The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data.

Publication Overview
TitleThe genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data.
AuthorsNguyen DT, Hayes JE, Atieno J, Li Y, Baumann U, Pattison A, Bramley H, Hobson K, Roorkiwal M, Varshney RK, Colmer TD, Sutton T
TypeJournal Article
Journal NameTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Year2021
CitationNguyen DT, Hayes JE, Atieno J, Li Y, Baumann U, Pattison A, Bramley H, Hobson K, Roorkiwal M, Varshney RK, Colmer TD, Sutton T. The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data.. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2021 Oct 13.

Abstract

KEY MESSAGE
QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in diverse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple diversity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two diversity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1-FTa2-FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and diversity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the diversity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology.

Features
This publication contains information about 11 features:
Feature NameUniquenameType
UAD_Ca1_6027390UAD_Ca1_6027390genetic_marker
UAD_Ca1_6027522UAD_Ca1_6027522genetic_marker
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UAD_Ca4_13018167UAD_Ca4_13018167genetic_marker
UAD_Ca4_13024285UAD_Ca4_13024285genetic_marker
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1432-2242
eISSN1432-2242
DOI10.1007/s00122-021-03954-4
Copyright© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryGermany
Journal AbbreviationTheor Appl Genet
Publication Date2021 Oct 13
URLhttps://link.springer.com/article/10.1007/s00122-021-03954-4
Cross References
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DatabaseAccession
PMID: PubMedPMID:34643761