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Screening method of rice SNP sites and method for identifying rice varieties

A screening method, rice technology, applied in instrumentation, genomics, proteomics, etc., can solve problems such as inaccuracy, and achieve the effect of improving pertinence and effectiveness

Pending Publication Date: 2021-12-31
SOUTH CHINA AGRI UNIV +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, the purchase price of rice is different between indica rice and japonica rice. In the market, it is generally used to distinguish between indica rice and japonica rice by observing the grain shape, but this is not accurate. appears to be particularly important

Method used

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  • Screening method of rice SNP sites and method for identifying rice varieties
  • Screening method of rice SNP sites and method for identifying rice varieties
  • Screening method of rice SNP sites and method for identifying rice varieties

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] A method for screening rice core SNP sites is provided, which includes the following steps.

[0044] 1. Data acquisition

[0045] The rice genome DNA sequencing data published by NCBI (NCBI public sequencing data database, website: https: / / www.ncbi.nlm.nih.gov / sra / ) was selected, among which 44,697 sequencing data included in the Illumina sequencing platform were selected, accounting for the total 99.62% of the data volume.

[0046] 2. SNP detection

[0047] SNP detection uses bwa (version is not limited, http: / / bio-bwa.sourceforge.net / ) comparison software to compare the paired-end sequences, select the aln strategy or mem strategy for the comparison, and select the default parameters for the parameters. Use samtools (version is not limited, http: / / samtools.sourceforge.net / ) to sort the aligned sequences, use GATK (version is not limited, https: / / software.broadinstitute.org / gatk / ) for SNP detection, A total of 3.07M SNP sites were detected.

[0048] 3. PCA analysis...

Embodiment 2

[0061] A method for screening rice core SNP sites is provided, which is roughly the same as in Example 1, except that step 3: PCA analysis and sample screening is omitted.

Embodiment 3

[0063] A method for screening core SNP sites in rice is provided, which is roughly the same as that in Example 1, except that the threshold value of Hp is set <0.05.

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Abstract

The invention discloses a screening method of rice SNP (Single Nucleotide Polymorphism) sites and a method for identifying rice varieties, and relates to the technical field of biomolecules. Before the SNP sites for identifying the rice varieties are screened, rice samples used for obtaining the SNP sites are filtered, non-core population samples are filtered out, then the SNP sites are screened and detected, therefore, the pertinence and effectiveness of the SNP site on identification and analysis of specific rice varieties can be remarkably improved, and a way is provided for effective identification of the specific rice varieties and construction of a rice high-quality heterogeneity gene map.

Description

technical field [0001] The invention relates to the technical field of biomolecules, in particular to a method for screening rice SNP sites and a method for identifying rice varieties. Background technique [0002] Indica rice and japonica rice are the two most profound and main directions of differentiation of common cultivated rice. In general, indica and japonica are quite different in morphology and geographical distribution. The layout of south indica and north japonica was formed during the long rice planting process. However, with the acceleration of the modern breeding process, the discovery of compatibility genes and the continuous utilization of interspecific heterosis, the boundaries between indica and japonica have become increasingly blurred. [0003] Under the new situation, new requirements are put forward for the identification of indica and japonica. At present, the purchase price of rice is different between indica rice and japonica rice. In the market, ...

Claims

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Application Information

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IPC IPC(8): G16B20/20
CPCG16B20/20
Inventor 张群宇陈杰湖周峰王曼刘耀光王红梅袁健铭
Owner SOUTH CHINA AGRI UNIV
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