Mulberry Transcriptome Sequencing And Development And Identification Of SSR Markers

China is the birthplace of the world’s silk industry, and sericulture production has five thousand years history. The mulberry leaf acts as the sole food of silkworm, which is the material basis of cocoons and silk production. In recent years, mulberry not only plays an important role in the traditional sericulture industry, but also develops rapidly in comprehensive utilization of mulberry resource. Mulberry can be used for defensing wind and sand, landscaping; mulberry leaves can be used as herbal medicines and animal feed; mulberry fruit can be used for fruit juice and wine processing; mulberry branch and root is one of the herbal medicines, too. In brief, mulberry shows great potentials and economic benefits in many industries.China is a large country with diverse ecological environment and climate characteristics, mulberry resource distributes widely in various regions of China. Because of its wide distribution and has diverse geographical environment, mulberry forms a rich and diverse germplasm resource after a long time species evolution. Recently, with the development of molecular biology, research in mulberry germplasm using molecular methods has become a popular research direction.In this study, we sequence transcriptome of roots and leaves of mulberry variety "Kang Qing 10" using high-throughput sequencing technology, following bioinformatics analysis. Then, we analyze SSR markers based on transcriptome sequence information, and develop and select primers of SSR markers, to seek available mulberry SSR markers for establishment of mulberry core germplasm, analysis of genetic diversity, construction of genetic map. The main research contents of this study are as follows:(1) Sequencing transcriptome of roots and leaves of mulberry variety "Kang Qing 10" using Illumina high-throughput sequencing technology, we obtained 105 million 90 bp reads, 60,069 Unigene after assembling, with total length of 47.63 Mb. Blasting all unigenes with known protein databases Nr、 GO、 COG and Swissprot, the results showed that 42,218 unigenes matched successfully, 31,548 unigenes annotated to 55 GO functional classification, 7,790 unigenes classified as a homologous group, 23,188 unigenes divided into 128 biological metabolic pathway. Functional classification results showed that a large number of genes related to secondary metabolism reactions, especially in the biosynthesis process of flavonoids, terpenoids and alkaloids.(2) We developed 10,268 SSR markers based on the whole mulberry transcriptomesequence, and designed SSR primers according to its sequence features. We selected randomly 100 pairs of SSR primers for primers verification using PCR amplification. Agarose gel electrophoresis shows 87 pairs of primers can amplify product. Among them, the amplify product of 58 pairs of primers with the predicted length, 26 pairs had longer amplified band, and the rest 3 pairs had shorter amplified band. According to polyacrylamide gel analysis, it showed that most primers amplified one band, and SSR motifs with amplified bands more than 2 showed repetitions greater than 3.In summary, developing SSR markers and its primers based on transcriptome sequence database is feasible and efficient, which can be used for establishment of mulberry core germplasm, analysis of genetic diversity, construction of genetic map.