Genetic structure and gene flows within horses: a genealogical study at the french population scale

Abstract

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.

Figure 1. Current gene flows and founder origins for the three categories Race and riding horses (blue), Pony (green) and Draught Horses (pink).

Number of individuals (2002–2011) in parenthesis.

Figure 2. Phenogram of relations between the 55 breed origins, based on 1 – coancestry rate.

Figure 3. Current gene flows and founder origins for Race and riding horses populations.

Parental gene flows under 1% are not presented here. Number of individuals (2002–2011) in parenthesis.

Figure 4. Relation between genealogical coancestry rates and molecular Reynold distances based on relation matrix of 32 horse breeds.

Blue cross represent breed pairs with coancestry larger than 0, red circles represent breeds pairs with coancestry equal to 0.