Characterization of an incomplete leaf rust resistance gene and development of KASP markers for the leaf rust resistance gene Lr47 in wheat

Authors: Xu, Xiangyang; Li, Genqiao; Bai, Guihua; Bernardo, Amy; CARVER, BRETT - Oklahoma State University; St Amand, Paul; BIAN, RUOLIN - Kansas State University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2020
Publication Date: 3/24/2021
Citation: 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.
DOI: https://doi.org/10.1094/PHYTO-07-20-0308-R

Interpretive Summary: Leaf rust is one of the most common wheat diseases worldwide. Although a considerable number of leaf rust resistance genes have been identified, most of them have lost effectiveness in the Great Plains of the USA and new leaf rust resistance genes are urgently needed to enhance leaf rust resistance in this region. A RIL population from CI 17884/Bainong 418 was evaluated for leaf rust resistance and genotyped using the genotyping by sequencing approach. QTL analysis revealed an incomplete leaf rust resistance gene, designated QLr.stars-1BS, on the short arm of chromosome 1B in Bainong 418, as well as the leaf rust resistance gene Lr47 on chromosome 7A in CI 17884. Lr47 is one of a few genes that are still effective in the Great Plains, while the combination of Lr47 and QLr.stars-1BS significantly enhanced leaf rust resistance. Therefore,Lr47 and QLr.stars-1BS are valuable for breeding leaf rust resistant cultivars in the Great Plains. One and two diagnostic KASP markers were further developed for QLr.stars-1BS and Lr47, respectively, to facilitate their introgression into elite wheat cultivars or breeding lines.

Technical Abstract: Leaf rust, caused by Puccininia triticina (Pt), is one of the most common wheat diseases in the Great Plains of the USA. Although a considerable number of leaf rust resistance genes have been identified, most of them have lost effectiveness in the region and new leaf rust resistance genes are urgently needed to enhance leaf rust resistance in this region. A population of recombinant inbred lines (RILs) from CI 17884 x Bainong 418 was evaluated for responses to leaf rust race Pt race Pt52-2 (phenotyped as MMPSD) and genotyped using single nucleotide polymorphism (SNP) markers generated by the genotyping-by-sequencing (GBS). Quantitative trait analysis (QTL) analysis identified a minor gene for resistance to leaf rust, designated QLr.stars-1BS, on the short arm of chromosome 1B of Bainong 418 and another leaf rust resistance gene Lr47 on chromosome 7A of CI 17884. QLr.stars-1BS resides on a wheat-rye 1BL.1RS translocation segment. Lr47 was originally identified from a wheat-T. speltoides translocation segment 7S#1 in CI 17884 etc. and is one of the only a few genes that are still effective in the Great Plains. The 7S#1 segment was previously shortened using the ph1 mutation, leading to the generation of wheat-T. speltoides translocation 7S#1S. A set of 7A-specific simple sequence repeat (SSR) markers were developed and used to genotype CI 17884, PI 603918, and Pavon F76. Haplotype analysis indicated that the estimated length of 7S#1S was 157.23 to 174.42 Mb, accounting for about 22.5% of the 7A chromosome. Two SNPs on 7S#1S and 4 SNPs on the 1RS chromosome arm were converted to KASP markers, which were subsequently validated in a panel of 91 cultivars and recently released elite breeding lines. Of these, the resistance alleles of KASP-Lr47-1 and KASP-Lr47-2 were only present in wheat accessions carrying Lr47, while the resistance allele of KASP-1RS-1 was only detected in wheat accessions with the 1BL.1RS translocation, indicating that they can be used to introgress Lr47 and QLr.stars-1BS into locally adapted wheat cultivars or breeding lines.