Analysis of SSR and SNP Loci in Corm Transcriptome of Amorphophallus bulbifer at Different Dormancy Stages
To understand the SSR and SNP information in corm transcriptome of Amorphophallus bulbifer,RNA-Seq was carried out with corm of A.bulbifer at three different dormancy stages(dormancy stage,germina-tion stage and budding stage).MISA and Varscan were used to identify and analyze the features of SSR and SNP in unigenes from RNA-Seq.The results showed that 292 086 unigenes contained 52 324 SSRs and 807 836 SNPs.The frequency of SSR was 17.91％respectively.The proportions of single nucleotide(33.97％),dinucleotide(47.83％),and trinucleotide(16.77％)repeats were notably high,with repeats occurring 6 to 11 times comprising 65.71％of the total.There were 130 types of repeat units;among these,the dinucleotide repeat unit AG/CT was the dominant type,representing 30.64％of the total SSRs.SSRs with a unit length of 10～20 bp accounted for 80.33％of all SSRs.In terms of SNP mutation types,transitions(523 617)far exceeded transversions(284 219).The SSR and SNP sites obtained from the corm of A.bulbifer based on the analysis of transcriptional sequencing were abun-dant in number,which can provide scientific datas for breaking dormancy analysis and molecular assisted breeding of the A.bulbifer.
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