Abstract
Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.
Highlights
Vicia amoena is an herbaceous, allotetraploid (2n=24), perennial legume species native to Eastern Asia (Siberia, Mongolia, China, Japan, and Korea) that is especially widely dispersed in northern China [1, 2]
The sequencing data generated in the present study have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (PRJNA742214)
The development and polymorphism of simple sequence repeat (SSR) markers Genetic research on V. amoena has developed slowly due to a lack of sufficient genetic information and effective molecular marker systems
Summary
Vicia amoena is an herbaceous, allotetraploid (2n=24), perennial legume species native to Eastern Asia (Siberia, Mongolia, China, Japan, and Korea) that is especially widely dispersed in northern China [1, 2]. It has high nutritional quality, strong abiotic stress tolerance, and wide adaptability. The protein content and the amino acid content of V. amoena are comparable to those of Microsatellites or simple sequence repeat (SSR) markers are a powerful molecular method for quantifying genetic variation in plants due to their high. A large number of SSR markers have been developed by high-throughput sequencing in many plants, such as Medicago sativa [16], Vicia sativa [15], Elymus sibiricus [17], Onobrychis viciifolia [18], Angelica gigas [19], Lentinula edodes [20], and Spondias tuberosa [21]
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