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

Pandey, M K and Khan, A W and Singh, V K and Vishwakarma, M K and Shasidhar, Y and Kumar, V and Garg, V and Bhat, R S and Chitikineni, A and Janila, P and Guo, B and Varshney, R K (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. pp. 1-15. ISSN 1467-7644

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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: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Resequencing, trait mapping, QTL-seq analysis, candidate gene discovery, diagnostic markers, groundnut, peanut, sequencing, leaf spot resistance
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 13 Apr 2017 04:48
Last Modified: 13 Apr 2017 04:48
URI: http://oar.icrisat.org/id/eprint/9956
Official URL: http://dx.doi.org/10.1111/pbi.12686
Acknowledgement: The work has been undertaken as a part of World Bank-assisted Karnataka Watershed Development Project-II (KWDP-II) funded by Government of Karnataka (GoK), India, Bill & Melinda Gates Foundation (BMGF) funded Tropical Legumes III (TL III) and the Peanut Foundation, USA. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium.
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