Analysis of SSR information in pear peel transcriptome

Abstract：【Objective】Pear (Pyrus spp.) is an economically important fruit tree worldwide.The number of SSR markers is still quite limited for sake of the increasing needs of researchers.In this study, the SSR molecular markers were developed for pear genetic research and gene mapping based on the transcriptome data of the mixed fruit peel samples of‘Mantianhong'בHongxiangsu'hybrid.【Methods】The MISA software was used to search for the gene sequence to find out the SSR sequence.The primers were designed using Primer 3 software, and the reference information of the genetic position of the SSR loci, from which the primers were successfully designed, was defined by using the scaffold information containing the SSR markers.【Results】Among 23 863 genes, 2 972 gene sequences contained3 555 SSRs, accounting for 12.45% of the total number of identified genes.In the SSR of 1-6 base motifs, the 3 base motif types appeared most frequently, accounting for 63.09% of the total number of the SSRs, followed by the 2 base and the single base motif types, accounting for 20.14% and 15.22%, respectively.Among the 1 and 2 base motif types, A/T (87.80 %) and AG/CT (84.64%) were dominant;among the 3 base motif types, the number of AGG/CCT was the largest, only accounting for 23.00%.Among the 4-6 base motifs, the number of each type was small.Gene GO functional classification showed that 2 972 pear fruit peel transcriptome genes containing SSR loci were enriched into 2 644 GO Term in 3 ontology categories, and the biological processes ontology categories included the most GO terminology (1 512) .A total of 2 911 primer pairs of the SSR loci (81.88%) were successfully designed, among which 864 SSR loci (2-6 base motif types) were successfully pooled into 17 linkage groups.【Conclusion】SSRs were successfully identified from the transcriptome gene sequence data of pear peel and the primers were developed, which can provide markers for researches on pear fingerprint construction, genetic diversity and molecular marker-assisted breeding.