Murdoch University Research Repository

Welcome to the Murdoch University Research Repository

The Murdoch University Research Repository is an open access digital collection of research
created by Murdoch University staff, researchers and postgraduate students.

Learn more

QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)

Pandey, M.K., Khan, A.W., Singh, V.K., Vishwakarma, M.K., Shasidhar, Y., Kumar, V., Garg, V., Bhat, R.S., Chitikineni, A., Janila, P., Guo, B. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2017) QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal, 15 (8). pp. 927-941.

[img]
Preview
PDF - Published Version
Download (1MB) | Preview
Free to read: https://doi.org/10.1111/pbi.12686
*No subscription required

Abstract

Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co-occurrence leads to significant yield loss in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling resistance to rust and LLS, whole-genome resequencing (WGRS)-based approach referred as ‘QTL-seq’ was deployed. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent and the resistant and susceptible bulks for rust and LLS. Sequence analysis of bulks for rust and LLS with reference-guided resistant parent assembly identified 3136 single-nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of ≥7 in the identified genomic region on pseudomolecule A03. Detailed analysis identified 30 nonsynonymous SNPs affecting 25 candidate genes for rust resistance, while 14 intronic and three synonymous SNPs affecting nine candidate genes for LLS resistance. Subsequently, allele-specific diagnostic markers were identified for three SNPs for rust resistance and one SNP for LLS resistance. Genotyping of one RIL population (TAG 24 × GPBD 4) with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of QTL-seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.

Item Type: Journal Article
Publisher: Blackwell Publishing Inc.
Copyright: © 2016 The Authors.
URI: http://researchrepository.murdoch.edu.au/id/eprint/61144
Item Control Page Item Control Page

Downloads

Downloads per month over past year