Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Abstract

Mitochondria follow non‐Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.

Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs

“…In commercial pig breeds, only two alleles of this SNP were found, such as G>A mutation in Large White pigs and the C>G mutation in Duroc pigs, which may be due to the strong artificial selection of commercial pigs (Bosse et al, 2015). Zhang et al performed a comprehensive analysis of the mitogenome of native Henan pig breeds with 58 worldwide pig breeds and identified a mutation (g.314delins T>AC/AT/C) in the 12S rRNA gene that could be used to distinguish Henan pigs from other pig breeds (Zhang et al, 2022). This indicated that the genetic diversity of native pig breeds in China is greater than that of commercial pigs.…”

“…Zhang et al. performed a comprehensive analysis of the mitogenome of native Henan pig breeds with 58 worldwide pig breeds and identified a mutation (g.314delins T>AC/AT/C) in the 12S rRNA gene that could be used to distinguish Henan pigs from other pig breeds (Zhang et al., 2022). This indicated that the genetic diversity of native pig breeds in China is greater than that of commercial pigs.…”

Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations

“…In the absence of a reproductive barrier between East Asian and European domestic pigs, hybridisation between East Asian and European and later American pig breeds has been successfully used to increase pig production [11][12][13]. Previous studies clearly demonstrated a hybrid origin of the European Large White breed with Asian pigs [14].…”