Research On Key Technologies Of Plant Poly SSR Database Construction

As a kind of DNA molecular marker,SSR(simple sequence repeats)plays an important role in gene expression and population genetic diversity.In recent years,with the development of high-throughput sequencing technology,a large number of species have completed genome or transcriptome sequencing respectively.On the basis of these sequence data,using SSR site recognition program and primer design tools to develop markers,and then constructing molecular marker database has become an important research content in the field of bioinformatics.In this paper,the key technologies in the construction of plant polymorphism ssr database are studied,and the main research contents and achievements are as follows:(1)A SSR recognition algorithm SO-SSR based on sequence offset and pattern matching is proposed.This paper analyzes the main problems in SSR recognition,such as maximum tandem repeat,divisor repeat and code shift repeat.According to the characteristics of SSR sequence,a SSR site recognition algorithm combining traditional pattern matching and sequence offset is designed.Compared with other algorithms,SO-SSR has more advantages in space occupation.(2)The development method of plant polymorphic SSR markers based on SO-SSR algorithm was studied.By analyzing the underlying implementation of the existing polymorphic SSR marker development tools,combining with the relevant references,we developed plant SSR markers,and evaluated the polymorphism of markers from the quantitative perspective.In this process,the NCBI is designed and developed by analyzing the problems in data collection of web crawler and combining the depth first and breadth first strategies SRA data acquisition and screening system;studied the basic theory and core algorithm of transcriptome assembly,discussed a suitable assembly process from m RNA to transcriptome;selected citrus and kiwifruit assembly for processing and analysis,determined the feasibility of the method,and verified the reliability of so-ssr algorithm in SSR recognition.(3)The plant polymorphism SSR database PPSD was constructed and the background management system was developed.Using the SO-SSR algorithm,28943 species SSRs and 6655 species SSRs were obtained from 48 plant species.Each SSR provided three pairs of primers.On the basis of these marked data,the ppsd database is constructed by using springboot framework,caffeine and activator components,and the corresponding background management system is developed.Security framework is used for security control and real-time performance monitoring of ppsd.PPSD can provide researchers in the field of plant genetic diversity with information retrieval of SSR markers polymorphism,and then targeted screening of potential SSR markers according to the target species/cultivars.In this study,SO-SSR algorithm based on sequence offset was proposed,and combined with sequence alignment and polymorphism evaluation index,the feasibility of using so-ssr to develop plant polymorphic SSR markers on gene sequences of multiple species / varieties was verified.Finally,ppsd of plant polymorphic SSR database was constructed using java language.The purpose of this study is to provide a low memory consumption SSR identification algorithm,and provide polymorphic molecular marker data service for researchers in plant genetics and breeding,gene mapping and variety identification.