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United States Department of Agriculture

Agricultural Research Service

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Research Project: Defining the Genetic Diversity and Structure of the Soybean Genome and Applications to Gene Discovery in Soybean, Wheat and Common Bean Germplasm

Location: Soybean Genomics & Improvement Laboratory

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

Genome-wide association analysis for drought tolerance and associated traits in common bean - (Peer Reviewed Journal)

Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea - (Peer Reviewed Journal)
Schneider, R., Rolling, W., Song, Q., Cregan, P., Dorrance, A.E., Mchale, L.K. 2016. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea. BMC Genomics. 17:607. doi:10.1186/s12864-016-2918-5.

Genome-wide association study of anthracnose resistance in Andean beans - (Peer Reviewed Journal)
Zuiderveen, G.H., Padder, B.A., Kamfwa, K., Song, Q., Kelly, J.D. 2016. Genome-wide association study of anthracnose resistance in Andean beans. PLoS One. 11(6):e0156391.

Multi-population selective genotyping to identify soybean (Glycine max (L.) Merr.) seed protein and oil QTLs - (Peer Reviewed Journal)
Phansak, P., Soonsuwon, W., Hyten, D., Song, Q., Cregan, P.B., Graef, G.L., Broman, K.W., Specht, J.E. 2016. Multi-Population Selective Genotyping to Identify Soybean (Glycine max (L.) Merr.) Seed Protein and Oil QTLs. Genes, Genomes, Genetics. doi:10.1534/g3.116.027656.

Classical and molecular genetic mapping - (Book / Chapter)

Mapping snap bean (Phaseolus vulgaris L.) pod and color traits, in a dry bean x snap bean recombinant inbred population - (Peer Reviewed Journal)
Hagerty, C.H., Cuesta-Marcos, A., Cregan, P., Song, Q., Mcclean, P., Myers, J.R. 2016. Mapping snap bean (Phaseolus vulgaris L.) pod and color traits, in a dry bean x snap bean recombinant inbred population. Journal of the American Society for Horticultural Science. 141(2):131-138.

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 Reprint Icon - (Peer Reviewed Journal)
Song, Q., Jenkins, J., Jia, G., Hyten, D., Pantalone, V., Jackson, S.A., Schmutz, J., Cregan, P. 2016. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. Biomed Central (BMC) Genomics. 17:33-44.

Identify and validate a quantitative trait locus underlying stearic acid on chromosome 14 in a soybean landrace using recombinant inbred lines and resident heterozygous lines - (Peer Reviewed Journal)
Yan, L., Deng, Y., Song, Q., Cregan, P., Chen, P., Lei, Y., Chen, Q., Di, R., Liu, B., Zhang, M. 2016. Identify and validate a quantitative trait locus underlying stearic acid on chromosome 14 in a soybean landrace using recombinant inbred lines and resident heterozygous lines. Journal of Crop Improvement. 30(2):152-164.

Estimation of genetic parameters and their sampling variances of quantitative traits in the type 2 modified augmented design - (Peer Reviewed Journal)
You, F.M., Song, Q., Yanzhao, C., Duguid, S., Booker, H., Cloutier, S. 2016. Estimation of genetic parameters and their sampling variances of quantitative traits in the type 2 modified augmented design. The Crop Journal. doi: 10.1016/j.cj.2016.01.003.

Genetic dissection of heterosis using epistatic QTL mapping in partial NCII mating design - (Peer Reviewed Journal)
Wen, J., Bu, S., Wu, G., Xiang, D., Yi, C., Zhang, J., Song, Q., Zhang, T., Zhang, Y. 2015. Genetic dissection of heterosis using epistatic QTL mapping in partial NCII mating design. Scientific Reports. 5:18376. doi: 10.1038/srep18376.

Genome-wide association study and marker-based selection for seed weight in soybean (Glycine max) - (Peer Reviewed Journal)
Zhang, J., Song, Q., Cregan, P., Jiang, G. 2015. Genome-wide association study and marker-based selection for seed weight in soybean (Glycine max). Theoretical and Applied Genetics. doi: 10.1007/s00122-015-2614-x.

SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research - (Peer Reviewed Journal)
Song, Q., Jia, G., Hyten, D.L., Jenkins, J., Hwang, E., Schroeder, S.G., Schmutz, J., Jackson, S.A., Mcclean, P., Cregan, P. 2015. SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research. G3, Genes/Genomes/Genetics. doi: 10.1534/g3.115.020594.

Genomic consequences of selection and genome-wide association mapping in soybean Reprint Icon - (Peer Reviewed Journal)
Wen, Z., Boyse, J.F., Song, Q., Cregan, P., Wang, D. 2015. Genomic consequences of selection and genome-wide association mapping in soybean. Biomed Central (BMC) Genomics. 16:671.

Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris) Reprint Icon - (Peer Reviewed Journal)
Hagerty, C.H., Cuesta-Marcos, A., Cregan, P., Song, Q., Mcclean, P.E., Noffsinger, S., Myers, J.R. 2015. Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris). Crop Science. 55(5):1969-1977.

Fingerprinting soybean germplasm and its utility in genomic research Reprint Icon - (Peer Reviewed Journal)
Song, Q., Hyten, D.L., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., Cregan, P. 2015. Fingerprinting soybean germplasm and its utility in genomic research. G3, Genes/Genomes/Genetics. 5(9):1-17.

A population structure and genome-wide association analysis on the USDA soybean germplasm collection Reprint Icon - (Peer Reviewed Journal)
Bandillo, N., Jarquin, D., Song, Q., Cregan, P., Nelson, R.L., Specht, J., Lorenz, A. 2015. A population structure and genome-wide association analysis on the USDA soybean germplasm collection. The Plant Genome. 8(3):1-13.

Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris) - (Peer Reviewed Journal)
Hagerty, C.H., Cuesta-Marcos, A., Cregan, P.B., Song, Q., Mcclean, P.E., Noffsinger, S., Myers, J.R. 2015. Mapping Fusarium solani and Aphanomyces euteiches root rot resistance and root architecture quantitative trait loci in common bean (Phaseolus vulgaris). Crop Science. 55:1969-1977.

Fine mapping and characterization of candidate genes that control resistance to Cercospora Sojina K. Hara in two soybean germplasm accessions Reprint Icon - (Peer Reviewed Journal)
Pham, A., Harris, D., Buck, J., Serrano, J., Abdel-Haleem, H., Song, Q., Cregan, P.B., Borema, H.R., Li, Z. 2015. Fine mapping and characterization of candidate genes that control resistance to Cercospora Sojina K. Hara in two soybean germplasm accessions. PLoS One. DOI:10.1371/journal.pone.0126753.

Genome-wide association mapping of flowering time and maturity dates in early mature soybean germplasm - (Peer Reviewed Journal)
Zhang, J., Song, Q., Cregan, P.B., Nelson, R.L., Wu, J., Jiang, G. 2015. Genome-wide association mapping of flowering time and maturity dates in early mature soybean germplasm. Biomed Central (BMC) Genomics. 16(1):217. doi:10.1186/s12864-015-1441-4.

Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method - (Peer Reviewed Journal)
Ling, Z., Shi-B0, W., Rongjun, H., Qing-Chun, G., Jia, W., Song, Q., Zhenzhen, W., Guang-Jun, L., Yu-Qin, L., Jianbo, J., Yuan, N., Li, Z., Wen-Long, R., Yuan-Ming, Z. 2015. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Scientific Reports. 5:9350.

Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean - (Peer Reviewed Journal)
Wen, Z., Tan, R., Yuan, J., Bales, C., Du, W., Zhang, S., Chilvers, M., Schmidt, C., Song, Q., Cregan, P.B., Kull, L., Wang, D. 2014. Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean. Biomed Central (BMC) Genomics. 15:809.

Quantitative trait locus analysis of seed sulfur containing amino acids in two recombinant inbred line populations of soybean - (Peer Reviewed Journal)
Xianzhi, W., Jiang, G., Song, Q., Cregan, P.B., Scott, R.A., Zhang, J., Yen, Y., Brown, M. 2014. Quantitative trait locus analysis of seed sulfur containing amino acids in two recombinant inbred line populations of soybean. Euphytica. DOI 10.1007/s10681-014-1223-0.

A roadmap for functional structural variants in the soybean genome - (Peer Reviewed Journal)
Anderson, J.E., Kantar, M.B., Kono, T.Y., Fu, F., Stec, A.O., Song, Q., Cregan, P.B., Specht, J.E., Diers, B.W., Cannon, S.B., McHale, L.K., Stupar, R.M. 2014. A roadmap for functional structural variants in the soybean genome. Genes, Genomes, Genetics. DOI:10.1534/g3.114.011551.

Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred populations of soybean - (Peer Reviewed Journal)
Wang, X., Jiang, G., Green, M., Scott, R.A., Song, Q., Hyten, D.L., Cregan, P.B. 2014. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred populations of soybean . Molecular Genetics and Genomics. DOI: 10.1007/s00438-014-0865-x.

Distinct copy number, coding sequence and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode - (Peer Reviewed Journal)
Cook, D.E., Bayless, A., Wang, K., Guo, X., Song, Q., Jiang, J., Bent, A.F. 2014. Distinct copy number, coding sequence and locus methylation patterns underlie Rhg1-mediated soybean resistance to soybean cyst nematode. Plant Physiology. 164(4):1-54 DOI:10.1104/pp.114.235952.

Last Modified: 2/23/2016
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