The genetic diversity and population structure of Kudouzi (Sophora alopecuroides) population were revealed by using SNP markers combined with seed phenotypic traits

Background: Sophora alopecuroides L. is a perennial herb of Leguminosae. It is mainly distributed in northwest China and has important medicinal, feeding and ecological restoration values. However, in recent years, due to the intensification of human activities, its wild population resources have plummeted and genetic diversity has continued to decline. In order to fully reveal the genetic diversity and population structure characteristics of S. alopecuroides in the natural distribution area. In this study, Single nucleotide polymorphism (SNP) molecular markers combined with seed phenotypic traits were used to systematically study 65 wild samples of S. alopecuroides in northwest China. Results: The results showed that the coefficient of variation (CV) of 8 phenotypic traits of S. alopecuroides seeds ranged from 2.87 % to 7.94 %, and the diversity index (H) ranged from 1.639 to 1.767. There was a significant correlation between phenotypic traits (P < 0.01), indicating that the phenotypic diversity of S. alopecuroides seeds was rich. Cluster analysis based on phenotypic traits divided the S. alopecuroides population into two groups. At the same time, based on SNP molecular markers, the genetic diversity of S. alopecuroides was relatively low. The average values of expected heterozygosity (He), observed heterozygosity (Ho) and single nucleotide diversity index (Pi) were 0.22, 0.17 and 0.19, respectively. The results of molecular variance analysis (AMOVA) showed that the level of variation between individuals (132.83%) was higher than that between populations and within populations. The Pairwise population differentiation (Fst) was between 0.00 and 0.04, which confirmed that there was no obvious differentiation among the populations. Population structure analysis, principal component analysis (PCA) and phylogenetic tree analysis roughly divided all populations into two clusters, which was consistent with the phenotypic clustering results. It is worth noting that the distribution patterns of the samples in the Southern Tianshan Mountains (TSNL) and the Altai Mountains (ARTS) are more complex. In addition, redundancy analysis (RDA) showed that the cumulative interpretation rates of environmental factors on phenotypic traits and genetic diversity were 99.75 % and 67.89 %, respectively. Among them, the mean temperature of the driest quarter (MTD) and annual mean wind speed (YWS) were identified as the primary factors influencing phenotypic traits, while the precipitation of the coldest quarter (PC), isothermality (ISO), and precipitation of the wettest quarter (PWE) have an important impact on genetic diversity. Conclusions: This study provides a foundation for the genetic evaluation and conservation of S. alopecuroides genetic resources in China and offers important insights for its breeding programs.