Genome‐wide association studies for two exterior traits in Chinese Dongxiang spotted pigs

Wang, Chengbin; Wang, Xiaopeng; Tang, Jiaxi; Chen, Hao; Zhang, Junjie; Li, Yiping; Lei, Shengrong; Ji, Huayuan; Yang, Bin; Ren, Jun; Ding, Nengshui

doi:10.1111/asj.13003

Cited by 7 publications

(5 citation statements)

References 27 publications

(25 reference statements)

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“…The most notable observation is the locus around 30.6 Mb on chromosome 7, which shows significant effects on multiple growth and carcass traits. It is needed to mention that the region on chromosome 7 was also identified in other local Chinese pig populations that have completely different genetic background with Bamaxiang pigs, these included Duroc × Erhualian F 2 resource population and Erhualian (He et al, ) and Dongxiang spotted pigs (Wang et al, ). However, the region was not identified for respective traits in pig breeds of mainly European origin like Large White and Landrace and Duroc, Cerdo Iberico, Large Black, Hampshire, Pietrain, and Schwabisch‐Hallisch (Rothammer et al, ), which suggested that the QTL segregate in Chinese indigenous pigs but not in the commercial pigs like Duroc, Large White and Landrace or above‐mentioned European indigenous pigs.…”

Section: Discussionmentioning

confidence: 99%

Unravelling the genetic loci for growth and carcass traits in Chinese Bamaxiang pigs based on a 1.4 million SNP array

Gong

Xiao

et al. 2018

J Animal Breeding Genetics

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Bamaxiang pig is from Guangxi province in China, characterized by its small body size and two‐end black coat colour. It is an important indigenous breed for local pork market and excellent animal model for biomedical research. In this study, we performed genomewide association studies (GWAS) on 43 growth and carcass traits in 315 purebred Bamaxiang pigs based on a 1.4 million SNP array. We observed considerable phenotypic variability in the growth and carcass traits in the Bamaxiang pigs. The corresponding SNP based heritability varied greatly across the 43 traits and ranged from 9.0% to 88%. Through a conditional GWAS, we identified 53 significant associations for 35 traits at p value threshold of 10−6. Among which, 26 associations on chromosome 3, 7, 14 and X passed a genomewide significance threshold of 5 × 10−8. The most remarkable loci were at around 30.6 Mb on chromosome 7, which had growth stage‐dependent effects on body lengths and cannon circumferences and showed large effects on multiple carcass traits. We discussed HMGA1 NUDT3, EIF2AK1, TMEM132C and AFF2 that near the lead SNP of significant loci as plausible candidate genes for corresponding traits. We also showed that including phenotypic covariate in GWAS can help to reveal additional significant loci for the target traits. The results provide insight into the genetic architecture of growth and carcass traits in Bamaxiang pigs.

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Section: Discussionmentioning

confidence: 99%

Unravelling the genetic loci for growth and carcass traits in Chinese Bamaxiang pigs based on a 1.4 million SNP array

Gong

Xiao

et al. 2018

J Animal Breeding Genetics

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“…The phenotypic values were regressed on sex and batch, and the residuals were used as the new phenotypes. Then, a univariate linear mixed model regression was executed with phenotypic trait, genotype, and relatedness matrix files (Wang et al, 2018). The threshold of genomic significance was set by the Bonferroni method: 0.05/the number of tested SNPs (Yang et al, 2005).…”

Section: Methodsmentioning

confidence: 99%

Whole-Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs

Zheng

Huang

et al. 2019

Front. Genet.

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The Duroc × (Landrace × Large White) hybrid pig (DLY) is the most popular commercial pig used in the Chinese pig industry. DLY pigs are usually white but sometimes show colored phenotypes. Colored DLY pigs are not favored by slaughterhouses and retailers, thus causing certain economic losses to farmers in China. In this study, we first conducted a genome-wide association study and RNA sequencing to demonstrate that KIT variants are responsible for diversifying coat color phenotypes segregating in a DLY population. We then defined the precise sizes and locations of four duplications (DUP1-4), four candidate causative mutations at the KIT locus, in the pig reference genome using the whole-genome sequence data of representative colored individuals. The sequence data also enabled us to identify a list of new KIT alleles. By investigating the association between these new alleles and coat color phenotypes, we provide further evidence that DUP2 is another causative mutation for the solid white coat color in pigs. DUP1 (the KIT gene duplication), DUP2 and the splice mutation are all required for the manifestation of a solid white coat color. DUP4 had a more significant effect on the formation of the belt phenotype compared with DUP3. Given the necessity of DUP2 for the solid white coat color, we detected IN/IN homozygotes lacking DUP2 in Large White and Landrace pigs and found that French Landrace pigs had the highest frequency (8.98%) of IN/IN individuals. This study not only advances our understanding of the molecular mechanism of the color phenotype in pigs, but also establishes a simple and accurate method for the screening of KIT IN/IN homozygotes in Large White and Landrace that would cause colored DLY pigs.

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“…Samples were collected from ear tissues of 96 Dongxiang spotted pigs as described in our previous report [19]. Briefly, these 96 pigs were sampled from the nucleus population of Dongxiang spotted pigs in a national conservation farm in Dongxiang county, Jiangxi Province, China.…”

Section: Methodsmentioning

confidence: 99%

“…DNA quality was measured by spectrophotometry and agarose gel electrophoresis and was finally diluted to a concentration of 50 ng/μL. All 96 pigs were genotyped with a customized Affymetrix Axiom Pig1.4M array plate as previously described [19]. Briefly, a total of 1,362,630 SNPs were successfully genotyped for these 96 pigs.…”

Section: Methodsmentioning

confidence: 99%

Identification of copy number variations using high density whole-genome single nucleotide polymorphism markers in Chinese Dongxiang spotted pigs

Wang

Chen

Wang

et al. 2019

Asian-Australas J Anim Sci

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ObjectiveCopy number variations (CNVs) are a major source of genetic diversity complementary to single nucleotide polymorphism (SNP) in animals. The aim of the study was to perform a comprehensive genomic analysis of CNVs based on high density whole-genome SNP markers in Chinese Dongxiang spotted pigs.MethodsWe used customized Affymetrix Axiom Pig1.4M array plates containing 1.4 million SNPs and the PennCNV algorithm to identify porcine CNVs on autosomes in Chinese Dongxiang spotted pigs. Then, the next generation sequence data was used to confirm the detected CNVs. Next, functional analysis was performed for gene contents in copy number variation regions (CNVRs). In addition, we compared the identified CNVRs with those reported ones and quantitative trait loci (QTL) in the pig QTL database.ResultsWe identified 871 putative CNVs belonging to 2,221 CNVRs on 17 autosomes. We further discarded CNVRs that were detected only in one individual, leaving us 166 CNVRs in total. The 166 CNVRs ranged from 2.89 kb to 617.53 kb with a mean value of 93.65 kb and a genome coverage of 15.55 Mb, corresponding to 0.58% of the pig genome. A total of 119 (71.69%) of the identified CNVRs were confirmed by next generation sequence data. Moreover, functional annotation showed that these CNVRs are involved in a variety of molecular functions. More than half (56.63%) of the CNVRs (n = 94) have been reported in previous studies, while 72 CNVRs are reported for the first time. In addition, 162 (97.59%) CNVRs were found to overlap with 2,765 previously reported QTLs affecting 378 phenotypic traits.ConclusionThe findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.

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Genome‐wide association studies for two exterior traits in Chinese Dongxiang spotted pigs

Cited by 7 publications

References 27 publications

Unravelling the genetic loci for growth and carcass traits in Chinese Bamaxiang pigs based on a 1.4 million SNP array

Unravelling the genetic loci for growth and carcass traits in Chinese Bamaxiang pigs based on a 1.4 million SNP array

Whole-Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs

Identification of copy number variations using high density whole-genome single nucleotide polymorphism markers in Chinese Dongxiang spotted pigs

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