A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth

Chen, Biao; Xu, Jiguo; He, Xiaomei; Xu, Haiping; Li, Guihuan; Du, Hongwu; Nie, Qinghua; Zhang, Xiquan

doi:10.1371/journal.pone.0137087

Cited by 42 publications

(39 citation statements)

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“…(NA: BWA did not detect any BAM alignment across the reference provided.) [17,[42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60] analyzing sequencing data derived from PacBio RS II and Illumina MiSeq sequencing technologies. The only difference detected in our assembled locus sequence relative to the Gallus Gallus (v5) is a 5 bp insertion in the intronic region of chIFITM3.…”

Section: Discussionmentioning

confidence: 99%

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

et al. 2017

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BackgroundInterferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. The chicken IFITM (chIFITM) genes are clustered on chromosome 5 and to date four genes have been annotated, namely chIFITM1, chIFITM3, chIFITM5 and chIFITM10. However, due to poor assembly of this locus in the Gallus Gallus v4 genome, accurate characterization has so far proven problematic. Recently, a new chicken reference genome assembly Gallus Gallus v5 was generated using Sanger, 454, Illumina and PacBio sequencing technologies identifying considerable differences in the chIFITM locus over the previous genome releases.MethodsWe re-sequenced the locus using both Illumina MiSeq and PacBio RS II sequencing technologies and we mapped RNA-seq data from the European Nucleotide Archive (ENA) to this finalized chIFITM locus. Using SureSelect probes capture probes designed to the finalized chIFITM locus, we sequenced the locus of a different chicken breed, namely a White Leghorn, and a turkey.ResultsWe confirmed the Gallus Gallus v5 consensus except for two insertions of 5 and 1 base pair within the chIFITM3 and B4GALNT4 genes, respectively, and a single base pair deletion within the B4GALNT4 gene. The pull down revealed a single amino acid substitution of A63V in the CIL domain of IFITM2 compared to Red Jungle fowl and 13, 13 and 11 differences between IFITM1, 2 and 3 of chickens and turkeys, respectively. RNA-seq shows chIFITM2 and chIFITM3 expression in numerous tissue types of different chicken breeds and avian cell lines, while the expression of the putative chIFITM1 is limited to the testis, caecum and ileum tissues.ConclusionsLocus resequencing using these capture probes and RNA-seq based expression analysis will allow the further characterization of genetic diversity within Galliformes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3801-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

et al. 2017

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“…Even though increasing numbers of SNPs, genes and regions have been found to be associated with chicken skeletal muscle development by GWAS, none of the new candidate genes has been verified to be involved in skeletal muscle development. The significant associated loci identified in the genome by these studies are very different, indicating that the loci associated with muscle [58] . This could be because the mRNA level of FOXO3 is expressed more highly in the skeletal muscle of XH than that in WRR chickens, and reduced FOXO3 expression can upregulate growth-related genes expression in DF-1 cells [58] .…”

Section: Single Nucleotide Polymorphisms In the Myogenic Genes Relatementioning

confidence: 73%

“…The significant associated loci identified in the genome by these studies are very different, indicating that the loci associated with muscle [58] . This could be because the mRNA level of FOXO3 is expressed more highly in the skeletal muscle of XH than that in WRR chickens, and reduced FOXO3 expression can upregulate growth-related genes expression in DF-1 cells [58] . In addition to WRR and XH chickens, skeletal muscle from sex-linked dwarf (SLD) chicken and normal chicken have been used to discover genes or pathways related to chicken muscle development [59,60] .…”

Section: Single Nucleotide Polymorphisms In the Myogenic Genes Relatementioning

confidence: 73%

The genetic regulation of skeletal muscle development: insights from chicken studies

Luo¹,

Abdalla²,

Nie³

et al. 2017

Front. Agr. Sci. Eng.

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Skeletal muscle development is a complex multi-process trait regulated by various genetic factors. The chicken embryo is an ideal model system for studying skeletal muscle development. However, only a small proportion of the genetic factors affecting skeletal muscle development have been identified in chicken. The aim of this review is to summarize recent knowledge about the genetic factors involved in the regulation of skeletal muscle development in the chicken, such as gene polymorphisms, epigenetic modification, noncoding RNAs and transcription factors, which can influence skeletal muscle development at the genome, epigenome, transcriptome and proteome levels. Research on the regulation of skeletal muscle development in chicken is not yet comprehensive and most of the candidate genes and single nucleotide polymorphisms related to chicken muscle growth remain to be verified in experimental studies. In addition, the data derived from transcriptome sequencing and genome-wide association studies still require further investigation and analysis and comprehensive studies on the regulation of chicken skeletal muscle development will continue as a major research focus.

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“…GH and IGF‐1 were suggested to regulate growth rate and body weight (Jia et al, ). FOXO3 was also reported to influence chicken growth (Chen et al, ). However, the underlying molecular mechanism of meat growth and quality remains poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Small RNA sequencing of pectoral muscle tissue reveals microRNA‐mediated gene modulation in chicken muscle growth

Zhang

Qiu

et al. 2020

Animal Physiology Nutrition

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Sichuan mountainous black‐bone (SMB) chicken is a small‐sized black‐feathered chicken breed with low amount of meat, while Dahen (DH) chicken has a larger body size and a faster growth rate. MicroRNAs (miRNAs) are involved in various physiological processes, but their role in chicken muscle growth remains unclear. We aimed to investigate the miRNAs and pathways participating in the muscle growth of chicken. MiRNA profiles of four SMB chickens and four DH chickens were detected by small RNA sequencing. A total of 994 known miRNAs were identified, among which gga‐miR‐1a‐3p, gga‐miR‐148‐3p and gga‐miR‐133a‐3p exhibited the highest enrichment in both breeds of chickens. Thirty‐two miRNAs were differently expressed between SMB and DH chickens. The differently expressed miRNAs were mainly associated with fatty acid metabolism, immunity and MAPK activation‐related processes. Kyoto encyclopaedia of genes and genomes (KEGG) analysis showed that miRNAs were involved in the immunity‐related and MAPK signalling pathways. Moreover, miR‐204 was downregulated in DH chicken compared with SMB chicken, and significantly inhibited the expression of MAP3K13, which is involved in the MAPK pathway. It was confirmed through luciferase reporter assays that miR‐204 specifically inhibited the activity of MAP3K13. Our results helped demonstrate the potential molecular mechanisms of muscle growth in chickens and provide valuable information for chicken breeding.

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A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth

Cited by 42 publications

References 50 publications

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes

The genetic regulation of skeletal muscle development: insights from chicken studies

Small RNA sequencing of pectoral muscle tissue reveals microRNA‐mediated gene modulation in chicken muscle growth

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