Combining genome-wide association analyses and gene interaction networks to reveal new genes associated with carcass traits, meat quality and fatty acid profiles in pigs

Amaral, Andreia J.; Bressan, Maria Cristina; Almeida, José; Bettencourt, C. M. V.; Moreira, Olga; Sá, João Moura e; Gama‐Carvalho, Margarida; Bessa, Rui J. B.; Gama, L. T.

doi:10.1016/j.livsci.2018.12.025

Cited by 9 publications

(7 citation statements)

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“…The results of genotyping using the Illumina 50K SNP chip showed that only about 68% of the assayed SNPs are polymorphic for this breed, which is in accordance with other studies with local cattle breeds that were not included in the SNP chip discovery panel [14,17], and indicate that ascertainment bias may be a concern when SNP chips are applied to minor breeds.…”

Section: Discussionsupporting

confidence: 88%

“…This was carried out based on the information reported for humans and only cattle orthologous genes were considered for the networks. The Reactome database was used ( ) to perform analyses of pathway enrichment as described in [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

“…The p-values were then corrected by multiplying observed p-values by the deflation factor λ obtained in GWAS [29]. We used the two higher level genome-wide significance thresholds defined by Teyssedre et al (2012) [30] and used by [14,29,31]. The used thresholds were 5 × 10 −6 and 5 × 10 −5 , where the first corresponds to 10,000 independent Bonferroni corrected tests and the second was proposed as the threshold allowing the detection of moderate associations [30].…”

Section: Association Analysismentioning

confidence: 99%

“…In this study, we used the 50K v3 Illumina Beadchip to assess the threats to genetic diversity in Ramo Grande, by estimating the occurrence of ROH, as well as the levels of LD and the corresponding Ne in past generations. Moreover, in order to identify polymorphisms significantly associated with relevant traits, we used a genome-wide association analysis, and investigated the functional impact of the identified associations by examining gene-interaction networks, allowing a better understanding of the genetic influences and candidate genes affecting the traits of interest [14].…”

Section: Introductionmentioning

confidence: 99%

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Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Amaral

Pavão

Gama

2020

Animals

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Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

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Section: Discussionsupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Association Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Amaral

Pavão

Gama

2020

Animals

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“…To better understand the genetic basis for variation in phenotypic traits in local pig breeds, several genome-wide association studies focused on detecting possible associations of loci with different phenotypic attributes, such as morphological, production or meat quality traits (11)(12)(13)(14). However, these studies worked with small number of samples, increasing the risk to give false negative results due to low statistical power (15).…”

Section: Introductionmentioning

confidence: 99%

Discovering genomic regions associated with the phenotypic differentiation of European local pig breeds

Poklukar

Mestre

Škrlep

et al. 2022

Preprint

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BackgroundIntensive selection of modern pig breeds resulted in genetic improvement of productive traits while local pig breeds remained less performant. As they have been bred in extensive systems, they have adapted to specifical environmental conditions resulting in a rich genotypic and phenotypic diversity. In this study, European local pig breeds were genotypically and phenotypically characterised using DNA-pool sequencing data and breed level phenotypes related to stature, fatness, growth and reproductive performance traits. These data were analysed using a dedicated approach to detect selection signatures linked to phenotypic traits in order to uncover potential candidate genes that may be under adaptation to specific environments.ResultsGenetic data analysis of European pig breeds revealed four main axes of genetic variation represented by Iberian and modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian and Portuguese Alentejano breeds. Principal component analysis of phenotypic data distinguished between larger and leaner breeds with better growth potential and reproductive performance on one hand and breeds that were smaller, fatter, and had low growth and reproductive efficiency on the other hand. Linking selection signatures with phenotype identified 561 significant genomic regions. Among them, several regions contained candidate genes with possible biological effect on stature, fatness, growth and reproduction performance traits. For example, strong associations were found for stature in two regions containing ANXA4 and ANTXR1 genes, for growth performance containing TLL1 gene, for fatness containing DNMT3A and POMC genes and for reproductive performance containing HSD17B7 gene.ConclusionsThe present study on European local pig breeds used a newly developed approach for searching selection signatures supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems. Results can be useful to define conservation programs of local pig breeds.

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Genetic Bases of Complex Traits: From Quantitative Trait Loci to Prediction

Ahmadi

2022

Methods in Molecular Biology

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Combining genome-wide association analyses and gene interaction networks to reveal new genes associated with carcass traits, meat quality and fatty acid profiles in pigs

Cited by 9 publications

References 62 publications

Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Discovering genomic regions associated with the phenotypic differentiation of European local pig breeds

Genetic Bases of Complex Traits: From Quantitative Trait Loci to Prediction

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