Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses

Abstract

Pedigree collected by the Interbeef service allowed genetic diversity to be assessed by using pedigree analyses for the European Charolais (CHA) and Limousin (LIM) cattle populations registered in national herdbooks in Denmark (DNK), France (FRA), Ireland (IRL), Sweden (SWE), and, solely for the LIM breed, the United Kingdom (UK). The CHA data set included 2,563,189 calves with weaning performance, of which 96.1% were recorded in FRA, 3.0% in SWE, 0.5% in IRL, and 0.4% in DNK. The LIM data set included 1,652,734 calves with weaning performance, of which 91.9% were recorded in FRA, 4.9% in UK, 1.8% in DNK, 0.9% SWE, and 0.5% in IRL. Pedigree files included 3,191,132 CHA and 2,409,659 LIM animals. Gene flows were rather limited between populations, except from FRA toward other countries. Pedigree completeness was good in all subpopulations for both breeds and allowed the pedigree to be traced back to the French population. A relatively high level of genetic diversity was assessed in each CHA and LIM subpopulation by estimating either effective population sizes (N(e) >244 and N(e) >345 in the CHA and LIM subpopulations, respectively), relationship coefficients within subpopulations (<1.3% in both breeds), or probability of gene origins. However, in each subpopulation, it was shown that founders and also ancestors had unbalanced genetic contributions, leading to a moderate but continuous reduction in genetic diversity. Analyses between populations suggested that all European CHA and LIM populations were differentiated very little. The Swedish CHA population was assessed as genetically more distant from the other CHA populations because of fewer gene flows from other countries and because of the use of North American sires to introgress the polled phenotype. In each European subpopulation, most of the main ancestors, which explained 50% of gene origin, were born in FRA. However, those main ancestors were different between countries. Moreover, in both breeds, the main ancestors, which explained 50% of the gene origin in DNK, IRL, SWE, and UK for the LIM breed, were found to be infrequently used in FRA. Those results were consistent with the low relationship coefficients estimated between subpopulations (<0.6% in both the CHA and LIM breeds). Therefore, in both breeds, each subpopulation may constitute a reservoir of genetic diversity for the other ones.

PHYSIOLOGY AND ENDOCRINOLOGY SYMPOSIUM: How single nucleotide polymorphism chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females1,2,3,4

“…With individual breeds having effective population sizes between 64 and 445 (Cleveland et al, 2005;McParland et al, 2007;Márquez et al, 2010), several hundred to a few thousand observations may be adequate for withinbreed whole-genome prediction of age at puberty, but tens of thousands of records are needed for lower heritability traits, such as first service AI pregnancy rate and breeding season pregnancy rate. The number of records required may increase by an order of magnitude for whole-genome predictions applicable to heifers representing a wide variety of genetic backgrounds or to breeds with larger effective population sizes (Bouquet et al, 2011). With this need for a large number of records, and a price of approximately $100 per 50K SNP assay, the cost of individually genotyping females to enable accurate prediction of fertility traits remains prohibitive.…”

Genetic structure and connectivity analysis in a large domestic livestock meta‐population: The case of the Pura Raza Español horses

“…Namely, the implementation of mating plans, the increase of gene flow between small herds by the use of reproductive techniques, and the establishment of the breeding programme in 2003, which allowed greater use of other PRE lines instead of the emblematic Carthusian individuals (Valera et al, 2005). Heterogeneity among the genetic contribution of founders to different countries could also reflect the different history of each founder and the origin of contributions (Bouquet et al, 2011). In this sense, founder contribution varied significantly in our PRE horse MP.…”

“…Heterogeneity among the genetic contribution of founders to different countries could also reflect the different history of each founder and the origin of contributions (Bouquet et al., ). In this sense, founder contribution varied significantly in our PRE horse MP.…”

“…Besides, fragmentation may lead to population isolation, reducing census, effective population size as well as genetic variation and increasing inbreeding levels, which reduce the individuals' robustness when exposed to stressful environmental conditions, ultimately leading to population extinction (Kristensen, Hoffmann, Pertoldi, & Stronen, 2015). Under these premises, gene flow across subpopulations could help maintain genetic diversity in the global population (Bouquet et al, 2011;Fernández, Toro, & Caballero, 2008).…”

Admixture analysis in relation to pedigree studies of introgression in a minorityBritish cattle breed: theLincolnRed

“…2BAD and DIYABC however yielded unrealistically high estimates of effective population size (compare, for example, those found for Limousin of 345 by Bouquet et al . , and for Lincoln Red of 107 in 2001 and 82 in 2007 according to T. Roughsedge unpublished). The relatively low effective population size values for the more highly selected Limousin and Aberdeen Angus deduced using 2BAD might indicate a greater sensitivity of this method to the selection history of introgressing breeds.…”