Identification of growth trait related genes in a Yorkshire purebred pig population by genome wide association studies

Meng, Qingkai; Wang, Kejun; Zhou, Haishen; Liu, Xu; Wang, Zhaojun; Fang, Meiying

doi:10.5713/ajas.16.0548

Cited by 37 publications

(29 citation statements)

References 35 publications

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“…Furthermore, MAP2K6 participates in the gonadotropin signalling pathway, which has been identified to be associated with divergent growth traits according to a multiomics analysis in an F 2 Charolais × Holstein population (Widmann et al., ). Regarding pigs, MAP2K6 has been associated with growth traits in the purebred Yorkshire strain (Meng et al., ) and with foot and leg structural soundness traits in domestic pigs in general (Meng et al., ).…”

Section: Discussionmentioning

confidence: 99%

Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

Miao

Wang

Bao³

et al. 2018

J Animal Breeding Genetics

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Bone weight, defined as the total weight of the bones in all the forequarter and hindquarter joints, can reflect somebody conformation traits and skeletal diseases. To gain a better understanding of the genetic determinants of bone weight, we used a composite strategy including multimarker and rare-marker association to perform genomewide association studies (GWAS) for that character in Simmental cattle. Our strategy consisted of three models: (i) A traditional linear mixed model (LMM) was applied (Q+K-LMM); (ii) single nucleotide polymorphisms (SNPs) with p-values less than .05 from the LMM were selected to undergo the least absolute shrinkage and selector operator (Lasso) in the second stage (LMM-Lasso); (iii) genes containing two or more rare SNPs were examined by performing the sequence kernel association test (gene-based SKAT). A total of 1,225 cattle were genotyped with an Illumina BovineHD BeadChip containing 770,000 SNPs. After the quality-control procedures, 1,217 individuals with 608,696 common SNPs and 105,787 rare SNPs (with 0.001 < minor allele frequency [MAF] <0.05) remained in the sample for analysis. A traditional LMM successfully mapped three genes associated with bone weight, while LMM-Lasso identified nine genes, which included all genes found by traditional LMM. Only a single gene, EPHB3, surpassed the significance threshold after Bonferroni correction in gene-based SKAT. In conclusion, based on functional annotation and results from previous endeavours, we believe that LCORL, RIMS2, LAP3, PRKAR2B, CHSY1, MAP2K6 and EPHB3 are candidate genes for bone weight. In general, such a comprehensive strategy for GWAS may be useful for researchers seeking to probe the full genetic architecture underlying economic traits in livestock.

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Section: Discussionmentioning

confidence: 99%

Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

Miao

Wang

Bao³

et al. 2018

J Animal Breeding Genetics

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“…For their use in biomedical research, pigs with small body size are preferred (Michael Swindle, Bradley, & Hepburn, ). Genomewide association studies (GWAS) have helped to identify significant loci for growth and carcass traits in different pig populations including Yorkshire, Duroc and Landrace purebred pigs (Meng et al, ; Sanchez et al, ; Sato et al, ), Duroc × Erhualian F 2 cross and Sutai pigs (Qiao et al, ), and purebred Chinese breeds like Laiwu pigs and Erhualian pigs (He et al, ; Zhou et al, ). These studies provide useful genetic variants that can be used in marker‐assisted selection in pig breeding programmes, as well as candidate genes for understanding molecular mechanism underlying growth and carcass traits in pigs.…”

Section: Introductionmentioning

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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“…Nevertheless, only a handful of quantitative trait nucleotides for these traits have been identified as the confidence intervals of most QTL are greater than 20 cM, hampering the characterization of quantitative trait nucleotides (Tabor et al ). With the emergence of high‐density SNP arrays, GWAS have identified a list of significant loci for growth and fatness traits in different pig populations, including Duroc and Yorkshire pigs (Sato et al ; Meng et al ), Chinese indigenous breeds like Erhualian and Bamaxiang pigs (Zhou et al ; Gong et al ), F 2 intercross populations and Chinese synthetic breeds (Qiao et al ). Significant loci are mainly located on pig chromosomes (SSC) 4 and 7, and a number of candidate genes such as GRM4 , HMGA1 and PLAG1 have been identified at the mapped loci (Qiao et al ; Ji et al ; Gong et al ).…”

Section: Genome‐wide Significant Snps Associated With Two Growth and mentioning

confidence: 99%

Genome‐wide association study for growth and fatness traits in Chinese Sujiang pigs

Tao

et al. 2020

Animal Genetics

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Summary Growth and fatness traits are complex and economically important traits in the pig industry. The molecular basis underlying porcine growth and fatness traits remains largely unknown. To uncover genetic loci and candidate genes for these traits, we explored the GeneSeek GGP Porcine 80K SNP chip to perform a GWAS for seven growth and fatness traits in 365 individuals from the Sujiang pig, a recently developed breed in China. We identified two, 17, one and 11 SNPs surpassing the suggestively significant threshold (P < 1.86 × 10−5) for body weight, chest circumference, chest width and backfat thickness respectively. Of these SNPs, 20 represent novel genetic loci, and five and four SNPs were respectively associated with chest circumference and backfat thickness at a genome‐wide significant threshold (P < 9.31 × 10−7). Eight SNPs had a pleiotropic effect on both chest circumference and backfat thickness. The most remarkable locus resided in a region between 72.95 and 76.27 Mb on pig chromosome 4, harboring a number of previously reported quantitative trait loci related to backfat deposition. In addition to two reported genes (PLAG1 and TAS2R38), we identified four genes including GABRB3, ZNF106, XKR4 and MGAM as novel candidates for body weight and backfat thickness at the mapped loci. Our findings provide insights into the genetic architecture of porcine growth and fatness traits and potential markers for selective breeding of Chinese Sujiang pigs.

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Identification of growth trait related genes in a Yorkshire purebred pig population by genome wide association studies

Cited by 37 publications

References 35 publications

Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

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

Genome‐wide association study for growth and fatness traits in Chinese Sujiang pigs

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