Optimization of Swine Breeding Programs Using Genomic Selection with ZPLAN+

Abstract

The objective of this study was to evaluate the present conventional selection program of a swine nucleus farm and compare it with a new selection strategy employing genomic enhanced breeding value (GEBV) as the selection criteria. The ZPLAN+ software was employed to calculate and compare the genetic gain, total cost, return and profit of each selection strategy. The first strategy reflected the current conventional breeding program, which was a progeny test system (CS). The second strategy was a selection scheme based strictly on genomic information (GS1). The third scenario was the same as GS1, but the selection by GEBV was further supplemented by the performance test (GS2). The last scenario was a mixture of genomic information and progeny tests (GS3). The results showed that the accuracy of the selection index of young boars of GS1 was 26% higher than that of CS. On the other hand, both GS2 and GS3 gave 31% higher accuracy than CS for young boars. The annual monetary genetic gain of GS1, GS2 and GS3 was 10%, 12%, and 11% higher, respectively, than that of CS. As expected, the discounted costs of genomic selection strategies were higher than those of CS. The costs of GS1, GS2 and GS3 were 35%, 73%, and 89% higher than those of CS, respectively, assuming a genotyping cost of $120. As a result, the discounted profit per animal of GS1 and GS2 was 8% and 2% higher, respectively, than that of CS while GS3 was 6% lower. Comparison among genomic breeding scenarios revealed that GS1 was more profitable than GS2 and GS3. The genomic selection schemes, especially GS1 and GS2, were clearly superior to the conventional scheme in terms of monetary genetic gain and profit.

Bayesian model combining linkage and linkage disequilibrium analysis for low density-based genomic selection in animal breeding

“…Under a genomic selection approach, Jiao et al (2014) working with Duroc pigs reported the heritability estimated obtained through Bayes A equal to 0.32 (0.09). Lopez et al (2016) reported heritability estimates for FCR closest to 0.30, and concluded that genomic selection for FCR is clearly superior to the conventional scheme in terms of monetary genetic gain and profit. According to Akanno et al (2013), when using genomic selection for feed conversion in pigs assuming heritability equal to 0.32, the accuracy of selection index ranged from 0.38 to 0.66, whereas the conventional selection provides accuracies between 0.10 and 0.64.…”

Application of Genomic Data for Reliability Improvement of Pig Breeding Value Estimates

“…The inclusion of genomic evaluation in the system implies additional costs incurred by the business. In this regard, there are a number of questions about the economic feasibility of implementing such a method [23,24]. Since genomic prediction is an addition to the conventional assessment of breeding value, it is necessary to plan in advance the payback period of obtaining animals' genomic data (sample collection, genotyping and data processing) and reference population size needed for sufficient assessment accuracy and effectiveness of genomic prediction for traits due to reference population size.…”

Development of a low-density panel for genomic selection of pigs in Russia1

“…The 3 layers are represented by the nucleus layer which include high-quality purebred animals, the multiplier level at which purebred animals from different lines are multiplied and crossed to obtain the F1 crossbred animals, and the production (commercial) level, at which F1 sows are crossed with purebred sires, the progeny of these crosses being used for pork production. Selection takes place at the nucleus and partially at the multiplier levels ( Visscher et al, 2000 ; Lopes, 2016 ; Lopez et al, 2016 ). The use of breeding programs of this kind leads to a certain genetic improvement lag, which is the time taken for genetic improvements achieved in the higher layer to reach the next layers ( Bichard, 1971 ; See, 1995 ), between the nucleus level at which selection and testing mostly occurs and the commercial level at which terminal (slaughter) hybrids are produced which should have the desired qualities.…”