Research Project: Improvement of Disease and Pest Resistance in Barley, Durum, Oat, and Wheat Using Genetics and Genomics

Location: Cereal Crops Improvement Research

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

Haplotype analysis identified key genes associated with improved salt stress tolerance in wheat (Triticum aestivum L.) - (Abstract Only)
Gudi, S., Gill, H., Collins, S., Singh, J., Sandhu, D., Sehgal, S., Upinder, G., Gupta, R. 2025. Haplotype analysis identified key genes associated with improved salt stress tolerance in wheat (Triticum aestivum L.). Meeting Abstract. Poster No.59974.

Identification of stem rust resistance genes in monogenic lines derived from wheat cultivar Waldron - (Peer Reviewed Journal)
Klindworth, D.L., Saini Sharma, J., Faris, J.D., Friesen, T.L., Peters Haugrud, A.R., Xu, S.S. 2025. Identification of stem rust resistance genes in monogenic lines derived from wheat cultivar Waldron. Crop Science. https://doi.org/10.1002/csc2.70010.

Leveraging historical trials to predict Fusarium head blight resistance in wheat breeding programs - (Peer Reviewed Journal)
Brault, C., Conley, E., Green, A., Glover, K., Cook, J., Gill, H., Read, A.C., Fiedler, J.D., Anderson, J. 2025. Leveraging historical trials to predict Fusarium head blight resistance in wheat breeding programs. The Plant Genome. 18(1). https://doi.org/10.1002/tpg2.20559.

Breeding strategies to enhance ß-glucan content in oats (Avena sativa L.) - (Peer Reviewed Journal)
Bazzzer, S., Oliveira, G., Fiedler, J.D., Nandety, R., Jannink, J., Caffe, M. 2025. Breeding strategies to enhance ß-glucan content in oats (Avena sativa L.). BMC Genomics. Article 0001a. https://doi.org/10.1186/s12864-024-11174-5.

Metabolic engineering of lipid biosynthesis enhances oil composition in oat - (Abstract Only)
Zhou, Z., Kaur, R., Donoso, T., Ohm, J., Gupta, R., Lefsrud, M., Singh, J. 2025. Metabolic engineering of lipid biosynthesis enhances oil composition in oat. Meeting Abstract.

Genetic and physical localization of Hessian fly resistance genes in barley - (Abstract Only)
Karki, M., Robbani, M., Nandety, R.S., Fiedler, J.D., Liu, Z., Yang, S. 2025. Genetic and physical localization of Hessian fly resistance genes in barley. Plant & Animal Genome Conference; San Diego, California. Poster No. P472.

Deciphering the genetic basis of salt stress tolerance in wheat (Triticum aestivum L.) through association studies and SNP-based haplotype analysis - (Abstract Only)
Gudi, S., Gill, H., Collins, S., Singh, J., Sandhu, D., Sehgal, S., Upinder, G., Gupta, R. 2025. Deciphering the genetic basis of salt stress tolerance in wheat (Triticum aestivum L.) through association studies and SNP-based haplotype analysis. Meeting Abstract. Poster No. PO0414.

Insights into the resistance mechanisms of Aegilops umbellulata against leaf rust and bacterial leaf streak using transcriptomics - (Abstract Only)
Singh, J., Gudi, S., Shi, G., Liu, Z., Gupta, R., Upinder, G. 2025. Insights into the resistance mechanisms of Aegilops umbellulata against leaf rust and bacterial leaf streak using transcriptomics. Plant and Animal Genome Conference. Poster No. PO0420.

A barley MLA receptor is targeted by a specialized non-ribosomal peptide effector of the necrotrophic spot blotch fungus to induce disease susceptibility - (Peer Reviewed Journal)
Leng, Y., Kummel, F., Zhao, M., Molnar, I., Dolezel, J., Logemann, E., Kochner, P., Xi, P., Yang, S., Moscou, M.J., Fiedler, B.A., Du, Y., Steuernagel, B., Meinhardt, S., Steffenson, B., Schulze-Lefert, P., Zhong, S. 2024. A barley MLA receptor is targeted by a specialized non-ribosomal peptide effector of the necrotrophic spot blotch fungus to induce disease susceptibility. New Phytologist. https://doi.org/10.1111/nph.20289.

Evaluation of durum and hard red spring wheat panels for sensitivity to necrotrophic effectors produced by Parastagonospora nodorum - (Peer Reviewed Journal)

Genetic mapping of QTLs for resistance to bacterial leaf streak in hexaploid wheat - (Peer Reviewed Journal)
Acharya, K., Liu, Z., Schachterle, J., Manan, F., Xu, S.S., Green, A., Faris, J.D. 2024. Genetic mapping of QTLs for resistance to bacterial leaf streak in hexaploid wheat. Theoretical and Applied Genetics. 137:article 265. https://doi.org/10.1007/s00122-024-04767-x.

Genome-wide dissection and haplotype analysis identified superior haplotypes for improved salt stress tolerance in wheat (Triticum aestivum L.) - (Abstract Only)
Gudi S, Gill H, Collins S, Singh J, Sandhu D, Sehgal S, Gill U and Gupta R (2024) Genome-wide dissection and haplotype analysis identified superior haplotypes for improved salt stress tolerance in wheat (Triticum aestivum L.) [Abstract]. ASA, CSSA & SSSA International Annual Meetings, November 10-13, 2024, San Antonio, Texas, USA

Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement - (Peer Reviewed Journal)
Singh, J., Gudi, S., Maughan, J., Liu, Z., Kolmer, J.A., Chen, X., Rouse, M.N., Sehgal, S., Gupta, R., Upinder, G., Fiedler, J.D., Choulet, F., Acevedo, M. 2024. Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.14470.

Metabolic engineering-induced transcriptome reprogramming enhance oil composition and content in oat (Avena sativa L.) - (Peer Reviewed Journal)
Zhou, Z., Kaur, R., Donoso, T., Ohm, J., Kushwaha, A., Gupta, R., Lefsrud, M., Singh, J. 2024. Metabolic engineering-induced transcriptome reprogramming enhance oil composition and content in oat (Avena sativa L.). Plant Biotechnology Journal. p. 1-14. https://doi.org/10.1111/pbi.14467.

Elucidating genetic determinants for salt tolerance in spring wheat (Triticum aestivum L.) - (Abstract Only)
Gudi, S., Gill, H.S., Collins, S., Singh, J., Sandhu, D., Sehgal, S., Upinder, G., Gupta, R. 2024. Elucidating genetic determinants for salt tolerance in spring wheat (Triticum aestivum L.). Meeting Abstract. Poster No. 20.

Can GWAS information from oat breeding programs be used to develop higher-yield oat varieties? A case study in the SDSU Oat Breeding Program - (Abstract Only)
Oliveira, G., Bazzer, S., Ayana, G., Fiedler, J.D., Nandety, R., Cafee, M. 2024. Can GWAS information from oat breeding programs be used to develop higher-yield oat varieties? A case study in the SDSU Oat Breeding Program. Meeting Abstract.

Vegetative indices data boost genomic selection models in predicting oat grain yield - (Abstract Only)
Oliveira, G., Bazzer, S., Maimaitijiang, M., Nandety, R., Chang, J., Fiedler, J.D., Cafee, M. 2024. Vegetative indices data boost genomic selection models in predicting oat grain yield. Meeting Abstract.

Species-specific microsymbiont discrimination mediated by a Medicago receptor kinase - (Peer Reviewed Journal)
Yu, X., Liu, J., Qin, Q., Zribi, I., Yu, J., Yang, S., Dinkins, R.D., Fei, Z., Kereszt, A., Zhu, H. 2024. Species-specific microsymbiont discrimination mediated by a Medicago receptor kinase. Science Advances. 10(31). https://doi.org/10.1126/sciadv.adp6436.

Understanding the genetic basis of stem rust resistance in southeastern US oat through genome wide association stud - (Abstract Only)
Acharya, J., Babar, M., Khan, N., Mcbreen, J., Signorini, V., Kunwar, S., Adewale, S., Esvelt Klos, K.L., Harrison, S., Dewitt, N., Furlan, F., Fiedler, J.D., Nandety, R., Osenga, M.M., Boyles, R. 2025. Understanding the genetic basis of stem rust resistance in southeastern US oat through genome wide association stud. Meeting Abstract.

Dissection of nonhost resistance in barley to the heterologous leaf rust pathogen Puccinia triticinay - (Abstract Only)
Ritzinger, M., Zhong, S., Yang, S. 2024. Dissection of nonhost resistance in barley to the heterologous leaf rust pathogen Puccinia triticinay. Meeting Abstract. 2024 Annual Meeting of the North Central Division of the American Phytopathological Society.

Genomic regions associated with spot blotch (SB) resistance in barley in the interspecific cytonuclear multi-parent population (CMPP) - (Abstract Only)
Pawar, T., Tilstra, J., Ahmad, M., Beery, A., Bodenheimer, S., Yang, S., Solanki, S., Shyam, E., Ameen, G. 2024. Genomic regions associated with spot blotch (SB) resistance in barley in the interspecific cytonuclear multi-parent population (CMPP). Meeting Abstract. 2024 Annual Meeting of the North Central Division of the American Phytopathological Society.

Genetic mapping of a recessive resistance to stripe rust in barley - (Abstract Only)
Kaur, S., Liu, Z., Yang, S. 2024. Genetic mapping of a recessive resistance to stripe rust in barley. Meeting Abstract. 2024 Annual Meeting of the North Central Division of the American Phytopathological Society.

Discovering bacterial leaf streak disease resistance loci in barley in the interspecific Cytonuclear Multi-Parent Population (CMPP) - (Abstract Only)
Tilstra, J., Ahmad, M., Pawar, T., Beery, A., Bodenheimer, S., Yang, S., Solanki, S., Fridman, E., Ameen, G. 2024. Discovering bacterial leaf streak disease resistance loci in barley in the interspecific Cytonuclear Multi-Parent Population (CMPP). Meeting Abstract. 2024 Annual Meeting of the North Central Division of the American Phytopathological Society.

Map-based cloning of the Nec50 gene which regulates programmed cell death in barley - (Abstract Only)
D'Eustachio, A., Liu, Z., Yang, S. 2024. Map-based cloning of the Nec50 gene which regulates programmed cell death in barley. Meeting Abstract. 2024 Annual Meeting of the North Central Division of the American Phytopathological Society.

Fine mapping of a QTL conferring susceptibility to spot blotch in barley - (Abstract Only)
Amusan, O., Leng, Y., Yang, S., Zhong, S. 2024. Fine mapping of a QTL conferring susceptibility to spot blotch in barley. Meeting Abstract. 2024 Annual Meeting of the North Central Division of the American Phytopathological Society.

Association analysis identified candidate genomic regions for heat stress tolerance in bread wheat (Triticum aestivum L.) - (Abstract Only)
Gudi, S., Singh, J., Gill, H., Sehgal, S., Upinder, G., Gupta, R. 2024. Association analysis identified candidate genomic regions for heat stress tolerance in bread wheat (Triticum aestivum L.). Plant Biology Conference. Poster No. 100-71.

Evolution, diversity, and function of the disease susceptibility gene Snn1 in wheat - (Peer Reviewed Journal)
Seneviratne, S., Shi, G., Szabo-Hever, A., Zhang, Z., Peters Haugrud, A.R., Running, K., Singh, G., Nandety, R.S., Fiedler, J.D., Mcclean, P., Xu, S.S., Friesen, T.L., Faris, J.D. 2024. Evolution, diversity, and function of the disease susceptibility gene Snn1 in wheat. The Plant Journal. 119(4):1720-1736. https://doi.org/10.1111/tpj.16879.

Identification of two QTL for Hessian fly resistance in tetraploid wheat - (Abstract Only)
Peters Haugrud, A.R., Anderson, K.M., Harris, M., Faris, J.D., Xu, S.S. 2024. Identification of two QTL for Hessian fly resistance in tetraploid wheat. Meeting Abstract. Poster No. 260.

Implementing multi-trait genomic selection to improve grain milling quality in oats (Avena sativa L.) - (Peer Reviewed Journal)
Dhakal, A., Poland, J., Adhikari, L., Faryna, E., Fiedler, J.D., Rutkoski, J., Arbelaez, J. 2024. Implementing multi-trait genomic selection to improve grain milling quality in oats (Avena sativa L.). The Plant Genome. 17(2). https://doi.org/10.1002/tpg2.20457.

Future of durum wheat research and breeding: insights from early career researchers - (Review Article)
Peters Haugrud, A.R., Achilli, A., Martinez-Pena, R., Klymiuk, V. 2024. Future of durum wheat research and breeding: insights from early career researchers. The Plant Genome. https://doi.org/10.1002/tpg2.20453.

The Hessian fly resistance gene HvRHF1 is localized in an NBS-LRR gene cluster in barley - (Peer Reviewed Journal)
Karki, M., Robbani, M., Chu, C.N., Xu, S.S., Liu, Z., Yang, S. 2024. The Hessian fly resistance gene HvRHF1 is localized in an NBS-LRR gene cluster in barley. Theoretical and Applied Genetics. 137. Article 71. https://doi.org/10.1007/s00122-024-04581-5.

The USDA-SoyWheOatBar-3K: a rapid, inexpensive genotyping platform to enable genomics-assisted breeding of small grains - (Abstract Only)
Fiedler, J.D., Brault, C., Conley, E., Beaubien, K., Bazzer, S., Caffe, M., Smith, K., Anderson, J. 2024. The USDA-SoyWheOatBar-3K: a rapid, inexpensive genotyping platform to enable genomics-assisted breeding of small grains. Meeting Abstract. Poster No. PO0345.

Haplotype and transcriptome analyses reveal genes and gene regions that promote FHB resistance in spring wheat - (Abstract Only)
Thapa, S., Poudel, B., Bai, G., Xu, S.S., Fiedler, J.D. 2024. Haplotype and transcriptome analyses reveal genes and gene regions that promote FHB resistance in spring wheat. Meeting Abstract. Poster Number PE0378.

Development of epigenetic landscape and gene expression atlas of oats - (Abstract Only)
Ajayi-Moses, O., Gudi, S., Carlson, C.H., Esvelt Klos, K.L., Gupta, R., Nandety, R. 2024. Development of epigenetic landscape and gene expression atlas of oats (abstract). Plant and Animal Conference. Poster No. PO0359.

Exploratory genomic sequence analysis reveals structural differences at key loci for growth habit, seed dormancy, and rust resistance in barley - (Abstract Only)
Massman, C., Maughn, P.J., Nandety, R., Clare, S.J., Fiedler, J.D., Hayes, P.M. 2024. Exploratory genomic sequence analysis reveals structural differences at key loci for growth habit, seed dormancy, and rust resistance in barley (abstract). Poster No. PE0348.

Genetic mapping of resistance QTLs to bacterial leaf streak in wheat - (Abstract Only)
Acharya, K., Green, A., Liu, Z., Schachterle, J., Kumari, P., Manan, F., Faris, J.D. 2024. Genetic mapping of resistance QTLs to bacterial leaf streak in wheat. Meeting Abstract. Poster No. PO0389.

Identification of QTLs associated with yield components, agronomic traits, and kernel parameters in hard red spring wheat - (Abstract Only)
Kumari, P., Peters Haugrud, A.R., Xu, S.S., Zhang, Q., Green, A., Faris, J.D. 2024. Identification of QTLs associated with yield components, agronomic traits, and kernel parameters in hard red spring wheat. Meeting Abstract. Poster No. PE0379.

Molecular cloning of the septoria nodorum blotch susceptibility gene Snn2 in wheat - (Abstract Only)
Seneviratne, S., Zhang, Z., Running, K., Peters Haugrud, A.R., Szabo-Hever, A., Singh, G., Acharya, K., Fiedler, J.D., Mclean, P., Xu, S.S., Yang, S., Friesen, T.L., Faris, J.D. 2024. Molecular cloning of the septoria nodorum blotch susceptibility gene Snn2 in wheat. Meeting Abstract. Poster No. PE0390.

Molecular mapping of a novel genetic locus governing enhanced susceptibility to tan spot in durum wheat - (Abstract Only)
Pfaff, T., Singh, G., Running, K., Szabo-Hever, A., Faris, J.D. 2024. Molecular mapping of a novel genetic locus governing enhanced susceptibility to tan spot in durum wheat. Meeting Abstract. Poster No. PO0379.

Towards improving oil composition and content in oat through metabolic engineering - (Abstract Only)
Zhou, Z., Kaur, R., Donoso, T., Ohm, J., Kushwaha, A., Gupta, R., Lefsrud, M., Singh, J. 2024. Towards improving oil composition and content in oat through metabolic engineering (abstract). Paper No.52034.

Telomere-to-telomere genome assembly and resequencing of 20 Aegilops umbellulata genomes reveals broad genetic and phenotypic diversity for novel disease resistance traits - (Abstract Only)
Singh, J., Gudi, S., Maughan, J., Liu, Z., Kolmer, J.A., Chen, X., Rouse, M.N., Sehgal, S., Fiedler, J.D., Choulet, F., Acevedo, M., Gupta, R., Upinder, G. 2024. Telomere-to-telomere genome assembly and resequencing of 20 Aegilops umbellulata genomes reveals broad genetic and phenotypic diversity for novel disease resistance traits (abstract). Poster No. PE0420.

Genome-wide association study unravel the genetic basis of seedling heat stress tolerance in wheat (Triticum aestivum L.) - (Abstract Only)
Gudi, S., Singh, J., Gill, H.S., Sehgal, S., Upinder, G., Gupta, R. 2024. Genome-wide association study unravel the genetic basis of seedling heat stress tolerance in wheat (Triticum aestivum L.)(abstract). Poster No. PE0414.

Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation - (Peer Reviewed Journal)
Nandety, R., Wen, J., Mysore, K. 2023. Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation. Fundamental Research. 3(2):219-224. https://doi.org/10.1016/j.fmre.2022.06.018.