Characterization of SSRs and SNPs Based on Transcriptome of ⁢Ranunculus asiaticus⁢ L. and Development of Anthocyanin-Related SSRs and SNPs

Ranunculus asiaticus L. has good economic importance, research value, and particularly, great diversity in flower coloring. However, marker-related background of Ranunculus asiaticus L. is little known. We identified and located SSR and SNP markers based on 151,136 petal transcriptome-derived unigenes with the aid of MISA, GATK3 and annotation tools. 18,060 SSRs with 228 repeat motif types and average length of 17.1 bp were detected in 16,328 unigenes, where A/T, AG/CT and AAG/CTT ranked the top three, indicating our SSRs had high polymorphism; 586 SSRs located in coding regions and mostly were tri-nucleotide motif; gene expression decreased along with the increase in SSR size according to their 'Pearson correlation coefficient' of -0.979. Average quantity of SNPs was 446,785 with the span of 4.19 SNPs/kb, including 62.30% transition type. Among the 116 unigenes of 8 families of key enzyme genes of anthocyanin biosynthesis, 19 SSRs and 127 SNPs were identified in 17 unigenes and 49 unigenes, respectively. ANS was free of SSRs or SNPs while DFR had the largest quantity of SSRs and SNPs. All the SSRs were in non-coding region and 53.13% SNPs were in coding region including 41 synonymous types. Owing to transcriptome sequencing, we broke the obstacle of genome or EST information absence of Ranunculus asiaticus L. to develop SSRs and SNPs, which can pave the way for future researches.