Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs

Huang, Min; Zhang, H.; Wu, Zhongzhen; Wang, X.P.; Li, D.S.; Liu, S.J.; Zheng, Sumei; Yang, Lin; Liu, B.B.; Li, G.X.; Jiang, Yongchuang; Chen, Hao; Ren, Jun

doi:10.1016/j.animal.2021.100354

Cited by 11 publications

(8 citation statements)

References 35 publications

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“…For a better comparison, similar to a previous study ( 30 ), we defined the ROH hotspots with a frequency of SNP occurrences exceeding 80% (top 1.96% in AD pigs and top 1.46% in CD pigs) as significant regions putatively under selection. In addition, we retrieved the 50 K SNP data of 11 European wild boars (EWB) from a previous study ( 43 ). Following the quality control mentioned above (MAF > 0.01), a total of 34,196 SNPs remained.…”

Section: Methodsmentioning

confidence: 99%

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Wang

Ruan

et al. 2022

Front. Vet. Sci.

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Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

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Section: Methodsmentioning

confidence: 99%

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Wang

Ruan

et al. 2022

Front. Vet. Sci.

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“…Nucleotide diversity (π) was calculated using VCFtools v0.1.13 (Danecek et al 2011). PLINK v1.90 (Purcell et al 2007) was used to calculated the proportion of polymorphic markers ( P N ), observed heterozygosity ( H o ), expected heterozygosity ( H e ), ROH, and LD for all SNP pairs, following the approach used in previous studies (Huang et al 2020; Huang et al 2021).…”

Section: Methodsmentioning

confidence: 99%

“…The range of nIBD values varied between 0 (indicating no IBD detected) and 1 (indicating all individuals in the group share IBD). The threshold for extreme IBD to be considered as putative introgression windows was set to top 1% of rIBD values (Chen et al 2020; Huang et al 2021).…”

Section: Methodsmentioning

confidence: 99%

Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

Qiu,

Liu,

Huang

et al. 2023

Preprint

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Historically, Chinese indigenous pigs were introduced to Europe centuries ago with the aim of enhancing economically important traits in European breeds. In recent decades, there has been a reciprocal introduction of European commercial breeds to China for indigenous pig breeding. Our study investigated the genomes of 418 pigs, revealing a genomics landscape of bi-directional introgression patterns between Chinese and European pig populations. We noted a common occurrence of incomplete linkage disequilibrium between structural variations (SVs) and adjacent single-nucleotide polymorphisms (SNPs) in our population, suggesting that conventional SNP-based analyses might not adequately capture the effect of SVs. Therefore, we examine both the roles of population-level SNPs and SVs in bi-directional introgression patterns, and highlight a show case centered around theBMP2gene. We identified introgressed haplotypes and SVs originating from Southern Chinese indigenous pigs, dispersing widely across various European pig breeds. Concurrently, we noted that the introgressed European haplotypes and SVs have attained high frequencies in Northern Chinese indigenous breeds, likely contributing to improvements in body size. In summary, these findings underscore the significant role of introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.

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“…Jinhua ( JH ), Chun’an ( CA ), Longyou Black ( LY ), and Shengxian Spotted ( SX ) pigs originated in eastern China and have similar characteristics to other indigenous breeds, e.g., improved meat quality, disease resistance, and high fertility in comparison with intensively-reared commercial pig breeds (e.g., Large white, Landrace, and Duroc pig breeds) [24] , [25] , [26] . These excellent characteristics mark them as the best material to uncover the genetic mechanism of economic traits and support the sustainable development of the pig industry [27] . It is well reported that Chinese indigenous pigs have excellent litter sizes and contribute to the improvement of fertility in intensively-reared commercial pig breeds [28] , [29] .…”

Section: Introductionmentioning

confidence: 99%

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs

Chen

Zhang

Wang

et al. 2022

Computational and Structural Biotechnology Journal

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Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs

Cited by 11 publications

References 35 publications

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs

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