Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances

Li, X; Yang, Shulin; Dong, Kunzhe; Tang, Zhonglin; Li, K; Fan, Bin; Wang, Z; Liu, B

doi:10.1111/age.12574

Cited by 9 publications

(8 citation statements)

References 47 publications

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“…The most frequent long ROH island in Western pig breeds contained the ADAMTSL3 gene, which was previously identified as having a strong selection signal for body length in Yorkshire pigs (Li et al . ). Correspondingly, a reproduction‐trait‐related gene, PRM1, was included in the Chinese pigs’ most significant long ROH island, which was discovered in a region with high haplotype similarity shared among Chinese indigenous pigs (Wang et al .…”

Section: Discussionmentioning

confidence: 97%

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Zhang

Xiao

et al. 2018

Animal Genetics

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Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reducedrepresentation sequencing method. After imputation and quality control, 60 850 highconfidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH-related variables were compared between imputed and non-missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction-related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.

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Section: Discussionmentioning

confidence: 97%

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Zhang

Xiao

et al. 2018

Animal Genetics

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“…We found the ADAMTS Like 3 (ADAMTSL3) gene at 52-53 Mb on SSC7. ADAMTSL3 is a member of the ADAMTS superfamily of proteins, and this gene was previously reported as a candidate gene for body length in Large White pigs (Li et al, 2017) and height in humans (Weedon et al, 2008). In addition, we located the Cytoplasmic Polyadenylation Element Binding Protein 1 (CPEB1) gene at 52-53 Mb on SSC7.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

et al. 2022

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A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

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“…These genes may have played a crucial role in duck domestication by altMangmoolering glucose and lipid metabolism. Differences in glucose and lipid metabolism between wild and domesticated animals due to directional selection were also observed in pigs [25] and chickens [3]. Enpp3 and Prkar2b were identi ed as the targets of selection during the domestication of Pekin ducks and other indigenous Chinese ducks [26,27].…”

Section: Selection For Domesticationmentioning

confidence: 96%

Whole-genome Resequencing Provides Insights into the Population Structure and Domestication Signatures of Ducks in Eastern China

Feng

Zeng

Yang

et al. 2020

Preprint

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Background: Ducks are an ancient domesticated animal with high economic value, uesd for its meat, eggs, and feathers. However, the origin of indigenous Chines ducks remains elusive. To address this question, we performed whole-genome resequencing to explore the genetic relationships among the domestic ducks and wild ducks in eastern China and to identify the genomic differences shaped by artificial selections. Results: The whole genomes of 60 ducks from eastern China were sequenced, with an average effective sequencing depth of ~6× per individual. The results of population and demographic analysis indicate that all individuals from the same breed gather together, and domestic ducks form a cluster separating from wild ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks.Conclusion: Genetic structure analysis showed that the domesticated ducks were not direct descendants of the mallard or Spot-billed duck and probably originated from an unknown population. During the long history of artificial selection, domesticated ducks have developed a complex biological adaptation to captivity.

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Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances

Cited by 9 publications

References 47 publications

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

Whole-genome Resequencing Provides Insights into the Population Structure and Domestication Signatures of Ducks in Eastern China

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