Allelic variants of EFL3 and their association with early flowering traits in chickpea (Cicer arietinum L.)

Allele mining of the ELF3 gene, associated with flowering time in chickpeas, was conducted using whole genome resequencing data from 254 chickpea genotypes within the chickpea reference set, utilizing the GATK tool. A total of 671 genetic variants were identified within the ELF3 genic region, encompassing not only its genic region but also its 1 kb promoter region and intergenic regions. Among these, biallelic SNPs were predominant (641), followed by multi-allelic InDels (19), multi-allelic SNPs (9) and least of biallelic Indels (2). Out of these 641 biallelic SNPs, 44 SNPs were located across 4 exons of ELF3 gene [exon 2 (16), exon 5 (10), exon1 (9) and exon 4 (9)] while exon 3 displayed no genetic variants. Remarkably, the distinctive 11 bp deletion within the first exon of ICC96029’s Elf3 was not detected in this analysis. Instead, a missense mutation within ELF3 was identified within the studied chickpea reference set. Utilizing a candidate gene-based association mapping approach, 20 variants (comprising 18 biallelic SNPs and 2 InDels) were employed based on their presence in at least 95% of genotypes. Employing a general linear model (GLM) approach with three years of phenotypic data, a total of 4 significant marker-trait associations (MTAs) were identified. Specifically, the variants SNP_021164.1_36025048 (G/A) and SNP_021164.1_36021869 (A/C) exhibited associations with the FLD/s trait. Additionally, the SNP locus SNP_021164.1_36011429 (C/T), located within exon 5 of ELF3a, and SNP_021164.1_36013862 (C/A) located within intron 2, displayed associations with the pod_D/S trait. These allelic variants, particularly the missense mutation, carry significant importance due to their potential impact on the interaction of ELF3 with interacting proteins that eventually lead to variations in flowering time within the chickpea population.