Candidate Gene Identification of Feed Efficiency and Coat Color Traits in a C57BL/6J × Kunming F2 Mice Population Using Genome-Wide Association Study

Miao, Yuanxin; Soudy, Fathia; Xu, Zhong; Liao, Mingxing; Song, Zhao; Li, Xinyun

doi:10.1155/2017/7132941

Cited by 8 publications

(7 citation statements)

References 55 publications

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“…A previous study reported that TYR showed the greatest level of differential expression in the skin of black versus white chickens [24]. In humans [25][26][27] and mice [28], several genome-wide studies have also shown signals of association for skin or coat color in the genomic regions encompassing the GRM5 and TYR genes. On GGA1, there were three other significant markers close to the RAB38 gene whose products is a Ras-related protein.…”

Section: Discussionmentioning

confidence: 96%

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Mastrangelo

Cendron

Sottile

et al. 2020

Animals

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Simple Summary: In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait.Abstract: Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (F ST ) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and F ST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

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Section: Discussionmentioning

confidence: 96%

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Mastrangelo

Cendron

Sottile

et al. 2020

Animals

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“…However, there was no clear signal associated with the hernia even when the cutoff P value was < 0.05. In consideration of different statistical models that tend to perform differently from various datasets [40], a case-control model implemented in PLINK, which has been previously reported [41], was employed to ascertain the remarkable SNPs associated with inguinal/scrotal hernias, and 7 significant association loci and 2 candidate genes (CPNE5, MAP7D2) were identified. Some studies have reported that case-control analysis by PLINK controlled the population structure and kinship among individuals as covariates to reduce false positives, but the use of covariates and testing markers may cause confounding, which could produce false negatives [42].…”

Section: Discussionmentioning

confidence: 99%

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Zou¹,

Zuo²,

Zhu³

et al. 2017

Oncotarget

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Inguinal and scrotal hernias are the most frequent congenital disorders in pigs, and they may cause severe economic loss in the pig breeding industry. Genetic factors play a significant role in the susceptibility to hernias, but the genetic mechanisms of inguinal/scrotal hernia are poorly understood. In this study, we performed a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) on 120 (59 cases and 61 controls) full and half sib pigs to identify genetic loci underlying variations in inguinal/scrotal hernias. A total of 218,460 high-quality SNPs were generated for further statistical analysis with casecontrols and the farmCPU model. Based on these two methods, a total of 59 SNPs were significantly (P < 0.01) associated with inguinal/scrotal hernia. Finally, 14 novel candidate genes implicated in the defect were identified, and 5 genes (CPNE5, DEGS1, PLCG2, PRKCE and NUAK1) were related to cell apoptosis, which is one of the pivotal pathogenesis factors of inguinal/scrotal hernia. In addition, 4 of them were shown strong associations with the hernia were confirmed in 270 samples (P < 0.05). This finding provides new evidence that genes related to cell apoptosis may be associated with inguinal/scrotal hernias.

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“…Genes suspected to be associated to feed efficiency were extracted, including the Fto gene which is known to be related to obesity (e.g., Church et al, 2009), Stat6 gene which is thought to be related to lipid production (e.g., Ricardo‐Gonzalez et al, 2010) and Phospho1 gene encoding enzyme possibly regulating thermogenesis, insulin resistance and obesity (e.g., Jiang, Chavarria, Yuan, Lodish, & Huang, 2020; Suchacki et al, 2020). Genes previously reported as candidate causal ones for feed efficiency and related traits were also included, such as Etv4 (e.g., Brunes et al, 2021; Weber et al, 2016), Fgd6 (e.g., Ghoreishifar et al, 2020), Fgf10 (e.g., Miao et al, 2017), Ghs r (e.g., Jin et al, 2014) and Igf2bp1 genes (e.g., Chen et al, 2019; Liu, Xu, Lan, Cao, & Pan, 2021). These findings might support the difference in chemical components, feed efficiency and MER between the lines reported by Darhan et al (2017).…”

Section: Resultsmentioning

confidence: 99%

Genetic and genomic analysis of oxygen consumption in mice

Ogawa

Darhan

Suzuki

2022

J Animal Breeding Genetics

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We estimated genetic parameters for oxygen consumption (OC), OC per metabolic body weight (OCMBW) and body weight at three through 8 weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. With respect to OC, estimated direct heritability was moderate (0.32) and the estimated proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance was very low (0.01), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes through selective signature detection with the results of pooled whole‐genome resequencing using pooled DNA samples from high and low OC mice. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP‐binding proteins (Ndufa12, Sdhc, Atp10b, etc.), Prr16 encoding Largen protein, Cry1 encoding a key component of the circadian core oscillator and so on. The results, although careful interpretation must be required, could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement, and therefore feed efficiency.

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Candidate Gene Identification of Feed Efficiency and Coat Color Traits in a C57BL/6J × Kunming F2 Mice Population Using Genome-Wide Association Study

Cited by 8 publications

References 55 publications

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

WITHDRAWN: Genome-wide association analysis of inguinal/scrotal hernia in pigs using specific length amplified fragment (SLAF) sequencing

Genetic and genomic analysis of oxygen consumption in mice

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