Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea

Publication Overview
TitleTranscriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea
AuthorsSrivastava R, Bajaj D, Malik A, Singh M, Parida SK
TypeJournal Article
Journal NameScientific reports
Volume6
Year2016
Page(s)33616
CitationSrivastava R, Bajaj D, Malik A, Singh M, Parida SK. Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea. Scientific reports. 2016; 6:33616.

Abstract

The RNA-sequencing followed by de-novo transcriptome assembly identified 11621 genes differentially xpressed in roots vs. shoots of a wild perennial Cicer microphyllum. Comparative analysis of transcriptomes between microphyllum and cultivated desi cv. ICC4958 detected 12772 including 3242 root- and 1639 shoot-specific microphyllum genes with 85% expression validation success rate. Transcriptional reprogramming of microphyllum root-specific genes implicates their possible role in regulating differential natural adaptive characteristics between wild and cultivated chickpea. The transcript-derived 5698 including 282 in-silico polymorphic SSR and 127038 SNP markers annotated at a genome-wide scale exhibited high amplification and polymorphic potential among cultivated (desi and kabuli) and wild accessions suggesting their utility in chickpea genomics-assisted breeding applications. The functional significance of markers was assessed based on their localization in non-synonymous coding and regulatory regions of microphyllum root-specific genes differentially expressed predominantly in ICC 4958 roots under drought stress. A high-density 490 genic SSR- and SNP markers-anchored genetic linkage map identified six major QTLs regulating drought tolerance-related traits, yield per plant and harvest-index in chickpea. The integration of high-resolution QTL mapping with comparative transcriptome profiling delineated five microphyllum root-specific genes with non-synonymous and regulatory SNPs governing drought-responsive yield traits. Multiple potential key regulators and functionally relevant molecular tags delineated can drive translational research and drought tolerance-mediated chickpea genetic enhancement.

Features
This publication contains information about 41 features:
Feature NameUniquenameType
SNP103CmSNP103Cmgenetic_marker
SNP104CmSNP104Cmgenetic_marker
SNP171CmSNP171Cmgenetic_marker
SNP172CmSNP172Cmgenetic_marker
SNP173CmSNP173Cmgenetic_marker
SNP229CmSNP229Cmgenetic_marker
SNP231CmSNP231Cmgenetic_marker
SNP265CmSNP265Cmgenetic_marker
SNP266CmSNP266Cmgenetic_marker
SNP268CmSNP268Cmgenetic_marker
SNP364CmSNP364Cmgenetic_marker
SNP365CmSNP365Cmgenetic_marker
SNP367CmSNP367Cmgenetic_marker
SNP420CmSNP420Cmgenetic_marker
SNP421CmSNP421Cmgenetic_marker
SNP422CmSNP422Cmgenetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Chickpea-Transcriptome_Agronomic_Traits-Srivastava-2016
Featuremaps
This publication contains information about 1 maps:
Map Name
Chickpea-ICC4958_x_ICC17163-RIL-2016
Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
ICC 4958ICC 4958accession
ICC 17163ICC 17163accession
ICC4958_x_ICC17163ICC4958_x_ICC17163population
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN2045-2322
eISSN2045-2322
Publication Date2016
Journal AbbreviationSci Rep
Elocation10.1038/srep33616
LanguageEnglish
Language AbbrENG
Publication TypeJournal Article