Genomic characterization and conservation of genetic diversity in cattle

Research output: Thesisinternal PhD, WU

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.     

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Veerkamp, Roel, Promotor
  • Windig, Jack, Co-promotor
Award date18 Sep 2020
Place of PublicationWageningen
Publisher
Print ISBNs9789463954235
DOIs
Publication statusPublished - 2020

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