The method of perfecting ssr map based on rad map

Abstract

The invention relates to a method for perfecting an SSR map on basis of an RAD map. The SSR map and the RAD map of a sample are obtained, real linkage groups and conflict linkage groups corresponding to all scaffolds are judged, and a one-to-one correspondence relation between an SSR linkage group and an RAD linkage group is established; according to marked genetic distances of conflict-free scaffolds and physical locations marked on the scaffolds, sort orders and directions of all the scaffolds in the linkage groups are determined through calculation, the SSR linkage group and the RAD linkage group which are in one-to-one correspondence relation is established, other scaffolds except common scaffolds in the RAD linkage group are supplemented to the SSR linkage group in the SSR map with the scaffolds in the SSR linkage group in the SSR map as a framework, an integrated map is assembled, and therefore a chromosome assembly sequence is obtained. According to the method for perfecting the SSR map on the basis of the RAD map, information of the SSR map and information of the RAD map are integrated and mutually corrected and complemented, map precision can be effectively improved, and the map length can be effectively increased.

Description

technical field [0001] The invention relates to a processing method for sequencing results, in particular to a method for perfecting SSR map connection and assisting assembly based on RAD maps, and belongs to the field of bioinformatics. Background technique [0002] Simple Sequence Repeats (Simple Sequence Repeats) marker is a molecular marker technology based on specific primer PCR developed in recent years, also known as microsatellite DNA (Microsatellite DNA), is a class of DNA consisting of several nucleotides ( Generally 1 to 6) is a tandem repeat sequence of dozens of nucleotides consisting of repeating units. The sequences flanking each SSR are generally relatively conserved single-copy sequences. At present, this technology is widely used in the construction of genetic linkage maps, germplasm identification, genetic diversity, and gene mapping and cloning. It has the following advantages: (1) abundant in quantity; (2) multi-allelic characteristics, providing high ...

AI Technical Summary

Problems solved by technology

However, SSR markers still have the following shortcomings: (1) The development of SSR markers is limited to species with known genome information; (2) There are certain limitations in sequence deredundancy splicing software and SSR search and primer design software, thus Affect the accuracy of SSR markers; (3) SSR marker polymorphism is low; (4) SSR marker density is generally low

However, the accuracy of the RAD map is somewhat different from that of the SSR map

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