Development of diagnostic markers for a wheat leaf rust resistance gene Lr42 using RNA-sequencing
Yang Liu,
Hui Chen,
Chunxin Li,
Lirong Zhang,
Mingqin Shao,
Yuhui Pang,
Xiangyang Xu,
Guihua Bai
Affiliations
Yang Liu
Institute of South Subtropical Crops, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524013, Guangdong, China; Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
Hui Chen
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
Chunxin Li
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; Henan Academy of Agricultural Science, Zhengzhou 450002, Henan, China
Lirong Zhang
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; College of Plant Protection, Hebei Agricultural University, Baoding 071000, Hebei, China
Mingqin Shao
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
Yuhui Pang
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; College of Agriculture, Henan University of Science and Technology, Luoyang 471023, Henan, China
Xiangyang Xu
USDA-ARS Wheat, Peanut, and Other Field Crop Research Unit, Stillwater, OK 74075, USA
Guihua Bai
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; USDA-ARS, Hard Winter Wheat Genetic Research Unit, Manhattan, KS 66506, USA; Corresponding author.
Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gene identified from Aegilops tauschii and is still effective against current predominant leaf rust races in the United States and many other countries. In this study, we developed diagnostic DNA markers for Lr42 using the sequence polymorphisms of a differentially expressed gene (TaRPM1) encoding a putative NB-ARC protein in the Lr42 candidate region identified by RNA-sequencing of two near-isogenic lines contrasting in Lr42 alleles. Markers were designed based on a deletion mutation and a single nucleotide polymorphism (SNP) in the gene. Haplotype analyses of the newly developed markers in the three diversity panels demonstrated that they are diagnostic for Lr42, and superior to previously used markers in selection accuracy. These markers have the advantages of low cost and easy assay, and they are suitable for marker-assisted selection in breeding programs with either high- or low-throughput marker screening facilities.
