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

OAR@ICRISAT

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Relation http://oar.icrisat.org/12631/
https://link.springer.com/article/10.1007/s00122-021-03954-4
https://doi.org/10.1007/s00122-021-03954-4
 
Title The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data
 
Creator Nguyen, D T
Hayes, J E
Atieno, J
Li, Y
Baumann, U
Pattison, A
Bramley, H
Hobson, K
Roorkiwal, M
Varshney, R K
Colmer, T D
Sutton, T
 
Subject Chickpea
Genetics and Genomics
 
Description 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.
 
Publisher Springer Verlag
 
Date 2021-10-13
 
Type Article
PeerReviewed
 
Identifier Nguyen, D T and Hayes, J E and Atieno, J and Li, Y and Baumann, U and Pattison, A and Bramley, H and Hobson, K and Roorkiwal, M and Varshney, R K and Colmer, T D and Sutton, T (2021) The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data. Theoretical and Applied Genetics, 135. pp. 107-124. ISSN 0040-5752