Genome‐wide association studies for hematological traits in swine

Wang, J. Y.; Luo, Y. R.; Fu, Weixuan; Lü, Xiaohong; Zhou, Jie; Ding, Xiangdong; Liu, J.; Zhang, Q.

doi:10.1111/j.1365-2052.2012.02366.x

Cited by 37 publications

(43 citation statements)

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“…From a statistically significant standpoint, there was an association with serum hemoglobin traits [6], supporting results of an earlier study that showed GYPC to regulate the mechanical stability of red blood cells [7]. According to comparative genomic studies, as well as significant signals in the GWAS, we postulate that the GYPC gene might be a good target gene for serum hemoglobin traits in pigs.…”

Section: Introductionsupporting

confidence: 83%

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A post-genome-wide association study validating the association of the glycophorin C gene with serum hemoglobin level in pig

Liu

Yang

et al. 2017

Asian-Australas J Anim Sci

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ObjectiveThis study aimed to validate the statistical evidence from the genome-wide association study (GWAS) as true-positive and to better understand the effects of the glycophorin C (GYPC) gene on serum hemoglobin traits.MethodsOur initial GWAS revealed the presence of two single nucleotide polymorphisms (SNPs) (ASGA0069038 and ALGA0084612) for the hemoglobin concentration trait (HGB) in the 2.48 Mb region of SSC15. From this target region, GYPC was selected as a promising gene that associated with serum HGB traits in pigs. SNPs within the GYPC gene were detected by sequencing. Thereafter, we performed association analysis of the variant with the serum hemoglobin level in three pig populations.ResultsWe identified one SNP (g.29625094 T>C) in exon 3 of the GYPC gene. Statistical analysis showed a significant association of the SNP with the serum hemoglobin level on day 20 (p<0.05). By quantitative real-time polymerase chain reaction, the GYPC gene was expressed in eight different tissues.ConclusionThese results might improve our understanding of GYPC function and provide evidence for its association with serum hemoglobin traits in the pig. These results also indicate that the GYPC gene might serve as a useful marker in pig breeding programs.

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Section: Introductionsupporting

confidence: 83%

“…Up until now, most genome-wide association studies have identified genomic regions or SNPs associating with erythroid traits in pigs [11,19]. In our initial GWAS, the GYPC gene was identified [6]. …”

Section: Discussionmentioning

confidence: 99%

A post-genome-wide association study validating the association of the glycophorin C gene with serum hemoglobin level in pig

Liu

Yang

et al. 2017

Asian-Australas J Anim Sci

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“…Fortunately this problem could be avoided by fitting the statistical model with the known breeds [38] or the PCs [37]. both of which could correct the population structure, while we ignored this problem in our previous study [39].…”

Section: Resultsmentioning

confidence: 99%

Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

Hao

Plastow

et al. 2017

BMC Genet

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BackgroundPiglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. The current study focused on identifying loci associated with PSL through a genome-wide association study (GWAS) performed with the Illumina Porcine60 SNP Beadchip v2.0. The study was a case/control design with four pig populations (Duroc, Landrace, Yorkshire and one crossbred of Landrace × Yorkshire).ResultAfter quality control of the genotyping data, 185 animals (73 cases, 112 controls) and 43,495 SNPs were retained for further analysis. Principal components (PCs) identified from the genomic kinship matrix were included in the statistical model for correcting the effect of population structure. Seven chromosome-wide significant SNPs were identified on Sus scrofa chromosome 1 (SSC1), SSC2 (2 SNPs), SSC7, SSC15 (2 SNPs) and SSC16 after strict Bonferroni correction. Four genes (HOMER1 and JMY on SSC2, ITGA1 on SSC16, and RAB32 on SSC1) related to muscle development, glycogen metabolism and mitochondrial dynamics were identified as potential candidate genes for PSL.ConclusionsWe identified seven chromosome-wide significant SNPs associated with PSL and four potential candidate genes for PSL. To our knowledge, this is the first pilot study aiming to identify the loci associated with PSL using GWAS. Further investigations and validations for those findings are encouraged.

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“…Genome-wide association studies (GWAS) have been used to identify genetic loci that affect complex traits in pigs, such as traits related to body composition [10], hematology [11], and disease susceptibility [12]. In a previous study, we conducted a large-scale White Duroc × Chinese Erhualian F 2 cross, measured a variety of traits and obtained 60 K genotypes from more than 1000 F 2 individuals.…”

Section: Introductionmentioning

confidence: 99%

Sexually dimorphic genetic architecture of complex traits in a large-scale F2 cross in pigs

Cui

Zhang

et al. 2014

Genet Sel Evol

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BackgroundIt is common for humans and model organisms to exhibit sexual dimorphism in a variety of complex traits. However, this phenomenon has rarely been explored in pigs.ResultsTo investigate the genetic contribution to sexual dimorphism in complex traits in pigs, we conducted a sex-stratified analysis on 213 traits measured in 921 individuals produced by a White Duroc × Erhualian F2 cross. Of the 213 traits examined, 102 differed significantly between the two sexes (q value <0.05), which indicates that sex is an important factor that influences a broad range of traits in pigs. We compared the estimated heritability of these 213 traits between males and females. In particular, we found that traits related to meat quality and fatty acid composition were significantly different between the two sexes, which shows that genetic factors contribute to variation in sexual dimorphic traits. Next, we performed a genome-wide association study (GWAS) in males and females separately; this approach allowed us to identify 13.6% more significant trait-SNP (single nucleotide polymorphism) associations compared to the number of associations identified in a GWAS that included both males and females. By comparing the allelic effects of SNPs in the two sexes, we identified 43 significant sexually dimorphic SNPs that were associated with 22 traits; 41 of these 43 loci were autosomal. The most significant sexually dimorphic loci were found to be associated with muscle hue angle and Minolta a* values (which are parameters that reflect the redness of meat) and were located between 9.3 and 10.7 Mb on chromosome 6. A nearby gene i.e. NUDT7 that plays an important role in heme synthesis is a strong candidate gene.ConclusionsThis study illustrates that sex is an important factor that influences phenotypic values and modifies the effects of the genetic variants that underlie complex traits in pigs; it also emphasizes the importance of stratifying by sex when performing GWAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-014-0076-2) contains supplementary material, which is available to authorized users.

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Genome‐wide association studies for hematological traits in swine

Cited by 37 publications

References 50 publications

A post-genome-wide association study validating the association of the glycophorin C gene with serum hemoglobin level in pig

A post-genome-wide association study validating the association of the glycophorin C gene with serum hemoglobin level in pig

Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

Sexually dimorphic genetic architecture of complex traits in a large-scale F2 cross in pigs

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