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Research paper | Open Access

Development of diagnostic markers for a wheat leaf rust resistance gene Lr42 using RNA-sequencing

Yang Liua,b, Hui Chenb, Chunxin Lib,c, Lirong Zhangb,d, Mingqin Shaob, Yuhui Pangb,e, Xiangyang Xuf, Guihua Baib,g( )
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
Henan Academy of Agricultural Science, Zhengzhou 450002, Henan, China
College of Plant Protection, Hebei Agricultural University, Baoding 071000, Hebei, China
College of Agriculture, Henan University of Science and Technology, Luoyang 471023, Henan, China
USDA-ARS Wheat, Peanut, and Other Field Crop Research Unit, Stillwater, OK 74075, USA
USDA-ARS, Hard Winter Wheat Genetic Research Unit, Manhattan, KS 66506, USA
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Abstract

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.

Keywords

KASPAegilops tauschiiTriticum tauschiiLr42Diagnostic marker

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The Crop Journal
Volume 9 Issue 6,
December 2021
Pages 1357-1366
DOI: 10.1016/j.cj.2021.02.012
Cite this article:
Liu Y, Chen H, Li C, et al. Development of diagnostic markers for a wheat leaf rust resistance gene Lr42 using RNA-sequencing. The Crop Journal, 2021, 9(6): 1357-1366. https://doi.org/10.1016/j.cj.2021.02.012

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Received: 20 October 2020
Revised: 11 December 2020
Accepted: 17 March 2021
Published: 06 April 2021
© 2021 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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