Development of genic SSR markers from transcriptome sequencing of pear buds

Abstract

A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116 282 transcriptomic unigenes in this study. Dinucleotide repeat motifs were the most common with a frequency of 65.11%, followed by trinucleotide (32.81%). A total of 4100 primer pairs were designed from the SSR loci. Of these, 343 primer pairs (repeat length ≥15 bp) were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions. After the preliminary test, 104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11% (101) of these. Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions. These markers displayed a high level of polymorphism. The number of alleles at these SSR loci ranged from 2 to 17, with a mean of 9.43 alleles per locus, and the polymorphism information content (PIC) values ranged from 0.26 to 0.91. The UPGMA (unweighted pair-group method with arithmetic average) cluster analysis grouped the 28 Pyrus accessions into two groups: Oriental pears and Occidental pears, which are congruent to the traditional taxonomy, demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships, enriching rare Pyrus EST-SSR resources, and confirming the potential value of a pear transcriptome database for the development of new SSR markers.

Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)

“…According to the previously-described criterion, the three categories were defined as high (PIC > 0.5), moderate (0.25 < PIC < 0.5), and low (PIC < 0.25) [34,35], and a total of 16 (72.73%) primers displayed a high level of PIC. In contrast to other plants, the Na and PIC values for the Welsh onion were lower than those reported in pear buds [36], 9.42 vs. 0.75, respectively. However, the values were higher than those for sweet potato (2.94 and 0.35, respectively) [25], cowpea (3.06 and 0.53, respectively) [37], and mung bean (3 and 0.34, respectively) [16].…”

Pursuit for est microsatellites in a tetraploid model from de novo transcriptome sequencing

“…Nine developed markers represent only a small part of the minable EST-SSRs: the mining process has discovered 31,561 contigs harboring trinucleotide, tetranucleotide, pentanucleotide and hexanucleotide motifs. Although being a common class of microsatellites (YUE et al, 2014) we did not mine for dinucleotide motifs due to possible difficulties in scoring different alleles using presented methodology.…”

Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry (Myrica rubra) and their application in seedling identification

“…Nowadays, it is much easier to develop SSR markers from genome or transcriptome databases (Jiao et al, 2012;Yue et al, 2014). They have been routinely used in the construction of molecular linkage maps, and in genetic diversity analysis, marker-assisted selection, fingerprinting and cultivar identification in fruit trees such as apple (Celton et al, 2009) and peach (Testolin et al, 2000).…”