A method for estimating genomic breeding value integrating dominance effects

A genome and breeding value technology, which is applied in the field of livestock and poultry genetic selection, can solve the problems of not considering the dominant effect and the accuracy of the genome estimation breeding value, etc., and achieve the effects of easy convergence, fast calculation speed and improved accuracy

Active Publication Date: 2018-12-28
ANIMAL SCI RES INST GUANGDONG ACADEMY OF AGRI SCI
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  • Application Information

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Problems solved by technology

Although the dominant effect is an important genetic effect, the commonly used genome breeding value estimation method does not consider the dominant effect, but only considers the additive effect
Some scholars have also studied the dominant effect, but the model assumes that the additive effect and the dominant effect are independent of each other, which is inconsistent with the fact that there is a certain relationship between the two effects, which causes the accuracy of the genome to estimate the breeding value to decrease. one of the reasons
[0004] The invention integrates and introduces the dominant effect from the gene marker end to estimate the genome breeding value, which has not been reported in domestic and foreign animal and plant genetic selection

Method used

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  • A method for estimating genomic breeding value integrating dominance effects
  • A method for estimating genomic breeding value integrating dominance effects
  • A method for estimating genomic breeding value integrating dominance effects

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0038] Example 1 Method for Estimating Genome Breeding Value of Yellow Feather Broiler AH Population Weight

[0039] In order to verify the effect of the method of the present invention, we use the cross-validation method to divide the reference population and the candidate population, and compare the accuracy of the genome estimation breeding value of the method of the present invention and other two common methods.

[0040] The AH population of yellow-feathered broiler chickens was designed and constructed by the F2 design of high-quality broiler A line and Huiyang bearded chickens. In this embodiment, a total of 582 genotyped individuals were used, including 20 individuals of the F0 generation, 51 individuals of the F1 generation, and 511 individuals of the F2 generation. The F2 generation came from 8 half-sib families, all with 12-week body weight records.

[0041] In this example, the target trait is body weight at 12 weeks. The 10-fold cross-validation method was used ...

Embodiment 2

[0078] Example 2 Method for Estimating Breeding Value of Pig Population Genome

[0079] The pig data used in the examples are disclosed in the document "A Common Dataset for Genomic Analysis of Livestock Populations.G3: Genes|Genomes|Genetics 2012, 2(4):429-435."

[0080] The pig group comes from a core strain of the PIC Breeding Pig Improvement International Group Company. The specific name of the core strain and the detailed names of the measured traits are not disclosed in the pig herd data set. The measured traits are named after the symbols T1, T2, T3, T4 and T5 Instead, all phenotype values ​​have been subjected to fixed effects removal. In this example, "T1" is selected as the target trait, which is a trait with low heritability, the heritability is 0.07, and there are 2804 phenotype records in total. The 10-fold cross-validation method was used to randomly divide the population into 10 uniform groups, including 6 groups with 280 pigs and 4 groups with 281 pigs. Among...

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Abstract

The invention discloses a genome breeding value estimation method for integrating dominant effect, which relates to the technical field of livestock and poultry genetic selection. The method comprisessteps identifying a reference group and a candidate group, the phenotype of the target traits of the reference population was determined, Genome-wide marker typing of reference population, quality control of gene marker of reference population, statistics of heterozygous marker deviation of reference population, formulation of genome marker re-coding rules, genome-wide marker typing of candidatepopulation, quality control of gene marker of candidate population, re-coding of genome marker and estimation of genome breeding value, etc. Based on the deviation degree between the phenotype of theheterozygous genotype and the phenotype of the homozygous genotype, the invention formulates coding rules, starts from the genomic marker end, re-codes the heterozygous genotype, causes the gene marker coding to include dominant effect, and then estimates the genomic breeding value. The invention is adapted to the needs of livestock and poultry genetic breeding, and can greatly improve the accuracy of genome estimation breeding value without increasing the complexity of the model.

Description

technical field [0001] The invention relates to the technical field of genetic selection and breeding of livestock and poultry, in particular to a genome breeding value estimation method integrating dominant effects. Background technique [0002] Hybridization technology is widely used in the genetic selection and breeding of animals and plants such as pigs, chickens, cattle, rice and corn. Its application mainly has two aspects: on the one hand, it is used for the cultivation of new varieties, and the excellent characteristics of the parents are combined to form new varieties through hybridization technology. Another aspect is to use heterosis to improve production efficiency. Heterosis refers to the phenomenon that heterozygous offspring are better than the average value of their parents. Dominance effect is one of the most important causes of hybrid vigor, which refers to the effect of the interaction between alleles in the same gene locus. With the continuous developme...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/20
Inventor 刘天飞瞿浩罗成龙王艳计坚舒鼎铭
Owner ANIMAL SCI RES INST GUANGDONG ACADEMY OF AGRI SCI
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