Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs

Wang, Xiaopeng; Zhang, Hui; Huang, Min; Tang, Jiaxi; Yang, Lijuan; Yu, Zhiqiang; Li, Desen; Li, Guixin; Jiang, Yongchuang; Sun, Yanxiao; Wei, Shudong; Xu, Pao; Ren, Jun

doi:10.1111/eva.13124

Cited by 27 publications

(27 citation statements)

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“…To identify the genomic regions with high ROH frequency, we first calculated the frequency of SNP occurrence in the ROH and selected the top 1% among those with the highest frequency (present in at least 33.3% of the samples) ( Figure 3 ). There were four adjacent SNPs on SSC4 at ∼35 Mb with the highest frequency of 60.2%, which is similar to the findings of Wang et al (2021) , but no gene has been mapped in this region according to the reference genome (Sscrofa11.1). Neighboring selected SNPs that constitute regions with the highest frequency of ROH are called ROH islands.…”

Section: Resultssupporting

confidence: 73%

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Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Fang

Hao

et al. 2021

Front. Genet.

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Laiwu pigs, distinguished by their high intramuscular fat of 7–9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1–5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.

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Section: Resultssupporting

confidence: 73%

“…The average H o and H e of this Laiwu pig population were 0.27 and 0.38, respectively. The value of H o is lower than the result reported before (0.284), whereas H e is higher (0.281) ( Wang et al, 2021 ). In addition, the N e of this population was 52.6, which suggests it is quite likely that inbreeding has happened.…”

Section: Resultscontrasting

confidence: 70%

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Fang

Hao

et al. 2021

Front. Genet.

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“…Chinese and EUR pigs in the population structure analysis. Interestingly, LWH pig breed is one of Chinese local pig breed classi ed to NCN also investigated here, which proved to have genetic components introgressed from EUR pigs [52], which supported by genetic evidence and historical evidence that EUR pigs were then introduced to the Shandong province and crossed with local breeds during the colonization of Yantai and Qingdao cities of Shandong Province by Britain and Germany at the early 20th century. Similarly, for PDW, EUR pigs such as Yorkshire were introduced to the Shanghai and crossed with local breeds subsequently since the Opium War with the opening of Shanghai [15].…”

Section: Discussionsupporting

confidence: 72%

Whole-Genome Resequencing Reveals Genetic Structure and Introgression in Chinese Pudong White Pigs

Huang

Wang

et al. 2021

Preprint

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Background: Pudong white (PDW) pigs originating from Shanghai, are the only Chinese indigenous pigs with white coat color except Rongchang (RC) pigs. However, there is limited information about its overall genetic structure, relationship with other breeds especially the East Chinese (ECN) and European pig due to the white coat of PDW. Whole-genome sequencing provides the effective approach to get the unique information of genome. The high-depth whole-genome sequencing data of 26 global pig breeds, European Wild boars (EWB), Chinese Wild boars (CWB) and out group (OUT) were implemented to detect the genetic structure, signature of selection and potential exotic introgression in PDW pigs.Results: The PDW pigs belonging to ECN pigs based on genetic relationship, and harbor lower genetic diversity and higher inbreeding coefficient compared to other Chinese indigenous pigs. Both the f3 and D-statistics analysis demonstrated that PDW pigs shared apparent alleles with Large White (LW) pigs. Then, two statistics, haplotype heat-map, copy number variation (CNV) and rIBD analysis further revealed that PDW pigs carry the same KIT genotype and share haplotypes at PARG-MARCHF8 locus with LW pigs, suggesting that the lineage of European (EUR) pigs in PDW originated from LW pigs. After detecting the KIT mutations in different pig breeds, PDW was confirmed to be same with LW at DUP1, DUP2 and the splicing mutation on intron 17 of KIT which determine the white coat color phenotype in European white pigs.Conclusions: This study shows that ECN pigs crossed with LW pigs after introduced to China about 110-164 years ago, where the offspring carrying KIT genotype that caused white coat color phenotype, and then were selected due to the rare white coat color in Chinese indigenous pigs, gradually forming PDW pig breed. To our knowledge, this study gives the first thorough description of the genetic structure of PDW pig via whole-genome resequencing data. This study not only advances our understanding of genetic structure, molecular phylogeny, and molecular origin of PDW pigs, but also provides a basis for facilitating the development of a national project for the conservation and utilization of this unique Chinese local population.

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“…Selection may strongly affect the distribution of ROH, and regions of genomic loci under selection tend to generate a high frequency of ROH (hotspots) (5). An increasing number of studies have confirmed that ROH hotspots are due to positive selection for economically important traits in cattle (6,7), pigs (8)(9)(10), chickens (11,12), goats (13,14), and sheep (15,16). Therefore, the identification and characterization of ROH in a population can provide new insights for uncovering the demographic history and the genetic basis of germplasm characteristics.…”

Section: Introductionmentioning

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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Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 27 publications

References 84 publications

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Whole-Genome Resequencing Reveals Genetic Structure and Introgression in Chinese Pudong White Pigs

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

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