Population structure and genome characterization of local pig breeds in Russia, Belorussia, Kazakhstan and Ukraine

Abstract

BackgroundIt is generally accepted that domestication of pigs took place in multiple locations across Eurasia; the breeds that originated in Europe and Asia have been well studied. However, the genetic structure of pig breeds from Russia, Belorussia, Kazakhstan and Ukraine, which represent large geographical areas and diverse climatic zones in Eurasia, remains largely unknown.ResultsThis study provides the first genomic survey of 170 pigs representing 13 breeds from Russia, Belorussia, Kazakhstan and Ukraine; 288 pigs from six Chinese and seven European breeds were also included for comparison. Our findings show that the 13 novel breeds tested derived mainly from European pigs through the complex admixture of Large White, Landrace, Duroc, Hampshire and other breeds, and that they display no geographic structure based on genetic distance. We also found a considerable Asian contribution to the miniature Siberian pigs (Minisib breed) from Russia. Apart from the Minisib, Urzhum, Ukrainian Spotted Steppe and Ukrainian White Steppe breeds, which may have undergone intensive inbreeding, the breeds included in this study showed relatively high genetic diversity and low levels of homozygosity compared to the Chinese indigenous pig breeds.ConclusionsThis study provides the first genomic overview of the population structure and genetic diversity of 13 representative pig breeds from Russia, Belorussia, Kazakhstan and Ukraine; this information will be useful for the preservation and management of these breeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0196-y) contains supplementary material, which is available to authorized users.

Genetic diversity, population structure and phylogenetic relationships of three indigenous pig breeds from Jiangxi Province, China, in a worldwide panel of pigs

“…; Traspov et al . ). Five breeds from North China (Min, Hetao Daer, Laiwu, Bamei and Gansu Tibetan), especially Min, displayed a signature of admixture with European breeds, as evidenced by their paraphyletic grouping patterns in the NJ tree (Fig.…”

Pudong White pig: a unique genetic resource disclosed by sequencing data

“…The white phenotype of the Rongchang pig is a recessive trait (Lai et al, 2007) and there is high conservation-related interest in investigating the origin of the PW breed. Knowledge of the genetic structure, based on genomic data, has been important in revealing the demographic and evolutionary history of pig breeds worldwide (Ai et al, 2013;Herrero-Medrano et al, 2013;Pham et al, 2014;Traspov et al, 2016). However, to date, the genetic structure of PW has scarcely been investigated, despite the specific, desirable qualities of this breed, including high prolificacy, high meat quality and good adaptability.…”

“…Previous studies have implied that the genetic distance of pig breeds from China may be influenced by their geographical distribution (Megens et al, 2008;Traspov et al, 2016). Thus, for further exploration of the relationship between PW and Taihu pig breeds may benefit from the inclusion of more breeds distributed in the area adjacent to Pudong.…”

CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

“…Among the European commercial breeds Duroc, Landrace, and Yorkshire, two AHR gene copies were detected in 46.1, 67.0, and 66.9%, respectively, of the tested population. Previous studies indicated the Landrace and Large White were much more closely related than Duroc at the genome-wide level [54,55], thus the higher proportion in Landrace and Yorkshire compared to Duroc could be attributed to the differences in the genome level among the three breeds. Landrace and Yorkshire were commonly used as maternal pigs, which are selected in the artificial breeding process based on large litter size.…”