Das, S. and Singh, M. and Srivastava, R. and Bajaj, D. and etl, .
(2015)
mQTL-seq delineates functionally relevant
candidate gene harbouring a major QTL
regulating pod number in chickpea.
DNA Research.
pp. 1-13.
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Abstract
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 mQTLseq-
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.
| Item Type: |
Article
|
| Uncontrolled Keywords: |
Chickpea, mQTL-seq, pod number, SNP, wild accessions |
| Author Affiliation: |
National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India |
| Subjects: |
Crop Improvement |
| Divisions: |
Chickpea |
| Depositing User: |
Mr T L Gautham
|
| Date Deposited: |
04 Nov 2016 03:51 |
| Last Modified: |
04 Nov 2016 03:51 |
| URI: |
http://eprints.icrisat.ac.in/id/eprint/14485 |
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