Identification of CtE1 gene nucleotide polymorphisms and development of SNP-based KASP markers in guar (Cyamopsis tetragonoloba (L.) Taub.)

Guar (Cyamopsis tetragonoloba (L.) Taub), is an important short-day legume crop, whose cultivation is limited at high latitudes due its photoperiod sensitivity, that negatively impacts flowering and maturation of this industrial oriented crop. In its close relative, soybean, the E₁ gene has been highly associated with the regulation of flowering time under long-day conditions. In this study we investigated the natural diversity of the E₁ homologue gene (CtE₁) in a panel of 144 guar accessions. For this purpose, the CtE₁ gene was amplified and sequenced using Illumina. As a result, five novel SNPs were identified in the 5’-untranslated region, coding region, and 3’-untranslated region of the CtE₁ gene. One non-synonymous SNP was located in the coding region causing a conservative Arg→Lys substitution. Based on the identified SNP, five KASP markers linked to polymorphism in the target gene were developed and tested in the guar collection. No significant associations were detected between discovered SNPs and available data on variability in flowering time or vegetation period length in the cohort of 144 accessions. These findings suggest that natural variation of the CtE₁ gene in the studied germplasm collection has minimal effect on flowering or maturation. The limited functional allelic diversity observed in the CtE₁ gene of guar compared to the E₁ gene in soybean likely reflects differences in their evolutionary histories, domestication bottlenecks, and selection pressures.

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