Efficiency of genomic selection in a purebred pig male line

Abstract

Stochastic simulation was used to compare the efficiency of 3 pig breeding schemes based on either traditional genetic evaluation or genomic evaluation. The simulated population contained 1,050 female and 50 male breeding animals. It was selected for 10 yr for a synthetic breeding goal that included 2 traits with equal economic weights and heritabilities of 0.2 or 0.4. The reference breeding scheme, named BLUP-AM, was based on the phenotyping of all candidates (13,770 animals/yr) for Trait 1 and of relatives from 10% of the litters (270 animals/yr) for Trait 2 and on BLUP-Animal Model genetic evaluations. Under the first alternative scenario, named GE-1TP, selection was based on genomic breeding values (GBV) estimated with one training population (TP) made up of candidate relatives phenotyped for both traits, with a size increasing from 1,000 to 3,430 over time. Under the second alternative scenario, named GE-2TP, the GBV for Trait 2 were estimated using a TP identical to that of GE-1TP, but the GBV for Trait 1 were estimated using a large TP made up of candidates that increased in number from 13,770 to 55,080 over time. Over the simulated period, both genomic breeding schemes generated 39 to 58% more accurate EBV for Trait 2 than the reference scheme, resulting in 78 to 128% (GE-1TP) and 63 to 84% (GE-2TP) greater average annual genetic trends for this trait. For Trait 1, GE-1TP was 18 to 24% less accurate than BLUP-AM, reducing average annual genetic trends by 27 to 44%. By contrast, GE-2TP generated 35 to 43% more accurate EBV and 8 to 22% greater average annual genetic trends for Trait 1 than the reference scheme. Consequently, GE-2TP was 27 to 33% more efficient in improving the global breeding goal than BLUP-AM whereas GE-1TP was globally as efficient as the reference scheme. Both genomic schemes reduced the inbreeding rate, the greatest decrease being observed for GE-2TP (-49 to -60% compared with BLUP-AM). In conclusion, genomic selection could substantially and durably improve the efficiency of pig breeding schemes in terms of reliability, genetic trends, and inbreeding rate without any need to modify their current structure. Even though it only generates a small TP, limited annual phenotyping capacity for traits currently only recorded on relatives would not be prohibitive. A large TP is, however, required to outperform the current schemes for traits recorded on the candidates in the latter.