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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #434147

Research Project: Gene Discovery and Designing Soybeans for Food, Feed, and Industrial Applications

Location: Plant Genetics Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

A fast and cost-effective procedure for reliable measurement of trypsin inhibitor activity in soy and soy products - (Peer Reviewed Journal)

Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession Reprint Icon - (Peer Reviewed Journal)
Yang, Y., La, T., Gillman, J.D., Lyu, Z., Joshi, T., Usovsky, M., Song, Q., Scaboo, A. 2022. Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession. Frontiers in Plant Science. 13. Article 938100. https://doi.org/10.3389/fpls.2022.938100.

Soybean seed proteomics: methods for the isolation, detection, and identification of low aabundance proteins - (Peer Reviewed Journal)

Utilization of plant architecture genes in soybean to positively impact adaptation to high yield environments Reprint Icon - (Peer Reviewed Journal)
Kim, J., Scaboo, A., Pantalone, V., Li, Z., Bilyeu, K.D. 2022. Utilization of plant architecture genes in soybean to positively impact adaptation to high yield environments. Frontiers in Plant Science. 13. Article 891587. https://doi.org/10.3389/fpls.2022.891587.

Candidate genes modulating reproductive timing in elite US soybean lines identified in soybean alleles of Arabidopsis flowering orthologs with divergent latitude distribution Reprint Icon - (Peer Reviewed Journal)
Dietz, N., Chan, Y., Scaboo, A., Graef, G., Hyten, D., Happ, M., Diers, B., Lorenz, A., Wang, D., Joshi, T., Bilyeu, K.D. 2022. Candidate genes modulating reproductive timing in elite US soybean lines identified in soybean alleles of Arabidopsis flowering orthologs with divergent latitude distribution. Frontiers in Plant Science. 13. Article 889066. https://doi.org/10.3389/fpls.2022.889066.

A reverse GWAS approach with accuracy accentuation in soybean reveals the landscape of association for genomic variants and phenotypes - (Peer Reviewed Journal)

Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations Reprint Icon - (Peer Reviewed Journal)
Basnet, P., Meinhardt, C.G., Usovsky, M., Gillman, J.D., Joshi, T., Song, Q., Diers, B., Mitchum, M.G., Scaboo, A. 2022. Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations. Theoretical and Applied Genetics. 135:2025-2039. https://doi.org/10.1007/s00122-022-04091-2.

Confocal fluorescence microscopy investigation for the existence of subdomains within protein storage vacuoles in soybean cotyledons Reprint Icon - (Peer Reviewed Journal)
Krishnan, H.B., Jurkevich, A. 2022. Confocal fluorescence microscopy investigation for the existence of subdomains within protein storage vacuoles in soybean cotyledons. International Journal of Molecular Sciences. 23(7). Article 3664. https://doi.org/10.3390/ijms23073664.

Genomic prediction models for traits differing in heritability for soybean, rice, and maize Reprint Icon - (Peer Reviewed Journal)
Kaler, A.S., Purcell, L., Beissinger, T., Gillman, J.D. 2022. Genomic prediction models for traits differing in heritability for soybean, rice, and maize. Biomed Central (BMC) Plant Biology. 22. Article 87. https://doi.org/10.1186/s12870-022-03479-y.

Breeding of ‘DND358’: a new soybean cultivar for processing soy protein isolate with a hypocholesterolemic effect similar to that of fenofibrate Reprint Icon - (Peer Reviewed Journal)
Song, B., Qiu, Z., Li, M., Luo, T., Wu, Q., Krishnan, H.B., Wu, J., Xu, P., Zhang, S., Liu, S. 2022. Breeding of ‘DND358’: a new soybean cultivar for processing soy protein isolate with a hypocholesterolemic effect similar to that of fenofibrate. Journal of Functional Foods. 90. Article 104979. https://doi.org/10.1016/j.jff.2022.104979.

Phenotyping and quantitative trait locus analysis for the limited transpiration trait in an upper-mid south soybean recombinant inbred line population (“Jackson” × “KS4895”): high throughput aquaporin inhibitor screening Reprint Icon - (Peer Reviewed Journal)
Sarkar, S., Shekoofa, A., Mcclure, A., Gillman, J.D. 2022. Phenotyping and quantitative trait locus analysis for the limited transpiration trait in an upper-mid south soybean recombinant inbred line population (“Jackson” × “KS4895”): high throughput aquaporin inhibitor screening. Frontiers in Plant Science. 12. Article 779834. https://doi.org/10.3389/fpls.2021.779834.

Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean Reprint Icon - (Peer Reviewed Journal)
Dietz, N., Combs-Giroir, R., Cooper, G., Stacey, M., Miranda, C., Bilyeu, K.D. 2021. Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean. Biomed Central (BMC) Plant Biology. 21. Article 441. https://doi.org/10.1186/s12870-021-03197-x.

Utilization of tofu processing wastewater as a source of the bioactive peptide lunasin Reprint Icon - (Peer Reviewed Journal)
Nieto-Veloza, A., Zhong, Q., Kim, W., D'Souzaa, D., Krishnan, H.B., Dia, V.P. 2021. Utilization of tofu processing wastewater as a source of the bioactive peptide lunasin. Food Chemistry. 362. Article 130220. https://doi.org/10.1016/j.foodchem.2021.130220.

Development of soybean experimental lines with enhanced protein and sulfur amino acid content - (Peer Reviewed Journal)

Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes Reprint Icon - (Peer Reviewed Journal)
Zeng, S., Skrabisova, M., Lyu, Z., Chan, Y., Dietz, N., Bilyeu, K.D., Joshi, T. 2021. Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes. International Journal of Data Mining and Bioinformatics. 25(1-2):65-85. https://doi.org/10.1504/IJDMB.2021.116886.

Adenanthera pavonina, a potential plant-based protein resource: seed protein composition and immunohistochemical localization of trypsin inhibitors Reprint Icon - (Peer Reviewed Journal)
Krishnan, H.B., Kim, S., Pereira, A.E., Jurkevich, A., Hibbard, B.E. 2022. Adenanthera pavonina, a potential plant-based protein resource: seed protein composition and immunohistochemical localization of trypsin inhibitors. Food Chemistry: X. 13. Article 100253. https://doi.org/10.1016/j.fochx.2022.100253.

Title: Hypermethylation of miRNA genes during nodule development Reprint Icon - (Peer Reviewed Journal)
Piya, S., Lopes-Caitar, V., Kim, W., Pantalone, V., Krishnan, H.B., Hewezi, T. 2021. Title: Hypermethylation of miRNA genes during nodule development. Frontiers in Molecular Biosciences. 8. Article e616623. https://doi.org/10.3389/fmolb.2021.616623.

Genomic prediction using training population design in interspecific soybean populations Reprint Icon - (Peer Reviewed Journal)
Beche, E., Gillman, J.D., Song, Q., Nelson, R.L., Beissinger, T., Decker, J., Shannon, G., Scaboo, A.M. 2021. Genomic prediction using training population design in interspecific soybean populations. Molecular Breeding. 41. Article e15. https://doi.org/10.1007/s11032-021-01203-6.

SNPViz v2.0: A web-based tool for enhanced haplotype analysis using large scale resequencing datasets and discovery of phenotypes causative gene using allelic variations Reprint Icon - (Proceedings)
Zeng, S., Skrabisova, M., Lyu, Z., Chan, Y., Bilyeu, K.D., Joshi, T. 2021. SNPViz v2.0: A web-based tool for enhanced haplotype analysis using large scale resequencing datasets and discovery of phenotypes causative gene using allelic variations. Bioinformatics. 1408-1415. https://doi.org/10.1109/BIBM49941.2020.9313539.

Quantitative trait locus mapping for resistance to heat-induced seed degradation and low seed phytic acid in soybean Reprint Icon - (Peer Reviewed Journal)
Gillman, J.D., Chebrolu, K., Smith, J.R. 2021. Quantitative trait locus mapping for resistance to heat-induced seed degradation and low seed phytic acid in soybean. Crop Science. 61(3):2023–2035. https://doi.org/10.1002/csc2.20419.

Lunasin protease inhibitor concentrate decreases proinflammatory cytokines and improves histopathological markers in dextran sodium sulfate-induced ulcerative colitis - (Peer Reviewed Journal)

Molecular-assisted breeding for soybean with high oleic/low linolenic acid and elevated vitamin e in the seed oil Reprint Icon - (Peer Reviewed Journal)
Hagely, K., Konda, A.R., Kim, J., Cahoon, E., Bilyeu, K.D. 2021. Molecular-assisted breeding for soybean with high oleic/low linolenic acid and elevated vitamin e in the seed oil. Molecular Breeding. 41. Article e3. https://doi.org/10.1007/s11032-020-01184-y.

Overexpression of ATP sulfurylase improves the sulfur amino acid content, enhances the accumulation of Bowman-Birk protease inhibitor and suppresses the accumulation of the b-subunit of b-conglycinin in soybean seeds Reprint Icon - (Peer Reviewed Journal)
Kim, W., Kim, S.N., Oehrle, N.W., Jez, J.M., Krishnan, H.B. 2020. Overexpression of ATP sulfurylase improves the sulfur amino acid content, enhances the accumulation of Bowman-Birk protease inhibitor and suppresses the accumulation of the b-subunit of b-conglycinin in soybean seeds. Scientific Reports. 10. Article e14989. https://doi.org/10.1038/s41598-020-72134-z.

Effect of heat stress on seed protein composition and ultrastructure of protein storage vacuoles in the cotyledonary parenchyma cells of soybean genotypes that are either tolerant or sensitive to elevated temperatures Reprint Icon - (Peer Reviewed Journal)
Krishnan, H.B., Kim, W., Oehrle, N.W., Smith, J.R., Gillman, J.D. 2020. Effect of heat stress on seed protein composition and ultrastructure of protein storage vacuoles in the cotyledonary parenchyma cells of soybean genotypes that are either tolerant or sensitive to elevated temperatures. International Journal of Molecular Sciences. 21(13). Article 4775. https://doi.org/10.3390/ijms21134775.

Soybean mutants lacking abundant seed storage proteins are impaired in mobilization of storage reserves and germination Reprint Icon - (Peer Reviewed Journal)
Wei, X., Kim, W., Song, B., Oehrle, N.W., Liu, S., Krishnan, H.B. 2020. Soybean mutants lacking abundant seed storage proteins are impaired in mobilization of storage reserves and germination. ACS Omega. 5(14):8065-8075. https://doi.org/10.1021/acsomega.0c00128.

The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments Reprint Icon - (Peer Reviewed Journal)
Miranda, C.A., Scaboo, A., Cober, E., Denwar, N., Bilyeu, K.D. 2020. The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments. Biomed Central (BMC) Plant Biology. 20:65. https://doi.org/10.1186/s12870-020-2276-y.

Nested association mapping of important agronomic traits in three interspecific soybean populations Reprint Icon - (Peer Reviewed Journal)
Beche, E., Gillman, J.D., Song, Q., Nelson, R.L., Beissinger, T., Decker, J., Shannon, G., Scaboo, A.M. 2020. Nested association mapping of important agronomic traits in three interspecific soybean populations. Theoretical and Applied Genetics. 133:1039-1054. https://doi.org/10.1007/s00122-019-03529-4.

Comparing different statistical models and multiple testing corrections for association mapping in soybean and maize Reprint Icon - (Peer Reviewed Journal)
Kaler, A.S., Gillman, J.D., Beissinger, T., Purcell, L.C. 2020. Comparing different statistical models and multiple testing corrections for association mapping in soybean and maize. Frontiers in Plant Science. 10:1794. https://doi.org/10.3389/fpls.2019.01794.

Field performance of high oleic soybeans with mutant FAD2-1A and FAD2-1B genes in Tennessee Reprint Icon - (Peer Reviewed Journal)
Darr, L., Cunicelli, M., Bhandari, H., Bilyeu, K.D., Chen, F., Hewezi, T., Li, Z., Sams, C., Pantalone, V. 2020. Field performance of high oleic soybeans with mutant FAD2-1A and FAD2-1B genes in Tennessee. Journal of the American Oil Chemists' Society. 97:49-56. https://doi.org/10.1002/aocs.12306.

Proteomic comparison of three extraction methods reveals the abundance of protease inhibitors in the seeds of grass pea, a unique orphan legume Reprint Icon - (Peer Reviewed Journal)
Miranda, C.A., Xu, Q., Oehrle, N.W., Islam, N., Garrett, W.M., Natarajan, S.S., Gillman, J.D., Krishnan, H.B. 2019. Proteomic comparison of three extraction methods reveals the abundance of protease inhibitors in the seeds of grass pea, a unique orphan legume. Journal of Agricultural and Food Chemistry. 67(37):10296-10305. https://doi.org/10.1021/acs.jafc.9b04307.

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 Reprint Icon - (Peer Reviewed Journal)
Gillman, J.D., Biever, J.J., Ye, S., Spollen, W.G., Givan, S.A., Lyu, Z., Joshi, T., Smith, J.R., Fritschi, F.B. 2019. 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. BMC Research Notes. 12:522. https://doi.org/10.1186/s13104-019-4559-7.

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 a-linolenic acid phenotype in soybean Reprint Icon - (Peer Reviewed Journal)
Do, P.T., Nguyen, C.X., Bui, H.T., Tran, L.T., Stacey, G., Gillman, J.D., Zhang, Z.J., Stacey, M.G. 2019. 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 a-linolenic acid phenotype in soybean. Biomed Central (BMC) Plant Biology. 19:311. https://doi.org/10.1186/s12870-019-1906-8.

BG-4 from bitter gourd (Momordica charantia) differentially affects inflammation in vitro and in vivo Reprint Icon - (Peer Reviewed Journal)
Nieto-Veloza, A., Wang, Z., Zhong, Q., Krishnan, H.B., Dia, V.P. 2019. BG-4 from bitter gourd (Momordica charantia) differentially affects inflammation in vitro and in vivo. Antioxidants. 8(6):175. https://doi.org/10.3390/antiox8060175.

Biochemical and anatomical investigation of Sesbania herbacea (Mill.) McVaugh nodules grown under flooded and non-flooded conditions Reprint Icon - (Peer Reviewed Journal)
Krishnan, H.B., Oehrle, N.W., Alaswad, A.A., Stevens, W., John, M.K., Luthria, D.L., Natarajan, S.S. 2019. Biochemical and anatomical investigation of Sesbania herbacea (Mill.) McVaugh nodules grown under flooded and non-flooded conditions. International Journal of Molecular Sciences. 20(8):1824. https://doi.org/10.3390/ijms20081824.

Novel alleles of FAD2-1A induce high levels of oleic acid in soybean oil Reprint Icon - (Peer Reviewed Journal)
Combs, R., Bilyeu, K.D. 2019. Novel alleles of FAD2-1A induce high levels of oleic acid in soybean oil. Molecular Breeding. 39:79. https://doi.org/10.1007/s11032-019-0972-9.

Environmental stability study of soybeans with modified carbohydrate profiles in maturity groups 0 to V Reprint Icon - (Peer Reviewed Journal)
Jo, H., Lorenz, A., Rainey, K., Shannon, J., Chen, P., Bilyeu, K.D. 2019. Environmental stability study of soybeans with modified carbohydrate profiles in maturity groups 0 to V. Crop Science. 59(4):1531-1543. https://doi.org/10.2135/cropsci2018.09.0600.

Draft genome sequence of bradyrhizobium sp. Strain LVM 105, a nitrogen-fixing symbiont of chamaecrista fasciculata (michx) greene Reprint Icon - (Peer Reviewed Journal)
Krishnan, H.B., Kim, W., Givan, S.A. 2019. Draft genome sequence of bradyrhizobium sp. Strain LVM 105, a nitrogen-fixing symbiont of chamaecrista fasciculata (michx) greene. Microbiology Resource Announcements. 8(14):e00132-19. https://doi.org/10.1128/MRA.00132-19.

Classical soybean (Glycine max (L.) Merr) symbionts, Sinorhizobium fredii USDA191 and Bradyrhizobium diazoefficiens USDA110, reveal contrasting symbiotic phenotype on pigeon pea (Cajanus cajan (L.) Millsp) Reprint Icon - (Peer Reviewed Journal)
Alaswad, A.A., Oehrle, N.W., Krishnan, H.B. 2019. Classical soybean (Glycine max (L.) Merr) symbionts, Sinorhizobium fredii USDA191 and Bradyrhizobium diazoefficiens USDA110, reveal contrasting symbiotic phenotype on pigeon pea (Cajanus cajan (L.) Millsp). International Journal of Molecular Sciences. 20(5):1091. https://doi.org/10.3390/ijms20051091.

Impact of co-expression of maize 11 and 18 kDa delta-zeins and 27 kDa gamma-zein in transgenic soybeans on protein body structure and sulfur amino acid content Reprint Icon - (Peer Reviewed Journal)
Kim, W., Krishnan, H.B. 2018. Impact of co-expression of maize 11 and 18 kDa delta-zeins and 27 kDa gamma-zein in transgenic soybeans on protein body structure and sulfur amino acid content. Plant Science. 280:340-347. https://doi.org/10.1016/j.plantsci.2018.12.016.

Transcriptomic profiling of Lathyrus sativus L. metabolism of ß-ODAP, a neuroexcitatory amino acid associated with neurodegenerative lower limb paralysis Reprint Icon - (Peer Reviewed Journal)
Xu, Q., Liu, F., Qu, R., Gillman, J.D., Bi, C., Hu, X., Chen, P., Krishnan, H.B. 2018. Transcriptomic profiling of Lathyrus sativus L. metabolism of ß-ODAP, a neuroexcitatory amino acid associated with neurodegenerative lower limb paralysis. Plant Molecular Biology Reporter. 36(5-6):832-843. https://doi.org/10.1007/s11105-018-1123-x.

Context-specific genomic selection strategies outperform phenotypic selection for soybean quantitative traits in the progeny row stage Reprint Icon - (Peer Reviewed Journal)
Smallwood, C., Saxton, A., Gillman, J.D., Bhandari, H., Wadl, P.A., Fallen, B., Hyten, D., Song, Q., Pantalone, V. 2019. Context-specific genomic selection strategies outperform phenotypic selection for soybean quantitative traits in the progeny row stage. Crop Science. 59(1):54-67. https://doi.org/10.2135/cropsci2018.03.0197.

Identification and characterization of beta-lathyrin, an abundant glycoprotein of grass pea (Lathyrus sativus L.), as a potential allergen Reprint Icon - (Peer Reviewed Journal)
Xu, Q., Song, B., Liu, F., Song, Y., Chen, P., Liu, S., Krishnan, H.B. 2018. Identification and characterization of beta-lathyrin, an abundant glycoprotein of grass pea (Lathyrus sativus L.), as a potential allergen. Journal of Agricultural and Food Chemistry. 66(32):8496-8503. https://doi.org/10.1021/acs.jafc.8b02314.