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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
Paul St Amand
Hard Winter Wheat Genetics Research
Geneticist Plants

Phone: (785) 532-7350
Fax:

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Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Enhancing the potential of phenomic and genomic prediction in winter wheat breeding using high-throughput phenotyping and deep learning Reprint Icon - (Peer Reviewed Journal)
Kaushal, S., Gill, H., Billah, M., Khan, S., Halder, J., Bernardo, A.E., St Amand, P.C., Bai, G., Glover, K., Maimaitijiang, M., Sehgal, S.K. 2024. Enhancing the potential of phenomic and genomic prediction in winter wheat breeding using high-throughput phenotyping and deep learning. Frontiers in Plant Science. 15. Article 1410249. https://doi.org/10.3389/fpls.2024.1410249.
Integrating genomics, phenomics, and deep learning improves the predictive ability for Fusarium head blight-related traits in winter wheat Reprint Icon - (Peer Reviewed Journal)
Thapa, S., Gill, H., Halder, J., Rana, A., Ali, S., Maimaitijiang, M., Gill, U., Bernardo, A.E., St Amand, P.C., Bai, G., Sehgal, S. 2024. Integrating genomics, phenomics, and deep learning improves the predictive ability for Fusarium head blight-related traits in winter wheat. The Plant Genome. Article.e20470. https://doi.org/10.1002/tpg2.20470.
Development and validation of diagnostic markers for the reduced height gene Rht8 in wheat Reprint Icon - (Peer Reviewed Journal)
Xu, Y., St Amand, P.C., Chai, L., Li, Y., Ni, Z., Carver, B., Bai, G. 2024. Development and validation of diagnostic markers for the reduced height gene Rht8 in wheat. Crop Science. 64(1):278-286. https://doi.org/10.1002/csc2.21153.
Genetic architecture of quantitative trait loci (QTL) for FHB resistance and agronomic traits in a hard winter wheat population Reprint Icon - (Peer Reviewed Journal)
Xu, Y., Li, Y., Bian, R., Fritz, A., Zhang, G., Dong, Y., Zhao, L., Xu, Y., Ghori, N., Bernardo, A.E., St Amand, P.C., Shoup-Rupp, J.L., Bruce, M., Wang, W., Akhunov, E., Carver, B., Bai, G. 2023. Genetic architecture of quantitative trait loci (QTL) for FHB resistance and agronomic traits in a hard winter wheat population. The Crop Journal. 11:1836-1845. https://doi.org/10.1016/j.cj.2023.09.004.
Genetic characterization of root architectural traits in barley (Hordeum vulgare L.) using SNP markers Reprint Icon - (Peer Reviewed Journal)
Farooqi, M., Moody, D., Bai, G., Bernardo, A.E., St Amand, P.C., Diggle, A., Rengel, Z. 2023. Genetic characterization of root architectural traits in barley (Hordeum vulgare L.) using SNP markers. Frontiers in Plant Science. 14:1265925. https://doi.org/10.3389/fpls.2023.1265925.
Skim exome capture genotyping in wheat Reprint Icon - (Peer Reviewed Journal)
Wang, H., Bernardo, A.E., St. Amand, P.C., Bai, G., Bowden, R.L., Guttieri, M.J., Jordan, K. 2023. Skim exome capture genotyping in wheat. The Plant Genome. 16(4). Article.e20381. https://doi.org/10.1002/tpg2.20381.
Haplocatcher: A package for prediction of haplotypes Reprint Icon - (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.
Multi-trait genomic selection improves the prediction accuracy of end-use quality traits in hard winter wheat Reprint Icon - (Peer Reviewed Journal)
Gill, H.S., Brar, N., Halder, J., Hall, C., Seabourn, B.W., Chen, Y., St Amand, P.C., Bernardo, A.E., Bai, G., Glover, K., Turnipseed, B., Sunish, S.K. 2023. Multi-trait genomic selection improves the prediction accuracy of end-use quality traits in hard winter wheat. The Plant Genome. 16:e20331. https://doi.org/10.1002/tpg2.20331.
QTL analysis of yield and end-use quality traits in Texas hard red winter wheat Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.) Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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) Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.