A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

Scientific Reports
Deepak BajajSwarup K Parida

Abstract

High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally rele...Continue Reading

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Citations

Dec 22, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Shouvik DasSwarup K Parida
Mar 5, 2016·Plant Science : an International Journal of Experimental Plant Biology·Deepak BajajSwarup K Parida
Sep 24, 2015·Plant Molecular Biology·Hari D UpadhyayaSwarup K Parida
Apr 6, 2016·Frontiers in Plant Science·Hari D UpadhyayaSwarup K Parida
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Aug 12, 2015·Scientific Reports·Sabiha ParweenDebasis Chattopadhyay
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Jul 29, 2017·Frontiers in Plant Science·Rishi SrivastavaSwarup K Parida
Jun 4, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Su Ryun ChoiYong Pyo Lim

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Methods Mentioned

BETA
genotyping
PCR
Assay

Software Mentioned

Circos
GenTrain
GeneMapper
Illumina Assay Design Tool ( ADT )
Illumina BeadArray Express Reader
QTL Cartographer
Illumina GenomeStudio Genotyping
JoinMap
QTL Network
SPSS

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