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Algorithm for assessing heritability through genome data

A technology of genome and heredity, applied in the field of genetic engineering, can solve problems such as large errors and cumbersome genealogy records, achieve accurate genealogy information, and solve the effect of cumbersome genealogy records

Active Publication Date: 2016-04-20
JIMEI UNIV
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  • Abstract
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AI Technical Summary

Problems solved by technology

[0003] The purpose of the present invention is to provide a method to overcome the problems of large errors in traditional heritability estimation and cumbersome pedigree records.

Method used

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  • Algorithm for assessing heritability through genome data
  • Algorithm for assessing heritability through genome data
  • Algorithm for assessing heritability through genome data

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Experimental program
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Effect test

Embodiment 1

[0035] 1. The test subjects were 500 large yellow croakers. Using the artificial egg-promoting technology, all large yellow croakers were born on the same day, that is, all of the same age; the test time was when the large yellow croakers were two years old, and the measurement characteristics were the weight and body length of all large yellow croakers. .

[0036] 2. Use GBS (genotyping-by-sequencing) sequencing technology to perform genome sequencing on all individuals to be studied, and screen qualified SNP sites. The parameters are controlled as follows: MAF > 0.05, Hardy-Weinberg balance test P-value > 0.001, and the marker sites whose deletion rate of a single site is lower than 20% are left; finally, a total of 29,748 qualified SNP markers are screened out, and the missing sites are completed by the imputation program of software Beagle3.3.2 version.

[0037] 3. Among all 500 individuals, randomly sample 20% of them, that is, 100 individuals, as the estimated population...

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Abstract

The invention discloses an algorithm for assessing heritability through genome data. The algorithm comprises the steps that for a certain quantitative character, marker effect estimation is conducted on a whole genome with different numbers of reference group individuals through a GBLUP algorithm, the breeding value of an estimated group is further obtained, and estimation accuracy is calculated; curve linearization fitting is conducted through genome estimation accuracy and the size of reference groups, and the reciprocal of the intercept of a regression equation obtained through fitting serves as the estimated value of heritability. According to the algorithm for assessing heritability through the genome data, heritability of the quantitative character is assessed through the genome data, the research achievement can be directly applied to quantitative character breeding of animals and plants, genealogy recording is not conducted on the individuals, but sequencing is conducted on each individual genome, heritability of the character is predicted through whole genome marks, the heritability estimation result is mainly applied to breeding work in the future, in addition, Mendel sampling errors can be captured through sequencing, and compared with genealogy data recording, more accurate genealogy information can be obtained.

Description

technical field [0001] The invention relates to the field of genetic engineering, in particular to an algorithm for evaluating heritability through genome data. Background technique [0002] The current heritability evaluation methods mainly use the genetic relationship between individuals, and use various statistical methods, such as variance analysis, correlation analysis, etc. to infer. This method requires a complete pedigree record. However, for some species, the pedigree The workload of recording is very heavy or even difficult to achieve, such as aquatic animals; in addition, the traditional method of heritability assessment treats genome information as a "black box", which cannot capture the specific information of genes passed from parents to offspring. That is, it is impossible to prepare to capture Mendelian sampling errors, resulting in large estimation errors; in order to solve the problems of heavy workload of pedigree records and inability to accurately captur...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 肖世俊董林松王志勇
Owner JIMEI UNIV
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