Restrictive two-stage genome-wide association study (GWAS) method based on SNPLDB mark

A whole-genome, association analysis technology, applied in the field of molecular quantitative genetics and molecular breeding, can solve the problems of missing heritability, kinship sensitivity, and reduced GWAS efficacy, so as to reduce multiple test problems, reduce false positives, and improve The effect of detection power

Inactive Publication Date: 2015-05-27
NANJING AGRICULTURAL UNIVERSITY
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Problems solved by technology

Practical research usually uses all molecular markers to estimate this kind of kinship matrix, but the latest research shows that if the molecular markers used in kinship estimation include genetic locus SNP markers, the power of GWAS will be re

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  • Restrictive two-stage genome-wide association study (GWAS) method based on SNPLDB mark
  • Restrictive two-stage genome-wide association study (GWAS) method based on SNPLDB mark
  • Restrictive two-stage genome-wide association study (GWAS) method based on SNPLDB mark

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Embodiment Construction

[0030] The invention will be further described below in conjunction with the accompanying drawings of the description.

[0031] like figure 1 As shown, a flow chart of a restrictive two-stage genome-wide association analysis method based on SNPLDB markers, and the implementation process of the method is designed. These three steps of the two-stage association analysis under the locus model.

[0032] a) Construction of genome-wide SNPLDB markers

[0033] The genotype data of 145558 SNP molecular markers distributed in the whole genome are obtained after simplified genome sequencing (RAD-seq) and a series of quality control procedures. The minimum allele frequency of each SNP is greater than 1%. Haploview software was used to define the haplotype blocks of SNP molecular markers, the threshold was set to D'>0.7, and the window was set to 200kb. Based on the distribution of 145558 SNP molecular markers in the whole genome of Chinese soybean germplasm resources containing 1024 ma...

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Abstract

The invention discloses a restrictive two-stage genome-wide association study (GWAS) method based on an SNPLDB mark, and aims at solving the problems that a traditional method cannot be used for estimating multiple allele information, and is high in false positive rate and low in efficiency of detection on inbreeding crops. By combination of the SNPLDB mark constructed on the basis of a haplotype block, correction of deviation of an inbreeding population relation analysis model and a two-stage relation analysis strategy under a multi-site model, the GWAS method suitable for conventional breeding of inbreeding crops is built; the SNPLDB mark is applied to GWAS, so that a method is provided for multiple allele estimation; candidate sites are screened on the basis of a single-site model in the first stage, and are further screened on the basis of a progressive regression analysis method in the multi-site model in the second stage, so as to balance the problems of missing of heritability and over-high heritability estimation. Therefore, the interpretation ratio of a final genetic model is controlled at trait heritability. The positioning accuracy and efficiency are improved by a feature vector and an appropriate significant level of a similarity coefficient matrix estimated by the SNPLDB mark by GWAS.

Description

technical field [0001] The invention belongs to the technical field of molecular quantitative genetics and molecular breeding, and specifically relates to a restricted two-stage genome-wide association analysis method based on SNPLDB markers. Background technique [0002] The Green Revolution bred high-yielding varieties through population plant type transformation is the success of the development of conventional breeding technology. Conventional breeding is mainly to create super-parent recombination, but in the past, breeders can only design combinations and indirectly track super-parent recombination through phenotypic evaluation. The rapid development of molecular technology provides the possibility to directly identify super-parental recombination genotypes. [0003] Genome-wide association analysis (GWAS) based on germplasm populations provides a method for comprehensively analyzing the genetic basis of agronomic traits. In the past, the main purpose of GWAS researc...

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Application Information

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IPC IPC(8): C12Q1/68G06F19/18
CPCG16B20/00
Inventor 盖钧镒贺建波孟珊管荣展赵团结
Owner NANJING AGRICULTURAL UNIVERSITY
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