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

This research article examines a method for quantifying the contribution of horse color subpopulations to the overall genetic diversity within the Spanish Purebred horse population. The study found that balancing the horse color subpopulations increases the genetic diversity by 12.5%.

Objective and Methodology

• The main aim of the research was to devise a technique that could quantify the subpopulation’s contribution to the total genetic diversity of a population. In this case, the ‘subpopulations’ are groups of horses distinguished by their coat colors.
• This method involved the use of pedigree information and creating a standardization for between- and within-subpopulation mean coancestries, in order to consider the different sizes of the subpopulations.
• The research utilized data from 166,264 horses registered in the Spanish Purebred (SPB) Studbook. The ‘reference population’ included animals born over an 11-year period (1996 to 2006).

Grouping and Differentiations

• The horses were grouped into eight different subpopulations based on their coat colors: grey, bay, black, chestnut, buckskin, roan, isabella, and white.
• The contributions of these subpopulations to the total genetic diversity were evaluated first in their existing proportions and then in scenarios where all subpopulations were equal in size.
• Ancestor analysis showed similar origins for all groups, except for six ancestors who were unique to one group and likely provided the unique color.

Findings and Implications

• The coancestry matrix showed a tight genetic relationship between the bay and chestnut subpopulations.
• Before adjustment, there was little differentiation between the groups, but after adjustment, the white, roan, and grey individuals appeared less differentiated.
• Standardization demonstrated that balancing coat colors would contribute to preserving the breed’s genetic diversity.
• Size standardization increased global genetic diversity by 12.5%, showing that increasing the proportions of less common coat colors would be beneficial for the breed’s genetic diversity.
• The methodology utilized in this study could also be valuable for investigating the genetic structures of different unevenly-sized subpopulations and predicting their genetic importance based on their contribution to genetic variability.