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Institut für Nutztierwissenschaften

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    Selection methods for local breeds with historical introgression
    (2018) Wang, Yu; Bennewitz, Jörn
    For the management of local breeds with historical introgression, both genetic gain and the long-term evolution of genetic variability have to be taken into consideration. Traditional optimum contribution selection (traditional OCS) aims at maximizing genetic gain while controlling the rate of inbreeding by optimizing the genetic contribution of each selection candidate to the next generation. It is also a promising approach to maintain genetic diversity since the average kinship of selection candidates is restricted. However, for the breeds with historical introgression, this diversity may be caused by introducing genetic material from other breeds, which can be a risk of the conservation of small local populations. Therefore, the breeding objectives should not only focus on increasing genetic gain but also on maintaining the diversity of native alleles. The main aim of this project was to resolve the existing conflicts in the current breeding program of local breeds with historical introgression. Chapter 1 gave a brief introduction and background of the topic and formulated the objective of the thesis. In chapter 2, the current inbreeding status of German Angler cattle was evaluated based on both pedigree (F_PED) and genomic information. The genomic inbreeding coefficients of 182 Angler cattle were estimated via analyzing the genome proportion of run of homozygosity (F_ROH) and using the genomic relationship matrix (F_GRM). On average, the inbreeding level of Angler is relatively low compared to the other breeds ((F_PED ) ̅:0.013;(F_GRM ) ̅:-0.015; (F_(ROH>1Mb) ) ̅:0.031). Moderate to strong correlations (0.607–0.702) were found between F_PED and F_ROH based on different length categories of ROH segments. Moreover, it proved that F_ROH is a robust estimating method owing to its ability to capture both ancient and recent inbreeding. Although traditional OCS may achieve higher genetic gain with the restriction of the defined rate of inbreeding, in this case, inbreeding is not the main problem in the current breeding program and the advantage of OCS may be limited since the level of inbreeding may be lower than the threshold. In chapter 3, we developed the advanced optimum contribution selection strategy by considering migrant contribution and conditional kinship at native alleles in the OCS procedure. Different scenarios were compared for both functions of production and conservation based on pedigree information. It has been proved that the advanced OCS approach can effectively maintain the diversity of native alleles and genetic originality while ensuring genetic improvement with appropriate settings of constraint values. The availability of high-density single-nucleotide polymorphism (SNP) markers provides a solution for achieving accurate estimates of both coancestry and breed composition. In chapter 4 and chapter 5, we evaluated the long-term performance of advanced OCS strategies in both production and conservation function via simulating several subsequent generations based on genomic information. In chapter 4, we found that traditional OCS procedure has slight advantages in increasing genetic gain whilst controlling relatedness compared to truncation selection. However, the introgression of foreign genetic material by traditional OCS is not desirable in the local breed conservation. In the long run, constraining migrant contribution and kinship at native alleles in the OCS procedure is a promising approach to increase genetic gain whilst maintaining genetic uniqueness and diversity. Chapter 5 mimics a conservation program which aims at increasing the value of a breed for conservation by removing exogenous genetic material, maintaining within-breed genetic diversity, and increasing the genetic diversity among breeds. Simply minimizing the exogenous genetic contribution leads to the loss of both within and between population diversity. Moreover, the recovery process ended at a plateau after several generations. The best scenario was able to increase the native contribution from 0.317 to 0.706 before a segment-based kinship level of 0.10 was reached. This scenario maximized the native contribution, constrained the increase in kinship, and the increase in kinship at native alleles. Moreover, it constrained the mean kinship in a multi-breed core set to the current level, which is desirable for the conservation program. This thesis ends with a general discussion.