Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding

Abstract

The effects of increased pedigree inbreeding in dairy cattle populations have been well documented and result in a negative impact on profitability. Recent advances in genotyping technology have allowed researchers to move beyond pedigree analysis and study inbreeding at a molecular level. In this study, 5,853 animals were genotyped for 54,001 single nucleotide polymorphisms (SNP); 2,913 cows had phenotypic records including a single lactation for milk yield (from either lactation 1, 2, 3, or 4), reproductive performance, and linear type conformation. After removing SNP with poor call rates, low minor allele frequencies, and departure from Hardy-Weinberg equilibrium, 33,025 SNP remained for analyses. Three measures of genomic inbreeding were evaluated: percent homozygosity (FPH), inbreeding calculated from runs of homozygosity (FROH), and inbreeding derived from a genomic relationship matrix (FGRM). Average FPH was 60.5±1.1%, average FROH was 3.8±2.1%, and average FGRM was 20.8±2.3%, where animals with larger values for each of the genomic inbreeding indices were considered more inbred. Decreases in total milk yield to 205d postpartum of 53, 20, and 47kg per 1% increase in FPH, FROH, and FGRM, respectively, were observed. Increases in days open per 1% increase in FPH (1.76 d), FROH (1.72 d), and FGRM (1.06 d) were also noted, as well as increases in maternal calving difficulty (0.09, 0.03, and 0.04 on a 5-point scale for FPH, FROH, and FGRM, respectively). Several linear type traits, such as strength (-0.40, -0.11, and -0.19), rear legs rear view (-0.35, -0.16, and -0.14), front teat placement (0.35, 0.25, 0.18), and teat length (-0.24, -0.14, and -0.13) were also affected by increases in FPH, FROH, and FGRM, respectively. Overall, increases in each measure of genomic inbreeding in this study were associated with negative effects on production and reproductive ability in dairy cows.

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

“…The comparison of ROH is not straightforward since different studies used different criteria in particular for the minimum length of ROH and the minimum number of SNPs involved in ROH. Furthermore, the number of SNPs, density of the SNP chip and selection criteria for SNPs used to determine the genomic inbreeding can have a huge effect on these values (Bjelland et al, 2013). Ferenčaković et al (2013a) found higher number of ROH in four analyzed cattle breeds probably because of the shorter length considered to define the ROH (>1 Mb).…”

“…SNPs that did not satisfy these quality criteria were excluded. Moreover, considering that high linkage disequilibrium (LD) can lead to detection of ROH that are not Runs of homozygosity in three local cattle breeds truly IBD, LD pruning was also performed before the ROH call to increase power, as suggested by Purcell et al (2007) and applied by several authors (Howrigan et al, 2011;Bjelland et al, 2013). Therefore, unlinked SNPs were selected using -indep option of PLINK with the following parameters: 50 SNPs/window, a shift of five SNPs between windows and r 2 threshold of 0.5.…”

The most important sires in Pinzgau population

“…As a consequence of mating closely related individuals, inbreeding manifests itself phenotypically as a loss in general level of performance and fitness of the progeny (Charlesworth and Willis 2009;Bjelland et al, 2013). It leads to the loss of genetic variation within population and accumulation of recessive mutations, which may be associated with several lethal effects (Bjelland et al, 2013).…”

Genomic Determination of the Most Important Father Lines of Slovak Pinzgau Cows

“…The inbreeding coefficient is defined as the probability that a pair of alleles is identical by descent (IBD). Historically, geneticists have estimated this probability using pedigree data though genomic information should lead to a more accurate depiction (Bjelland et al, 2013). Increased levels of inbreeding would appear genomically as an increase in the frequency of homozygous alleles.…”

“…A problem with this method is that alleles that are IBD and identical by state (IBS) cannot be distinguished and are both included in this measure of inbreeding. An alternative method involving genomic runs of homozygosity (ROH) attempts to distinguish these differences and has been used in human (Kirin et al, 2010) as well as cattle genomics (Bjelland et al, 2013;Ferenčaković et al, 2013), examining population history. The ROH are consequence of inbreeding and relatively close relationships between parent pairs, especially in small endangered populations (Mészáros et al, 2015).…”