Abstract
Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.
Highlights
Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs
The results show that genealogical coancestry was a very good predictor of molecular coancestry as expected, and, and contrary to what it has been observed in previous studies using microsatellites, molecular coancestry was very accurate in predicting genealogical coancestry
The prediction of genealogical coancestry from single nucleotide polymorphisms (SNPs) was more accurate than that from microsatellites. As it was observed from the analysis using the whole dataset, the prediction of molecular coancestry from genealogical coancestry was more precise than the prediction of genealogical coancestry from molecular coancestry (Figure 3)
Summary
Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. In the specific context of livestock species, the maintenance of genetic diversity is critical for addressing current and future challenges to food security, for rural development and for the environment as stressed in the Interlaken Declaration on Animal Genetic Resources (FAO, 2007). The Iberian breed (Sus scrofa meridionalis) is the most emblematic in the Mediterranean area and one of the most important worldwide from an economic point of view [2]. The breed has an important role in shaping and maintaining the Dehesa, a richly diverse agrosilvopastoral system of great economic and social importance in the southwest of the Iberian Peninsula [4]. Iberian pigs are well adapted to the strong oscillations in feeding and climate conditions, typical of this geographical area, because of their capacity to accumulate fat
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