Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds

Wang, Jue; Liu, Chengkun; Chen, Jie; Bai, Ying; Wang, Kejun; Wang, Yubei; Fang, Meiying

doi:10.3390/genes11030275

Cited by 12 publications

(15 citation statements)

References 58 publications

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“…Collectively, these findings revealed the clear signature of admixture of Chinese indigenous pigs with European pigs, especially in Henan indigenous pigs (CDh). This result was also consistent with previous evidence of European pig introgression with MIN pigs (MIN), Laiwu black pigs (LWH), Hetao pigs (HTDE), and Tibetan pigs (TT) (Chen et al, 2020;Wang et al, 2020).…”

Section: Inference Of Population Structuresupporting

confidence: 92%

“…Evidence from TreeMix also indicated significant gene flow from DU into CDh (HN, QS, and NY), consistent with the results of our outgroup-f3 analysis. We also observed weak introgression from DU to MIN, HTDE, TT, and LWH, which was consistent with the previous introgression results based on SNP chip data (Wang et al, 2020).…”

Section: Gene Flow Of Duroc Pigs To Henan Indigenous Pigssupporting

confidence: 92%

“…Moreover, Chinese pigs were imported into America to improve the production performance of American indigenous pigs through crossbreeding, and this accounts for about 33% of the genome on average (Fang and Andersson, 2006). Several studies based on genetic data have revealed evidence for introgression between sub-populations (Yang et al, 2009(Yang et al, , 2014Jiang et al, 2012;Wang et al, 2020). However, the genomic differences and functions introduced by introgression are still not well understood.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

et al. 2021

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Introgression of genetic features from European pigs into Chinese pigs was reported possibly contributing to improvements in productivity traits, such as feed conversion efficiency and body size. However, the genomic differences from European pigs and the potential role of introgression in Henan indigenous pigs remains unclear. In this study, we found significant introgression from European pigs into the genome of Chinese indigenous pigs, especially in Henan indigenous pigs. The introgression in Henan indigenous pigs, particularly in the Nanyang black pig, was mainly derived from Duroc pigs. Most importantly, we found that the NR6A1, GPD2, and CSRNP3 genes were introgressed and reshaped by artificial selection, and these may have contributed to increases in pig body size and feed conversion efficiency. Our results suggest that human-mediated introgression and selection have reshaped the genome of Henan pigs and improved several of their desired traits. These findings contribute to our understanding of the history of Henan indigenous pigs and provide insights into the genetic mechanisms affecting economically important traits in pig populations.

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Section: Inference Of Population Structuresupporting

confidence: 92%

Section: Gene Flow Of Duroc Pigs To Henan Indigenous Pigssupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

et al. 2021

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“…f dM is a conservative version of the f statistic that is particularly appropriate for analysis of small genomic windows ( Malinsky et al, 2018 ). The f dM statistics ( Malinsky et al, 2015 ) was estimated using a sliding window size of 10 SNPs and a step size of two SNPs ( Wang et al, 2020 ) as follows:

Where

stands for the numerator of Patterson’s D, and

is equivalent to the f dM numerator when

and

, depending on which of

populations has the higher frequency of the derived allele. Under the null hypothesis, i.e., no introgression, the f dM value is symmetrically distributed around zero, and it can equally quantify shared variation between P3 and P2 (positive values) or between P3 and P1 (negative values) ( Malinsky et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Vahedi

Ardestani²,

Afshari³

et al. 2022

Front. Genet.

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Genetic introgression from interbreeding hybridization of European Bos taurus taurus (EBT) and Indian Bos taurus indicus (IBI) cattle breeds have been widely used to combine the climatic resilience of the IBI cattle and the higher productivity of EBT when forming new composite beef cattle (CB) populations. The subsequent breeding strategies have shifted their initial genomic compositions. To uncover population structure, signatures of selection, and potential introgression events in CB populations, high-density genotypes [containing 492,954 single nucleotide polymorphisms (SNPs) after the quality control] of 486 individuals from 15 cattle breeds, including EBT, IBI, and CB populations, along with two Bos grunniens genotypes as outgroup were used in this study. Then, in-depth population genetics analyses were performed for three CB breeds of Beefmaster, Brangus, and Santa Gertrudis. Neighbor-joining, principal components, and admixture analyses confirmed the historical introgression of EBT and IBI haplotypes into CB breeds. The fdM statistics revealed that only 12.9% of CB populations’ genetic components are of IBI origin. The results of signatures of selection analysis indicated different patterns of selection signals in the three CB breeds with primary pressure on pathways involved in protein processing and stress response in Beefmaster, cell proliferation regulation and immune response in Brangus, and amino acids and glucose metabolisms in Santa Gertrudis. An average of >90% of genomic regions underlying selection signatures were of EBT origin in the studied CB populations. Investigating the CB breeds’ genome allows the estimation of EBT and IBI ancestral proportions and the locations within the genome where either taurine or indicine origin alleles are under selective pressure. Such findings highlight various opportunities to control the selection process more efficiently and explore complementarity at the genomic level in CB populations.

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“…Previous genome-wide association studies (GWAS) focused on the examination of significant variants and evolutionary genomic analysis to determine the selective genomic regions by comparing the two breeds. Cross-population extended haplotype homozygosity (XP-EHH), cross-population composite likelihood ratio (XP-CLR), and hapFLK were used as selective sweep study methods in these studies (Manunza et al 2016 ; Sun et al 2018 ; Wang et al 2020 ). When a beneficial mutation arises and subsequently spreads in the genome, a selective sweep occurs which generates higher population differentiation, higher frequencies of segregating sites, and linkage disequilibrium (LD) (Grossman et al 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

Lee

Son

Heo

et al. 2021

Animal Cells and Systems

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Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotype associated variant (XP-PAV) analysis as a novel method to determine the genomic variants with different effects between the two populations. XP-PAV analysis could reveal the differential genetic variants between the two populations by considering the gene effect and selection signal simultaneously. In this study, we used daily weight gain (DWG) and back fat thickness (BF) as phenotypes and the Landrace and Yorkshire populations were used for XP-PAV analysis. The main aim was to reveal the differential selection by considering the gene effect between Landrace and Yorkshire pigs. In the gene ontology analysis of XP-PAV results, differential selective genes in DWG analysis were involved in the regulation of interleukin-2 production and cell cycle G2/M transition. The protein modification and glycerophospholipid biosynthetic processes were the most enriched terms in the BF analysis. Therefore, we could identify genetic differences for immune and several metabolic pathways between Landrace and Yorkshire breeds using the XP-PAV analysis. In this study, we expect that XP-PAV analysis will play a role in determining useful selective variants with gene effects and provide a new interpretation of the genetic differences between the two populations.

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Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds

Cited by 12 publications

References 58 publications

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

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