Genome‐wide association study reveals regions associated with gestation length in two pig populations

Hidalgo, A.M.; Lopes, M.S.; Harlizius, B.; Bastiaansen, J.W.M.

doi:10.1111/age.12395

Cited by 10 publications

(9 citation statements)

References 16 publications

(21 reference statements)

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“…The development of single nucleotide polymorphism (SNP) panels has provided the opportunity to narrow down the confidence interval and to identify novel associated variants via genome‐wide association studies (GWASes) (Hidalgo et al . ). However, very few studies have been performed to identify the related genes and mutations on a genome‐wide scale for ear size in sheep (Jawasreh et al .…”

Section: Suggestively Significant (005mentioning

confidence: 97%

Genome‐wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed

et al. 2018

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Microtia is a congenital deformity of the outer ear with phenotypes varying from a small auricle to total absence (anotia). The genetic basis is still poorly understood, and very few studies have been performed in sheep. Valle del Belice sheep is a breed showing microtia. The aim of this study was to identify the potential genomic regions involved in microtia in sheep. A total of 40 individuals, 20 with microtia and 20 normal, were genotyped with the Illumina OvineSNP50 BeadChip. The comparison among the results from a genome-wide association study, Fisher's exact test and F analysis revealed a single strong association signal: rs419889303 on chromosome 1, located within intron 3 of the CLRN1 gene. Our study suggests for the first time that this novel candidate gene is responsible for microtia in sheep. Additional analysis based on the sequencing would help confirm our findings and allow for the proposal of a precise genetic basis for microtia in sheep.

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Section: Suggestively Significant (005mentioning

confidence: 97%

Genome‐wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed

et al. 2018

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“…; Hidalgo et al . ). The objective of the current study was to identify markers and genomic regions that are associated with GL in maternal line females at different parities.…”

Section: Single Marker Association Results Between Snps That Explainementioning

confidence: 97%

A genome‐wide association study for gestation length in swine

et al. 2019

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Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska-Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1-GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions. Chromosome:position in number of base pairs. 2 Percentage of additive genetic variance explained. 3Least squares means estimates with matching superscripts differ significantly (P < 0.01). The alleles, 1 or 2, were designated by alphabetical order. 4 P-value for the overall test effect of genotypes.

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“…With the development of high throughput SNP genotyping technologies, the GWAS has become a routine approach for investigating mutations underlying complex traits. Results from the GWAS have been successfully applied in identifying functional genes involved in important economical traits in pigs [15,16]. Numerous candidate SNP loci associating with respective target traits have been identified by the GWAS.…”

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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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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Genome‐wide association study reveals regions associated with gestation length in two pig populations

Cited by 10 publications

References 16 publications

Genome‐wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed

Genome‐wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed

A genome‐wide association study for gestation length in swine

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

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