Genomic correlation: harnessing the benefit of combining two unrelated populations for genomic selection

Genetics Selection Evolution

Research Article

Sigrid A. Lehnert¹  Laercio R. Porto-Neto¹  Antonio Reverter¹  John M. Henshall¹  Sean M. McWilliam¹  William Barendse¹ 

[1] CSIRO Agriculture, Queensland Bioscience Precinct, 4067, St. Lucia, QLD, Australia;

关键词: Quantitative Trait Locus;    Genetic Correlation;    Genomic Selection;    Genomic Prediction;    Genomic Estimate Breeding Value;   

DOI  :  10.1186/s12711-015-0162-0

 received in 2015-02-05, accepted in 2015-10-16,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe success of genomic selection in animal breeding hinges on the availability of a large reference population on which genomic-based predictions of additive genetic or breeding values are built. Here, we explore the benefit of combining two unrelated populations into a single reference population.MethodsThe datasets consisted of 1829 Brahman and 1973 Tropical Composite cattle with measurements on five phenotypes relevant to tropical adaptation and genotypes for 71,726 genome-wide single nucleotide polymorphisms (SNPs). The underlying genomic correlation for the same phenotype across the two breeds was explored on the basis of consistent linkage disequilibrium (LD) phase and marker effects in both breeds.ResultsThe proportion of genetic variance explained by the entire set of SNPs ranged from 37.5 to 57.6 %. Estimated genomic correlations were drastically affected by the process used to select SNPs and went from near 0 to more than 0.80 for most traits when using the set of SNPs with significant effects and the same LD phase in the two breeds. We found that, by carefully selecting the subset of SNPs, the missing heritability can be largely recovered and accuracies in genomic predictions can be improved six-fold. However, the increases in accuracy might come at the expense of large biases.ConclusionsOur results offer hope for the effective implementation of genomic selection schemes in situations where the number of breeds is large, the sample size within any single breed is small and the breeding objective includes many phenotypes.

【 授权许可】

CC BY   
© Porto-Neto et al. 2015

【 图 表 】

12864_2017_4186_Article_IEq16.gif

12864_2017_4186_Article_IEq14.gif

12864_2017_4186_Article_IEq11.gif

12864_2017_4186_Article_IEq8.gif

12864_2017_4186_Article_IEq9.gif

12645_2016_25_Article_IEq19.gif

12864_2015_2055_Article_IEq84.gif

12864_2017_3910_Article_IEq2.gif

12711_2017_362_Article_IEq40.gif

12864_2017_3496_Article_IEq2.gif

12864_2017_3487_Article_IEq4.gif

12864_2015_2055_Article_IEq79.gif

12864_2016_3440_Article_IEq35.gif

12864_2016_2463_Article_IEq5.gif

12864_2015_2296_Article_IEq100.gif

12864_2016_2463_Article_IEq4.gif

12864_2016_2682_Article_IEq45.gif

12864_2017_4025_Article_IEq6.gif

12864_2017_4274_Article_IEq1.gif

12864_2017_4130_Article_IEq10.gif

12864_2015_2198_Article_IEq38.gif

12864_2017_4130_Article_IEq9.gif

12864_2015_2198_Article_IEq36.gif

12864_2016_2821_Article_IEq30.gif

12864_2017_4020_Article_IEq36.gif

12864_2016_2848_Article_IEq20.gif

12864_2017_3655_Article_IEq27.gif

12864_2017_4020_Article_IEq34.gif

12864_2017_3655_Article_IEq26.gif

12864_2016_3440_Article_IEq28.gif

12864_2016_2848_Article_IEq16.gif

12864_2017_4025_Article_IEq5.gif

12864_2017_3500_Article_IEq12.gif

12864_2017_4025_Article_IEq4.gif

12864_2016_2443_Article_IEq15.gif

12864_2015_2055_Article_IEq66.gif

12864_2017_4260_Article_IEq1.gif

12864_2017_4130_Article_IEq8.gif

12864_2016_2798_Article_IEq11.gif

12864_2017_4130_Article_IEq7.gif

12864_2016_3098_Article_IEq43.gif

12864_2015_2198_Article_IEq33.gif

12864_2016_2821_Article_IEq27.gif

12864_2017_3655_Article_IEq25.gif

12864_2017_4020_Article_IEq33.gif

12864_2017_3655_Article_IEq24.gif

12864_2016_2821_Article_IEq7.gif

12864_2016_3440_Article_IEq27.gif

12864_2017_3655_Article_IEq22.gif

12864_2016_2682_Article_IEq39.gif

12894_2015_Article_81_TeX2GIF_IEq2.gif

12864_2015_2118_Article_IEq5.gif

12893_2017_312_Article_IEq1.gif

12864_2017_3785_Article_IEq2.gif

12864_2017_3604_Article_IEq5.gif

12864_2015_2118_Article_IEq2.gif

12864_2017_3604_Article_IEq4.gif

12864_2017_4309_Article_IEq13.gif

12864_2017_4130_Article_IEq3.gif

12864_2015_1994_Article_IEq14.gif

12864_2016_3210_Article_IEq1.gif

12864_2015_2055_Article_IEq60.gif