Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs

Abstract

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G × E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low ( h 2 = 0.05) and moderate heritability ( h 2 = 0.30). GEBV were calculated for different accuracies (r mg ), and G × E interactions were considered by modifying originally simulated true breeding values in the range from r g = 0.5 to 1.0. For both traits ( h 2 = 0.05 and 0.30) and r mg ⩾ 0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G × E interactions. Only for pronounced G × E interactions ( r g = 0.5), and for highly accurate GEBV for natural service bulls ( r mg > 0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

Genetic parameters for stayability of Holsteins in US organic herds

“…In the absence of genetic evaluations specific to the organic environment, genetic improvement in cow fitness could be facilitated through selection for fitness traits derived primarily from conventional herd data if positive genetic correlations exist. Previous research for genotype × environment interactions between conventionally managed herds and organic herds in the United States is sparse; studies comparing health or fitness in Europe are available but results are inconsistent (Ahlman et al, 2011;Yin et al, 2014). Recent results from a German study indicate that selection based on genetic merit estimates from conventional herds may not be optimal in organic herds, particularly for health traits (Yin et al, 2014).…”

“…Previous research for genotype × environment interactions between conventionally managed herds and organic herds in the United States is sparse; studies comparing health or fitness in Europe are available but results are inconsistent (Ahlman et al, 2011;Yin et al, 2014). Recent results from a German study indicate that selection based on genetic merit estimates from conventional herds may not be optimal in organic herds, particularly for health traits (Yin et al, 2014). However, Ahlman et al (2011) found that genetic correlations for survival between organic and conventional Swedish Holsteins did not differ from unity.…”

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

“…The frequency of deleterious alleles including recessive lethal alleles can rise in populations as a consequence of drift due to small effective population size, but also due to selection [ 1 ]. Inherited defects usually derive from unique “founder” mutations [ 2 ]. Especially in cattle breeds, several high frequency lethal alleles have been described [ 3 , 4 ] reaching carrier frequencies up to 32% [ 5 ], that can be traced back to prime bulls that were used extensively in the past decades.…”

Population dynamics of potentially harmful haplotypes: a pedigree analysis

“…Although the potential role of mutation, demography, and selection on the frequency of deleterious alleles has been discussed before [ 7 ], little is known about the dynamics of potentially lethal haplotypes. Assuming that genetic variants causing inherited defects should expand in a population from founder events involving carriers [ 16 ], this research aims at the ascertainment of segregation patterns of haplotypes with low probabilities of being observed at a homozygous state using a small pedigree of the highly inbred Gochu Asturcelta pig breed.…”