Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

Abstract

We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (FIS), population differentiation (FST), and Nei’s genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher FIS, and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies.

A High Throughput Genotyping Approach Reveals Distinctive Autosomal Genetic Signatures for European and Near Eastern Wild Boar

“…Both parameters displayed values that are in the lower range of what has been reported so far. In this sense, Zhang and Plastow [11] described values of 0.54 (range: 0.35–0.65) and 0.57 (range: 0.35–0.71) for observed and expected heterozygosities in European pig populations genotyped with the Illumina Porcine SNP60 BeadChip. The low heterozygosity values we have observed in Iberian pigs and European and Near Eastern wild boar cannot be explained in terms of limited sampling ( Table S1 ).…”

Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays

“…As shown in Table 1, the CNV number detected per individual varies greatly, ranging from 2 (MS8) to 13 (D2). Chinese indigenous breeds have larger genetic diversity than European breeds [30], and it is expected more CNVs would existed in them. Contrary to expectations, in our study, fewer CNVs per pig were detected in Chinese indigenous and wild pigs (average 5.5) than in the modern commercial breeds (average 10.5).…”

“…Chinese indigenous breeds have larger genetic diversity and higher average heterozygosity than European breeds [30], which can help to detect fruitful breed-specific CNVs which have segregated among different populations in the course of evolution and selection. In the present study, a genome-wide CNV detection based on the PorcineSNP60 BeadChip was performed in 14 individual selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds.…”

Evaluation of quantitative trait loci affecting intramuscular fat and reproductive traits in pigs using marker‐assisted introgression

“…). Zhang & Plastow () reported that the average LD in improved pig breeds extended to 1–3 cM – much larger than those observed in humans (<30 kb) and cattle (<100 kb), but less than in sheep (<10 cM).…”