Exploiting Illumina Sequencing for the Development of 95 Novel Polymorphic EST-SSR Markers in Common Vetch (Vicia sativa subsp. sativa)

Abstract

Abstract:The common vetch (Vicia sativa subsp. sativa), a self-pollinating and diploid species, is one of the most important annual legumes in the world due to its short growth period, high nutritional value, and multiple usages as hay, grain, silage, and green manure. The available simple sequence repeat (SSR) markers for common vetch, however, are insufficient to meet the developing demand for genetic and molecular research on this important species. Here, we aimed to develop and characterise several polymorphic EST-SSR markers from the vetch Illumina transcriptome. A total number of 1,071 potential EST-SSR markers were identified from 1025 unigenes whose lengths were greater than 1,000 bp, and 450 primer pairs were then designed and synthesized. Finally, 95 polymorphic primer pairs were developed for the 10 common vetch accessions, which included 50 individuals. Among the 95 EST-SSR markers, the number of alleles ranged from three to 13, and the polymorphism information content values ranged from 0.09 to 0.98. The observed heterozygosity values ranged from 0.00 to 1.00, and the expected heterozygosity values ranged from 0.11 to 0.98. These 95 EST-SSR markers developed from the vetch Illumina transcriptome could greatly promote the development of genetic and molecular breeding studies pertaining to in this species.

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

“…The decreased levels of polymorphism may be due to the smaller number or close geographic origin of the materials used in the study 12 . In the present study, 112 EST-SSR variations were found in the coding regions, whereas five were found in genes not associated with known proteins, which is similar to the location of EST-SSR markers in common vetch 15 .…”

“…To date, many SSRs have been developed in many plants through Illumina sequencing; these plants include alfalfa 13 14 , Vicia sativa 15 , and Indian sesame 16 . However, in the genus Elymus , the applications of SSRs have only been presented in a few species, including E. alaskanus 5 , E. caninus 17 , E. trachycaulus 18 , and E .…”

Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

“…Previous research reported that the occurrence of SSR in the coding regions seems to be limited by non-perturbation of ORFs [ 44 ], and the tri- and hexa-nucleotide repeats are dominant in protein-coding exons of all taxa [ 45 ]. Besides, the relative proportions of EST-SSR motif types observed in this study coincided with previous reports, such as the vetch ( Vicia sativa ) [ 46 ], Ma bamboo ( Dendrocalamus latiflorus ) [ 47 ] and alfalfa ( Medicago sativa ) [ 48 ]. Furthermore, since we found that Vicia cDNA-SSRs are highly polymorphic, thus, those retrieved cDNA-SSR, through the NGS sequencing technology, will be a valuable resource for research communities of the vetch breeding program.…”

Transcriptome Analysis of Methyl Jasmonate-Elicited Panax ginseng Adventitious Roots to Discover Putative Ginsenoside Biosynthesis and Transport Genes

“…The results from this study suggested that short reads from Illumina/Solexa sequencing can effectively be assembled through “Trinity” giving the advantage of a high assurance and reliable assembly of putative unigenes, including potential and valuable splice variant information. Therefore, de novo sequencing and assembly of transcriptomes or genomes has effectively been utilized for model [ 57 , 58 ] and non-model organisms [ 59 , 60 , 61 ].…”