. A total of 16,469 single nucleotide polymorphisms (SNPs) developed for the Illumina beadchip genotyping platform were used to construct a high resolution genetic linkage map. Among the 11 putative QTLs identified, two significant QTLs on chromosome 7 were determined to be associated with total root length (RL) and root surface area (RSA) with favorable alleles from the wild soybean parent. These seedling root traits, RL (BARC_020495_04641 ~ BARC_023101_03769) and RSA (SNP02285 ~ SNP18129_Magellan), could be potential targets for introgression into cultivated soybean background to improve both tap and lateral roots. The RL QTL region harbors four candidate genes with higher expression in root tissues: Phosphofructokinase (Glyma.07g126400), Snf7 protein (Glyma.07g127300), unknown functional gene (Glyma.07g127900), and Leucine Rich-Repeat protein (Glyma.07g127100). The novel alleles inherited from the wild soybean accession could be used as molecular markers to improve root system architecture and productivity in elite soybean lines.
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- 2020
48. Genome-wide association mapping of flooding tolerance in soybean
- Author
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Chengjun Wu, Grover Shannon, Pengyin Chen, David Moseley, Henry T. Nguyen, Wade Hummer, Heng Ye, and Leandro Mozzoni
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,business.industry ,fungi ,Flooding (psychology) ,Linear model ,food and beverages ,Single-nucleotide polymorphism ,Genome-wide association study ,Plant Science ,Biology ,Best linear unbiased prediction ,01 natural sciences ,Biotechnology ,03 medical and health sciences ,030104 developmental biology ,Genetics ,Cultivar ,Association mapping ,business ,Agronomy and Crop Science ,Molecular Biology ,010606 plant biology & botany - Abstract
Flooding threatens soybean production and limits soybean yields worldwide. The most effective and economic approach to decrease loss of yield due to flooding is to develop flood-tolerant soybean cultivars. The objective of this study was to identify genetic loci and candidate genes associated with flooding tolerance. A panel of 384 soybean plant introductions (PIs) was evaluated for flooding tolerance in two consecutive years in the field. The plant foliar damage score was used to index soybean response to flooding stress. A total of 42,291 SNP markers were obtained from the Illumina Infinium SoySNP50K BeadChip database. After filtration for quality control, 31,125 SNPs were used for genome-wide association mapping utilizing four different models (regression linear model (GLM), mixed linear model (MLM), compressed mixed linear model (CMLM), and enriched compressed mixed linear model (ECMLM)). Fourteen SNPs were identified to be associated with flooding tolerance across all environments and models at a significance level of −Log10 (P) ≥ 2.5. Five SNPs were located within the coding regions of five candidate genes. Several PIs with lower best linear unbiased prediction (BLUPs) of the breeding values and a large number of favorable flood-tolerant alleles were found as new genetic sources for use in soybean breeding programs.
- Published
- 2019
49. Assessment of Phenotypic Variations and Correlation among Seed Composition Traits in Mutagenized Soybean Populations
- Author
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Naoufal Lakhssassi, Khalid Meksem, Tri D. Vuong, Mallory A Cullen, Abdelhalim El Baz, Henry T. Nguyen, and Zhou Zhou
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,TILLING ,Ethyl methanesulfonate ,correlation analysis ,Carbohydrates ,Mutagenesis (molecular biology technique) ,Biology ,01 natural sciences ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,chemical mutagenesis ,Genetic variation ,Genetics ,Plant Oils ,Plant breeding ,Genetics (clinical) ,Mutation breeding ,business.industry ,Fatty Acids ,fungi ,food and beverages ,mutation breeding ,Breed ,soybean oil composition traits ,Biotechnology ,Plant Breeding ,Phenotype ,030104 developmental biology ,chemistry ,Ethyl Methanesulfonate ,Mutation ,Seeds ,Soybean Proteins ,Soybeans ,business ,soybean meal traits ,010606 plant biology & botany - Abstract
Soybean [Glycine max (L.) Merr.] seed is a valuable source of protein and oil worldwide. Traditionally, the natural variations were heavily used in conventional soybean breeding programs to select desired traits. However, traditional plant breeding is encumbered with low frequencies of spontaneous mutations. In mutation breeding, genetic variations from induced mutations provide abundant sources of alterations in important soybean traits, this facilitated the development of soybean germplasm with modified seed composition traits to meet the different needs of end users. In this study, a total of 2366 &lsquo, Forrest&rsquo, derived M2 families were developed for both forward and reverse genetic studies. A subset of 881 M3 families was forward genetically screened to measure the contents of protein, oil, carbohydrates, and fatty acids. A total of 14 mutants were identified to have stable seed composition phenotypes observed in both M3 and M4 generations. Correlation analyses have been conducted among ten seed composition traits and compared to a collection of 103 soybean germplasms. Mainly, ethyl methanesulfonate (EMS) mutagenesis had a strong impact on the seed-composition correlation that was observed among the 103 soybean germplasms, which offers multiple benefits for the soybean farmers and industry to breed for desired multiple seed phenotypes.
- Published
- 2019
- Full Text
- View/download PDF
50. Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics
- Author
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Louise O'Donoughue, Davoud Torkamaneh, Jérôme Laroche, Elroy R. Cober, Jeremy Schmutz, François Belzile, Ricardo Vilela Abdelnoor, Avinash Sreedasyam, Henry T. Nguyen, Istvan Rajcan, Babu Valliyodan, DEPARTEMENT DE PHYTOLOGIE, UNIVERSITE LAVAL, QUEBEC CITY, INSTITUT DE BIOLOGIE INTEGRATIVE ET DES SYSTEMES (IBIS), UNIVERSITE LAVAL, QUEBEC CITY, NATIONAL CENTER FOR SOYBEAN BIOTECHNOLOGY AND DIVISION OF PLANT SCIENCES, UNIVERSITY OF MISSOURI, COLUMBIA, CEROM, CENTRE DE RECHERCHE SUR LES GRAINS INC., SAINT-MATHIEU DE BELOEIL, AGRICULTURE AND AGRI-FOOD CANADA, OTTAWA, DEPARTMENT OF PLANT AGRICULTURE, UNIVERSITY OF GUELPH, GUELPH, RICARDO VILELA ABDELNOOR, CNPSO, INSTITUTE FOR BIOTECHNOLOGY, HUDSONALPHA, HUNTSVILLE, and DEPARTEMENT DE PHYTOLOGIE, UNIVERSITE LAVAL, QUEBEC CITY.
- Subjects
0106 biological sciences ,0301 basic medicine ,haplotype ,Genotype ,Soja ,loss‐of‐function mutation ,Genomics ,Single-nucleotide polymorphism ,imputation ,Plant Science ,Biology ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Genetic variation ,soybean ,Genoma ,Genetic variance ,Research Articles ,Genetics ,Whole genome sequencing ,genetic variants ,Haplotype ,food and beverages ,haplotype map ,Plant Breeding ,030104 developmental biology ,Haplotypes ,Soybeans ,whole‐genome sequencing ,Agronomy and Crop Science ,Functional genomics ,Imputation (genetics) ,010606 plant biology & botany ,Biotechnology ,Genome-Wide Association Study ,Research Article - Abstract
Summary Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole‐genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single‐nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1‐Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene‐centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss‐of‐function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
- Published
- 2019
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