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

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. Abstract 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.

Fine Mapping of a Vigor QTL in Chickpea (Cicer arietinum L.) Reveals a Potential Role for Ca4_TIFY4B in Regulating Leaf and Seed Size

“…In cool, short-season environments, increasing vigor is a key priority of breeding programs to improve competitive ability during crop establishment and yield. Genetic studies in many different crops have mapped vigor-related loci and assessed their impact under a range of growing conditions including irrigated, drought, salt, and disease pressure ( Collins et al, 1999 ; Graham et al, 2011 ; Platten et al, 2013 ; Sivasakthi et al, 2018 ; Taylor et al, 2019 ; Atieno et al, 2021 ; Nguyen et al, 2021 ). In chickpea, vigor has been reported to contribute either positively ( Subbarao et al, 1995 ; Turner et al, 2001 ) or negatively ( Zaman-Allah et al, 2011 ) to yield.…”

“…Recently, quantitative trait locus (QTL) mapping and association studies across multiple environments identified major genetic regions for vigor-related traits on chromosomes (Ca) 1, 3, and 4 in chickpea ( Nguyen et al, 2021 ). The vigor QTL on Ca4 ( Ca4_Vqtl ) overlapped with a “hotspot” region of QTL previously reported for drought tolerance ( Varshney et al, 2014 ; Jaganathan et al, 2015 ; Kale et al, 2015 ; Singh et al, 2016 ) and vigor ( Sivasakthi et al, 2018 ).…”

“…The vigor QTL on Ca4 ( Ca4_Vqtl ) overlapped with a “hotspot” region of QTL previously reported for drought tolerance ( Varshney et al, 2014 ; Jaganathan et al, 2015 ; Kale et al, 2015 ; Singh et al, 2016 ) and vigor ( Sivasakthi et al, 2018 ). The overlapping QTL region also colocated with a region for seed size in both the ICC4958/ICC1882 ( Varshney et al, 2014 ; Sivasakthi et al, 2018 ) and Rupali/Genesis836 recombinant inbred line (RIL) mapping populations ( Atieno et al, 2021 ; Nguyen et al, 2021 ). A positive impact of seed size on vigor has been reported in both cereal and legume species, including wheat ( Triticum aestivum L.) ( Sloane, 1999 ; Zhao et al, 2019 ), rice ( Oryza sativa L.) ( Roy et al, 1996 ), maize ( Zea mays L.) ( Yusuf et al, 2014 ), barley ( Hordeum vulgare L.) ( Massimi, 2018 ), birdsfoot trefoil ( Lotus corniculatus L.) and alfalfa ( Medicago sativa L.) ( Carleton and Cooper, 1972 ), chickpea ( Cicer arietinum L.), lupin ( Lupinus angustifolius L.) and pea ( Pisum sativum L.) ( Kamboozia, 1994 ), and soybean ( Glycine max (L.) Merr.)…”

“…The Ca4_Vqtl region is estimated between 12.65 and 13.06 Mb of chromosome 4 ( CDC Frontier Ref V2.6.3 ; Edwards, 2016 ; Ruperao, 2016 ) and contains 39 genes ( Nguyen et al, 2021 ), making it difficult to prioritize candidates for further investigation and functional confirmation. Further fine mapping was necessary to prioritize candidates with roles in plant vigor.…”

“…This was achieved using heterogeneous inbred families (HIFs) derived from selfed F 4 RILs of Rupali/Genesis836, confirmed as heterozygous across the Ca4_Vqtl interval. High-depth sequence capture ( Nguyen et al, 2021 ) was used to identify sequence variation. We identified a variant of the gene Ca4_TIFY4B in the high-vigor Rupali RIL parent, proposed to alter the regulation of seed size and other plant organs including leaves and roots and contribute to differences in plant vigor.…”