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

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Relation http://oar.icrisat.org/9956/
http://dx.doi.org/10.1111/pbi.12686
10.1111/pbi.12686
 
Title QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)
 
Creator 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
Varshney, R K
 
Subject Groundnut
Genetics and Genomics
 
Description 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.
 
Publisher John Wiley & Sons
 
Date 2017-02
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/9956/1/Pandey_et_al-2017-Plant_Biotechnology_Journal.pdf
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