Genetic Diversity and Ancestral History of the German Angler and the Red-and-White Dual-Purpose Cattle Breeds Assessed through Pedigree Analysis

Abstract

Local cattle breeds continue to decline in numbers partly due to the use of high performing breeds in advanced production systems where genetic material of elite animals is widely spread. The objective of this study was to assess the within and across breed genetic diversity of the Angler and Red-andWhite dual-purpose (DP) cattle breeds applying different inbreeding concepts. Classical and ancestral inbreeding coefficients were computed from pedigree data using the gene dropping method. Effective population size was calculated based on the increase of classical inbreeding, and based on ancestral inbreeding to obtain what was termed as ancestral effective population size. Furthermore, the effective number of founders and ancestors were computed to assess the disequilibrium of founder contribution in the reference populations. The analyses were performed separately for each breed and for a combined dataset. The Angler pedigree was more complete (88%) in the first parental generation but completeness declined with increasing pedigree depth. Average classical inbreeding coefficients of inbred individuals were 2.19%, 1.94% and 2.07%, while average Ballou's ancestral inbreeding coefficients were 3.69%, 1.39% and 2.21% for the Angler, Red-and-White DP and the combined breed pedigree analyses, respectively. Ancestral history coefficient is a novel coefficient and its estimates were similar and strongly correlated to Ballou's coefficients (r = 0.99, p < 0.001). The effective population size estimates ranged from 156 to 170 for the classical inbreeding based method, and as low as from 50 to 54 for the ancestral history coefficient based method. The effective number of founders and ancestors ranged from 310 to 532, and

Historical Changes and Description of the Current Hungarian Hucul Horse Population

“…The ancestral history coefficient has been only rarely studied yet. Our estimated values were higher for all birth-year groups than published for Angler and Red-and-White cattle breeds [ 33 ]. The tendencies of the estimated correlations of the different inbreeding parameters in our study were similar to those of reported for Angler and Red-and-White cattle [ 33 ].…”

The benefit of native uniqueness in a local red cattle breed from Northern Germany

“…Since year 2006 candidates’ plateaus are reflected from mostly female candidates, which show a stronger genetic relation (Figure ) and smaller variation of NC itself (Figure ). Moreover, the influence of RH as one major migrant breed (Table ) has been confirmed and is in accordance with the studies from Addo et al () and Schäler et al ().…”

“…Especially, small local breeds often reveal a poor pedigree quality. In case of the RDP, the pedigree file showed large gaps and a high rate of incompleteness regarding dams as mentioned by Addo, Schäler, Hinrichs, and Thaller () and Schäler et al (). In addition, different amounts of migrant breeds’ contribution (Table ), distinct NC variations per cohort (Figure ), and a low correlation between NC PED and NC SEG (Table ) strengthen previous assumptions.…”

Coancestry rate’s estimate of effective population size for genetic variability monitoring

“…In the first case, it is difficult to quantify the level of overestimation, however, restricting the number of considered generations is expected to increase the bias. In the latter case, recent genealogical studies have shown wide ranges in amount of pedigree knowledge and unbalanced pedigree, with EqG and percent of unknown parents ranging from < 2 to more than 10 generations, and from 0 to more than 30% respectively (Leroy et al 2006(Leroy et al , 2013Bartolomé et al 2011;Santana et al 2016;Addo et al 2017;Kumpulainen et al 2017). From our simulations, genealogies with more than 10% of unknown parents are expected to provide N e estimates with substantial overestimations regardless of the metrics chosen, and we may, nevertheless, recommend to restrict the number of generations considered for N e estimation in order to limit the extent of bias.…”