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ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Soybean Genomics & Improvement Laboratory People





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- Qijian Song RL
- Bret Cooper
- Marcial Pastor Corrales
- Savithiry Natarajan
- Mark Tucker

Qijian  Song    Research Geneticist Research LeaderSoybean Genomics and Improvement LaboratoryBeltsville Agricultural Research CenterUSDA-ARSBldg. 006 Rm. 10010300 Baltimore Ave,Beltsville, MD 20705, USA(301) 504-5337 **Description of Research Activities:** Research involves: Discovery of  genetic variants in soybean, wheat and common bean genomes through high throughput DNA and RNA sequence analysis; Development and application of molecular genetic markers and genomic research tools such as gene chips to identify QTL and genes controlling biotic and abiotic stress resistance, agronomic and quality traits; Identification of desirable genetic diversity for germplasm improvement; Application of knowledge of bioinformatics, biostatistics to breeding practice, genetics and genomics research; and Development of algorithms and computer programs for the genetic analysis of large datasets containing high throughput sequences and genotyping data. **Publications:**  Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Loss-of-function of an a-SNAP gene confers resistance to soybean cyst nematode-(Peer Reviewed Journal) Usovsky, M., Gamage, V.A., Meinhardt, C.G., Dietz, N., Triller, M., Basnet, P., Gillman, J.D., Bilyeu, K.D., Song, Q., Dhital, B., Nguyen, A., Mitchum, M.G., Scaboo, A. 2023. Loss-of-function of an a-SNAP gene confers resistance to soybean cyst nematode. Nature Communications. 14. Article 7629. https://doi.org/10.1038/s41467-023-43295-y.Cataloging SCN resistance loci in north american public soybean breeding programs-(Peer Reviewed Journal) Mahmood, A., Bilyeu, K.D., Skrabisova, M., Biova, J., De Meyer, E., Meinhardt, C., Usovsky, M., Song, Q., Lorenz, A., Mitchum, M., Shannon, G., Scaboo, A. 2023. Cataloging SCN resistance loci in north american public soybean breeding programs. Frontiers in Plant Genetics and Genomics. 14. Article 1270546. https://doi.org/10.3389/fpls.2023.1270546.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.Whole genome sequencing enables the molecular dissection and candidate gene identification of the rust resistance gene R12 in sunflower (Helianthus annuus L.)-(Peer Reviewed Journal) Ma, G., Talukder, M.I., Song, Q., Li, X., Qi, L. 2023. Whole genome sequencing enables the molecular dissection and candidate gene identification of the rust resistance gene R12 in sunflower (Helianthus annuus L.). Journal of Theoretical and Applied Genetics. 136. Article 143. https://doi.org/10.1007/s00122-023-04389-9.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.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.Analysis of the mitochondrial genome sequences of Diaporthe longicolla (syn. Phomopsis longicolla) isolates causing Phomopsis seed decay in soybean-(Abstract Only) Li, S., Hu, X., Song, Q., Arias, R.S. 2023. Analysis of the mitochondrial genome sequences of Diaporthe longicolla (syn. Phomopsis longicolla) isolates causing Phomopsis seed decay in soybean. Plant and Animal Genome Conference. https://plan.core-apps.com/pag_2023/abstract/963d7d6c9252da3647857a6b5d0808ac.Isoflavone composition of germinated soybeans after freeze-thaw-(Peer Reviewed Journal) Ji, W., Yang, T., Song, Q., Ma, M. 2022. Isoflavone composition of germinated soybeans after freeze-thaw. Food Research International. 16. Article 100493. https://doi.org/10.1016/j.fochx.2022.100493.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.Genetic insight into disease resistance gene clusters by using sequencing-based fine mapping in sunflower (Helianthus annuus L.)-(Peer Reviewed Journal) Ma, G., Song, Q., Li, X., Qi, L. 2022. Genetic insight into disease resistance gene clusters by using sequencing-based fine mapping in sunflower (Helianthus annuus L.). International Journal of Molecular Sciences. 23(17):9516. https://doi.org/10.3390/ijms23179516.Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession-(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.POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean-(Peer Reviewed Journal) Goettel, H.W., Zhang, H., Li, Y., Qiao, Z., Jiang, H., Hou, D., Song, Q., Pantalone, V., Song, B., Yu, D., An, Y. 2022. POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean. Nature Communications. 13. Article 3051. https://doi.org/10.1038/s41467-022-30314-7.Genome-wide association study and genomic selection for proteinogenic methionine in soybean seeds-(Peer Reviewed Journal) Singer, W.M., Shea, Z., Yu, D., Huang, H., Mian, R.M., Rosso, M.L., Song, Q., Zhang, B. 2022. Genome-wide association study and genomic selection for proteinogenic methionine in soybean seeds. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.859109.Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations-(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.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.Impact of multiple selective breeding programs on genetic diversity in soybean germplasm-(Peer Reviewed Journal) Gomes Viana, J.P., Fang, Y., Avalos, A., Song, Q., Nelson, R., Hudson, M.E. 2022. Impact of multiple selective breeding programs on genetic diversity in soybean germplasm. Theoretical and Applied Genetics. 135(5):1591–1602. https://doi.org/10.1007/s00122-022-04056-5.Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes-(Peer Reviewed Journal) Zhang, H., Jiang, H., Hu, Z., Song, Q., An, Y. 2022. Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes. BMC Genomics. 23. Article 250. https://doi.org/10.1186/s12864-022-08326-w.Registration of USDA-N7005 soybean germplasm with high yield and 62.5% pedigree from Japanese accessions Tamahikari and PI 416937-(Peer Reviewed Journal) Bagherzadi, L., Fallen, B.D., Gillen, A.M., Mcneece, B.T., Mian, R.M., Song, Q., Taliercio, E.W., Zenglu, L., Carter, T. 2022. Registration of USDA-N7005 soybean germplasm with high yield and 62.5% pedigree from Japanese accessions Tamahikari and PI 416937. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20209.Mining QTL for elevated protein and other major seed composition traits from diverse soybean germplasm-(Peer Reviewed Journal) Arnold, B., Menke, E., Mian, R.M., Song, Q., Buckley, B., Li, Z. 2021. Mining QTL for elevated protein and other major seed composition traits from diverse soybean germplasm. Molecular Breeding. https://doi.org/10.1007/s11032-021-01242-z.QTL mapping of seed quality traits including cooking time, flavor, and texture in a yellow dry bean (Phaseolus vulgaris L.) population-(Peer Reviewed Journal) Bassett, A.N., Katuuramu, D.N., Song, Q., Cichy, K.A. 2021. QTL mapping of seed quality traits including cooking time, flavor, and texture in a yellow dry bean (Phaseolus vulgaris L.) population. Frontiers in Plant Science. 12:670284. https://doi.org/10.3389/fpls.2021.670284.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.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.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.Genomic prediction using training population design in interspecific soybean populations-(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.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.A versatile resource of 1500 diverse wild and cultivated soybean genomes for post-genomics research-(Pre-print Publication) Zhang, H., Jiang, H., Hu, Z., Song, Q., An, Y. 2020. A versatile resource of 1500 diverse wild and cultivated soybean genomes for post-genomics research. bioRxiv. https://doi.org/10.1101/2020.11.16.383950.Comparative analysis of mitochondrial genomes of soybean cytoplasmic male sterile lines and their maintainer lines-(Peer Reviewed Journal) He, T., Ding, X., Zhang, H., Chen, L., Wang, T., Yang, L., Nie, Z., Song, Q., Gai, J., Yang, S. 2021. Comparative analysis of mitochondrial genomes of soybean cytoplasmic male sterile lines and their maintainer lines. Frontiers in Plant Science. 21(1):43-57. https://doi.org/10.1007/s10142-020-00760-x.Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing-(Peer Reviewed Journal) Valliyodan, B., Brown, A.V., Wang, J., Patil, G., Liu, Y., Otyama, P.I., Nelson, R., Vuong, T., Song, Q., Musket, T.A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D.M., Bayer, P., Roorkiwal, M., Varshney, R.K., Liu, X., Edwards, D., Xu, D., Joshi, T., Cannon, S.B., Nguyen, H.T. 2020. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data. 8. Article 50. https://doi.org/10.1038/s41597-021-00834-w.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.Fine mapping of an anthracnose-resistance locus in Andean common bean cultivar Amendoim Cavalo-(Peer Reviewed Journal) Gilio, T., Hurtado-Gonzales, O.P., Goncalves-Vidigal, M.C., Valentini, G., Ferreira Elias, J.C., Song, Q., Pastor Corrales, M.A. 2020. Fine mapping of an anthracnose-resistance locus in Andean common bean cultivar Amendoim Cavalo. PLOS ONE. 15(10):0239763. https://doi.org/10.1371/journal.pone.0239763.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.QTL for resistance to angular leaf spot and rust in Tanzania vs South Africa for the Andean panel & Rojo/Cal 143 RIL population-(Research Notes) Miklas, P.N., Chilagane, L., Fourie, D., Nchimbi, S., Soler-Garzon, A., Hart, J., Mcclean, P., Pastor Corrales, M.A., Song, Q., Porch, T.G. 2020. QTL for resistance to angular leaf spot and rust in Tanzania vs South Africa for the Andean panel & Rojo/Cal 143 RIL population. Bean Improvement Cooperative Annual Report. 63: 83-84.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.Nested association mapping of important agronomic traits in three interspecific soybean populations-(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.Genome sequencing and analysis of Diaporthe aspalathi isolate MS-SSC91 causing stem canker in soybean-(Abstract Only)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.Molecular dissection of resistance gene cluster and candidate gene identification of Pl17 and Pl19 in sunflower by whole-genome resequencing-(Peer Reviewed Journal) Ma, G.J., Song, Q., Underwood, W., Zhang, Z.W., Fiedler, J.D., Xuehui, L., Qi, L. 2019. Molecular dissection of resistance gene cluster and candidate gene identification of Pl17 and Pl19 in sunflower by whole-genome resequencing. Scientific Reports. 9:14974. https://doi.org/10.1038/s41598-019-50394-8.Construction and comparison of three new reference-quality genome assemblies for soybean-(Peer Reviewed Journal) Valliyodan, B., Cannon, S.B., Bayer, P.E., Shu, S., Brown, A.V., Ren, L., Jenkins, J., Chung, C.Y.L., Chan, T.F., Daum, C.G., Plott, C., Hastie, A., Baruch, K., Barry, K.W., Huang, W., Gunvant, P., Varshney, R.K., Hu, H., Batley, J., Yuan, Y., Song, Q., Stupar, R.M., Goodstein, D.M., Stacey, G., Lam, H.M., Jackson, S.A., Schmutz, J., Grimwood, J., Edwards, D., Nguyen, H.T. 2019. Construction and comparison of three new reference-quality genome assemblies for soybean. Plant Journal. 100(5):1066-1082. https://doi.org/10.1111/tpj.14500.Genetic diversity and phylogenetic relationships of annual and perennial Glycine species-(Peer Reviewed Journal) Hwang, E., Schroeder, S.G., Fickus, E.W., Quigley, C.V., Cregan, P., Song, Q. 2019. Genetic diversity and phylogenetic relationships of annual and perennial Glycine species. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.119.400220.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.Mapping and marker development for Ur-5 rust resistance locus-(Trade Journal) Hurtado-Gonzales, O.P., Valentini, G., Song, Q., Pastor Corrales, M.A. 2019. Mapping and marker development for Ur-5 rust resistance locus. Bean Improvement Cooperative Annual Report. 62:25-26.Haplotype analysis of a major and stable QTL underlying soybean (Glycine max) seed oil content reveals footprint of artificial selection-(Peer Reviewed Journal) Yan, L., Di, R., Wu, C., Hou, W., Zhao, Q., Liu, B., Shi, X., Yang, C., Song, Q., Zhang, M. 2019. Haplotype analysis of a major and stable QTL underlying soybean (Glycine max) seed oil content reveals footprint of artificial selection. Molecular Breeding. 39:57. https://doi.org/10.1007/s11032-019-0951-1.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.Context-specific genomic selection strategies outperform phenotypic selection for soybean quantitative traits in the progeny row stage-(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.Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing-(Peer Reviewed Journal) Chen, L., Ding, X., Zhang, H., He, T., Li, Y., Wang, T., Li, X., Jin, L., Song, Q., Yang, S., Gai, J. 2018. Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing. BMC Genomics. 9(1):663.Characterization of a USDA core collection of wild soybean (Glycine soja Siebold & Zucc.) accessions for seed composition and agronomic traits-(Peer Reviewed Journal) La, T., Large, E., Taliercio, E.W., Song, Q., Gillman, J.D., Xu, D., Nguyen, H., Shannon, G., Scaboo, A. 2018. Characterization of a USDA core collection of wild soybean (Glycine soja Siebold & Zucc.) accessions for seed composition and agronomic traits. Frontiers in Plant Science. https://doi.org/10.2135/cropsci2017.08.0514.Genetic architecture of soybean yield and agronomic traits-(Peer Reviewed Journal) Diers, B.W., Specht, J., Rainey, K., Cregan, P., Song, Q., Ramasubramanian, V., Graef, G., Nelson, R., Schapaugh, W., Wang, E., Shannon, G., McHale, L., Kantartzi, S., Xavier, A., Mian, R.M., Stupar, R., Michno, J., An, Y., Goettel, W., Ward, R., Fox, C., Lipka, A.E., Hyten, D., Cary, T., Beavis, W.D. 2018. Genetic architecture of soybean yield and agronomic traits. G3, Genes/Genomes/Genetics. 8(10):3367-3375. https://doi.org/10.1534/g3.118.200332.Fine mapping of genes conferring resistance to rust and anthracnose of common bean-(Trade Journal) Hurtado-Gonzales, O.P., Valentini, G., Gilio, T., Quigley, C.V., Song, Q., Goncalves-Vidigal, M.C., Pastor Corrales, M.A. 2018. Fine mapping of genes conferring resistance to rust and anthracnose of common bean. Bean Improvement Cooperative Annual Report. 61:27-28.High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R15, in sunflower (Helianthus annuus L.)-(Peer Reviewed Journal) Ma, G.J., Song, Q.J., Markell, S.G., Qi, L.L. 2018. High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R15, in sunflower (Helianthus annuus L.). Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-018-3087-5.Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean-(Peer Reviewed Journal) Wen, Z., Tan, R., Zhang, S., Collins, P.J., Yuan, J., Du, W., Gu, C., Ou, S., Song, Q., An, Y., Boyse, J.F., Chilvers, M.I., Wang, D. 2018. Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean. Plant Biotechnology. https://doi.org/10.1111/pbi.12918.Pyramiding different aphid-resistance genes in elite soybean germplasm to combat dynamic aphid populations-(Peer Reviewed Journal) Zhang, S., Wen, Z., Difonzo, Song, Q., Wang, D. 2018. Pyramiding different aphid-resistance genes in elite soybean germplasm to combat dynamic aphid populations. Molecular Breeding. 38(3)29. https://doi.org/10.1007/s11032-018-0790-5.Genome-wide scan for seed composition provides insights into the improvement of soybean quality and the impacts of domestication and modern breeding-(Peer Reviewed Journal) Zhang, J., Lu, Y., Bhussa, S.J., Song, Q., Yen, Y., Brown, M., Jiang, G. 2018. Genome-wide scan for seed composition provides insights into the improvement of soybean quality and the impacts of domestication and modern breeding. Molecular Plant. https://doi.org/10.1016/j.molp.2017.12.016.Genome-wide footprints of grain yield stability and environmental interactions in a multi-parental soybean population-(Peer Reviewed Journal) Xavier, A., Jarquin, D., Howard, R., Ramasubramanian, V., Specht, J.E., Graef, G.L., Beavis, W.D., Diers, B.W., Song, Q., Cregan, P., Nelson, R.L., Mian, R.M., Shannon, J.G., Mchale, L., Wang, D., Schapaugh, W., Lorenz, A.J., Zu, S., Muir, W.M., Rainey, K.M. 2017. Genome-wide footprints of grain yield stability and environmental interactions in a multi-parental soybean population. G3, Genes/Genomes/Genetics. 8(2):519-529.Development of SSR markers for genetic diversity and phylogenetic studies of Phomopsis longicolla causing Phomopsis seed decay in soybean-(Abstract Only) Li, S., Song, Q. 2018. Development of SSR markers for genetic diversity and phylogenetic studies of Phomopsis longicolla causing Phomopsis seed decay in soybean. Annual International Plant & Animal Genome Conference. Available: http://intlpag.org/2018/images/pdf/PAGXXVI-abstracts-posters.pdf. Paper No. P0786.Identifying and exploring significant genomic regions associated with soybean yield, seed fatty acids, protein, and oil-(Peer Reviewed Journal) Smallwood, C.J., Gillman, J.D., Saxton, A.M., Bhandari, H.S., Wadl, P.A., Fallen, B.D., Hyten, D.L., Song, Q., Pantalone, V.R. 2017. Identifying and exploring significant genomic regions associated with soybean yield, seed fatty acids, protein, and oil. Journal of Crop Science and Biotechnology. 20(4):243-253. https://doi.org/10.1007/s12892-017-0020-0.Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32-(Peer Reviewed Journal) Zhang, S., Zhang, Z., Wen, Z., Gu, C., An, Y., Bales, C., DiFonzo, C., Song, Q., Wang, D. 2017. Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32. Theoretical and Applied Genetics. 130(12):2601-2615. https://doi.org/10.1007/s00122-017-2979-0.Genome-wide Association Mapping of Resistance to Phytophthora sojae in a Soybean [Glycine max (L.) Merr.] Germplasm Panel from Maturity Groups IV and V-(Peer Reviewed Journal) Qin, J., Song, Q., Shi, A., Li, S., Zhang, M., Zhang, B. 2017. Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from Maturity Groups IV and V. PLoS One. 12(9):e0814613. https://doi.org/10.1371/journal.pone.0184613.Molecular mapping and genomics of soybean seed protein: A review and perspective for the future-(Peer Reviewed Journal) Patil, G., Mian, R.M., Vuong, T., Pantalone, V., Song, Q.J., Shannon, G., Carter Jr, T.E., Chen, P., Nguyen, H. 2017. Molecular mapping and genomics of soybean seed protein: A review and perspective for the future. Journal of Theoretical and Applied Genetics 130:(10):1975-1991. doi:10.1007/s00122-017-2955-8.Analysis of the Genome Sequence of Phomopsis longicolla Type Strain TWH P74 Causing Phomopsis Seed Decay in Soybean-(Abstract Only)Genome-wide association study of soybean cyst nematode (Heterodera glycines Ichinohe) HG type 2.5.7 (race 1) resistance in wild soybean (Glycine soja Sieb. & Zucc.)-(Peer Reviewed Journal) Xhang, H., Song, Q., Song, B. 2017. Genome-wide association study of soybean cyst nematode (Heterodera glycines Ichinohe) HG type 2.5.7 (race 1) resistance in wild soybean (Glycine soja Sieb. & Zucc.). Molecular Genetics and Genomics. https://doi.org/10.1007/s00438-017-1345-x.Genome-wide detection of genetic loci associated with soybean aphid resistance in soybean germplasm PI 603712-(Peer Reviewed Journal) Bhusal, S.J., Jiang, G., Song, Q., Cregan, P., Wright, D., Gonzalez=Hernandez, J.L. 2017. Genome-wide detection of genetic loci associated with soybean aphid resistance in soybean germplasm PI 603712. Euphytica. 213:144. https://doi.org/10.1007/s10681-017-1933-1.An RNA-Seq study reveals genetic responses of diverse wild soybean accessions to increased ozone levels-(Peer Reviewed Journal) Waldeck, N., Taliercio, E.W., Burkey, K.O., Carter Jr, T.E., Song, Q., Dickey, D. 2017. An RNA-Seq study reveals genetic responses of diverse wild soybean accessions to increased ozone levels. BMC Genomics. 18:498.Genome-wide linkage and association mapping of halo blight resistance in common bean to race 6 of the globally important bacterial pathogen-(Peer Reviewed Journal) Tock, A., Fourie, D., Walley, P.G., Holub, E.B., Soler, A., Cichy, K.A., Pastor Corrales, M.A., Song, Q., Porch, T.G., Hart, J.P., Vaconcellos, R., Vicente, J.G., Barker, G.C., Miklas, P.N. 2017. Genome-wide linkage and association mapping of halo blight resistance in common bean to race 6 of the globally important bacterial pathogen. Frontiers in Plant Science. 8:1170. https://doi.org/10.3389/fpls.2017.01170.Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions-(Peer Reviewed Journal) Mao, T., Li, J., Wen, Z., Wu, T., Wu, C., Sun, S., Jiang, B., Hou, W., Li, W., Song, Q., Wang, D., Han, T. 2017. Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions. Biomed Central (BMC) Genomics. 18(1):415. https://doi.org/10.1186/s12684-017-3778-3.High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases-(Peer Reviewed Journal) Valentini, G., Goncalves-Vidigal, M., Cregan, P., Song, Q., Pastor Corrales, M.A. 2017. High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases. Theoretical and Applied Genetics. doi: 10.1007/s00122-017-2920-6.Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.)-(Peer Reviewed Journal) Ma, G.J., Markell, S.G., Song, Q.J., Qi, L.L. 2017. Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.). Theoretical and Applied Genetics. 130(7):1519-1529.Genetics and mapping of a new anthracnose resistance Locus in Andean common bean Paloma-(Peer Reviewed Journal) Castro, S., Goncalves-Vidigal, M., Gilio, T., Giselly, F., Valentini, G., Ramos Martins, V., Song, Q., Marta, Z., Hurtado-Gonzales, O.P., Pastor Corrales, M.A. 2017. Genetics and mapping of a new anthracnose resistance Locus in Andean common bean Paloma. Biomed Central (BMC) Genomics. 18:306.Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses-(Peer Reviewed Journal) Yan, L., Hofmann, N., Li, S., Ferreira, M., Song, B., Jiang, G., Ren, S., Quigley, C.V., Fickus, E.W., Cregan, P., Song, Q. 2017. Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses. Biomed Central (BMC) Genomics. 18:529. https://doi.org/10.1186/s12864-017-3922-0.Simple sequence repeat DNA markers linked with genes for resistance to major diseases of common bean-(Trade Journal) Valentini, G., Goncalves-Vidigal, M.C., Cregan, P., Song, Q., Pastor Corrales, M.A. 2017. Simple sequence repeat DNA markers linked with genes for resistance to major diseases of common bean. Bean Improvement Cooperative Annual Report. 60:29-30.Fine mapping the borad spectrum anthracnose resistance gene in Amendoim Cavalo-(Trade Journal) Gilio, T., Hurtado-Gonzales, O.P., Valentini, G., Castro, S.A., Elias, H., Song, Q., Goncalves-Gidigal, C.M., Pastor Corrales, M.A. 2017. Fine mapping the borad spectrum anthracnose resistance gene in Amendoim Cavalo. Bean Improvement Cooperative Annual Report. 60:3-4.Simple sequence repeat DNA markers linked with genes for resistance to major diseases of common bean-(Trade Journal) Giseli, V., Goncalves-Vidigal, M.C., Cregan, P., Song, Q., Pastor Corrales, M.A. 2017. Simple sequence repeat DNA markers linked with genes for resistance to major diseases of common bean. Bean Improvement Cooperative Annual Report. 60:29-30.Meta-QTL for resistance to white mold in common bean-(Peer Reviewed Journal) Vasconcellos, R., Blessing, O., Soler, A., Arkwazee, H., Myers, J., Ferreira, J., Song, Q., McClean, P., Miklas, P.N. 2017. Meta-QTL for resistance to white mold in common bean. PLoS One. 12(2):e0171685. doi: 10.1371/journal.pone.0171685.Genetic characterization of the soybean Nested Association Mapping (NAM) population-(Peer Reviewed Journal) Song, Q., Yan, L., Quigley, C.V., Jordan, B.D., Fickus, E.W., Schroeder, S.G., Song, B., An, Y., Hyten, D., Nelson, R.L., Rainey, K., Beavis, W.D., Specht, J., Diers, B., Cregan, P. 2017. Genetic characterization of the soybean Nested Association Mapping (NAM) population. The Plant Genome. 10(2). doi: 10.3835/plantgenome2016.10.0109.Integration of least angle regression with empirical Bayes
for multi-locus genome-wide association studies-(Peer Reviewed Journal) Zhang, J., Feng, J., Wen, Y., Niu, Y., Tamba, C., Yue, C., Song, Q., Zhang, Y. 2017. Integration of least angle regression with empirical Bayes for multi-locus genome-wide association studies. Heredity. 118:517-524.Validation of the quantitative trait locus underlying soybean plant height using residual heterozygous lines and near isogenic lines across multi-environments-(Peer Reviewed Journal) Yan, L., Zhang, Y., Song, Q., Cregan, P., Yang, C., An, Y., Wu, C., Chen, Q., Liu, B., Di, R., Zhang, M. 2017. Validation of the quantitative trait locus underlying soybean plant height using residual heterozygous lines and near isogenic lines across multi-environments. Euphytica. 213:32. doi:10.1007/s10681-016-1833.Fine mapping of Ur-3, a historically important rust resistance locus in common bean-(Peer Reviewed Journal) Hurtado-Gonzales, O.P., Valentini, G., Gilio, T., Martins, A., Song, Q., Pastor Corrales, M.A. 2016. Fine mapping of Ur-3, a historically important rust resistance locus in common bean. G3, Genes/Genomes/Genetics. 7(2):557-569.Registration of Wyandot × PI 567301B soybean recombinant inbred line population-(Peer Reviewed Journal) Lee, S., Tae-Hwan, J., Mchale, L., Michel, A., Dorrance, A., Song, Q., Mian, R.M. 2017. Registration of Wyandot × PI 567301B soybean recombinant inbred line population. Journal of Plant Registrations 11(3):324-327. doi:10.3198/jpr2016.09.0042crmp.QTL analysis of symbiotic nitrogen fixation in a black bean RIL population-(Peer Reviewed Journal) Heilig, J.A., Wright, E.M., Kelly, J.D., Beaver, J.S., Song, Q. 2016. QTL analysis of symbiotic nitrogen fixation in a black bean RIL population. Crop Science. 57:1-12.Genome-wide association analysis for drought tolerance and associated traits in common bean-(Peer Reviewed Journal) Hoyos-Villegas, V., Song, Q., Kelly, J.D. 2016. Genome-wide association analysis for drought tolerance and associated traits in common bean. The Plant Genome. 10(1)):1-17.SNP discovery and QTL mapping of Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing (GBS)-(Peer Reviewed Journal) Zahirul, T.I., Seiler, G.J., Song, Q., Ma, G., Qi, L. 2016. SNP discovery and QTL mapping of Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing (GBS). The Plant Genome. 9(3). doi:10.3835/plantgenome 2016.03.0035.Genome-wide association study identifies candidate loci underlying seven agronomic traits in Middle American diversity panel in common bean (Phaseolus vulgaris L.)-(Peer Reviewed Journal) Moghaddam, S., Mamidi, S., Osorno, J., Lee, R., Brick, M., Kelly, J., Miklas, P.N., Urrea, C., Song, Q., Cregan, P.B., Grimwood, J., Schmutz, J., McClean, P. 2016. Genome-wide association study identifies candidate loci underlying seven agronomic traits in Middle American diversity panel in common bean (Phaseolus vulgaris L.). The Plant Genome. 9:1-21.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.Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations-(Peer Reviewed Journal) Hoyos-Villegas, V., Song, Q., Wright, E.M., Beebe, S.E., Kelly, J.D. 2016. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Science. 56(5):2546-2563.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.Further characerization of the broad-spectrum anthraconse resistance in Andea common bean Amendoim Cavalo-(Trade Journal) Gilio, T., Nanami, D., Goncalves-Vidigal, M.C., Valentini, G., Song, Q., Pastor Corrales, M.A. 2016. Further characerization of the broad-spectrum anthraconse resistance in Andea common bean Amendoim Cavalo. Bean Improvement Cooperative Annual Report. 59:127-128.Classical and molecular genetic mapping-(Book / Chapter)Draft genome sequence of diaporthe aspalathi isolate ms-ssc91 a fungus causing stem canker in soybean-(Peer Reviewed Journal) Li, S., Song, Q., Martin, A., Cregan, P.B. 2016. Draft genome sequence of diaporthe aspalathi isolate ms-ssc91 a fungus causing stem canker in soybean. Genomics Data. 7:262-263.Characterization of soybean storage and allergen protein affected by environmental and genetic factors-(Peer Reviewed Journal) Natarajan, S.S., Khan, F., Song, Q., Lakshman, S., Cregan, P., Scott, R.A., Shipe, E., Garrett, W.M. 2016. Characterization of soybean storage and allergen protein affected by environmental and genetic factors. Journal of Agricultural and Food Chemistry. 64(6):1433-1445.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-(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.Identification of a soybean rust resistance gene in PI 567104B-(Peer Reviewed Journal) Liu, M., Li, S., Swaminathan, S., Sahu, B., Leandro, L., Cardinal, A., Bhattacharyya, M., Song, Q., Walker, D.R., Cianzio, S.R. 2016. Identification of a soybean rust resistance gene in PI 567104B. Theoretical and Applied Genetics. 129:863-877.A novel phakopsora pachyrhizi resistance allele (rpp) contributed by PI 567068A-(Peer Reviewed Journal) King, Z.R., Harris, D.K., Pedley, K.F., Song, Q., Wang, D., Wen, Z., Buck, J.W., Li, Z., Boerma, H. 2015. A novel phakopsora pachyrhizi resistance allele (rpp) contributed by PI 567068A. Theoretical and Applied Genetics. 129:517-534.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 sequencing of phomopsis longicolla type strain twh p74 causing phomopsis seed decay in soybean-(Abstract Only) Li, S., Song, Q. 2016. Genome sequencing of phomopsis longicolla type strain twh p74 causing phomopsis seed decay in soybean. Annual International Plant & Animal Genome Conference. Paper No. 0989.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.Genome-wide association study of ureide concentration in diverse maturity group IV soybean [Glycine max (L.) Merr.] accessions-(Peer Reviewed Journal) Ray, J.D., Dhanapal, A.P., Singh, S.K., Hoyos-Villegas, V., Smith, J.R., Purcell, L.C., King, C.A., Boykin, D.L., Cregan, P.B., Song, Q., Fritschi, F.B. 2015. Genome-wide association study of ureide concentration in diverse maturity group IV soybean [Glycine max (L.) Merr.] accessions. G3, Genes/Genomes/Genetics. 5:2391-2403.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-(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)-(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-(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-(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.Interaction between the Ur-4 and Ur-5 bean rust resistance genes-(Trade Journal) Valentini, G., Cregan, P., Song, Q., Pastor Corrales, M.A. 2015. Interaction between the Ur-4 and Ur-5 bean rust resistance genes. Bean Improvement Cooperative Annual Report. 58:47-48.Using SNP genetic markers to elucidate the linkage of the Co-34/Phg-3 anthracnose and angular leaf spot resistance gene cluster with the Ur-14 resistance gene-(Trade Journal) Valentini, G., Gonçalves-Vidigal, M.C., Cregan, P., Song, Q., Pastor Corrales, M.A. 2015. Using SNP genetic markers to elucidate the linkage of the Co-34/Phg-3 anthracnose and angular leaf spot resistance gene cluster with the Ur-14 resistance gene  . Bean Improvement Cooperative Annual Report. 58:21-22.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-(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.Draft Genome Sequence of Phomopsis longicolla Type Strain TWH P74, a Fungus Causing Phomopsis Seed Decay in Soybean-(Peer Reviewed Journal) Li, S., Song, Q., Ji, P., Cregan, P.B. 2015. Draft Genome Sequence of Phomopsis longicolla Type Strain TWH P74, a Fungus Causing Phomopsis Seed Decay in Soybean. Genome Announcements. 3(1):e00010-15.Identification of quantitative trait loci for sucrose content in soybean seed-(Peer Reviewed Journal) Zeng, A., Chen, P., Shi, A., Wang, D., Zhang, B., Orazaly, M., Jaureguy, L., Florez, L., Brye, K., Cregan, P.B., Song, Q. 2015. Identification of quantitative trait loci for sucrose content in soybean seed. Crop Science. 54:554-564.The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations-(Peer Reviewed Journal) Vaughn, J.N., Nelson, R.L., Song, Q., Cregan, P.B., Boerma, R., Li, Z. 2014. The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations. Genes, Genomes, and Genomics. 4:2283-2294. doi: 10.1534/g3.114.013433.A comparison of protein and phenolic compounds in seed from GMO and non-GMO soybean-(Peer Reviewed Journal) Natarajan, S.S., Khan, F., Luthria, D.L., Tucker, M.L., Song, Q., Garrett, W.M. 2014. A comparison of protein and phenolic compounds in seed from GMO and non-GMO soybean. Journal of Data Mining in Genomics & Proteomics. 5(3):161-169.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.A reference genome for common bean and genome wide analysis of dual domestications-(Peer Reviewed Journal) Shmutz, J., Mcclean, P., Mamidi, S., Wu, A., Cannon, S.B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Geffroy, V., Moghaddam, S.M., Dongying, G., Abernathy, B., Barry, K., Blair, M., Brick, M.A., Chovatia, M., Gepts, P., Goodstein, D.M., Gonzales, M., Hellsten, U., Hyten, D.L., Gaofeng, J., Kelly, J., Kudrna, D., Lee, R., Manon, R.M., Miklas, P.N., Osorno, J.M., Rodrigues, J., Thareau, V., Urrea, C.A., Wang, M., Yu, Y., Zhang, M., Wing, R.A., Cregan, P.B., Rokhsar, D.S., Jackson, S.A. 2014. A reference genome for common bean and genome wide analysis of dual domestications. Nature Genetics. 46: 707-713. DOI: 10.1038/ng.3008.A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12-(Peer Reviewed Journal) Talukder, Z., Gong, L., Hulke, B.S., Pegadaraju, V., Song, Q., Schultz, Q., Qi, L. 2014. A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One. 9(7): e98628. Available http://dx.plos.org/10.1371/journal.pone.0098628.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.SSR DNA markers linked with Broad-Spectrum rust resistance in common bean discovered by bulk segregant analysis using a large set of SNP markers-(Trade Journal) Shin, S., Song, Q., Cregan, P.B., Pastor Corrales, M.A. 2014. SSR DNA markers linked with Broad-Spectrum rust resistance in common bean discovered by bulk segregant analysis using a large set of SNP markers. Bean Improvement Cooperative Annual Report. 57:187-188.Phytophthora root rot resistance in soybean E00003-(Peer Reviewed Journal) Zhang, A., Hao, J., Yuan, J., Song, Q., Hyten, D., Cregan, P.B., Zhang, G., Gu, C., Li, M., Wang, D. 2014. Phytophthora root rot resistance in soybean E00003. Crop Science. 54(2):492-499.A genome-wide association study in soybean-(Peer Reviewed Journal) Hwang, E., Song, Q., Jia, G., Specht, J.E., Hyten, D.L., Costa, J., Cregan, P.B. 2014. A genome-wide association study in soybean. Biomed Central (BMC) Genomics. 15:1-12.Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.-(Peer Reviewed Journal) Mafi_Moghaddam, S., Song, Q., Mamidi, S., Schmutz, J., Lee, R., Cregan, P.B., Osorno, J.M., Mcclean, P.E. 2013. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.. Frontiers in Plant Genetics and Genomics. DOI:10.3389/fpls.2013.00251.Mapping soybean aphid resistance genes in PI 567598B-(Peer Reviewed Journal) Bales-Arcelo, C., Zhang, A., Liu, M., Mensah, C., Gu, C., Song, Q., Hyten, D., Cregan, P.B., Wang, D. 2013. Mapping soybean aphid resistance genes in PI 567598B. Theoretical and Applied Genetics. 126:2081-2091.Development and evaluation of SoySNP50K, a high-density genotyping array for soybean-(Peer Reviewed Journal) Song, Q., Hyten, D., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., Cregan, P.B. 2013. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS Genetics. 8(1):e54985.Simple sequence repeats linked with Slow Darkening Trait in Pinto bean discovered by SNP assay and whole genome sequencing-(Peer Reviewed Journal) Felicetti, E.E., Song, Q., Jia, G., Cregan, P.B., Bett, K., Miklas, P.N. 2012. Simple sequence repeats linked with Slow Darkening Trait in Pinto bean discovered by SNP assay and whole genome sequencing. Crop Science. 52:1600-1608.Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean-(Peer Reviewed Journal) Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P.B., Ma, J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean. The Plant Cell. 24(1):21-32.Development and application of a multilocus sequence analysis method for the identification of genotypes within genus Bradyrhizobium and for establishing nodule occupancy of soybean (Glycine max L. Merr)-(Peer Reviewed Journal) Van Berkum, P.B., Elia, P.E., Song, Q., Eardly, B. 2012. Development and application of a multilocus sequence analysis method for the identification of genotypes within genus Bradyrhizobium and for establishing nodule occupancy of soybean (Glycine max L. Merr). Molecular Plant-Microbe Interactions. 25(3):321-330.


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