Opportunities for genome-wide selection for pig breeding in developing countries1

Abstract

Genetic improvement of exotic and indigenous pigs in tropical developing countries is desired. Implementations of traditional selection methods on tropical pig populations are limited by lack of data recording and analysis infrastructure. Genome-wide selection (GS) provides an approach for achieving faster genetic progress without developing a pedigree recording system. The implications of GS on long-term gain and inbreeding should be studied before actual implementation, especially where low linkage disequilibrium (LD) is anticipated in the target population. A simulation case study of this option was performed on the basis of the available 60,000 SNP panel for porcine genome. Computer simulation was used to explore the effects of various selection methods, trait heritability, and different breeding programs when applying GS. Genomic predictions were based on the ridge regression method. Genome-wide selection performed better than BLUP and phenotypic selection methods by increasing genetic gain and maintaining genetic variation while lowering inbreeding, especially for traits with low heritability. Indigenous pig populations with low LD can be improved by using GS if high-density marker panels are available. The combination of GS with repeated backcrossing of crossbreds to exotic pigs in developing countries promises to rapidly improve the genetic merit of the commercial population. Application of this novel method on a real population will need to be performed to validate these results.

Comparison of genomic predictions for carcass and reproduction traits in Berkshire, Duroc and Yorkshire populations in Korea

“…The TNB heritability was estimated as 0.15 in Berkshire, which was in good agreement with the heritability value in commercial pig populations reported by Cleveland et al [23] and Cleveland and Hickey [24]. In the three breed populations, heritability values for TNB were greater than those for NBA, which was also agreed with the previous reports [22,24].…”

“…In general, NBA has been reported to have very low heritability, i.e. <0.10 [22], which was in good agreement with the estimate in Berkshire in this study (Table 3). However, in Duroc, the heritability estimates for the reproductive traits were high, which may be partly due to a small sample size (Table 1).…”

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

“…Genomic selection might also assist to increase genetic gain in developing countries in which indigenous and exotic lines could be used for repeated backcrossing ( Akanno et al, 2013 ). The use of genomic information will, also in such schemes, assist to control inbreeding and avoid a possible loss of variation.…”

Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

“…Therefore, it is difficult to improve these traits more rapidly using traditional breeding methods. With the development of molecular breeding technology, marker-assisted selection (MAS) and genomic selection (GS) have become effective ways to improve pig breeding efficiency [ 2 ].…”