Abstract
Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS) technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%), followed by trinucleotide (31.96%), and dinucleotide (14.57%). A total of 2525 primer pairs were successfully designed, and 91 out of 311 tested primers were polymorphisms. Overall, 38 genic SSR markers were randomly selected to further validate the degree of genetic diversity, and 22 genic SSR markers (57.89%) showed high levels of polymorphism. The average polymorphism information content (PIC) value and the number of alleles (Na) were 0.63 and 5.27, respectively, and the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis grouped the 22 Allium accessions into three groups with Nei’s similarity coefficients ranging from 0.37 to 0.99. This result suggested that these genic SSR markers could be used to develop a higher resolution genetic map and/or to analyze the phylogenetic relationships among Allium plants in the near future.
Highlights
The Welsh onion (Allium fistulosum L. 2n = 16) is a cultivar of Alliaceae Allium sp., which are some of the most commercially-important biennial and perennial herbs, and its plump stalk, including the leaf sheath and tender leaf, they are consumed as vegetables and condiments worldwide [1].The plant is thought to have been derived from Northwestern China, and it is widely cultivated worldwide, in East Asian countries, such as Japan, China, and Korea [2,3]
Since the RNA-Seq next-generation sequencing (NGS) technology allows for lower cost and higher throughput transcriptome sequencing than traditional Sanger sequencing, it has been widely used in many non-model organisms, including Tapiscia sinensis, Cucurbita moschata, and Larix kaempferi [20,21,22]
The application of genic simple sequence repeats (SSR) markers to genetic diversity analysis and fingerprinting has recently been reported in several plant species [25,38,39,40]
Summary
More and more researchers have been attempting to develop molecular markers for the Welsh onion to construct a genetic map or for use in a marker-assisted selection (MAS) breeding system. A large number of genomic SSR markers have been developed in the Welsh onion [14,15], but genic SSR markers have largely been ignored until recently; Tsukazaki et al, described transcriptome shotgun assembly (TSA)-derived markers in Japanese bunching onion [10]. The priority of this study was to report on the development of genic SSR markers using a transcriptome approach, which provides new molecular markers for genetic diversity studies in the. These genic SSR markers will provide important resources for chromosome mapping and phylogenetic analysis of Allium plants, potentially contributing to target gene cloning, as well as the utilization of the MAS breeding
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