Approaches to the management of inbreeding and relationship in the German Holstein dairy cattle population

Koenig, Sven; Simianer, Henner

doi:10.1016/j.livsci.2005.12.009

Cited by 59 publications

(68 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…With the availability of pedigree information, pedigree analysis can offer a better understanding of the population structure and trends in inbreeding of these breeds. In dairy cattle, pedigree analysis has often been used in genetic diversity studies [8], [9], and in assessing the effect of inbreeding on differing phenotypic traits [10] [11] [12] [13]. Apart from a few studies [10] [13], most pedigree analyses involving dairy cattle were focused on classical in- [14], [15] are well established.…”

Section: Introductionmentioning

confidence: 99%

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

Addo¹,

Schäler²,

Hinrichs³

et al. 2017

View full text Add to dashboard Cite

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

show abstract

Section: Introductionmentioning

confidence: 99%

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

Addo¹,

Schäler²,

Hinrichs³

et al. 2017

View full text Add to dashboard Cite

show abstract

“…NBREEDING depression, the reduction in fitness observed in the progeny of genetically related individuals, plays a key role in population biology, affecting processes as diverse as the management of livestock and endangered wild species (Keller and Waller 2002;Koenig and Simianer 2006), the evolution of mating systems (Kelly 2005), and the dispersal strategies (Motro 1991;Gandon 1999). The population genetics of this depression is well understood (Lynch 1991;Charlesworth and Charlesworth 1999;Charlesworth and Willis 2009), but the genomic details about the mechanisms causing it are just starting to be unveiled (Paige 2010).…”

mentioning

confidence: 99%

Gene-Expression Changes Caused by Inbreeding Protect Against Inbreeding Depression in Drosophila

et al. 2012

View full text Add to dashboard Cite

We present a transcriptomic analysis aimed at investigating whether the changes in gene expression that occur under inbreeding generally reduce or enhance inbreeding depression. Discerning between these two alternatives can be addressed only when both changes in expression due to inbreeding and to inbreeding depression are estimated simultaneously. We used Affymetrix 2.0 arrays to study the changes in gene expression associated with both inbreeding and inbreeding depression for fitness in four sets of inbred sublines of Drosophila melanogaster. We found that for most genes showing changes in expression associated with inbreeding, the least depressed sublines were those showing the largest departures in expression from that of the outbred control. This suggests a pattern consistent with a protective role of expression changes against inbreeding effects, and would reveal a new dimension of the transcriptomics of inbreeding. The variation in depression observed could then be due not only to the genetic damages primarily originating that depression, but also possibly to differences in the ability to carry out the appropriate adjustments in gene expression to cope with the inbreeding. We also found that these expression changes with a putative protective role against inbreeding effects show a clear specificity on RNA synthesis and splicing and energy derivation functions. INBREEDING depression, the reduction in fitness observed in the progeny of genetically related individuals, plays a key role in population biology, affecting processes as diverse as the management of livestock and endangered wild species (Keller and Waller 2002;Koenig and Simianer 2006), the evolution of mating systems (Kelly 2005), and the dispersal strategies (Motro 1991;Gandon 1999). The population genetics of this depression is well understood (Lynch 1991;Charlesworth and Charlesworth 1999;Charlesworth and Willis 2009), but the genomic details about the mechanisms causing it are just starting to be unveiled (Paige 2010). In particular, it would be important to determine the relationship between gene regulation and inbreeding, as regulatory variation underlies much of phenotypic diversity (Wilson et al. 1974;Carroll 2005;Ranz and Machado 2006). Evidence has been provided for significant intraspecific variation in transcript abundance for a large fraction of the genome (Primig et al. 2000;Sandberg et al. 2000) and to show that much of such variation is heritable (Cavalieri et al. 2000;Karp et al. 2000;Jin et al. 2001), suggesting that regulatory variation is likely the main mediator of phenotypic divergence in evolution (King and Wilson 1975;Wray et al. 2003;Hoekstra and Coyne 2007). Therefore, genetic correlations between expression phenotypes and organismal phenotypes point to the molecular pathways that underlie the organismal phenotypes (Rockman and Kruglyak 2006). Thus, an understanding of the molecular basis of inbreeding depression requires knowledge of variation at the whole-genome level (Ayroles et al. 2009).Using whole-genome cD...

show abstract

“…This result applies to both the low (Figure 3a) and the moderate heritability trait (Figure 3b). Inbreeding coefficients in selected groups of elite animals, that is bull dams and bull sires, are generally higher than in milking cows in the population (König and Simianer, 2006). Nevertheless, intensively selected elite bulls and elite cows determine accumulation of inbreeding in the long term.…”

Section: Resultsmentioning

confidence: 99%

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

Yin

Wensch-Dorendorf²,

Simianer

et al. 2014

Animal

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Approaches to the management of inbreeding and relationship in the German Holstein dairy cattle population

Cited by 59 publications

References 34 publications

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

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

Gene-Expression Changes Caused by Inbreeding Protect Against Inbreeding Depression in Drosophila

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

Contact Info

Product

Resources

About