Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

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.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

“…Excluding mononucleotide repeats, trinucleotides were found to be the most abundant repeats in the present study. This result was consistent with previous studies in other plants, such as Curcuma alismatifolia [ 42 ], Vicia amoena [ 22 ], and Pseudotaxus chienii [ 55 ]. Importantly, the abundance of trinucleotides in coding regions does not change the coding frame and therefore may not affect the functions of the genes [ 56 , 57 ].…”

“…It has the advantages of good reproducibility, codominance, abundant polymorphisms, and easy detection [ 20 ]. In recent years, SSR markers have been widely used in genetic diversity analysis [ 21 , 22 ], linkage genetic map construction and QTL identification [ 23 , 24 ], and marker-assisted breeding [ 25 , 26 ].…”

Establishment of novel SSR markers from transcriptome data of Chimonanthus praecox and application in the variety identification

“…Traditional SSR development method is a di cult, costly and labour intensively process, but the next-generation sequencing technology can effectively identify a large number of SSRs at a small cost and effort compared to traditional methods. Its main advantage is the ability to generate a large amount of sequence data, from which a large number of whole genome and gene-based SSR loci can be isolated and developed [39,45]. As NGS techniques have become more advanced, different new methods of SSR marker development have been reported that can be grouped into genomic SSRs (gSSRs) distributed throughout the entire whole genome sequence and expression sequence tags SSRs (EST ssr) embedded in transcriptional sequences [46,47].…”

Transcriptome-derived SSR markers for DNA fingerprinting and inter-populations genetic diversity assessment of Atractylodes chinensis

“…gov/ sra/ PRJNA 698794). SSR marker detection, identification and primer design were performed as described by [31].…”

“…The three clusters formed in the dendrogram revealed that the geographic origin does not exactly corroborate genetic diversity. This phenomenon appeared in many SSR marker-based genetic diversities, such as Sesamum indicum [2,20], Camellia oleifera [4], Vicia amoena [31] and Trifolium repens [32]. Wu et al carried out genetic diversity analysis of Trifolium repens using PCoA, UPGMA and STRU CTU RE, and indicated that UPGMA analysis was implemented based on genetic distance, which provided more detailed relationships [32].…”