Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration

Abstract

BackgroundOptimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle.ResultsIn most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS.ConclusionsFor local breeds with historical introgressions, current breeding programs should focus on increasing genetic gain and controlling inbreeding, as well as maintaining the genetic originality of the breeds and the diversity of native alleles via the inclusion of MC and kinship at native alleles in the OCS process.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0320-7) contains supplementary material, which is available to authorized users.

Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds

“…The fraction BBL that may be unique in the Dutch gene bank is likely to be well covered in the BBL population in Belgium. To account for influences of breeds like HF and BBL in native cattle populations, OCS can be extended to minimize migrant contributions while maximizing genetic diversity [31]. In this extended OCS approach, a reference population (consisting of breeds that are likely to have contributed to the native breeds) is used to determine the migrant contributions.…”

Origin Specific Genomic Selection: a simple process to optimize the favourable contribution of parents to progeny

“…Therefore, OSGS can be complementary to optimal contribution selection as we could partition the kinship matrix into two matrices based on markers carrying favourable primary or secondary parent allele effects. Similar approach has been advocated for optimal contribution selection in rare breeds of livestock in the presence of introgression from cosmopolitan breeds (Wang et al 2017a, 2017b and 2019).…”

Advanced optimum contribution selection as a tool to improve regional cattle breeds: a feasibility study for Vorderwald cattle

“…Advanced OCS is implemented in the open-source R package optiSel (Wellmann, 2019) and allows for simultaneous management of the ΔG, ΔF, ΔF nat and MC (Wang et al, 2017a;Wellmann et al, 2012). Advanced OCS was used solely for the selection of proven sires for deployment in the breeding population.…”

“…Therefore, aOCS is of great interest for breeds under conservation. Basic research on the appropriate exploitation of aOCS procedures has already been carried out (Wellmann et al, 2012;Wang et al, 2017a and2017b). Thus, this study will examine the possibilities of implementing aOCS in the actual breeding scheme of Vorderwald cattle, a model population with historical introgression.…”