Genome‐wide analysis suggests multiple domestication events of Chinese local pigs

Peng, Yebo; Cai, Xinyu; Wang, Yuzhan; Liu, Zexuan; Zhao, Yiqiang

doi:10.1111/age.13183

Cited by 7 publications

(4 citation statements)

References 72 publications

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“…We predefined the groups of Chinese pigs according to our previous analysis (Peng et al, 2022) and their geographical origins (Wang et al, 2011) (Supplementary Figure S1). The NJ-tree, t-SNE dimensionality and global ancestry analysis were used to dissect the genetic structure of our samples.…”

Section: Genetic Structure Analysismentioning

confidence: 99%

Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds

et al. 2023

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Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68–98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.

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Section: Genetic Structure Analysismentioning

confidence: 99%

Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds

et al. 2023

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“…The workflow supports either Beagle v5 or greater 51 or shapeit4 v4.2.0 52 . In this study we applied Beagle (v5.2) with the following effective population sizes (Ne): 1000 for the cattle 25 , 358 for water buffalo 25 , 5000 for the African Buffalo 53 , 5000 for the pig 54 , 100 for horse 55 and, 230 for dog 56 .…”

Section: Methodsmentioning

confidence: 99%

The evolution and convergence of mutation spectra across mammals

Talenti,

Wilkinson,

Morrison

et al. 2023

Preprint

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Despite the key role genetic mutations play in shaping phenotypic differences between species, little is currently known about the evolution of germline mutation spectra across mammals. Domesticated species are likely particularly interesting case studies because of their high mutation rates and complex evolutionary histories, which can span multiple founding events and genetic bottlenecks. Here we have developed a new reusable workflow, nSPECTRa, that can undertake the key steps in characterising mutation spectra, from determining ancestral alleles to characterising multiple forms of variation. We apply nSPECTRa to seven species, including several that have undergone domestication, and highlight how nSPECTRa can provide important novel insights into mutation rate evolution. While mutation spectra most often show marked differences between species and even breeds, certain mutation types have risen to a high frequency in subpopulations of different species, indicative of convergent evolution in mutation rates. This includes the previously characterized TCC->TTC change enriched among European humans, which is also enriched among East Asian cattle. We show Indicine cattle are particularly interesting examples of how different mutation spectra segregate within a population and subsequently spread across the globe. Together, this work has important implications for understanding the control and evolution of mammalian mutation rates.

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“…China has a significant advantage in the genetic resources of domestic pigs because it has over one-third of the world's total pig breeds [8]. With its vast territory and diverse geographical environment, China has a wide variety of local pig breeds that have evolved genetic adaptations to different environmental conditions as people have migrated and domesticated them [9]. For example, the different temperatures and altitudes in the north and south have created differences in the size, hair, and physiological regulation of pig populations [10].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China

Wang

Zha

et al. 2023

Animals

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Tunchang pigs are one of the unique black pig breeds in the Hainan province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.

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Genome‐wide analysis suggests multiple domestication events of Chinese local pigs

Cited by 7 publications

References 72 publications

Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds

Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds

The evolution and convergence of mutation spectra across mammals

Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China

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