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

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...

AI Technical Summary

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 reduced, and on the contrary, false positives will increase

The researchers also proposed several methods to solve the problem of kinship sensitivity in GWAS based on the LMM method, but they did little to solve the problem of missing heritability.

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