Genome‐wide association studies reveal genetic loci associated with plasma cholinesterase activity in ducks

Xu, Yaxi; Liu, Hongyan; Jiang, Yue; Fan, Wenlei; Hu, Jianguo; Zhang, Y.; Guo, Zhanbao; Xie, Ming; Huang, Wei; Liu, X.; Zhou, Zhengkui; Hou, Shuisheng

doi:10.1111/age.12791

Cited by 3 publications

(3 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2018; Xu et al . 2019). Recently, we applied for the first time the genotyping‐by‐sequencing (GBS) method in ducks (Zhu et al .…”

Section: Trait Nbsnp Chr Position (Ps) Maf Beta P‐value Var (%) Candimentioning

confidence: 99%

“…Examining currently available meat quality studies, hundreds of QTL have been curated in pigs, cattle and chickens (Hu et al 2016). However, owing to a lack of microarray and cheap genotyping methods in ducks, few studies have been reported using the whole genome-sequencing data (Zhou et al 2018;Xu et al 2019). Recently, we applied for the first time the genotyping-by-sequencing (GBS) method in ducks (Zhu et al 2016;Deng et al 2019;Zhu et al 2019), which makes it possible to detect meat quality-related QTL.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Genome‐wide association study reveals novel loci associated with fat‐deposition and meat‐quality traits in Pekin ducks

et al. 2020

View full text Add to dashboard Cite

Meat-quality traits play an essential role in meat poultry production. To determine the genetic mechanisms of meat quality in Pekin ducks, we performed a large-scale GWAS to identify quantitative trait loci affecting meat quality in Pekin ducks. We measured 10 traits in 542 Pekin ducks and genotyped each duck using genotyping-by-sequencing. The genetic parameters (genomic heritability, genetic correlation) for 10 meat-quality related traits were evaluated. Based on the large genotype-phenotype dataset, we performed GWASs for all of these traits. A total of 33 significant QTL (P < 3.03 9 10 À5) across 13 chromosomes were identified by loci-based analysis. Some newly identified candidate genes were discovered for fat-deposition and meat-quality traits, including PAG1 for body weight and eviscerated weight, INTU and NUP35 for abdominal fat weight and ratio, NUP3 and ARHGDIB for skin fat weight and ratio, GOLGA5 for breast muscle toughness and breast tenderness, and CTDSPL and PKP1 for breast muscle thickness. The current study is the first systematic report regarding duck meat quality.

show abstract

“…2018; Xu et al . 2019). Recently, we applied for the first time the genotyping‐by‐sequencing (GBS) method in ducks (Zhu et al .…”

Section: Trait Nbsnp Chr Position (Ps) Maf Beta P‐value Var (%) Candimentioning

confidence: 99%

mentioning

confidence: 99%

Genome‐wide association study reveals novel loci associated with fat‐deposition and meat‐quality traits in Pekin ducks

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Examining currently available meat quality studies, hundreds of QTLs have been curated in pigs, cattle, and chickens [ 11 ]. However, owing to a lack of microarrays and cheap genotyping methods in ducks, few studies have been reported using whole genome-sequencing data [ 12 , 13 ]. Recently, we applied for the first time the genotyping-by-sequencing (GBS) method in ducks [ 14 – 16 ], which makes it possible to detect meat quality-related QTLs.…”

Section: Introductionmentioning

confidence: 99%

A novel candidate gene CLN8 regulates fat deposition in avian

Zhang

Sun

et al. 2023

J Animal Sci Biotechnol

View full text Add to dashboard Cite

Background The fat deposition has a crucial role in animal meat flavor, and fat deposition-related traits are vital for breeding in the commercial duck industry. Avian fat-related traits are typical complex phenotypes, which need a large amount of data to analyze the genetic loci. Results In this study, we performed a new phenotypic analysis of fat traits and genotyped whole-genome variations for 1,246 ducks, and combed with previous GWAS data to reach 1,880 ducks for following analysis. The carcass composition traits, subcutaneous fat weight (SFW), subcutaneous fat percentage (SFP), abdominal fat weight (AFW), abdominal fat percentage (AFP) and the body weight of day 42 (BW42) for each duck were collected. We identified a set of new loci that affect the traits related to fat deposition in avian. Among these loci, ceroid-lipofuscinosis, neuronal 8 (CLN8) is a novel candidate gene controlling fat deposition. We investigated its novel function and regulation in avian adipogenesis. Five significant SNPs (the most significant SNP, P-value = 21.37E−12) and a single haplotype were detected in the upstream of CLN8 for subcutaneous fat percentage. Subsequently, luciferase assay demonstrated that 5 linked SNPs in the upstream of the CLN8 gene significantly decreased the transcriptional activity of CLN8. Further, ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype. A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were constructed, and the core promoter area of CLN8 was finally identified in the −1,884/−1,207 bp region of the 5′ flanking sequences, which contains adipogenesis-related transcription factors binding sites. Moreover, the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in ICPs. Consistent with these, the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process during the adipogenesis was significantly enriched. Conclusions Our results demonstrated that CLN8 is a positive regulator of avian adipocyte differentiation. These findings identify a novel function of CLN8 in adipocyte differentiation, which provides important clues for the further study of the mechanism of avian fat deposition.

show abstract

A novel candidate gene CLN8 regulates fat deposition in avian

Zhang

Sun

et al. 2022

Preprint

View full text Add to dashboard Cite

Background The fat deposition has a crucial role in animal meat flavor, and fat deposition-related traits are vital for breeding in the commercial duck industry. Avian fat-related traits are typical complex phenotypes, which need a large amount of data to analyze the genetic loci. Results In this study, we newly phenotyped fat traits and genotyped whole-genome variations for 1246 ducks, and combed with previous GWAS data to reach 1880 ducks for following analysis. The carcass composition traits, subcutaneous fat weight (SFW), subcutaneous fat percentage (SFP), Abdominal fat weight (AFW), Abdominal fat percentage (AFP) and the body weight of day 42 (BW42) for each duck were collected. We identified a set of new loci that affect the traits related to fat deposition in avian. Among these loci, Ceroid-lipofuscinosis, neuronal 8 (CLN8) is a novel candidate gene controlling fat deposition. We investigated its novel function and regulation in avian adipogenesis.Five significant SNPs and a single haplotype were detected in the upstream of gene CLN8 and the most significant SNP (P-value = 21.37E-12) for subcutaneous fat percentage was obtained. Subsequently, luciferase assay demonstrated that five linkage mutations in the upstream of the CLN8 gene significantly decreased the transcriptional activity of CLN8. Further, ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype. A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were constructed, and the core promoter area of CLN8 was finally identified in the − 1884/-1207 bp region of the 5′ flanking sequences, which contains adipogenesis-related transcription factors binding sites. Moreover, the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in ICPs. Consistent with these, the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process during the adipogenesis was significantly enriched. Conclusions Our results demonstrated that CLN8 is a positive regulator of avian adipocyte differentiation. These findings identify a novel function of CLN8 in adipocyte differentiation, which provides important clues for the further study of the mechanism of avian fat deposition.

show abstract

Genome‐wide association studies reveal genetic loci associated with plasma cholinesterase activity in ducks

Cited by 3 publications

References 28 publications

Genome‐wide association study reveals novel loci associated with fat‐deposition and meat‐quality traits in Pekin ducks

Genome‐wide association study reveals novel loci associated with fat‐deposition and meat‐quality traits in Pekin ducks

A novel candidate gene CLN8 regulates fat deposition in avian

A novel candidate gene CLN8 regulates fat deposition in avian

Contact Info

Product

Resources

About