Investigation of Gene Variants across More Than 60 Pig Breeds and Populations and Other Species Using Whole-Genome Sequencing Datasets.

Polymorphisms in the human gene determine the major blood classification system based on the three well-known forms: ; ; and . In pigs that carry only two main alleles in this gene ( and ), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the gene in different species, pig breeds, and populations and provide (i) a comprehensive distribution of the and alleles, (ii) evolutionary relationships of gene sequences across species, and (iii) an exploratory evaluation of the effect of the different gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele is likely under balancing selection, present in all species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions.