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European Pig Genomes Show Influence of Asian Breed Introgression on Litter Size

NEW YORK (GenomeWeb) – During the Industrial Revolution in Europe, pig breeders drew on imported Chinese pigs to increase meat quality and litter size of European breeds.

These signals of introgression can still be seen in European pigs, researchers from the Netherlands and the UK reported in Nature Communications today.

Researchers led by Wageningen University's Martien Groenen sequenced and genotyped 70 Sus scrofa, including both wild boars from Asia and Europe as well as domesticated pigs from Asia and Europe, and uncovered introgressed Asian haplotypes in the European breeds. In particular, the researchers found Asian-derived variants in the AHR gene, which is linked to increased litter size, throughout European pigs.

"Our findings provide a unique insight into the genomic haplotype patterns resulting from breeding practices from first domestication until the intensive breeding industry we know today," Groenen and his colleagues wrote in their paper.

As the Large White breed, a common commercial breed developed in the UK in the late 1800s, is thought to have a hybrid origin, the researchers searched for Asian pig haplotypes throughout its genome. They hypothesized that those haplotypes should be non-randomly distributed throughout the LW genome because of its deliberate introduction and subsequent artificial selection.

Indeed, they found haplotypes in the LW pigs were identical by descent with both European wild boars and Asian domestic pigs. All the LW pig individuals had roughly the same degree of admixture with Asian pigs across their genomes, though most of the LW genomes were, overall, more similar to European wild boars than to domesticated Asian pigs.

Still, some spots along the genome had stronger Asian ancestry signals while others had stronger European ancestry signals. This introgression pattern involving multiple sites suggests that the selection on Asian haplotypes involved complex, multi-genic traits, according to the researchers.

The genomic regions where the LW pigs shared more haplotypes with Asian pigs than with wild European boars are linked with commercial traits like meat quality and development, the researchers reported.

Chromosomes 8 and 9 both contain large consecutive regions of putative introgression, regions that also appear to contain genes associated with reproduction.

The highest peak of Asian haplotypes on chromosome 8 includes the PGRMC2 gene, which codes for the progesterone receptor. The hormone progesterone, they noted, is involved in female reproduction and maternal behavior.

The researchers genotyped a further 5,150 pigs from three European commercial pig lines using the Illumina Porcine 60K iSelect beadchip. Two of those lines had been developed by selecting for reproductive traits, while the other was developed for finishing traits, and those lines show distinct differences in SNP alleles in that region. This, the researchers said, supports the idea that Asian haplotypes in this region could be associated with fertility.

However, a large introgression signal in that same region lacks any annotated genes and underscores the possible role of drift or genetic hitchhiking.

In a region on chromosome 9, the LW haplotypes are nearly identical to haplotypes found in the Asian Jianquhai breed, the researchers said. This region, they added, includes members of the TWIST family, which are known to be involved in processes like embryonic development, as well as the AHR gene, which is linked to both toxicity response and fertility.

In closely related species, the ancestral haplotype — the Asian pig haplotype — is homozygous, and is found at high frequency in both Asian and European domesticated pigs, the researchers said. The derived haplotype, though, was present in European wild boars and at low frequency in Asian wild boars.

"This suggests a history of selection for the ancestral state in domestics, after the derived state reached high frequency in the wild populations," the authors said.

This change at AHR, Groenen and his colleagues found, affects reproductive success. Based on the genotyping data of those 5,150 pigs, they found that the Asian AHR variant was associated with an increase in the estimated breeding value for total number born for all three lines.

"As total number of piglets born is a complex multi-locus trait, an increase of 0.16 piglets born (across all three breeds) is substantial in the current breeding industry," the researchers said. "If the costs of maintaining a sow on a farm are spread over a larger number of piglets being weaned from that sow, the marginal cost reduction of producing a finishing pig is just over 3 euros per extra piglet, that is, 2 [percent] of that total."

This association with increased EBV for total is, the researchers argued, a strong indicator for the allele to be under selection after introgression.