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

Abstract

In the middle of the 20th century, increasing inbreeding rates were identified as a threat to livestock breeding. Consequences include reduced fertility, fitness and phenotypic expression of lethal alleles. An important step in mitigating this inbreeding was the introduction of optimum contribution selection (OCS). OCS facilitates the simultaneous management of genetic gain and inbreeding rates. However, using a standard OCS methodology for regional breeds with historical introgression for upgrading reasons could lead to reinforced selection on introgressed genetic material since those alleles improve the rate of genetic gain and reduce the average kinship in the population. Consequently, regional breeds may become genetically extinct if a standard OCS approach is used. Thus, the advanced OCS (aOCS) approach takes introgressed genetic material into account. The major goals of this study were to (i) gather key information on the feasibility of aOCS under practical conditions of the actual breeding scheme of Vorderwald cattle, (ii) identify superior strategies for implementing the actual scheme and (iii) examine whether historical breeding decisions to increase genetic gain by introgression from commercial breeds could have been avoided by using aOCS. Stochastic simulations were designed in this study to create populations from the historical gene pool by using aOCS. Simultaneously, all practical constraints of a breeding scheme were met. Thus, the simulated populations were comparable with real data. The annual genetic gain was higher in reality (1.56) than in the simulation scenarios (1.12–1.40). The introgressed genetic material increased to 61.3% in reality but was conserved at a final value of 15.3% (±0.78) across simulations. The classical rate of inbreeding and rate of native inbreeding were constrained to 0.092% on an annual basis. This value is equal to an effective population size of 100. The observed values for rates of inbreeding were 0.082–0.087% and 0.087–0.088% for classical and native kinship, respectively. The corresponding figures in reality were 0.067% and 0.184%, respectively. This study suggests that aOCS is feasible for Vorderwald cattle. Strategies for implementation are identified. Finally, we conclude that historical breeding decisions could have been avoided by using aOCS. The genetic gain would have been reduced by at least 12.2%, but the introgressed genetic material, genetic diversity and native genetic diversity would have been more desirable for a breed under conservation.

Implementation of advanced Optimum Contribution Selection in small-scale breeding schemes: prospects and challenges in Vorderwald cattle

“…Therefore, starting the management of MCs is imperative. This study continues the investigation of Kohl et al (2019). In that preceding article, a deeper insight in the underlying simulation process with explanations of the iterative phenotyping and breeding value estimation of the population under study is given.…”

“…Since sufficient marker data are not yet available, and will not be in the foreseeable future, the simulations rely on pedigree data. A detailed description of the simulation protocol and the breeding scheme can be found in Kohl et al (2019). The simulation process was iterated 21 times, whereby each iteration equalled 1 year.…”

“…The actual TMI is composed of performance traits in 44%, 44% and 12% for milk yield, fitness and meat production, respectively. Thus, we assumed a breedspecific TMI based on an individual's own performance, equivalent to a simulated trait with h 2 = 0.25 for our simulations (Kohl et al, 2019). In Germany, EBVs are standardised with mean 100 and a genetic SD of 12.…”

“…Introgressed alleles replaced native gene variants and lowered the probability that alleles at a locus are identical by descent. Thus, genetic gain (ΔG ) was achieved at a low rate of inbreeding (Δf ) (Kohl et al, 2019) but at the expense of decreasing genetic originality. The loss of genetic diversity can be measured in two different ways using: (I) the effective population size (N e ), which is the number of individuals in an idealised population under random mating that would cause the same amount of decrease in genetic diversity as the population under study and (II) the native effective population size (N e(nat) ), which is the corresponding parameter that quantifies how fast the genetic diversity at native alleles is decreasing (Wellmann et al, 2012).…”

“…Thus, a pedigree-based aOCS approach is of great interest to manage the native genetic diversity and originality of those breeds till marker data are affordable and methodologies are developed. The objectives of this study were (I) the development of strategies for practical implementation of an aOCS approach to manage the MC and Δf (nat) in breeding schemes of regional cattle breeds and (II) to examine the financial effects of implementing aOCS in connection with the modelled breeding scheme of Kohl et al (2019) in the Vorderwald cattle breed. On one hand, conservation or reduction of the MC is needed.…”