Total cost estimation for implementing genome-enabled selection in a multi-level swine production system

Abstract

BackgroundDetermining an animal’s genetic merit using genomic information can improve estimated breeding value (EBV) accuracy; however, the magnitude of the accuracy improvement must be large enough to recover the costs associated with implementing genome-enabled selection. One way to reduce costs is to genotype nucleus herd selection candidates using a low-density chip and to use high-density chip genotyping for animals that are used as parents in the nucleus breeding herd. The objective of this study was to develop a tool to estimate the cost structure associated with incorporating genome-enabled selection into multi-level commercial breeding programs.ResultsFor the purpose of this deterministic study, it was assumed that a commercial pig is created from a terminal line sire and a dam that is a cross between two maternal lines. It was also assumed that all male and female selection candidates from the 1000 sow maternal line nucleus herds were genotyped at low density and all animals used for breeding at high density. With the assumptions used in this analysis, it was estimated that genome-enabled selection costs for a maternal line would be approximately US$0.082 per weaned pig in the commercial production system. A total of US$0.164 per weaned pig is needed to incorporate genome-enabled selection into the two maternal lines. Similarly, for a 600 sow terminal line nucleus herd and genotyping only male selection candidates with the low-density panel, the cost per weaned pig in the commercial herd was estimated to be US$0.044. This means that US$0.21 per weaned pig produced at the commercial level and sired by boars obtained from the nucleus herd breeding program needs to be added to the genetic merit value in order to break even on the additional cost required when genome-enabled selection is used in both maternal lines and the terminal line.ConclusionsBy modifying the input values, such as herd size and genotyping strategy, a flexible spreadsheet tool developed from this work can be used to estimate the additional costs associated with genome-enabled selection. This tool will aid breeders in estimating the economic viability of incorporating genome-enabled selection into their specific breeding program.

Harnessing genomic information for livestock improvement

“…The rate of inbreeding did not seem to be affected. Although the gains are less than those in dairy cattle, GS has also been applied and deemed profitable in defined contexts in beef cattle 103,104 , pigs 105 , sheep [106][107][108] and layer chickens 109 . Another potential advantage of GS is that new traits can be included in selection indices to maximize genetic gain for profit.…”

Genomic selection in pigs: state of the art and perspectives

“…Actually, unlike in dairy cattle, where genomic selection is a reality nowadays, in pigs no great economic changes are expected with the introduction of genomic selection and the advantages should cover the extra financial costs associated to its implementation in pig breeding programmes (Tribout et al 2013). The primary expected benefit from incorporating genomic information into pig breeding value estimation is the improved accuracy and this increase should be large enough to recover the genotyping costs (Abell et al 2014). Differently from other species, as i.e.…”

“…ancillary expenses associated to genotyping, costs due to the additional time needed to develop and calculate EBV, and to the increased computer power necessary to predict GEBV (Abell et al 2014).…”

“…Bouquet et al (2015) assessed that imputation of LD to HD genotyping of crossbred pigs would result in a similar precision of imputation than those on purebred animals when both the parental lines are genotyped at HD and with similar values of precision than in the imputation of purebred lines when sufficient dense genotyping (at least 10K). Abell et al (2014) predicted the expenses associated to the incorporation of genomic selection into traditional pig breeding schemes while using two different types of genotyping densities (LD and HD chips). With the selection candidates genotyped at LD and all animals used for breeding genotyped at HD, costs resulted in US$0.164 (in a 1000 sow maternal line nucleus herd) or US$0.21 (in a 600 sow terminal sire line) per weaned piglets.…”

Effects of Genotypes for Igf2, Cckar and Mc4r on the Phenotypic Estimations and Breeding Values for Productive Traits in Pigs

“…If in livestock breeding the genomic selection programs are implemented on the basis of using SNP-arrays of medium density (MD) and high density (HD) [2,5,6], in pig breeding the application of MD-and HD-arrays is economically unjustified. The implementation of genomic selection of pigs is associated with the development of low density DNA-matrixes with inclusion of SNPs in them selected by the results of GWAS (genome-wide association studies) analysis using MD-and HD-arrays [7][8][9][10]. In order to increase the information content of LD-arrays, they additionally include SNPs localized in "primary" genes associated with QTL.…”