Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat

Authors: Lhamo, Dhondup; SUN, QUN - North Dakota State University; ZHANG, QIJUN - North Dakota State University; LI, XUEHUI - North Dakota State University; Fiedler, Jason; XIA, GUANGMIN - Shandong University; Faris, Justin; Gu, Yong; GILL, UPINDER - North Dakota State University; Cai, Xiwen; ACEVEDO, MARICELIS - Cornell University; Xu, Steven

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/7/2022
Publication Date: 1/22/2023
Citation: Lhamo, D., Sun, Q., Zhang, Q., Li, X., Fiedler, J.D., Xia, G., Faris, J.D., Gu, Y.Q., Gill, U., Cai, X., Acevedo, M., Xu, S.S. 2023. Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat. Theoretical and Applied Genetics. 136. Article 20. https://doi.org/10.1007/s00122-023-04281-6.
DOI: https://doi.org/10.1007/s00122-023-04281-6

Interpretive Summary: Wheat leaf rust is one of the most devastating fungal diseases of wheat. Although leaf rust can be effectively controlled by growing wheat varieties carrying leaf rust resistance (Lr) genes, new races of leaf rust pathogen are frequently emerging and make the Lr genes in the wheat varieties become ineffective. Therefore, finding new resistance sources are needed to sustain robust and durable resistance in wheat breeding and production. This study was conducted to identify the Lr genes presented in cultivated emmer wheat germplasm. By evaluating 180 cultivated emmer wheat lines for leaf rust resistance and analyzing them with DNA markers, we identified 90 chromosomal regions that are associated with seedling and adult plant resistances, respectively. Among these chromosomal regions, 24 possibly harbor the known Lr genes such as Lr3, Lr18, Lr28, Lr37, Lr45, Lr53, Lr64, etc., the remaining 66 regions potentially harbor new Lr genes with major and minor effects. The discovery from this study provides a foundation for further genetic analysis, cloning and functional analysis of the Lr genes in these chromosomal regions contributing to leaf rust resistance, which can then be utilized in resistance breeding of modern wheat varieties.

Technical Abstract: Leaf rust, caused by the fungal pathogen, Puccinia triticina (Pt), poses a serious threat to the global wheat production. To find new resistance sources, we assessed a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for seedling resistance to Pt race, BBBQD, in the greenhouse and for adult plant resistance to mixed Pt races, BBBQJ, CCMSS and MCDSS, in the field. Genotype-by-sequencing (GBS) method and 9K SNP Infinium array were used to genotype the emmer panel, and the subsequent filtering resulted in 46,383 and 4,331 SNPs (single nucleotide polymorphisms), respectively. By performing genome-wide association analyses (GWAS) using four statistical models, we identified 49 quantitative trait loci (QTL) for seedling resistance located largely on chromosomes 2A, 6B, 2B, 4A and 5B, and 41 distinct QTL for adult plant resistance on 2B, 3B, 5B and 3A. Of these, 11 QTL for seedling resistance were collocated or present near five catalogued Lr genes including Lr28, Lr37, Lr53, Lr64 and LrZH22, and five QTL for adult plant resistance were collocated or present near Lr3, Lr18 and Lr45. In addition, three QTL for seedling resistance and five QTL for adult plant resistance were found near the previously-reported QTL in wheat. The remaining QTL were novel loci that potentially harbor new Lr genes with major and minor effects. Further linkage analysis, cloning and functional genetics are necessary to determine the causal genes behind QTL contributing to leaf rust resistance, which can then be utilized in resistance breeding of modern wheat cultivars.