Genomic characterization and conservation of genetic diversity in cattle

Abstract

Genetic diversity in livestock populations is important, because it forms the basis for these populations to adapt to changing environments and human demands. Traditionally, livestock genetic diversity has been characterized and conserved with pedigree-based measures of inbreeding and kinship. Thanks to the increasing availability of genomic information, in particular single nucleotide polymorphism (SNP) data, we now have additional opportunities to better manage genetic diversity. In this thesis, I utilized SNP data to characterize and conserve genetic diversity in Dutch cattle, both in in situ populations and ex situ gene bank collections. The Holstein Friesian (HF) breed was the main breed of interest, because of its importance in the Dutch and global dairy cattle sector. First, it was demonstrated how changes in breeding practices in the past have been accompanied by changes in genetic diversity trends in the Dutch-Flemish HF breeding program. Among others, it was shown that the introduction of genomic selection has been accompanied by an increase in pedigree-based and SNP-based rates of inbreeding and kinship. Second, the negative effects of inbreeding on performance ("inbreeding depression") were quantified for yield, fertility and udder health traits of Dutch HF cows. It was shown that recent inbreeding may be more harmful than ancient inbreeding, although results were mixed. It was also shown that, based on SNP data, the negative effects of inbreeding are quite equally distributed across the genome and well captured by genome-wide homozygosity. Third, the value of the Dutch cattle gene bank collection was demonstrated. It was shown that old HF gene bank bulls can be used in the current or future HF breeding program to increase (or recover) genetic diversity, or to improve genetic merit given a certain level of diversity. It was also shown that Dutch native breeds in the gene bank collection harbor genetic diversity, both within and across breeds, although some breeds showed substantial overlap. Last, it was discussed how genomic information (in particular SNP data) can be used to maintain genetic diversity in livestock populations. Based on our current knowledge and the availability of SNP data, I recommend to limit the increase in SNP-by-SNP similarity (and, thus, homozygosity) while performing selection. For gene bank collections, I envision a transition towards bio-digital resource centers, in which large amounts of genomic and phenotypic data are stored in addition to physical germplasm material. Overall, the findings of this thesis improve our understanding of (conservation of) genetic diversity in livestock and, thereby, contribute to sustainable livestock production.

Opportunities of Genomics for the Use of Semen Cryo-Conserved in Gene Banks

“… Doekes (2020) stated that “a common strategy of national gene banks is to conserve all national breeds.” But funds are usually restricted, and choices between breeds often have to be made. This may depend on which other breeds are already conserved.…”

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

“…The change in use from local breeds to specialized breeds has been observed in many industrialized European countries including the Netherlands [4,5]. Until 1975, the Dutch Friesian cattle (DF) dominated the Dutch national cattle population (76%) [6,7]. By the late nineteenth century, the Dutch Friesians were internationally known as exceptionally productive dairy cattle.…”

Genomics applied to conservation of genetic diversity in Dutch livestock

“…Thirdly, the assumption when measuring genetic relationships based on pedigree information is that full siblings share exactly 50% of their alleles, while in reality they are subject to mendelian sampling that creates variation in the amount of allele sharing between full siblings; the same holds for other relationships. Fourthly, pedigrees are generally recorded per breed, making analysis of between-breed diversity by pedigree analysis impossible (Eusebi et al 2019;Doekes 2020;Galla et al 2022). With the wide availability of genomic data, it has become possible to study and quantify genetic diversity directly rather than using pedigree information to make statistical inferences.…”

“…Conserving genetic diversity is essential for the sustainability of populations. In livestock, the amount of genetic diversity should be large enough to enable the adaptation of populations to changing environments (such as production systems and climate) and market requirements, and for selection to genetically improve the economically important traits (FAO 2015;Woolliams and Oldenbroek 2017;Doekes 2020). Genetic diversity is important in stable environments as well.…”

“…The change in use from local breeds to specialized breeds has been observed in many industrialized European countries including the Netherlands(Oldenbroek 2007;Hiemstra et al 2010). Until 1975, the Dutch Friesian cattle (DF) dominated the Dutch national cattle population (76%)(van Breukelen et al 2019;Doekes 2020). By the late nineteenth century, the Dutch Friesians were internationally known as exceptionally productive dairy cattle.…”