Pedigree estimation of the (sub) population contribution to the total gene diversity: the horse coat colour case

Abstract

A method to quantify the contribution of subpopulations to genetic diversity in the whole population was assessed using pedigree information. The standardization of between-and within-subpopulation mean coancestries was developed to account for the different coat colour subpopulation sizes in the Spanish Purebred (SPB) horse population. The data included 166 264 horses registered in the SPB Studbook. Animals born in the past 11 years (1996 to 2006) were selected as the 'reference population' and were grouped according to coat colour into eight subpopulations: grey (64 836 animals), bay (33 633), black (9414), chestnut (1243), buckskin (433), roan (107), isabella (57) and white (37). Contributions to the total genetic diversity were first assessed in the existing subpopulations and later compared with two scenarios with equal subpopulation size, one with the mean population size (13 710) and another with a low population size (100). Ancestor analysis revealed a very similar origin for the different groups, except for six ancestors that were only present in one of the groups likely to be responsible for the corresponding colour. The coancestry matrix showed a close genetic relationship between the bay and chestnut subpopulations. Before adjustment, Nei's minimum distance showed a lack of differentiation among subpopulations (particularly among the black, chestnut and bay subpopulations) except for isabella and white individuals, whereas after adjustment, white, roan and grey individuals appeared less differentiated. Standardization showed that balancing coat colours would contribute preserving the genetic diversity of the breed. The global genetic diversity increased by 12.5% when the subpopulations were size standardized, showing that a progressive increase in minority coats would be profitable for the genetic diversity of this breed. The methodology developed could be useful for the study of the genetic structure of subpopulations with unbalanced sizes and to predict their genetic importance in terms of their contribution to genetic variability.

Genetic diversity within and gene flow between three draught horse breeds using genealogical information

“…= average coancestry and inbreeding coefficients for the entire metapopulation, respectively f = average coancestry coefficient of subpopulations -D = average genetic distance (Nei 1987) The F-statistics were standardized according to the sample size (Bartolome et al 2010). …”

One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed

“…Even if crossbreeding offered the opportunity to combine the desirable characteristics of Há's two ancestral breeds, PRE and PRá, potentially increased performance due to the complementary effects of heterosis [16]. Still, the planning of matings should be a priority.…”

500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data

“…Despite this, our results analysing the genetic diversity at the population level (studied across GD, a parameter that shows the global diversity when each of the subpopulations studied is removed (Bartolomé et al, 2010) demonstrated that the PRE_C group contributed with almost the same gene diversity to the complete population as PRE_CI_NC animals. Because the number of horses of the PRE_C subpopulation is…”