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mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea

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Title mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea
 
Creator Das, Shouvik
Singh, Mohar
Srivastava, Rishi
Bajaj, Deepak
Saxena, Maneesha S.
Rana, Jai C.
Bansal, Kailash C.
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject chickpea
mQTL-seq
pod number
SNP
wild accessions
 
Description Accepted date: 9 November 2015
The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.
The authors gratefully acknowledge the financial support for this study
provided by a research grant from the Department of Biotechnology (DBT),
Government of India (102/IFD/SAN/2161/2013-14). S.D. acknowledges the
DBT for Junior Research Fellowship award. The authors also acknowledge
the financial support provided by the Department of Agriculture and Cooperation (DAC), Government of India for developing wide cross populations
and their precise phenotyping under the National Food Security Mission. We
are thankful to the Editor and reviewers for critically evaluating the manuscript
and providing constructive comments.
 
Date 2016-01-28T08:36:18Z
2016-01-28T08:36:18Z
2016
 
Type Article
 
Identifier DNA Res., 23(1): 53-65
1756-1663
http://172.16.0.77:8080/jspui/handle/123456789/601
http://dnaresearch.oxfordjournals.org/content/early/2015/12/19/dnares.dsv036.long
10.1093/dnares/dsv036
 
Language en_US
 
Publisher Oxford University Press