Accounting for population structure in selective cow genotyping strategies

Perez, Bruno da Costa; Balieiro, J. C. C.; Carvalheiro, Roberto; Tirelo, Fabio; Júnior, Gerson A. Oliveira; Dementshuk, J.M.; Eler, Joanir Pereira; Ferraz, José Bento Sterman; Ventura, Ricardo Vieira

doi:10.1111/jbg.12369

Cited by 7 publications

(9 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, with the IBD‐GS approach, they suggested that with small inflation, bias would not be a problem in practice. Similarly, high bias of prediction of GEBV was also obtained for extreme phenotypic selective genotyping by Perez et al (). High bias of prediction in B25 and B50 was due to their minimal contribution to the subsequent generations.…”

Section: Discussionmentioning

confidence: 63%

“…Ødegård and Meuwissen () have studied the advantages of identity by descent genomic selection and found that inclusion of 5% most extreme sibs in the reference results in the extra genetic gain. Perez et al () studied the female selective genotyping strategy in GS. They reported that inclusion of extreme cow (pseudo) phenotypes in the reference is useful to accurately predict the most influential SNPs in genome‐wide association studies; however, the estimates of GEBVs were highly inflated in selection candidates.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Gowane

Lee

Clark

et al. 2019

J Animal Breeding Genetics

View full text Add to dashboard Cite

Reference populations for genomic selection usually involve selected individuals, which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is, Best Linear Unbiased Prediction of breeding values using pedigree-based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single-Step approach (SSGBLUP) using both. For a scenario with no-selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices. Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single-Step approach to obtain accurate and unbiased prediction of GEBV. K E Y W O R D Sgenomic selection, GWAS, prediction bias, selective genotyping, single-step GBLUP How to cite this article: Gowane GR, Lee SH, Clark S, Moghaddar N, Al-Mamun HA, van der Werf JHJ. Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction.

show abstract

Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Gowane

Lee

Clark

et al. 2019

J Animal Breeding Genetics

View full text Add to dashboard Cite

show abstract

“…The inclusion of females in the genotyped population was also found to be beneficial in species where the effect of female paths on genetic progress is strong, and the effect of genomic data on accuracy depends on the existing population structure (Lourenco et al, 2015). The effect of genotyped populations including female genomic information on genomic prediction accuracy has been thoroughly studied (Koivula et al, 2016;Uemoto et al, 2017;Perez et al, 2019), and also as a strategy to increase the genotyped population size into small populations (Jiménez-Montero et al, 2012;Lund et al, 2016;Jenko et al, 2017). Different strategies have been proposed to assess an optimal selection of individ-uals to be genotyped.…”

Section: Maximum Genotypingmentioning

confidence: 99%

“…Different strategies have been proposed to assess an optimal selection of individ-uals to be genotyped. Including genomic information of females selected based on a divergent strategy seems to be better than a random or directional approach (Jenko et al, 2017;Perez et al, 2019), and avoiding the inclusion of only selected individuals would reduce prediction bias (Vitezica et al, 2011;Koivula et al, 2016). In practical terms not all the strategies are feasible for animal breeding programs and even less for small populations.…”

Section: Maximum Genotypingmentioning

confidence: 99%

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Granado-Tajada

Varona

Ugarte

2021

Journal of Dairy Science

View full text Add to dashboard Cite

Genomic selection has been implemented over the years in several livestock species, due to the achievable higher genetic progress. The use of genomic information in evaluations provides better prediction accuracy than do pedigree-based evaluations, and the makeup of the genotyped population is a decisive point. The aim of this work is to compare the effect of different genotyping strategies (number and type of animals) on the prediction accuracy for dairy sheep Latxa breeds. A simulation study was designed based on the real data structure of each population, and the phenotypic and genotypic data obtained were used in genetic (BLUP) and genomic (single-step genomic BLUP) evaluations of different genotyping strategies. The genotyping of males was beneficial when they were genetically connected individuals and if they had daughters with phenotypic records. Genotyping females with their own lactation records increased prediction accuracy, and the connection level has less relevance. The differences in genotyping females were independent of their estimated breeding value. The combined genotyping of males and females provided intermediate accuracy results regardless of the female selection strategy. Therefore, assuming that genotyping rams is interesting, the incorporation of genotyped females would be beneficial and worthwhile. The benefits of genotyping individuals from various generations were highlighted, although it was also possible to gain prediction accuracy when historic individuals were not considered. Greater genotyped population sizes resulted in more accuracy, even if the increase seems to reach a plateau.

show abstract

“…Newborn bull-calves aged 8, 12, and 15 months were by the conventional method examined on the main measurements on the basis of which body-build indices were calculated [7].…”

Section: Methodsmentioning

confidence: 99%

Genotypical features of the exterior development of Hereford bull-calves

et al. 2020

View full text Add to dashboard Cite

An analysis of previous years shows that there is a gradual increase in the rate of breeding and pedigree work, its intensification, which is caused primarily by the implementation of new methods of biotechnology and population genetics. In this regard, the improvement and development of new criteria for cow evaluation taking into account created highly productive lines, types, and populations are relevant for science and practice. There was carried out scientific and economic research in order to characterize the main indicators of the breeding value of cows that belong to the created hornless Ural-type Hereford breed of domestic breeding. The influence of these indicators on the formation of the productivity of bull-calf progenies fell under the characterization as well. There were formed five groups of full-aged cows (5-8 years) different in productive qualities to determine the influence of the productive value of mother cows on the pedigree and productive qualities of progenies. Cows of all groups were inseminated by the deep-frozen seed of Hereford bull of the “elite-record” class produced by Golub 4168. Five groups of experimental bull-calves were formed by the method of groups-analogs from the resulting progeny. The analysis of weight and linear growth of the progeny bull-calves showed that all the animals normally developed being characterized with the general patterns of ontogenesis. At the same time, bull-calf progenies of cows different in productive value were inherent in some features - the average live weight of bulls of group III was larger than those of its peers from groups I, II, IV, and V by 27.4 kg (6.3 %, P>0.95), 64.1 kg (16.1 %, P>0.999), 28.9 kg (6.6 %, P>0.95), and 47.4 kg (11.4 %, P>0.999), respectively.

show abstract

Accounting for population structure in selective cow genotyping strategies

Cited by 7 publications

References 55 publications

Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Genotypical features of the exterior development of Hereford bull-calves

Contact Info

Product

Resources

About