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1. Genomic prediction models for traits differing in heritability for soybean, rice, and maize

Author:
Jason D. Gillman,   et al.   ; Avjinder S. Kaler; Larry C. Purcell; Timothy Beissinger;     Show all 4 Authors
Source:
BMC plant biology 2022 v.22 no.1 pp. 87
ISSN:
1471-2229
Subject:
Glycine max; Oryza sativa; Zea mays; corn; genomics; genotype; heritability; linkage disequilibrium; marker-assisted selection; models; plant biology; prediction; rice; soybeans
Abstract:
... BACKGROUND: Genomic selection is a powerful tool in plant breeding. By building a prediction model using a training set with markers and phenotypes, genomic estimated breeding values (GEBVs) can be used as predictions of breeding values in a target set with only genotype data. There is, however, limited information on how prediction accuracy of genomic prediction can be optimized. The objective of ...
DOI:
10.1186/s12870-022-03479-y

2. Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations

Author:
Jason D. Gillman,   et al.   ; Pawan Basnet; Clinton G. Meinhardt; Mariola Usovsky; Trupti Joshi; Qijian Song; Brian Diers; Melissa G. Mitchum; Andrew M. Scaboo;     Show all 9 Authors
Source:
Theoretical and applied genetics 2022 v.135 no.6 pp. 2025-2039
ISSN:
0040-5752
Subject:
Heterodera glycines; alleles; cultivars; epistasis; genetic resistance; inbred lines; markets; quantitative traits; soybeans; virulence
Abstract:
... KEY MESSAGE: An epistatic interaction between SCN resistance loci rhg1-a and rhg2 in PI 90763 imparts resistance against virulent SCN populations which can be employed to diversify SCN resistance in soybean cultivars. With more than 95% of the $46.1B soybean market dominated by a single type of genetic resistance, breeding for soybean cyst nematode (SCN)-resistant soybean that can effectively comb ...
DOI:
10.1007/s00122-022-04091-2

3. Quantitative trait locus mapping for resistance to heat‐induced seed degradation and low seed phytic acid in soybean

Author:
Jason D. Gillman,   et al.   ; Kranthi Chebrolu; James R. Smith;     Show all 3 Authors
Source:
Crop science 2021 v.61 no.3 pp. 2023-2035
ISSN:
0011-183X
Subject:
Glycine max; backcrossing; bioavailability; climate change; cultivars; drought; early development; germination; germplasm; greenhouses; heat tolerance; inbred lines; introduced plants; marker-assisted selection; mutants; phosphorus; phytic acid; quantitative trait loci; seed quality; soybeans; water stress
Abstract:
... Soybean [Glycine max (L.) Merr.] reproductive structures are temperature‐sensitive, with a reproductive optimum of 22 to 24 °C. Currently, parts of the US soybean growing region experience consistent late‐season drought stress, resulting in the adoption of agronomic practices that favor early maturity groups. This approach is the Early Soybean Production System and has boosted yields and on‐farm r ...
Handle:
10113/7709381
DOI:
10.1002/csc2.20419

4. Genomic prediction using training population design in interspecific soybean populations

Author:
Jason D. Gillman,   et al.   ; Eduardo Beche; Qijian Song; Randall Nelson; Tim Beissinger; Jared Decker; Grover Shannon; Andrew M. Scaboo;     Show all 8 Authors
Source:
Molecular breeding 2021 v.41 no.2 pp. 15
ISSN:
1380-3743
Subject:
additive effect; alleles; gene pool; genetic improvement; genomics; germplasm; grain yield; introgression; marker-assisted selection; models; oils; phenotypic selection; population size; prediction; soybeans
Abstract:
... Agronomically important traits generally have complex genetic architecture, where many genes have a small and largely additive effect. Genomic prediction has been demonstrated to increase genetic gain and efficiency in plant breeding programs beyond marker-assisted selection and phenotypic selection. The objective of this study was to evaluate the impact of allelic origin, marker density, training ...
DOI:
10.1007/s11032-021-01203-6

5. Nested association mapping of important agronomic traits in three interspecific soybean populations

Author:
Jason D. Gillman,   et al.   ; Eduardo Beche; Qijian Song; Randall Nelson; Tim Beissinger; Jared Decker; Grover Shannon; Andrew M. Scaboo;     Show all 8 Authors
Source:
Theoretical and applied genetics 2020 v.133 no.3 pp. 1039-1054
ISSN:
0040-5752
Subject:
Glycine max; Glycine soja; alleles; chromosomes; gene pool; genetic background; genetic improvement; genetic variation; germplasm; grain yield; plant height; seed yield; soybeans
Abstract:
... KEY MESSAGE: Glycine soja germplasm can be used to successfully introduce new alleles with the potential to add valuable new genetic diversity to the current elite soybean gene pool. Given the demonstrated narrow genetic base of the US soybean production, it is essential to identify beneficial alleles from exotic germplasm, such as wild soybean, to enhance genetic gain for favorable traits. Nested ...
DOI:
10.1007/s00122-019-03529-4

6. Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Author:
Jason D. Gillman,   et al.   ; Thang La; Edward Large; Earl Taliercio; Qijian Song; Dong Xu; Henry T. Nguyen; Grover Shannon; Andrew Scaboo;     Show all 9 Authors
Source:
Crop science 2019 v.59 no.1 pp. 233-251
ISSN:
0011-183X
Subject:
Glycine max; Glycine soja; USDA; cultivars; genetic variation; genotype; germplasm conservation; grain yield; linolenic acid; oleic acid; phenotype; phenotypic variation; raffinose; seed oils; seed weight; soybeans; stachyose; Missouri; North Carolina
Abstract:
... The relatively low genetic variation of current US soybean [Glycine max (L.) Merr.] cultivars constrains the improvement of grain yield and other agronomic and seed composition traits. Recently, a substantial effort has been undertaken to introduce novel genetic diversity present in wild soybean (Glycine soja Siebold & Zucc.) into elite cultivars, in both public and private breeding programs. The ...
DOI:
10.2135/cropsci2017.08.0514

7. Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections

Author:
Jason D. Gillman,   et al.   ; Greg Ziegler; Randall Nelson; Stephanie Granada; Hari B. Krishnan; Ivan Baxter;     Show all 6 Authors
Source:
Plant direct 2018 v.2 no.1 pp. e00033
ISSN:
2475-4455
Subject:
USDA; genes; genetic analysis; germplasm; germplasm conservation; ionomics; linkage disequilibrium; nutritive value; soybeans
Abstract:
... The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elementa ...
DOI:
10.1002/pld3.33

8. Genotyping-by-sequencing-based investigation of the genetic architecture responsible for a ~sevenfold increase in soybean seed stearic acid

Author:
Jason D. Gillman,   et al.   ; Crystal B. Heim;     Show all 2 Author
Source:
G3-GenesGenomesGenetics 2017 v.7 no.1 pp. 299-308
ISSN:
2160-1836
Subject:
chromosome mapping; chromosomes; crossing; cultivars; functional properties; gene deletion; genes; hydrogenated oils; hydrogenation; inheritance (genetics); missense mutation; mutants; oxidative stability; quantitative trait loci; saturated fats; seed yield; soybean oil; soybeans; stearic acid; trans fatty acids
Abstract:
... Soybean oil is highly unsaturated but oxidatively unstable, rendering it nonideal for food applications. Until recently, the majority of soybean oil underwent partial chemical hydrogenation, which produces trans fats as an unavoidable consequence. Dietary intake of trans fats and most saturated fats are conclusively linked to negative impacts on cholesterol levels and cardiovascular health. Two ma ...
Handle:
10113/5607534
DOI:
10.1534/g3.116.035741
PubMed:
27866151
PubMed Central:
PMC5217118

9. Demonstration of highly efficient dual gRNA CRISPR/Cas9 editing of the homeologous GmFAD2–1A and GmFAD2–1B genes to yield a high oleic, low linoleic and α-linolenic acid phenotype in soybean

Author:
Jason D. Gillman,   et al.   ; Phat T. Do; Cuong X. Nguyen; Hien T. Bui; Ly T. N. Tran; Gary Stacey; Zhanyuan J. Zhang; Minviluz G. Stacey;     Show all 8 Authors
Source:
BMC plant biology 2019 v.19 no.1 pp. 311
ISSN:
1471-2229
Subject:
Agrobacterium; CRISPR-Cas systems; DNA; alleles; allotetraploidy; alpha-linolenic acid; breeding; crops; exons; fatty acid composition; gene editing; genotyping; homologous recombination; homozygosity; linoleic acid; mutants; mutation; oleic acid; phenotype; rhizogenesis; seeds; soybeans; stearoyl-CoA desaturase; transgenic plants
Abstract:
... BACKGROUND: CRISPR/Cas9 gene editing is now revolutionizing the ability to effectively modify plant genomes in the absence of efficient homologous recombination mechanisms that exist in other organisms. However, soybean is allotetraploid and is commonly viewed as difficult and inefficient to transform. In this study, we demonstrate the utility of CRISPR/Cas9 gene editing in soybean at relatively h ...
Handle:
10113/6540733
DOI:
10.1186/s12870-019-1906-8
PubMed:
31307375
PubMed Central:
PMC6632005

10. Transcriptomic Profiling of Lathyrus sativus L. Metabolism of β-ODAP, a Neuroexcitatory Amino Acid Associated with Neurodegenerative Lower Limb Paralysis

Author:
Jason D. Gillman,   et al.   ; Quanle Xu; Fengjuan Liu; Ruihong Qu; Chunxiao Bi; Xin Hu; Peng Chen; Hari B. Krishnan;     Show all 8 Authors
Source:
Plant molecular biology reporter 2018 v.36 no.5-6 pp. 832-843
ISSN:
0735-9640
Subject:
Lathyrus sativus; amino acids; gene expression regulation; metabolism; seed germination; seedlings; transcription (genetics); transcriptomics
Abstract:
... Grass pea (Lathyrus sativus L.) is a unique potential crop for marginal arid regions with untapped, exceptional biotic/abiotic stress tolerance, and high protein content seeds. High dietary intake of grass pea is associated with neurodegenerative lower limb paralysis, thought due to the compound β-N-oxalyl-L-α, β-diaminopropionic acid (β-ODAP). β-ODAP increases after seed germination and then decr ...
Handle:
10113/6275085
DOI:
10.1007/s11105-018-1123-x

11. Genetic analysis of teosinte alleles for kernel composition traits in maize

Author:
Jason D. Gillman,   et al.   ; Avinash Karn; Sherry A. Flint-Garcia;     Show all 3 Authors
Source:
G3 GenesGenomesGenetics 2017 v.7 no.4 pp. 1157-1164
ISSN:
2160-1836
Subject:
Zea mays subsp. parviglumis; agronomic traits; alleles; backcrossing; chromosome mapping; corn; domestication; genetic analysis; genetic variation; germplasm; isogenic lines; landraces; lipid content; near-infrared spectroscopy; nuclear magnetic resonance spectroscopy; oils; protein content; proteins; quantitative trait loci; seeds; starch; whole grain foods; Missouri; New York
Abstract:
... Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared to maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (teosinte NILs) was previously developed to broaden the resources for genetic diversity of mai ...
Handle:
10113/5700681
DOI:
10.1534/g3.117.039529
PubMed:
28188181
PubMed Central:
PMC5386864

12. Context‐Specific Genomic Selection Strategies Outperform Phenotypic Selection for Soybean Quantitative Traits in the Progeny Row Stage

Author:
Jason D. Gillman,   et al.   ; Christopher J. Smallwood; Arnold M. Saxton; Hem S. Bhandari; Phillip A. Wadl; Benjamin D. Fallen; David L. Hyten; Qijian Song; Vincent R. Pantalone;     Show all 9 Authors
Source:
Crop science 2019 v.59 no.1 pp. 54-67
ISSN:
0011-183X
Subject:
Glycine max; fatty acids; field experimentation; genotyping; inbred lines; lipid content; marker-assisted selection; oils; phenotype; phenotypic selection; prediction; progeny; quantitative traits; seed yield; single nucleotide polymorphism; soybeans; Tennessee
Abstract:
... Evaluating different breeding selection strategies for relative utility is necessary to choose those that maximize efficiency. Soybean [Glycine max (L.) Merr.] seed yield and fatty acid, protein, and oil contents are all commercially important traits that display complex quantitative inheritance. A soybean population consisting of 860 F₅–derived recombinant inbred lines (RILs), genotyped with 4867 ...
Handle:
10113/6471412
DOI:
10.2135/cropsci2018.03.0197

13. Proteomic Comparison of Three Extraction Methods Reveals the Abundance of Protease Inhibitors in the Seeds of Grass Pea, a Unique Orphan Legume

Author:
Jason D. Gillman,   et al.   ; Carrie Miranda; Quanle Xu; Nathan W. Oehrle; Nazrul Islam; Wesley M. Garrett; Savithiry S. Natarajan; Hari B. Krishnan;     Show all 8 Authors
Source:
Journal of agricultural and food chemistry 2019 v.67 no.37 pp. 10296-10305
ISSN:
1520-5118
Subject:
Lathyrus sativus; antinutritional factors; drought tolerance; enzymes; ethanol; famine; humans; isopropyl alcohol; legumes; mass spectrometry; nervous system diseases; neurotoxins; proteinase inhibitors; proteins; proteomics; seeds; spectral analysis
Abstract:
... Grass pea is an orphan legume that is grown in many places in the world. It is a high-protein, drought-tolerant legume that is capable of surviving extreme environmental challenges and can be a sole food source during famine. However, grass pea produces the neurotoxin β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a neurological disease. This crop is promising as a food source fo ...
DOI:
10.1021/acs.jafc.9b04307
CHORUS:
10.1021/acs.jafc.9b04307

14. A seed germination transcriptomic study contrasting two soybean genotypes that differ in terms of their tolerance to the deleterious impacts of elevated temperatures during seed fill

Author:
Jason D. Gillman,   et al.   ; Jessica Biever; Songqing Ye; William Spollen; Scott A. Givan; Zhen Lyu; Trupti Joshi; James R. Smith; Felix B. Fritschi;     Show all 9 Authors
Source:
BMC research notes 2019 v.12 no.522 pp. -
ISSN:
1756-0500
Subject:
Glycine max; filling period; gene expression; gene expression regulation; genotype; global warming; heat stress; heat tolerance; high-yielding varieties; landraces; physiological response; plant response; protein refolding; seed germination; soybeans; transcriptomics; Midwestern United States; Southeastern United States
Abstract:
... Objective: Soybean seed development is negatively impacted by elevated temperatures during seed fill, which can decrease seed quality and economic value. Prior germplasm screens identified an exotic landrace able to maintain ~95% seed germination under stress conditions that reduce germination dramatically (>50%) for typical soybean seeds. Seed transcriptomic analysis was performed for two soybean ...
Handle:
10113/6964455
DOI:
10.1186/s13104-019-4559-7

15. Identification of a New Soybean Kunitz Trypsin Inhibitor Mutation and Its Effect on Bowman−Birk Protease Inhibitor Content in Soybean Seed

Author:
Jason D. Gillman,   et al.   ; Won-Seok Kim; Hari B. Krishnan;     Show all 3 Authors
Source:
Journal of agricultural and food chemistry 2015 v.63 no.5 pp. 1352-1359
ISSN:
0021-8561
Subject:
Kunitz-type proteinase inhibitor; weight gain; polyacrylamide gel electrophoresis; antibodies; chymotrypsin; energy; essential amino acids; feed meals; gene overexpression; germplasm; heat treatment; homozygosity; mutants; mutation; proteome; seeds; soy protein; soybean meal; soybeans; trypsin
Abstract:
... Soybean seed contains antinutritional compounds that inactivate digestive proteases, principally corresponding to two families: Kunitz trypsin inhibitors (KTi) and Bowman–Birk inhibitors (BBI). High levels of raw soybean/soybean meal in feed mixtures can cause poor weight gain and pancreatic abnormalities via inactivation of trypsin/chymotrypsin enzymes. Soybean protein meal is routinely heat-trea ...
Handle:
10113/60531
DOI:
10.1021/jf505220p
CHORUS:
10.1021/jf505220p

16. Properties of Oleogels Formed With High‐Stearic Soybean Oils and Sunflower Wax

Author:
Jason D. Gillman,   et al.   ; Hong‐Sik Hwang; Jill K. Winkler‐Moser; Sanghoon Kim; Mukti Singh; Jeffrey A. Byars; Roque L. Evangelista;     Show all 7 Authors
Source:
The journal of the American Oil Chemists' Society 2018 v.95 no.5 pp. 557-569
ISSN:
0003-021X
Subject:
Helianthus annuus; ambient temperature; crystallization; firmness; hydrogenation; lipid content; oleogels; phase-contrast microscopy; soybean oil; soybeans; stearic acid; vegetables; viscoelasticity
Abstract:
... In an effort to develop alternatives for harmful trans fats produced by partial hydrogenation of vegetable oils, oleogels of high‐stearic soybean (A6 and MM106) oils were prepared with sunflower wax (SW) as the oleogelator. Oleogels of high‐stearic oils did not have greater firmness when compared to regular soybean oil (SBO) at room temperature. However, the firmness of high‐stearic oil oleogels a ...
DOI:
10.1002/aocs.12060

17. Identification of a plant introduction soybean line with genetic lesions affecting two distinct glycinin subunits and evaluation of impacts on protein content and composition

Author:
Jason D. Gillman,   et al.   ; Won-Seok Kim; Hari B. Krishnan;     Show all 3 Authors
Source:
Molecular breeding 2013 v.32 no.2 pp. 291-298
ISSN:
1380-3743
Subject:
Glycine max; fractionation; frameshift mutation; gene expression; genes; genetic lines; glycinin; introduced plants; messenger RNA; plant taxonomy; protein content; protein subunits; seeds; soybeans
Abstract:
... Unlike other oilseeds, soybean (Glycine max [L.] Merr) is also valuable due to its direct conversion into human food. One notable example is the cheese-like product tofu. The quality of tofu is improved when protein subunits derived from two glycinin genes, Gy1 and Gy4, are reduced or absent. Here we report the discovery that one exotic soybean plant introduction line, PI 605781 B, has not only a ...
DOI:
10.1007/s11032-013-9870-8

18. Phosphorus Partitioning of Soybean Lines Containing Different Mutant Alleles of Two Soybean Seed-Specific Adenosine Triphosphate-Binding Cassette Phytic Acid Transporter Paralogs

Author:
Jason D. Gillman,   et al.   ; Ivan Baxter; Kristin Bilyeu;     Show all 3 Authors
Source:
The plant genome 2013 v.6 no.1 pp. -
ISSN:
1940-3372
Subject:
ABC transporters; Glycine max; alleles; bioavailability; digestive enzymes; digestive tract; humans; minerals; missense mutation; mutants; new combination; nonsense mutation; phenotype; phosphates; phosphorus; phytic acid; poultry; seeds; single nucleotide polymorphism; soybean meal; soybeans; swine
Abstract:
... Seed phytate is a repository of P and minerals in soybean [Glycine max (L.) Merr.] seeds that limits P and mineral bioavailability for monogastric animals (e.g., humans, swine [Sus scrofa], and poultry [especially chicken, Gallus domesticus]) due to insufficient digestive tract phytase activity. We previously identified epistatic recessive mutations affecting two paralogous adenosine triphosphate- ...
Handle:
10113/55933
DOI:
10.3835/plantgenome2012.06.0010
CHORUS:
10.3835/plantgenome2012.06.0010

19. Identifying and exploring significant genomic regions associated with soybean yield, seed fatty acids, protein and oil

Author:
Jason D. Gillman,   et al.   ; Christopher J. Smallwood; Arnold M. Saxton; Hem S. Bhandari; Phillip A. Wadl; Benjamin D. Fallen; David L. Hyten; Qijian Song; Vincent R. Pantalone;     Show all 9 Authors
Source:
Journal of crop science and biotechnology 2017 v.20 no.4 pp. 243-253
ISSN:
1975-9479
Subject:
Glycine max; chromosomes; crop yield; field experimentation; genes; genomics; genotyping; inbred lines; linolenic acid; lipid content; pleiotropy; quantitative trait loci; single nucleotide polymorphism; soybean oil; soybeans; stearic acid; Tennessee
Abstract:
... Soybean [Glycine max (L.) Merrill] yield and seed fatty acids, protein, and oil content are important traits for which an improved understanding of significant genomic regions would be useful. To accomplish this, a soybean population consisting of 203 F5 derived recombinant inbred lines (RILs) was developed and genotyped with 11,633 polymorphic single nucleotide polymorphisms (SNPs). Each RIL was ...
Handle:
10113/5886728
DOI:
10.1007/s12892-017-0020-0

20. Impact of heat stress during seed development on soybean seed metabolome

Author:
Jason D. Gillman,   et al.   ; Kranthi K. Chebrolu; Felix B. Fritschi; Songqing Ye; Hari B. Krishnan; James R. Smith;     Show all 6 Authors
Source:
Metabolomics 2016 v.12 no.2 pp. 28
ISSN:
1573-3882
Subject:
Glycine max; antioxidants; climate change; genotype; genotype-environment interaction; germination; heat stress; heat tolerance; metabolites; metabolome; metabolomics; pathogens; seed development; seeds; soybeans; summer; temperature; tissues; United States
Abstract:
... Seed development is a temperature-sensitive process that is much more vulnerable than vegetative tissues to abiotic stresses. Climate change is expected to increase the incidence and severity of summer heatwaves, and the impact of heat stress on seed development is expected to become more widespread during the course of the 21st century. A recent change to soybean cultivation practices in the Mids ...
Handle:
10113/61846
DOI:
10.1007/s11306-015-0941-1