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Rice genome-wide breeding chip and its application

A whole-genome and rice technology, applied in the fields of genomics, molecular biology, bioinformatics and molecular plant breeding, can solve the problems of large-scale commercial breeding, cumbersome operation process, low throughput, etc., and achieve sequencing cost reduction, simple data analysis, and high throughput

Active Publication Date: 2016-11-02
CHINA NAT SEED GRP +3
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, traditional molecular marker technology has many limitations, such as low throughput, small quantity, cumbersome operation process, and cannot meet the needs of large-scale commercial breeding

Method used

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  • Rice genome-wide breeding chip and its application

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] Embodiment 1Rice60K rice whole genome breeding chip preparation method

[0044] The present invention utilizes the Illumina sequencing technology to test 211 rice varieties, see Table 1. Whole-genome sequencing was performed to obtain 2.5-fold genome coverage per sample. At the same time, the present invention also downloaded the sequencing data of 520 rice landraces from the public database (http: / / www.ebi.ac.uk / ena / , accession numbers ERP000106, ERP000235, ERP000236), each sample 1 times the genome Coverage (Huang et al., Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010, 42:961-967). A total of 731 rice cultivar genome sequencing data. Follow the steps below to identify and screen SNPs.

[0045] Table 1 Names of 211 rice varieties

[0046]

[0047]

[0048]

[0049] 1. 3,791,687 high-quality SNP sites were identified from the sequencing data of 731 rice varieties. High-quality SNP sites meet the following conditio...

Embodiment 2

[0057] Example 2 Application of Rice60K rice genome-wide breeding chip in detecting rice DNA samples

[0058] Rice genomic DNA extraction: Genomic DNA is extracted from rice seeds, leaves and other tissues according to the detection requirements. Among them, it is recommended to use Promega Plant Genome Extraction Kit (Wizard Magnetic 96DNAPlant System Kit, Cat. No. FF3760 or FF3761, Beijing Promega Biotechnology Co., Ltd.) for DNA extraction of young rice leaves, and it is recommended for DNA extraction of rice seed endosperm SurePlant Genome Extraction Kit (SurePlant DNA Kit, Cat. No. CW0555, Beijing Kangwei Century Biotechnology Co., Ltd.) was used for extraction.

[0059] DNA sample quality detection: use agarose gel electrophoresis detection with a mass fraction of 1-1.5% (W / W), and use a gel imaging system (Gel Doc XR System, Bio-Rad, USA) to systematically judge the electrophoresis results to ensure that the genome DNA integrity is good, and the length of the genomic D...

Embodiment 3

[0062] Example 3 Application of Rice60K Rice Whole Genome Breeding Chip in Genomic Fingerprint Analysis of Rice Germplasm Resources

[0063] The invention uses the Rice60K breeding chip to pair 270 varieties of micro-core rice germplasm resources, numbered WCR001-270, from China Seed Group Co., Ltd. Detection was carried out with reference to the method of Example 2, and 195 representative homozygous inbred varieties were selected for analysis according to the detection results. According to the genotype detected by the Rice60K breeding chip, the cluster analysis of these 195 varieties can be divided into three categories: indica rice, japonica rice and intermediate types (see figure 2 ), which is in good agreement with the classification according to the phenotype. The average numbers of polymorphic SNPs between any two varieties, between indica and japonica, between indica and indica, and between japonica and japonica were about 14,000, 19,000, 10,000, and 8,000, respectiv...

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Abstract

The present invention provides a rice genome-wide breeding chip and its application. The rice genome-wide breeding chip of the present invention is Rice60K, which is a SNP chip made based on Infinium chip manufacturing technology. Each chip can simultaneously detect 24 samples, including 58,290 SNPs These marker sites have the DNA sequence shown in SEQ ID NO.1-58290. The chip can perform molecular marker fingerprint analysis on rice variety resources, perform genotype identification on offspring of hybrid populations, and identify variety authenticity. The analysis and screening of the genetic background of breeding materials and the association analysis of agronomic traits have broad application prospects.

Description

technical field [0001] The invention relates to the fields of genomics, molecular biology, bioinformatics and molecular plant breeding, in particular to a rice genome-wide breeding chip and its application. Background technique [0002] In recent years, breakthroughs have been made in DNA sequencing technology. The development of second-generation DNA sequencing technology has greatly improved genome sequencing efficiency, greatly reduced sequencing time and cost, and brought great convenience to functional genome research. In terms of rice, Chinese rice molecular biologists used the second-generation sequencing technology to complete the resequencing of 517 Chinese rice landrace materials in 2010, and constructed a high-density rice haplotype map (HapMap). The genome association analysis (GWAS) research method carried out association analysis on 14 important agronomic traits of indica rice varieties, and determined the candidate gene loci related to these agronomic traits, ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C40B40/06C12N15/29C12N15/11C12Q1/68G16B30/00
CPCC12Q1/6837C12Q2600/156G16B30/00C12Q1/6895C12Q2600/13
Inventor 周发松陈浩东谢为博何航喻辉辉唐晓艳李菁周君莉何予卿陈伟张启发邓兴旺
Owner CHINA NAT SEED GRP
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