Development Of SSR Markers Based On Transcriptom And Genetic Diversity Analysis Of Wild Type Rosa Rugosa

Rosa rugosa,an important ornamental plant in genus Rosa,has great ornamental,economic and breeding values.In this study,we identified the SSR loci in Rosa rugosa and investigated their features according to the transcriptom data.Then,48 SSR primers were selected to develop polymorphic primers.19 SSR primers were identified as polymorphic primers and were used to analyze the genetic diversity of 46 Rosa rugosa materials originated from Muping and Hunchun.The main results were as follows:1.16,212 SSR loci were identified from Rosa rugosa transcriptom data,the occurring frequency(the number of unigenes which contain SSR locus/the number of total unigenes)was 17.94%,and the appearing frequency(the number of SSR locus/the number of total unigenes)was 22.70%.One SSR locus can be found in average of 4.21 Kb.2.Mono-nucleotide SSRs were the main type in Rosa rugosa transcriptom data and account for 40.49%of all SSRs,then the di-nucleotide and tri-nucleotide SSRs.The repeat number of mono-nucleotide SSRs was 12～16 while the repeat number of multi-nucleotide was 5～9.The maximum number of motif composition was AG/CT motif(5,495)which account for 33.89%of all SSRs;then the A/T motif.The dominant SSR motif type in plants was depended to the species while the dominant SSR motif composition was similar in the same SSR motif type in different species.3.48 primers which contain different motif type were selected from 7536 designed primers.Among them,19 primers exhibited polymorphic,the primer development efficiency was 39.58%.Two motif types,Penta-nucleotide repeats and hexa-nucleotide repeats had the maximum efficiency to develop SSR markers.The efficiency of them was 83.33%and 71.43%,respectively.4.The genetic diversity of 46 wild Rosa rugosa originated from Muping and Hunchun was analyzed by SSR markers developed in this study.The genetic diversity index(number of polymorphic alleles,genetic distance,Nei’s gene diversity index and Shannon information index)in Muping was higher than that in Hunchun,indicating that the genetic diversity of Muping was more abundant.However,the genetic diversity of wild Rosa rugosa was lower than that in cultivars.