Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein–Friesian breeding program from 1986 to 2015

Abstract

BackgroundIn recent decades, Holstein–Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015.MethodsPedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time.ResultsEffective population size estimates for the 1986–2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996–2000 and 2001–2005 periods.ConclusionsGenome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0385-y) contains supplementary material, which is available to authorized users.

Efficient use of genomic information for sustainable genetic improvement in small cattle populations

“…However, lower intensity of selection in small 369 populations stems from fewer tested animals, and not more selected, which reduces a genetic pool 370 for selection. Our results are more in line with Doekes et al (2018). They attribute the higher rates 371 of inbreeding with genomic selection to the fact, that the animals with a higher relatedness to the 372 reference population have more accurate genomic predictions and are more likely to deviate 373 substantially and therefore to be selected (Habier et al, 2007;Clark et al, 2012).…”

“…The results have implications also for large populations, namely they show that genomic selection is 437 increasing turnover of germplasm per year with positive effect on genetic gain and negative effect 438 on genetic variation. This has been already indicated in real large populations (Doekes et al, 2018). 439…”

Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds

“…Small population sizes in native breeds increase the risk on inbreeding and loss of genetic diversity through genetic drift [7]. Second, artificial selection, particularly in the Holstein Friesian breed, facilitated by techniques like artificial insemination and embryo transfer in combination with cryo storage, has further reduced genetic diversity [8,9].…”

Accounting for population structure in selective cow genotyping strategies

“…There has been considerable concern on controlling inbreeding in cattle populations in the genomics era (Howard, Pryce, Baes, & Maltecca, ). Doekes, Veerkamp, Bijma, Hiemstra, and Windig () have investigated genetic diversity trends in the Dutch–Flemish Holstein–Friesian bull population, and reported that after the implementation of GS, inbreeding and kinship have increased substantially. Especially in small populations, the loss in genetic variance stands as an obstacle to improve genetic gains when performing genomic selection for many generations (Jannink, ).…”