Identifying potential adaptive SNPs within combined DNA sequences in Genus Crocus L. (Iridaceae family): A multiple analytical approach

Abstract

The genus Crocus L. of Iridaceae family contains about 160 species and is considered as a complex group of plant taxa with regard to evolutionary and phylogenetic events. Inter-specific hybridization and gene flow contribute to species genetic homogeneity in one hand and high within species genetic variability and species genetic content overlaps caused species resolution a problem. In spite of extensive molecular phylogenetic studies in this genus, nothing is known about DNA sequences or Single nucleotide polymorphisms (SNPs) which are of adaptive nature. Moreover, nothing is known about which geographical or environmental factors plays role in species local adaptation and speciation events within Crocus L. genus. Therefore, the present study was conducted to answer the above said questions. We used a combined molecular data set of internal transcribed spacer (ITS) nuclear gene and trnL-F intergenic spacer (trnL-F) sequences of chloroplast genome. A multiple analytical method of Canonical correlation (CCA), Redundency analysis (RDA), and Latent Factor Mixed Model (LFMM)identified a few potential adaptive SNPs. Moreover, population criterions like Tajimas’ D, molecular clock test, as well as skyline-plot revealed a smooth and continuous genetic changes for most of the Crocus species, but the occurrence of a sudden deep nucleotide substitution for Crocus taxa of Iran. The impact of latitude was significantly higher on nucleotide changes compared to that of longitudinal distribution of Crocus species.