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Type: Journal article
Title: Genome analysis identified novel candidate genes for ascochyta blight resistance in chickpea using whole genome re-sequencing data
Author: Li, Y.
Ruperao, P.
Batley, J.
Edwards, D.
Davidson, J.
Hobson, K.
Sutton, T.
Citation: Frontiers in Plant Science, 2017; 8:359-1-359-13
Publisher: Frontiers Media S.A.
Issue Date: 2017
ISSN: 1664-462X
Statement of
Yongle Li, Pradeep Ruperao, Jacqueline Batley, David Edwards, Jenny Davidson, Kristy Hobson and Tim Sutton
Abstract: Ascochyta blight (AB) is a fungal disease that can significantly reduce chickpea production in Australia and other regions of the world. In this study, 69 chickpea genotypes were sequenced using whole genome re-sequencing (WGRS) methods. They included 48 Australian varieties differing in their resistance ranking to AB, 16 advanced breeding lines from the Australian chickpea breeding program, four landraces, and one accession representing the wild chickpea species Cicer reticulatum. More than 800,000 single nucleotide polymorphisms (SNPs) were identified. Population structure analysis revealed relatively narrow genetic diversity amongst recently released Australian varieties and two groups of varieties separated by the level of AB resistance. Several regions of the chickpea genome were under positive selection based on Tajima’s D test. Both Fst genome- scan and genome-wide association studies (GWAS) identified a 100 kb region (AB4.1) on chromosome 4 that was significantly associated with AB resistance. The AB4.1 region co-located to a large QTL interval of 7 Mb∼30 Mb identified previously in three different mapping populations which were genotyped at relatively low density with SSR or SNP markers. The AB4.1 region was validated by GWAS in an additional collection of 132 advanced breeding lines from the Australian chickpea breeding program, genotyped with approximately 144,000 SNPs. The reduced level of nucleotide diversity and long extent of linkage disequilibrium also suggested the AB4.1 region may have gone through selective sweeps probably caused by selection of the AB resistance trait in breeding. In total, 12 predicted genes were located in the AB4.1 QTL region, including those annotated as: NBS-LRR receptor-like kinase, wall-associated kinase, zinc finger protein, and serine/threonine protein kinases. One significant SNP located in the conserved catalytic domain of a NBS-LRR receptor-like kinase led to amino acid substitution. Transcriptional analysis using qPCR showed that some predicted genes were significantly induced in resistant lines after inoculation compared to non-inoculated plants. This study demonstrates the power of combining WGRS data with relatively simple traits to rapidly develop “functional makers” for marker-assisted selection and genomic selection.
Keywords: association study; re-sequencing; ascochyta blight; disease resistance; selective sweep; Fst; QTL
Rights: © 2017 Li, Ruperao, Batley, Edwards, Davidson, Hobson and Sutton. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
DOI: 10.3389/fpls.2017.00359
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