Dissection of genomic regions underlying early seedling vigour in chickpea through genome-wide association mapping

TL;DR

This study identifies genetic regions linked to early seedling vigour in chickpea, which could help develop better-performing varieties.

Contribution

The study reports novel marker-trait associations for early seedling vigour in chickpea using genome-wide association mapping.

Findings

34 marker-trait associations were identified for early seedling vigour traits in chickpea.

36 candidate genes linked to these associations were identified, including those involved in root formation and hormone signaling.

Highly vigorous genotypes like ICC15567 and ICC8318 were identified through phenotypic screening.

Abstract

Chickpea (Cicer arietinum L.) is the most important pulse in India and one of the most important worldwide. In order to increase the chickpea production area, the rainfed rice fallows are being targeted to adopt rice-chickpea cropping system. Early seedling vigour (ESV) is an important trait which enables the crop to have better germination, crop stand, utilization of residual soil moisture, faster biomass accumulation and better root growth under poor soil structure. Till date there has been no work done regarding the mapping of genomic regions controlling ESV in chickpea.

We conducted a genome-wide association study taking 13 traits related to ESV in a diverse panel of the reference set of ICRISAT. GWAS was conducted using FarmCPU and BLINK model and a total of 34 marker-trait associations (MTAs) were identified. We were able to identify putative 36 candidate genes linked to the MTAs such as Lateral Root Primordium 1, Auxin-Induced Protein 22D-Like, Transcription factor MYB3-like etc. Most of these genes are involved in primary and lateral root formation, development of meristem, hormone signaling and germination that ultimately regulate the seedling vigour in chickpea.

Our findings have identified substantial genetic variability for early seedling vigour traits in chickpea. Phenotypic screening has enabled to identification of highly vigorous genotypes like ICC15567, ICC8318. We also reported novel MTAs linked to ESV traits in chickpea, which can be further validated using functional genomic studies. The findings of this study will help in further understanding of ESV as a trait and the development of early vigorous chickpea varieties in future.

The online version contains supplementary material available at 10.1186/s12870-025-07814-x.

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