Valorization of feral pigs in the tropics, from the genetic characterization to the re-domestication

Abstract

Feral pigs may serve as a valuable genetic resource for the future, offering potential interesting gene pool for adaptation to climate change and the preservation of biodiversity. The main objective of this study was to identify the genetic structure of feral pigs from the Caribbean island of Martinique, measure the inbreeding rate of a Creole population re-domesticated in 2016 from captured feral pigs, and evaluate its evolution to the present day. We hypothesized that feral pigs, like Creole breeds of the Americas, have been shaped by a unique cross-breeding process linked to the historical context of the Caribbean. A total of 121 animals were genotyped and 76 were compared with referenced mainstream genotypes and Creole breeds from the Americas. Re-domestication efforts were carried out through a holistic approach, involving researchers, farmers, consultants, and development actors. The results showed that feral and semi-feral pigs in Martinique belong to the creole pig breeds, with more than 20% Iberian genetic admixture. The majority of domesticated pigs groups studied including re-domesticated creole pigs exhibit a significantly lower proportion of runs of homozygosity compared to feral pigs, suggesting a better control of inbreeding, thanks to structured breeding programs. The chosen conservation strategy was the result of a consensus between scientific evidence, practical experience, and field feasibility. A rotational mating system using sire lines among a minimum of five farmers was adopted. This approach is expected to generate, within five years, a pedigree containing information on a total of at least 150 reproducers on 8 generations.

Keywords: Admixture; Conservation strategy; Feral pig; Martinique; Re-domestication.

Fig. 1

Inbreeding coefficient (F) per farm. P-value (P). a, b, c, d: P < 0,001; e, f, g: P < 0,01 ; h : P < 0,05. Breeder 1,2,3 : Re-domesticated feral pigs by three volunteer farmers in the PNRM program; FM: Feral pigs are animals captured by hunters or PNRM staff; SfM: Pigs crossed with feral pigs by farmers and kept on their farms; FamM: Pigs reared in family farms in Martinique; FamP: Pigs raised on family farms that are potential parents of CRM re-domesticated feral pigs; ProM: Pigs that are reared by pig professional farmers; FamG: Pigs reared in family farms in Guadeloupe; INRAE: Creole pigs that are conserved at the INRAE experimental facilities. Each boxplot represents, from top to bottom: the maximum value, the third quartile, the median (in bold), the first quartile, and the minimum value.

Fig. 2

Proportion of the local pigs’genome in ROHs in per farm. P-value (P). a: P < 0,001; b, c, d, e: P < 0,01; f, g: P < 0,005. 194 ROH detected in 65 individuals among the 121 individuals genotyped in Martinique and Guadeloupe. Breeder 1,2,3 : Re-domesticated feral pigs by three volunteer farmers in the PNRM program; FM: Feral pigs are animals captured by hunters or PNRM staff; SfM: Pigs crossed with feral pigs by farmers and kept on their farms; FamM: Pigs reared in family farms in Martinique; FamP: Pigs raised on family farms that are potential parents of CRM re-domesticated feral pigs; ProM: Pigs that are reared by pig professional farmers; FamG: Pigs reared in family farms in Guadeloupe; INRAE: Creole pigs that are conserved at the INRAE experimental facilities. Each boxplot represents, from top to bottom: the maximum value, the third quartile, the median (in bold), the first quartile, and the minimum value.

Fig. 3

PCA of genetic distances between animals genotyped in Martinique and Guadeloupe (The two French Caribbean islands). Breeder 1,2,3 : Re-domesticated feral pigs by three volunteer farmers in the PNRM program; FID: Family identifier, FM: Feral pigs are animals captured by hunters or PNRM staff; SfM: Pigs crossed with feral pigs by farmers and kept on their farms; FamM: Pigs reared in family farms in Martinique; FamP: Pigs raised on family farms that are potential parents of CRM re-domesticated feral pigs; ProM: Pigs that are reared by pig professional farmers; FamG: Pigs reared in family farms in Guadeloupe; INRAE: Creole pigs that are conserved at the INRAE experimental facilities.

Fig. 4

Admixture: From top to bottom (a) unsupervised (K = 10); (b) supervised admixture (K = 8), (c) supervised admixture (K = 10).

Fig. 5

Rotational mating plan with maximum avoidance of inbreeding. Each small circle E represent a herd or a regional group of herds, arrows represent the rotation mating (from the first to the fifth generations for maximum avoidance of inbreeding scheme).

Fig. 6

Geographical distribution of pigs genotyped in Martinique.