Research Project: Characterization of Genetic Diversity in Soybean and Common Bean, and Its Application toward Improving Crop Traits and Sustainable Production

Location: Soybean Genomics & Improvement Laboratory

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

Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans - (Peer Reviewed Journal)
Vuong, T.D., Florez-Palacios, L., Mozzoni, L., Clubb, M., Quigley, C.V., Song, Q., Kamad, S., Yuan, A., Chan, T., Mian, R.M., Nguyen, H. 2023. Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans. The Plant Genome. Article e20400. https://doi.org/10.1002/tpg2.20400.

Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains - (Peer Reviewed Journal)
Araya, S., Elia, P.E., Quigley, C.V., Song, Q. 2023. Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains. BMC Genomics. 24, Article number: 520 (2023). https://doi.org/10.1186/s12864-023-09627-4.

Determining genetic markers and seed characteristics related to high test weight in Glycine max - (Peer Reviewed Journal)
Shea, Z., Singer, W., Rsso, L., Song, Q., Zhang, B. 2023. Determining genetic markers and seed characteristics related to high test weight in Glycine max. Plants. 12(16):2997. https://doi.org/10.3390/plants12162997.

Genomic selection of soybean (Glycine max) for genomic improvement of yield and seed composition in a breeding context - (Peer Reviewed Journal)
Miller, M., Song, Q., Li, Z. 2023. Genomic selection of soybean (Glycine max) for genomic improvement of yield and seed composition in a breeding context. The Plant Genome. Article 20384. https://doi.org/10.1002/tpg2.20384.

Identification of quantitative trait loci controlling soybean seed protein and oil content - (Peer Reviewed Journal)
Clevinger, E., Biyashev, R., Haak, D., Song, Q., Pilot, G., Saghai Maroof, M. 2023. Identification of quantitative trait loci controlling soybean seed protein and oil content. PLOS ONE. https://doi.org/10.1371/journal.pone.0286329.

Genomic prediction of optimal cross combinations to accelerate genetic improvement of soybean (Glycine Max) - (Peer Reviewed Journal)
Miller, M., Song, Q., Fallen, B.D., Li, Z. 2023. Genomic prediction of optimal cross combinations to accelerate genetic improvement of soybean (Glycine Max). Crop Science. 14. Article e1171135. https://doi.org/10.3389/fpls.2023.1171135.

Recombination hotspots in soybean (Glycine Max (L.) Merr.) - (Peer Reviewed Journal)
McConaughy, S., Amundsen, K., Quigley, C.V., Pantalone, V., Hyten, D. 2023. Recombination hotspots in soybean (Glycine Max (L.) Merr.). G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkad075.

Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean - (Peer Reviewed Journal)
Yang, Q., Zhang, J., Shi, X., Chen, L., Qin, J., Zhang, M., Yang, C., Song, Q., Yan, L. 2023. Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean. Molecular Breeding. 43(4):p26. https://doi.org/10.1007/s11032-023-01372-6.

Genome-wide detection of quantitative trait loci and prediction of candidate genes for seed sugar composition in early mature soybean - (Peer Reviewed Journal)
Hu, L., Wang, X., Zhang, J., Florz-Palacios, L., Song, Q., Jiang, G. 2023. Genome-wide detection of quantitative trait loci and prediction of candidate genes for seed sugar composition in early mature soybean. International Journal of Molecular Sciences. 24:3167. https://doi.org/10.3390/ijms24043167.

Genetic architecture of protein and oil content in soybean seed and meal - (Peer Reviewed Journal)
Diers, B., Specht, J., Graef, G., Song, Q., Rainey, K.M., Ramasubramanian, V., Liu, X., Myers, C., Stupar, R., An, Y., Beavis, W. 2023. Genetic architecture of protein and oil content in soybean seed and meal. The Plant Genome. 16(1). Article e20308. https://doi.org/10.1002/tpg2.20308.

Genome-wide association study reveals novel loci and candidate gene for resistance to frogeye leaf spot (Cercospora sojina) in soybean - (Peer Reviewed Journal)
McDonald, S., Buck, J., Song, Q., Li, Z. 2023. Genome-wide association study reveals novel loci and candidate gene for resistance to frogeye leaf spot (Cercospora sojina) in soybean. Molecular Genetics and Genomics. https://doi.org/10.1007/s00438-022-01986-z.

Development of molecular inversion probes for soybean progeny genomic selection genotyping - (Peer Reviewed Journal)
Wang, H., Campbell, B., Happ, M., McConaughy, S., Lorenz, A., Amundsen, K., Song, Q., Pantalone, V., Hyten, D. 2022. Development of molecular inversion probes for soybean progeny genomic selection genotyping. The Plant Genome. Article e20270. https://doi.org/10.1002/tpg2.20270.

Genotype imputation for soybean nested association mapping population to improve precision of QTL detection - (Peer Reviewed Journal)
Chen, L., Yang, S., Araya, S., Quigley, C.V., Taliercio, E.W., Mian, R.M., Specht, J., Diers, B., Song, Q. 2022. Genotype imputation for soybean nested association mapping population to improve precision of QTL detection. Theoretical and Applied Genetics. 135(5), pp.1797-1810. https://doi.org/10.1007/s00122-022-04070-7.

Identification of candidate genes controlling soybean cyst nematode resistance in ‘Handou 10’ based on genomic and transcriptome analyses - (Peer Reviewed Journal)
Wei, H., Zhang, H.Y., Liang, Y., Li, J.Y., Li, H.C., Song, Q., Wu, Y., Lei, C.F., Wang, S.W., Wang, J.S., Lu, W.G. 2022. Identification of candidate genes controlling soybean cyst nematode resistance in ‘Handou 10’ based on genomic and transcriptome analyses. Frontiers in Plant Science. 13. Article 860034. https://doi.org/10.3389/fpls.2022.860034.

Genome-wide association study and genomic prediction for soybean cyst nematode resistance in USDA common bean (Phaseolus vulgaris) core collection - (Peer Reviewed Journal)
Shi, A., Gepts, P., Song, Q., Xiong, H., Michaels, T.E. 2021. Genome-wide association study and genomic prediction for soybean cyst nematode resistance in USDA common bean (Phaseolus vulgaris) core collection. Frontiers in Plant Science. 12:624156. https://doi.org/10.3389/fpls.2021.624156.

Common bean (Phaseolus vulgaris L.) with increased cysteine and methionine concentration - (Peer Reviewed Journal)
Viscarra-Torrico, R., Pajak, A., Garzon, A., Zhang, B., Pandurangan, S., Diapari, M., Song, Q., Conner, R.L., House, J.D., Miklas, P.N., Hou, A., Marsolais, F. 2021. Common bean (Phaseolus vulgaris L.) with increased cysteine and methionine concentration. Legume Science. https://doi.org/10.1002/leg3.103.

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding - (Peer Reviewed Journal)
Bayer, P.E., Valliyodari, B., Hu, H., Marsh, J., Yuan, Y., Vuong, T.D., Patil, G., Song, Q., Batley, J., Varshney, R.K., Lam, H., Edwards, D., Nguyen, H.T. 2021. Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome. 15(1):e20109. https://doi.org/10.1002/tpg2.20109.

Identification and characterization of novel QTL conferring internal detoxification of aluminium in soybean - (Peer Reviewed Journal)
Li, Y., Ye, H., Song, L., Vuong, T.D., Song, Q., Zhao, L., Shannon, J., Li, Y., Nguyen, H.T. 2021. Identification and characterization of novel QTL conferring internal detoxification of aluminium in soybean. Journal of Experimental Botany. 72(13):4993-5009. https://doi.org/10.1093/jxb/erab168.

Identification of quantitative disease resistance Loci towards four Pythium species in soybean - (Peer Reviewed Journal)
Clevinger, E., Biyashev, R., Lerch, E., Yu, H., Quigley, C.V., Song, Q., Dorrance, A., Robertson, A., Maroof, S. 2021. Identification of quantitative disease resistance Loci towards four Pythium species in soybean. Frontiers in Plant Science. 12:514. https://doi.org/10.3389/fpls.2021.644746.

NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean - (Peer Reviewed Journal)
Soler-Garzon, A., Oladzadabbasabadi, A., Beaver, J., Beebe, S., Lee, R., Lobaton, J., Macea, E., Mcclean, P., Raatz, B., Rosas, J.C., Song, Q., Miklas, P.N. 2021. NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean. Frontiers in Plant Science. 12. Article 628443. https://doi.org/10.3389/fpls.2021.628443.

Development of breeder-friendly KASP markers for low concentration of kunitz trypsin inhibitor in soybean seeds - (Peer Reviewed Journal)
Rosso, L., Shang, C., Escamilla, D.M., Gillenwater, J., Song, Q., Zhang, B. 2021. Development of breeder-friendly KASP markers for low concentration of kunitz trypsin inhibitor in soybean seeds. International Journal of Molecular Sciences. 22:2675. https://doi.org/10.3390/ijms22052675.

Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection - (Peer Reviewed Journal)
Zhang, B., Wang, M., Sun, Y., Zhao, P., Liu, C., Qing, K., Hu, X., Zhong, Z., Cheng, J., Wang, H., Pemg, Y., Shi, J., Zhuang, L., Du, S., He, M., Wu, H., Liu, M., Chen, S., Wang, H., Chen, X., Fan, W., Tian, K., Wang, Y., Chen, Q., Wang, S., Dong, F., Yang, C., Zhang, M., Song, Q., Li, Y., Wang, X. 2021. Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection. Nature Plants. 7:73-86. https://doi.org/10.1038/s41477-020-00832-7.

Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean - (Peer Reviewed Journal)
Costa, L.C., Nalin, R.S., Dias, M.A., Ferreira, M.E., Song, Q., Pastor Corrales, M.A., Hurtado-Gonzales, O.P., Souza, E.A. 2020. Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean. Theoretical and Applied Genetics. 134:543-556. https://doi.org/10.1007/s00122-020-03713-x.

Selection of GmSWEET39 for oil and protein improvement in soybean - (Peer Reviewed Journal)
Zhang, H., Goettel, W., Song, Q., Jiang, H., Hu, Z., Wang, M.L., An, Y. 2020. Selection of GmSWEET39 for oil and protein improvement in soybean. PLoS Genetics. 16(11).e1009114. https://doi.org/10.1371/journal.pgen.1009114.

Evolutionary population structure model reveals pleiotropic effects of GmPDAT for seed oil- and size-related traits in soybean - (Peer Reviewed Journal)
Liu, J.Y., Zhang, Y.W., Han, X., Zuo, J.F., Zhang, Z.B., Shang, H.H., Song, Q., Zhang, Y.M. 2020. Evolutionary population structure model reveals pleiotropic effects of GmPDAT for seed oil- and size-related traits in soybean. Journal of Experimental Botany. 71(22):6988-7002. https://doi.org/10.1093/jxb/eraa426.

Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.) - (Peer Reviewed Journal)
Zhu, Q., Escamilla, D.M., Wu, X., Song, Q., Li, S., Rosso, L., Lord, N., Xie, F., Zhang, B. 2020. Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.). Theoretical and Applied Genetics. 133(1):3165-3176. https://doi.org/10.1007/s00122-020-03662-5.

Soybean BARCSoySNP6K - An assay for soybean genetics and breeding research - (Peer Reviewed Journal)
Song, Q., Yan, L., Quigley, C.V., Fickus, E.W., Wei, H., Chen, L., Dong, F., Arya, S., Liu, J., Hyten, D., Pantalone, V., Nelson, R.L. 2020. Soybean BARCSoySNP6K - An assay for soybean genetics and breeding research. Plant Journal. https://doi.org/10.1111/tpj.14960.

QTL Mapping of Post-Processing Color Retention in Two Black Bean Populations - (Peer Reviewed Journal)
Bornowski, N., Song, Q., Kelly, J. 2020. QTL Mapping of Post-Processing Color Retention in Two Black Bean Populations. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-020-03656-3.

New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar - (Peer Reviewed Journal)
Goncalves-Vidigal, M.C., Gilio, T., Valentini, G., Vaz-Bisneta, M., Vidigal Filho, P.S., Song, Q., Oblessuc, P.R., Melotto, M. 2020. New Andean source of resistance to anthracnose and angular leaf spot: fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar. PLoS One. 15(6):e0235215. https://doi.org/10.1371/journal.pone.0235215.

Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism - (Peer Reviewed Journal)
Rambani, A., Pantalone, V., Yang, S., Rice, H., Song, Q., Mazarei, M., Arelli, P.R., Meksem, K., Stewart, N., Hewezi, T. 2020. Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism. New Phytologist. 227(1):168-184. https://doi.org/10.1111/nph.16511.

Toward validation of QTLs associated with pod and seed size in common bean using two nested recombinant inbred line populations - (Peer Reviewed Journal)
Murube, E., Campa, A., Song, Q., Mcclean, P., Ferreira, J.J. 2019. Toward validation of QTLs associated with pod and seed size in common bean using two nested recombinant inbred line populations. Molecular Breeding. 40:7. https://doi.org/10.1007/s11032-019-1085-1.

Natural variation in Portuguese common bean germplasm reveals new sources of resistance against Fusarium oxysporum f. sp. phaseoli and resistance-associated candidate genes - (Peer Reviewed Journal)
Leitao, S., Malosetti, M., Song, Q., Eeuwijk, F., Rubiales, D., Patto, M. 2020. Natural variation in Portuguese common bean germplasm reveals new sources of resistance against Fusarium oxysporum f. sp. phaseoli and resistance-associated candidate genes. Phytopathology. 110(3):663-647.

Genome wide association study and genomic selection of amino acid concentrations in soybean seeds - (Peer Reviewed Journal)
Qin, J., Shi, A., Song, Q., Li, S., Wang, F., Cao, Y., Ravelombola, W., Yang, C., Zhang, M. 2019. Genome wide association study and genomic selection of amino acid concentrations in soybean seeds. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01445.

Genomic selection for yield and seed composition traits within an applied soybean breeding program - (Peer Reviewed Journal)
Stewart-Brown, B.B., Song, Q., Vaughn, J., Li, Z. 2019. Genomic selection for yield and seed composition traits within an applied soybean breeding program . G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.118.200917.

Physiological and QTL analysis of slow canopy wilting trait for improvement of drought tolerance in soybean - (Peer Reviewed Journal)
Ye, H., Song, L., Schapaugh, W.T., Ali, L., Riar, M.K., Raymond, R.N., Li, Y., Vuong, T., Valliyodan, B., Neto, A.P., Klepadlo, M., Song, Q., Shannon, G.J., Pengyin, C., Nguyen, H.T. 2019. Physiological and QTL analysis of slow canopy wilting trait for improvement of drought tolerance in soybean. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/jxb/erz150.

Different loci associated with root and foliar resistance to sudden death syndrome (Fusarium virguliforme) in soybean - (Peer Reviewed Journal)
Tan, R., Collins, P.J., Wang, J., Wen, Z., Boyse, J.F., Laurenz, R., Gu, C., Jacobs, J.L., Song, Q., Chilvers, M.I., Wang, D. 2018. Different loci associated with root and foliar resistance to sudden death syndrome (Fusarium virguliforme) in soybean. Theoretical and Applied Genetics. 132:501-513. https://doi.org/10.1007/s00122-018-3237-9.