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Identification of molecular pathways and candidate genes associated with cocks' comb size trait by genome-wide transcriptome analysis

ABSTRACT: Identification of molecular pathways and candidate genes associated with cocks' comb size trait by genome-wide transcriptome analysis

PROVIDER: PRJNA421483 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6357660_1.fastq.gz	Fastqsanger.gz
	SRR6357660_2.fastq.gz	Fastqsanger.gz
	SRR6357661_1.fastq.gz	Fastqsanger.gz
	SRR6357661_2.fastq.gz	Fastqsanger.gz
	SRR6357662_1.fastq.gz	Fastqsanger.gz

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Identification of molecular pathways and candidate genes associated with cocks' comb size trait by genome-wide transcriptome analysis

Project description:In this study, RNA sequencing (RNA-seq) was employed to compare the whole transcriptomic differences between six Partridge Shank chickens that are divergent in comb sizes and divided into two groups. A total of 563 differentially expressed genes (DEGs) were found in the two groups. Among these DGEs, 277 were up-regulated and 286 were down-regulated in the big comb group. According to the animal QTL database, eight DEGs including BMP2 and CHADL matched the QTLs associated with the chicken comb traits. Functional annotation analysis revealed that the DEGs were involved in cell communication and calcium signaling. Protein-protein interaction network analysis showed that STK32A, PI3KR1, EDN1, HSPA5 and HSPA8 might have great impact on comb growth. Moreover, potential alternative splicing (AS) events and single nucleotide polymorphisms (SNP) were also identified.

2017-12-08 | GSE107815 | GEO

Genome-wide association analysis and genome resequencing reveal a genomic duplication possibly concerning a novel chicken comb morphology

Project description:Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. After conducting a genome-wide association study (GWAS), a 36.5-kb candidate genomic region (chromosome 19:757,754-794,200) related to the Antler-comb phenotype was identified, which wholly and partially encompassed heat shock factor 5 (HSF5) and ring finger protein 43 (RNF43), respectively. HSF5 was ectopically expressed and RNF43 was up-regulated in Antler-comb chickens at embryo ages 7 and 9 (E7 and E9). We further genotyped the most significant single-nucleotide polymorphism (SNP) site, Chr19:794200, across 222 chickens of 16 breeds. We found that the major allele G in Antler-comb chickens remained highly significant across different breeds, and each Antler-comb chicken harbored an allele G. Whole-genome re-sequencing (WGS) involving 10 Hetian Antler-comb and 10 Wildtype-comb chickens reaffirmed the 36.5-kb candidate genomic region, and revealed a genomic duplication, which was 15.7 kb in length and pertained to the 5’-untranslated region and 5’-flanking region of HSF5 (Chr19:784,335-800,034), suggesting its possible role in inducing ectopic expression of HSF5 and altering expression of RNF43 during comb development (E7 and E9). The present study furthers our understanding of this novel chicken comb phenotype, and likely gives another example regarding interactions between genetic variation and phenotype.

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Identification of molecular pathways and candidate genes associated with cocks' comb size trait by genome-wide transcriptome analysis.

Project description:The comb of the male is an important secondary sexual characteristic. Although quantitative trait loci (QTLs) related to comb size have been identified, molecular mechanisms underlying this trait remain mostly unknown. In this study, RNA sequencing (RNA-seq) was employed to compare whole transcriptomic differences between two groups of Partridge Shank chickens that are divergent in comb sizes. A total of 563 differentially expressed genes (DEGs) were identified, including 277 up-regulated and 286 down-regulated DEGs. According to the animal QTL database, eight DEGs including BMP2 and CHADL matching the reported QTLs were associated with the comb size. Functional annotation analysis revealed that DEGs were involved in cell communication and calcium signaling. Protein-protein interaction network analysis showed that STK32A, PIK3R1, EDN1, HSPA5, and HSPA8 have an impact on comb growth. Moreover, potential alternative splicing events and single nucleotide polymorphisms were also identified. Our data provide a source for identifying genes and pathways with functions critical to comb size and accelerate studies involving molecular mechanisms of this sexual ornament.

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