Genome-wide population structure and genetic diversity of endemic species Pulsatiila tongkangensis (Ranunculaceae) inferred from GBS (Genotyping by Seuencing): Implications for conservation and management
Bo-Yun KimP1*, Young-Cheol Kim2, Hyun-Kyung Oh1, Young-In Kim3, Jung-Hoon Lee3,
Seonghyun Cho4, Ji-Won Yoon1, SunheeSim1
1Plant Resources Division, National Institute of Biological Resources; 2Research Center for Natural Science, Gangneung-WonjuNational Universityy; 3Multidisciplinary Genome Institute, HallymUniversity; 4Biological and Genetic Resources Utilization Division, National Institute of Biological Resource
Genotyping-by-Sequencing (GBS) is a powerful genomic approach for identification of genetic variation on a genome-wide scale for genetic diversity analysis of non-model plants. This study represents the first use of GBS application to genome-wide variants of Korean endemic and vulnerable species Pulsatilla tongkangensis and assessed the genetic diversity present in 172 individuals from 12 populations.A total of 1,442,563s were initially obtained, from which 26,070 high-confidence SNPs (MAF >5% SNP missing data < 30%, calling rate = 100% and biallelic SNPs etc) were selected to analysis genetic diversity and population structure. Compared to the previous study, the He value (0.029~0.188) of this species was observed relatively low, which is considered to be the cause of limited distribution and small size of populations. Analysis of molecular variance (AMOVA) identified 40.3% variance within populations, indicating a moderate level of gene flow (or low genetic differentiation) between population, and these variation resulted possibly from characteristics of the fruit carried by the wind within limited distribution. The significant genetic divergence (FST) and PCA clustering results observed in SC could be assumed to be due to genetic drift in specific isolated population. According to these results, management strategies should be focus on SC and AD populations to protect reduced genetic sources for the efficient conservation of P. tongkangensis.