Genomics applied to conservation of genetic diversity in Dutch livestock

Abstract

Hulsegge, I. (2023). Genomics applied to conservation of genetic diversity in Dutch livestock. PhD thesis, Wageningen University, the Netherlands 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 and market requirements, and for selection to genetically improve economically important traits. Unfortunately, the current trend in populations is often for reduced genetic diversity due to intense selection or random drift. Consequently, breeding methods and gene banks were developed to avoid the risk of losing genetic diversity. As genomic information becomes more accessible, we now have the option to better manage genetic diversity. In this thesis, I applied genomics to conservation practises. More specifically, I applied genomic tools and methods to prove their relevance for the conservation of Dutch livestock breeds. I demonstrated that the use of genomics led to a more detailed understanding of the genetic diversity conserved in gene banks or in living populations of numerically small breeds in The Netherlands. Moreover, I reported the implications for genetic diversity of (1) lines or supposed lines within a numerically small breed, (2) merging and terminating lines of the Dutch Landrace pig breed, and (3) the replacement over time of traditional local cattle breed (Dutch Friesian Cattle) with just productive breed (Holstein Friesian). Subsequently, I illustrated that only a small set of informative SNPs is needed to differentiate among Dutch local cattle breeds. Using such a small set of informative SNPs a genetic tool (DNA test) was developed for the determination of breed purity of cattle. Lastly, I addressed the recent developments in genomics and how they can be used effectively for genetic conservation, and in particular how gene banks can benefit from these developments, and I outline possible future directions for (a more effective) conservation of breeds using genomic methods. More specially, I propose a strategy for conservation and stated that gene banks should transform from "traditional gene banks" into "digital gene banks". Contents 9 1 -General introduction 15 2 -Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account 31 3 -Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs 51 4 -Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data 73 5 -Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle 91 6 -Development of a genetic tool for determining breed purity of cattle 111 7 -General discussion 125