Single nucleotide polymorphism and haplotype diversity of the gene NAC4 in grapevine

Abstract

The NAC gene family encodes a large plant-specific transcription factors that play diverse roles in plant development and stress regulation. In this study, nucleotide variation at gene NAC4 was surveyed by sequencing a sample of 50 wild grapevine accessions and 73 cultivars of Vitis vinifera L. A total of 11 bi-allelic single nucleotide polymorphisms were detected in the studied gene resulting in an average of 1 SNP every 63bp. Among the 11 detected SNPs, 2 SNPs were located in the coding region, SNP R373 results in a change in the encoded amino acid (Val⇒Ile) and the second is synonymous. The detected SNPs combine to 10 haplotypes with frequency varying from 0.4% to 53.3%. Genetic diversity level recorded for cultivated grapevine gene pools (11 SNP, 9 haplo, Hd=0.735±0.028, Pi=0.00492±0.00024) was higher than for wild germplasms (9 SNPs, 8 haplo, Hd=0.526±0.051, Pi=0.00236±0.00026). A search for selection signatures highlighted non deviations from the standard neutral model for this gene in wild sample. However patterns of nucleotide diversity were consistent with a balancing selection in cultivated gene pool which may provide evidence for adaptation at the molecular level and help elucidate genotype phenotype relationships. The presence of SNPs resulting in the change in the encoded amino acid in the studied gene can be interesting to highlight contribution of SNP in the evolution of candidate genes coding for functional trait in plants and can be a base for further genetic association studies.