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                    U.S. DEPARTMENT OF AGRICULTURE
 Hard Winter Wheat Genetics Research: Manhattan, KS
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                        Center for Grain and Animal Health Research: Manhattan, KS
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ARS Home Plains Area Manhattan, Kansas Center for Grain and Animal Health Research Hard Winter Wheat Genetics Research People & Locations







Paul  St Amand
                        Hard Winter Wheat Genetics Research

                        




                        
                        Geneticist Plants
                        Phone: (785) 532-7350
                        
                        
                        Fax: (Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            **Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Skim exome capture genotyping in wheat

- (Peer Reviewed Journal)Haplocatcher: A package for prediction of haplotypes
                                                        

- (Peer Reviewed Journal)Winn, Z.J., Hudson-Arns, E., Hammers, M., Dewitt, N., Lyerly, J., Bai, G., St Amand, P.C., Haley, S., Mason, R.E. 2023. Haplocatcher: A package for prediction of haplotypes. The Plant Genome. https://doi.org/10.1101/2023.07.20.549744.Exploiting multi-trait genomic selection to improve the prediction accuracy of processing and end-use quality traits in hard winter wheat breeding.

- (Peer Reviewed Journal)QTL analysis of yield and end-use quality traits in Texas hard red winter wheat
                                                        

- (Peer Reviewed Journal)Dogan, M., Wang, Z., Cerit, M., Valenzuela-Antelo, J., Dhakal, S., Chu, C., Xue, Q., Ibrahim, A., Rudd, J., Bernardo, A.E., St Amand, P.C., Bai, G., Zhang, H., Liu, S. 2023. QTL analysis of yield and end-use quality traits in Texas hard red winter wheat. Agronomy. Agronomy 13(3). Article 689. https://doi.org/10.3390/agronomy13030689.Quantitative trait loci for rolled leaf trait in a wheat EMS mutant from Jagger
                                                        

- (Peer Reviewed Journal)Ruolin, B., Liu, N., Xu, Y., Su, Z., Cai, L., Bernardo, A.E., St Amand, P.C., Fritz, A., Zhang, G., Rupp, J., Akhunov, E., Jordan, K., Bai, G. 2023. Quantitative trait loci for rolled leaf trait in a wheat EMS mutant from Jagger. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-023-04284-3.Development of diagnostic SNP markers for identification of rye 1RS translocations in wheat
                                                        

- (Peer Reviewed Journal)Liu, Z., Li, Y., Bernardo, A.E., St Amand, P.C., Zhang, P., Sehgal, S., Bai, G. 2022. Development of diagnostic SNP markers for identification of rye 1RS translocations in wheat. Crop Science. https://doi.org/10.1002/csc2.20841.Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits
                                                        

- (Peer Reviewed Journal)Gill, H., Halder, J., Zhang, J., Rana, A., Klienjan, J., St Amand, P.C., Bernardo, A.E., Bai, G., Sehgal, S. 2022. Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-022-04160-6.Multi-locus genome-wide association studies to characterize Fusarium head blight (FHB) resistance in hard winter wheat
                                                        

- (Peer Reviewed Journal)Zhang, J., Gill, H., Halder, J., Brar, N., Shaukat, A., Bernardo, A.E., St Amand, P.C., Bai, G., Turnipseed, B., Sehgal, S. 2022. Multi-locus genome-wide association studies to characterize Fusarium head blight (FHB) resistance in hard winter wheat. Frontiers in Plant Science. 13. Article 946700. https://doi.org/10.3389/fpls.2022.946700.Redox-engineering enhances maize thermotolerance and grain yield in the field
                                                        

- (Peer Reviewed Journal)Sprague, S., Tamang, T., Steiner, T., Wu, Q., Hu, Y., Kakeshpour, T., Park, J., Yang, J., Peng, Z., Bergkamp, B., Somayanda, I., Peterson, M., Garcia, E., Hao, Y., St Amand, P.C., Bai, G., Nakata, P., Rieu, I., Jackson, D., Cheng, N., Valent, B., Hirschi, K., Jagadish, K., Liu, S., White, F., Park, S. 2022. Redox-engineering enhances maize thermotolerance and grain yield in the field. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13866.Genomic prediction of Fusarium head blight resistance in early stages using advanced breeding lines in hard winter wheat
                                                        

- (Peer Reviewed Journal)Zhang, J., Gill, H., Brar, N., Halder, J., Ali, S., Liu, X., Bernardo, A.E., St Amand, P.C., Bai, G., Turnipseed, B., Sehgal, S. 2022. Genomic prediction of Fusarium head blight resistance in early stages using advanced breeding lines in hard winter wheat. The Crop Journal. https://doi.org/10.1016/j.cj.2022.03.010.Identification of a novel major QTL from Chinese wheat cultivar Ji5265 for Fusarium head blight resistance in greenhouse
                                                        

- (Peer Reviewed Journal)Li, H., Zhang, F., Zhao, J., Bai, G., St Amand, P.C., Bernardo, A.E., Ni, Z., Xun, Q., Su, Z. 2022. Identification of a novel major QTL from Chinese wheat cultivar Ji5265 for Fusarium head blight resistance in greenhouse. Journal of Theoretical and Applied Genetics. 135.1867–1877. https://doi.org/10.1007/s00122-022-04080-5.Genetic Architecture of the High Inorganic Phosphate Phenotype Derived from a Low Phytate Mutant in Winter Wheat (Triticum aestivum L.)
                                                        

- (Peer Reviewed Journal)Venegas, J., Guttieri, M.J., Boehm Jr, J.D., Graybosch, R.A., Bai, G., St. Amand, P.C., Palmer, N.A., Hussain, W., Blecha, S., Baenziger, P. 2022. Genetic architecture of the high inorganic phosphate phenotype derived from a low phytate mutant in winter wheat (Triticum aestivum L.). Crop Science. https://doi.org/10.1002/csc2.20738.Genotyping-by-sequencing based molecular genetic diversity of Pakistani bread wheat (Triticum aestivum L.) accessions
                                                        

- (Peer Reviewed Journal)Hussain, S., Habib, M., Ahmed, Z., Sadia, B., Bernardo, A.E., St Amand, P.C., Bai, G., Ghori, N., Khan, A., Awan, F., Maqbool, R. 2022. Genotyping-by-sequencing based molecular genetic diversity of Pakistani bread wheat (Triticum aestivum L.) accessions. Frontiers in Genetics. 13. Article 772517. https://doi.org/10.3389/fgene.2022.772517.Characterization of PmBN418, a wheat powdery mildew resistance gene on the rye 1RS chromosome arm
                                                        

- (Peer Reviewed Journal)Xu, X., Bai, G., Li, G., Cowger, C., Bernardo, A.E., Carver, B., St Amand, P.C., Bian, R. 2021. Characterization of PmBN418, a wheat powdery mildew resistance gene on the rye 1RS chromosome arm. Crop Science. 61(6):4194-4201. https://doi.org/10.1002/csc2.20637.Multi-trait multi-environment genomic prediction of agronomic traits in advanced breeding lines of winter wheat
                                                        

- (Peer Reviewed Journal)Gill, H., Halder, J., Zhang, J., Brar, N., Hall, C., Rai, T., Bernardo, A.E., St Amand, P.C., Bai, G., Olson, E., Ali, S., Turnipseed, B., Sehgal, S. 2021. Multi-trait multi-environment genomic prediction of agronomic traits in advanced breeding lines of winter wheat. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.709545.High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat
                                                        

- (Peer Reviewed Journal)Pang, Y., Wu, Y., Liu, C., Li, W., St Amand, P.C., Bernardo, A.E., Wang, D., Dong, L., Yung, X., Zhang, H., Zhao, M., Wang, L., He, F., Liang, Y., Yan, Q., Lu, Y., Yu, S., Wu, J., Li, A., Kong, L., Bai, G., Liu, S. 2021. High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat. Theoretical and Applied Genetics. 134:2857–2873. https://doi.org/10.1007/s00122-021-03863-6.Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using GWAS
                                                        

- (Peer Reviewed Journal)Hanif, U., Alipour, H., Gul, A., Li, J., Bihamta, R., Mohammadi, V., Peyghambari, S., Amir, R., Munir, F., Llyas, M., St. Amand, P.C., Bernardo, A.E., Bai, G. 2021. Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using GWAS. The Plant Genome. https://doi.org/10.1002/tpg2.20096.Characterization of an incomplete leaf rust resistance gene and development of KASP markers for the leaf rust resistance gene Lr47 in wheat
                                                        

- (Peer Reviewed Journal)Xu, X., Li, G., Bai, G., Bernardo, A.E., Carver, B.F., St Amand, P.C., Bian, R. 2021. Characterization of an incomplete leaf rust resistance gene and development of KASP markers for the leaf rust resistance gene Lr47 in wheat. Phytopathology. https://doi.org/10.1094/PHYTO-07-20-0308-R.Development of KASP markers for wheat greenbug resistance gene Gb5
                                                        

- (Peer Reviewed Journal)Xu, X., Li, G., Bai, G., Bernardo, A., Carver, B.F., St Amand, P., Armstrong, S. 2020. Development of KASP markers for wheat greenbug resistance gene Gb5. Crop Science. 61(1):490–499. https://doi.org/10.1002/csc2.20339.High resolution genome-wide association study identified genomic regions and candidate genes for important agronomic traits in wheat
                                                        

- (Peer Reviewed Journal)Pang, Y., Liu, C., Wang, D., St Amand, P.C., Bernardo, A.E., Li, W., He, F., Li, L., Wang, L., Yuan, X., Bai, G., et al. 2020. High resolution genome-wide association study identified genomic regions and candidate genes for important agronomic traits in wheat. Molecular Plant. https://doi.org/10.1016/j.molp.2020.07.008.Discovery of Alpha Kafirin Alleles Associated with Protein Digestibility in Grain Sorghum
                                                        

- (Peer Reviewed Journal)Understanding the genetic basis of spike fertility to improve grain number, harvest index, and grain yield in wheat under high temperature stress environments
                                                        

- (Peer Reviewed Journal)Pradhan, S., Babar, M., Robbins, K., Bai, G., Mason, R., Khan, J., Shahi, D., Avci, M., Guo, J., Hossain, M., Bhatta, M., Mergoum, M., Asseng, S., St. Amand, P.C., Gezan, S., Baik, B.V., Blount, A., Bernardo, A.E. 2019. Understanding the genetic basis of spike fertility to improve grain number, harvest index, and grain yield in wheat under high temperature stress environments. Frontiers in Plant Science. 10. Article 1481. https://doi.org/10.3389/fpls.2019.01481.Rapid identification of a novel wheat leaf rust resistance gene by selective genotyping of F2 plants using next-generation-sequencing

- (Abstract Only)Multiplex Restriction Amplicon Sequencing (MRASeq), a novel next generation sequencing based marker platform for high-throughput genotyping
                                                        

- (Peer Reviewed Journal)Bernardo, A., St Amand, P.C., Le, H., Su, Z., Bai, G. 2019. Multiplex Restriction Amplicon Sequencing (MRASeq), a novel next generation sequencing based marker platform for high-throughput genotyping. Nucleic Acids Research. https://doi.org/10.1111/pbi.13192.Genetic diversity, population structure, and linkage disequilibrium of pearl millet
                                                        

- (Peer Reviewed Journal)Serba, D.D., Muleta, K., St Amand, P.C., Bernando, A., Bai, G., Perumal, R., Bashir, E., Morris, G. 2019. Genetic diversity, population structure, and linkage disequilibrium of pearl millet. The Plant Genome. https://doi.org/doi:10.3835/plantgenome2018.11.0091.A deletion mutation in TaHRC confers Fhb1 resistance to Fusarium head blight in wheat
                                                        

- (Peer Reviewed Journal)Su, Z., Bernardo, A., Tian, B., Chen, H., Wang, S., Ma, H., Cai, S., Liu, D., Zhang, D., Li, T., Trick, H., St Amand, P.C., Yu, J., Zhang, Z., Bai, G. 2019. A deletion mutation in TaHRC confers Fhb1 resistance to Fusarium head blight in wheat. Nature Genetics. 51:1099-1105. https://doi.org/10.1038/s41588-019-0425-8.Persistence of rye (secale cereale L.) chromosome arm 1RS in wheat (triticum aestivum L.) breeding programs of the great plains of north america
                                                        

- (Peer Reviewed Journal)Graybosch, R.A., Bai, G., St Amand, P.C., Sarath, G. 2020. Persistence of rye (secale cereale L.) chromosome arm 1RS in wheat (triticum aestivum L.) breeding programs of the great plains of north america. Genetic Resources and Crop Evolution. 66:941-950. https://doi.org/10.1007/s10722-019-00742-4.Biofortification of hard red winter wheat by genes conditioning low phytate and high grain protein concentration
                                                        

- (Peer Reviewed Journal)Venegas, J.P., Graybosch, R.A., Wienhold, B.J., Rose, D.J., Waters, B.M., Baenziger, P.S., Eskridge, K., Bai, G., St Amand, P.C. 2018. Biofortification of hard red winter wheat (Triticum aestivum L.) by genes conditioning low phytate and high grain protein concentration. Crop Science. 58(5):1942-1953. https://doi.org/10.2135/cropsci2018.03.0175.Using next generation sequencing for multiplexed trait-linked markers in wheat
                                                        

- (Peer Reviewed Journal)Bernardo, A., Wang, S., St Amand, P.C., Bai, G. 2015. Using Next Generation Sequencing for Multiplexed Trait-linked Markers in Wheat. PLoS One. 10(12):e0143890. doi:10.1371/journal.pone.0143890.Identification of markers linked to genes for sprouting tolerance (independent of grain color) in hard white winter wheat (HWWW)
                                                        

- (Peer Reviewed Journal)Fakthongphan, J., Graybosch, R.A., Bai, G., St Amand, P., Baenziger, S.P. 2015. Identification of markers linked to genes for sprouting tolerance (independent of grain color) in hard white winter wheat (HWWW). Theoretical and Applied Genetics. PP 1-12.Registration of 'TAM 305' hard red winter Wheat

- (Peer Reviewed Journal)Ibrahim, A., Rudd, J., Devkota, R., Baker, J., Sutton, R., Simoneaux, B., Opena, G., Herrington, R., Rooney, L., Dykes, L., Awika, J., Nelson, L.R., Fritz, A., Bowden, R.L., Graybosch, R.A., Jin, Y., Seabourn, B.W., Chen, X., Kolmer, J.A., St Amand, P., Bai, G., Duncan, R. 2015. Registration of 'TAM 305' hard red winter Wheat. Journal of Plant Registrations. doi:10.3198/jpr2014.08.0054crc.Construction of dense linkage maps "on the fly" using early generation wheat breeding populations

- (Peer Reviewed Journal)Eckard, J., Gonzales-Hernandez, J., Chao, S., St Amand, P., Bai, G. 2014. Construction of dense linkage maps "on the fly" using early generation wheat breeding populations. Molecular Breeding. DOI:10.1007/s11032-014-0116-1.Molecular markers linked to genes important for Hard Winter Wheat production and marketing in the U.S. Great Plains

- (Peer Reviewed Journal)Liu, S., Rudd, J.C., Bai, G., Haley, S.D., Ibrahim, A., Xiu, Q., Hays, D.B., Graybosch, R.A., Devkota, R.N., St Amand, P. 2014. Molecular markers linked to genes important for Hard Winter Wheat production and marketing in the U.S. Great Plains. Crop Science. 54:1304-1321. DOI:10.2135/cropsci2013.08.0564.Release of ‘Mattern’ waxy (amylose-free) winter wheat
                                                        

- (Peer Reviewed Journal)Graybosch, R.A., Baenziger, P.S., Dantra, D., Regassa, T., Jin, Y., Kolmer, J.A., Wegulo, S., Bai, G., St Amand, P., Chen, X., Seabourn, B.W., Dowell, F.E., Bowden, R.L., Marshall, D.S. 2014. Release of ‘Mattern’ waxy (amylose-free) winter wheat. Journal of Plant Registrations. 8:43-48.Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley
                                                        

- (Peer Reviewed Journal)Mascher, M., Wu, S., St Amand, P., Rico, A., Sartori, A., Stein, N., Poland, J.A. 2013. Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley. PLoS One. DOI: 10.1371/journal.pone.0076925.Evaluation of genetic markers for prediction of pre-harvest sprouting tolerance in hard white winter wheats

- (Peer Reviewed Journal)Graybosch, R.A., St Amand, P., Bai, G. 2013. Evaluation of genetic markers for prediction of pre-harvest sprouting tolerance in hard white winter wheats. Plant Breeding. doi:10.1111/pbr.12071.Consensus mapping and identification of markers for marker-assisted selection of Wsm2 in wheat

- (Peer Reviewed Journal)Lu, H., Kottke, R., Devkota, R., St Amand, P., Bernardo, A., Bai, G., Byrne, P., Martin, T.J., Haley, S.D., Rudd, J. 2011. Consensus mapping and identification of markers for marker-assisted selection of Wsm2 in wheat. Crop Science. 52:720-728.Starch waxiness in hexaploid wheat (Triticum aestivum L.) by NIR reflectance spectroscopy

- (Peer Reviewed Journal)Delwiche, S.R., Graybosch, R.A., St Amand, P., Bai, G. 2011. Starch waxiness in hexaploid wheat (Triticum aestivum L.) by NIR reflectance spectroscopy. Journal of Agricultural and Food Chemistry. 59:4002-4008.


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