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Performance of genomic selection under a single‐step approach in autochthonous Spanish beef cattle populations
Author(s) -
Mouresan E.F.,
Altarriba J.,
Moreno C.,
Munilla S.,
GonzálezRodríguez A.,
Varona L.
Publication year - 2017
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12253
Subject(s) - selection (genetic algorithm) , beef cattle , heritability , best linear unbiased prediction , genotyping , population , genomic selection , biology , trait , statistics , artificial insemination , genetic gain , effective population size , zoology , genotype , genetics , mathematics , genetic variation , demography , single nucleotide polymorphism , computer science , machine learning , pregnancy , sociology , gene , programming language
Summary This study evaluated different strategies for implementing a single‐step genomic selection programme in two autochthonous Spanish beef cattle populations (Pirenaica—Pi and Rubia Gallega— RG ). The strategies were compared in terms of accuracy attained under different scenarios by simulating genomic data over the known genealogy. Several genotyping approaches were tested, as well as, other factors like marker density, effective population size, mutation rate and heritability of the trait. The results obtained showed gains in accuracy with respect to pedigree BLUP evaluation in all cases. The greatest benefit was obtained when the candidates to selection had their genotypes included in the evaluation. Moreover, genotyping the individuals with the most accurate predictions maximized the gains but other suboptimal strategies also yielded satisfactory results. Furthermore, the gains in accuracy increased with the marker density reaching a plateau at around 50,000 markers. Likewise, the effective population size and the mutation rate have also shown an effect, both increasing the accuracy with decreasing values of these population parameters. Finally, the results obtained for the RG population showed greater gains compared to the Pi population, probably attributed to the wider implantation of artificial insemination.