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Journal article
QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)
Plant Biotechnology Journal, Vol.15(8), pp.927-941
2017
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.
Details
- Title
- QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)
- Authors/Creators
- M.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA.W. Khan (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsV.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM.K. Vishwakarma (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsY. Shasidhar (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsV. Kumar (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsV. Garg (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.S. Bhat (Author/Creator) - University of Agricultural Sciences, DharwadA. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsP. Janila (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsB. Guo (Author/Creator) - Agricultural Research ServiceR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
- Publication Details
- Plant Biotechnology Journal, Vol.15(8), pp.927-941
- Publisher
- Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
- Identifiers
- 991005541740707891
- Copyright
- © 2016 The Authors.
- Murdoch Affiliation
- State Agricultural Biotechnology Centre; Centre for Crop and Food Innovation; Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science