Development of Simple Sequence Repeat(SSR) and Insertion/Deletion(InDel) Markers in Chinese Cabbage(Brassica rapa ssp. pekinesis) and Analysis of Their Transferability
Abstract：In order to analyze the SSR distribution in genomic sequence of Brassica rapa and develop new SSR markers, the DNA sequences of Chinese cabbage A10(16899818~17299817) were screened using SSRHunter software and 394 Simple sequence repeats(SSRs) were mined with an average distance of 1.02 kb. Dinucleotide and trinucleotide repeat SSRs were the dominant types, accounting for 79.44% and 18.78%, respectively, of the SSR obtained. In order to improve the accuracy and to test the transferability of the developed SSRs, the mined SSRs were blasted and 15 SSR sequences were selected and primers were designed. Morever, some differences of Insertion/Deletion(InDels) rather than SSRs were found in some SSRs sequences and 19 InDels primers were designed. The 34 resultant primer pairs were used for polymorphism analysis in 6 genotypes of Chinese cabbage(Brassica rapa ssp. pekinesis). Twenty eight primer pairs had expected PCR products, accounting for 82.35% of designed primers, and 27 primer pairs showed polymorphisms, accounting for 79.41% of the designed primers. PCR products from 4 random SSR primer pairs were used for sequence analysis. The results showed that 100% of the fragments contained target SSRs. The percentage of available SSRs and InDels amplified in cabbage(B. oleracea), rapeseed(B. napus) and radish(Raphanus sativus) samples were 85.71%, 100% and 77.78%, respectively. It showed that these SSRs and InDels had good polymorphisms and transferability among Brassicaceae. A subset of 6 validated primers was also used to assess genetic diversity in a collection of 48 elite Brassicaceae germplasms. The dendrogram revealed that all germplasms were obviously classified into 3 groups, including Brassica rapa and Brassica oleracea, Raphanus sativus and Brassica napus, and the result accorded with the conventional taxonomy. The SSR and InDel markers can be used in genetic analysis of Brassica rapa.
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