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Creation of rice multi-sample variation integration map osms-ivmap1.0

A multi-sample, variant technology, applied in the field of integrated maps, to speed up the breeding process and avoid technical limitations

Active Publication Date: 2021-12-28
INST OF CROP SCI CHINESE ACAD OF AGRI SCI +2
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The current rice map, from the earliest RFLP, to the later SSR, the physical map of a single sample, the sequence map of a single sample, etc., but there is still a lack of multi-sample variation integration that integrates multi-sample multi-dimensional variation on the same reference genome Atlas

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  • Creation of rice multi-sample variation integration map osms-ivmap1.0
  • Creation of rice multi-sample variation integration map osms-ivmap1.0
  • Creation of rice multi-sample variation integration map osms-ivmap1.0

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Embodiment Construction

[0028] The present invention will be further described below in conjunction with specific implementation examples. The methods used herein are conventional methods unless otherwise specified. The following examples do not limit the invention in any way.

[0029] (1) Genome information acquisition of parental materials

[0030] 1. Test materials

[0031] More than 3000 rice samples.

[0032] 2. DNA extraction and whole genome high-throughput sequencing

[0033] Referring to the DNA extraction method of Temnykh et al. (2000), genomic DNA was extracted from each individual plant.

[0034] Considering the cost, genome sequencing can be based on shot-gun sequencing technology, and the library construction and sequencing methods are the same as conventional. To obtain better quality data coverage, it is recommended to be above 10X. In order to ensure the quality of the sequencing data, if more than 50% of the bases in the original data have a base quality value less than 5 or ...

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Abstract

The invention relates to using the 3K genome data based on whole genome sequencing to compare the variation information of different dimensions including SNP, InDel and SV obtained by the reference genome Nipponbare, and through unified integration to generate a variety of rice varieties containing more than 3000 samples of variation information. This integrated map OsMS‑IVMap1.0. The creation process of the map is based on multiple genomic variation search methods based on multiple samples on the one hand; on the other hand, it uniformly formats the variation information of different dimensions. This map can be used to conduct an overall analysis of the important genetic variation of rice and efficiently compare the distribution of different types of genomic variation. It is mainly used in genome-wide variation detection, marker development and gene function in model organisms represented by rice. Research.

Description

technical field [0001] The invention relates to a method of creating an integrated map by using high-quality variation information such as SNP, InDel, and SV generated from multiple samples based on whole-genome sequencing. This method and the map OsMS-IVMap1.0 it creates belong to the field of crop molecular breeding, and are suitable for genome-wide variation detection, marker development, and gene function research in model organisms represented by rice. Background technique [0002] The combination of genome technology and information technology enables researchers to easily obtain the massive amount of genetic data they need and deeply mine related genetic information; how to mine useful variation information from multi-sample high-quality sequencing Effective integration with known reference maps and making them available to researchers in related fields is an important issue. [0003] Genome sequencing will generate massive amounts of data, which contain rich variati...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B30/10
CPCG16B25/00
Inventor 郑天清黎志康徐建龙王春超王文生赵秀琴陈凯
Owner INST OF CROP SCI CHINESE ACAD OF AGRI SCI