Dairy cattle breeds have been exposed to intense directional selection for milk production traits over the last fifty years. Intense selection can cause loss of genetic variability and increased inbreeding. Fast selection of breeding candidates via genomic data can boost yearly rate of inbreeding in the population. Inbreeding might in turn result in an excess of deleterious variants and inbreeding depression. Inbreeding is traditionally assessed by pedigree-based estimates (FPED). Nowadays, different measures of inbreeding can be estimated from genomic data. The objective of this study was to assess and compare the level of inbreeding in genotyped Italian Holstein dairy cows from pedigree and SNP data throughout a period of 14 years (2006-2019). A total of 40,921 Italian Holstein dairy cows with imputed high-density genotypes (287,329 SNP after quality control) were available. FPED and the complete generation equivalents (CGE) were computed in ENDOG 4.8. The genomic inbreeding (FROH) was calculated as the proportion of individual genome size covered by runs of homozygosity (ROH) in PLINK 1.9. Overall, genome-based inbreeding (mean FROH = 0.12) was higher than pedigree-based inbreeding (mean FPED = 0.07). As FPED largely relies on pedigree depth, pedigree incompleteness can result in an underestimation of the real inbreeding. Moderate Pearson correlation was observed between FROH and FPED (r = 0.60, P-value < 0.05). The low FPED might be related to the number of CGE registered in the pedigree. The highest correlation was found in the case of animals with highest CGE being equal to 10. Till 2012 the inbreeding per year slightly rose, whereas from 2013 a steep increase was observed. Finally, the rate of inbreeding per generation was equal to 1.67% and 1.58% in the last two generations for FPED and FROH. The identified increase of inbreeding in the breed has led to in-depth studies to evaluate the effect of inbreeding on milk yield and fertility traits.
Pedigree and genomic-based inbreeding in Italian Holstein dairy cows / Ablondi, Michela; Sabbioni, Alberto; CIPOLAT GOTET, Claudio; Malacarne, Massimo; Dadousis, Christos; van Kaam, Jan-Thijs; Summer, Andrea. - (2020). (Intervento presentato al convegno Virtual Meeting 71st Conventional and traditional livestock production systems tenutosi a Virtuale nel 1-4 December 2020).
Pedigree and genomic-based inbreeding in Italian Holstein dairy cows
Michela Ablondi;Alberto Sabbioni;Claudio Cipolat-Gotet;Massimo Malacarne;Christos Dadousis;Andrea Summer
2020-01-01
Abstract
Dairy cattle breeds have been exposed to intense directional selection for milk production traits over the last fifty years. Intense selection can cause loss of genetic variability and increased inbreeding. Fast selection of breeding candidates via genomic data can boost yearly rate of inbreeding in the population. Inbreeding might in turn result in an excess of deleterious variants and inbreeding depression. Inbreeding is traditionally assessed by pedigree-based estimates (FPED). Nowadays, different measures of inbreeding can be estimated from genomic data. The objective of this study was to assess and compare the level of inbreeding in genotyped Italian Holstein dairy cows from pedigree and SNP data throughout a period of 14 years (2006-2019). A total of 40,921 Italian Holstein dairy cows with imputed high-density genotypes (287,329 SNP after quality control) were available. FPED and the complete generation equivalents (CGE) were computed in ENDOG 4.8. The genomic inbreeding (FROH) was calculated as the proportion of individual genome size covered by runs of homozygosity (ROH) in PLINK 1.9. Overall, genome-based inbreeding (mean FROH = 0.12) was higher than pedigree-based inbreeding (mean FPED = 0.07). As FPED largely relies on pedigree depth, pedigree incompleteness can result in an underestimation of the real inbreeding. Moderate Pearson correlation was observed between FROH and FPED (r = 0.60, P-value < 0.05). The low FPED might be related to the number of CGE registered in the pedigree. The highest correlation was found in the case of animals with highest CGE being equal to 10. Till 2012 the inbreeding per year slightly rose, whereas from 2013 a steep increase was observed. Finally, the rate of inbreeding per generation was equal to 1.67% and 1.58% in the last two generations for FPED and FROH. The identified increase of inbreeding in the breed has led to in-depth studies to evaluate the effect of inbreeding on milk yield and fertility traits.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
