Rice whole genome SNP chip and application thereof

A whole genome and chip technology, applied in the field of rice whole genome SNP chip and preparation, rice SNP chip field, can solve the problems of limited use, high data analysis requirements, no chip, etc.

Active Publication Date: 2012-10-24
先正达集团股份有限公司
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  • Abstract
  • Description
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AI Technical Summary

Problems solved by technology

Although molecular marker technology based on second-generation sequencing technology has high throughput, flexibility and efficiency, short-segment sequencing relies on the reference genome sequence, and it is difficult to detect and analyze regions located in repetitive sequence regions or not on the reference genome. The processing of sequencing data Complicated processes such as sequence genome positioning and genotyping calculations have high requirements for data analysis, which require professional bioinformatics personnel to complete
These disadvantages somewhat limit the widespread use of this method, especially in molecular breeding on a large scale
Illumina Infinium SNP chips have been widely used in the study of genome variation in human, mouse, maize and other species, but no such chip has been reported in rice

Method used

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  • Rice whole genome SNP chip and application thereof
  • Rice whole genome SNP chip and application thereof
  • Rice whole genome SNP chip and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0054] Embodiment 1: RICE6K SNP chip preparation method

[0055] 1. Obtaining the first type of probes on the RICE6K SNP chip

[0056] The applicant used the Illumina next-generation sequencing technology to sequence the genome of the rice core parent material. In addition, at the end of 2010, Huang et al. published genome resequencing data of 520 rice landraces (Huang et al., Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010, 42: 961-967). The applicant downloaded this data from a public database and presented it as the Nipponbare Genome (MSU version 6.1, http: / / rice.plantbiology.msu.edu / ) as the reference sequence, using MAQ software ( http: / / sourceforge.net / projects / maq ) to match all species resequencing data to the reference sequence. The specific steps of probe design are as follows:

[0057] (2) First, 4,236,029 high-quality SNPs were identified according to the following criteria:

[0058] Sequences were used to identify ...

Embodiment 2

[0075] Example 2: Application of RICE6K Rice SNP Chip in Detection of Rice DNA Samples

[0076] 1. Rice genomic DNA extraction: Genomic DNA is extracted from rice seeds, leaves and other tissues according to the detection requirements. Among them, the DNA of young rice leaves was extracted using the Promega Plant Genome Extraction Kit according to the standard procedure (Wizard Magnetic 96 DNA Plant System Kit, Cat. No. FF3760 or FF3761, Promega, USA).

[0077] 2. DNA sample quality detection: detect with agarose gel electrophoresis with a mass fraction of 1% (W / W), use a gel imaging system (Gel Doc XR System, Bio-Rad, USA) to judge the electrophoresis results, and ensure that the genomic DNA The integrity is good, and the length of the genomic DNA fragment is greater than 10kb; use a UV spectrophotometer (NanoDrop2000, Thermo Scientific, USA) to measure the protein and organic matter pollution levels in the genomic DNA, and the genomic DNA A260 / 280 ratio should be between 1.8...

Embodiment 3

[0080] Example 3: Application of RICE6K Rice SNP Chip in Molecular Marker Fingerprint Analysis of Rice Germplasm Resources

[0081] Using the RICE6K SNP chip, the applicant conducted molecular marker fingerprint analysis on 106 micro-core rice germplasm resources. The RICE6K chip detected the genomic DNA of these 106 rice varieties. Among the 5,102 effective detection sites, 636 sites were detected as heterozygous sites in more than 3 varieties. The applicant believes that the detection ability of these sites is relatively low. Poor, the remaining 4466 high-quality loci were used for genotyping of 106 varieties. According to the genotyping results, the cluster analysis of these 106 rice varieties showed that all 18 japonica rice varieties were clustered into one category, and the other 88 indica rice varieties were clustered into another category. The applicant analyzed the number of polymorphic SNP sites between any two varieties that could be detected by this batch of RICE6...

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Abstract

The present invention discloses a rice whole genome SNP chip and an application thereof. A method for preparing the chip comprises: (1) obtaining a first class of probes on a chip, wherein sequencing is performed to obtain a parental genome sequence, resequencing data of other rice varieties in a public database are combined, a Nipponbare genome is adopted as a reference sequence, a MAQ software is adopted to match and analyze all the sequencing data, and finally a SNP marker is screened; (2) obtaining a second class of probes on the chip, wherein a rice function gene is obtained from the public database, sequence difference reflecting gene function is searched, and a SNP / INDEL probe is designed according to the sequence difference; (3) adopting an infinium chip manufacturing technology to produce a SNP chip; and (4) testing accuracy and application efficiency of the chip. The chip of the present invention can be applicable for rice germplasm resource molecule marker fingerprint analysis, seed authenticity detection, filial generation genotyping, and other related researches.

Description

technical field [0001] The invention relates to the fields of molecular biology, functional genomics, bioinformatics and genome breeding, and more specifically relates to a rice whole-genome SNP chip and a preparation method thereof, and also relates to the application of the rice SNP chip. Background technique [0002] Molecular markers refer to the technical method of using macromolecular compounds, proteins and DNA, to mark genetic variation by differences among biological individuals. Since the difference between individuals of protein is smaller than that of DNA, and it is difficult to detect, most molecular markers use genetic polymorphisms at the DNA level, also known as DNA molecular markers. Molecular marker technology mainly refers to molecular biology techniques for detecting DNA variation. Molecular marker technology is mainly used in the following four aspects in crop research: (1) construction of genetic linkage map and gene mapping; (2) germplasm resource res...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C40B40/06
Inventor 周发松谢为博喻辉辉李菁张启发
Owner 先正达集团股份有限公司
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