agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species

Klees, Selina; Heinrich, Felix; Schmitt, Armin O.; Gültaş, Mehmet

doi:10.3390/biology10080790

Cited by 10 publications

(28 citation statements)

References 62 publications

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“…Numerous studies have shown that SNP variation in coding regions, which affects the sequence of amino acids or the folding of peptide chains by changing codons, can alter certain phenotypic traits of organisms [ 38 – 40 ]. However, the effect of regulatory regions on animal phenotypes may be underestimated, and a growing number of studies have found the effects of regulatory regions on phenotypes [ 41 ]. In recent studies, regulatory regions have also been found to influence individual phenotypes by regulating gene expression.…”

Section: Discussionmentioning

confidence: 99%

A novel candidate gene CLN8 regulates fat deposition in avian

Zhang

Sun

et al. 2023

J Animal Sci Biotechnol

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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.

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Section: Discussionmentioning

confidence: 99%

A novel candidate gene CLN8 regulates fat deposition in avian

Zhang

Sun

et al. 2023

J Animal Sci Biotechnol

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“…Numerous studies have shown that SNP variation in coding regions, which affects the sequence of amino acids or the folding of peptide chains by changing codons, can alter certain phenotypic traits of organisms [38][39][40]. However, the effect of regulatory regions on animal phenotypes may be underestimated, and a growing number of studies have found the effects of regulatory regions on phenotypes [41]. In recent studies, regulatory regions have also been found to in uence individual phenotypes by regulating gene expression.…”

Section: Discussionmentioning

confidence: 99%

A novel candidate gene CLN8 regulates fat deposition in avian

Zhang

Sun

et al. 2022

Preprint

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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.

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“…In our previous work, we have established a pipeline for the detection of rSNPs [6], which requires as input for each species a SNP catalog (as GVF file [26,27]), a reference genome (as fasta file), and gene annotations (as GFF3 file [28]). For all species except for rapeseed, the input data were downloaded from Ensembl Plants [23], with genome assemblies listed in Table 1.…”

Section: Methodsmentioning

confidence: 99%

“…In the search for causality of disease-or trait-associated SNPs, one often encounters regulatory SNPs (rSNPs) that influence the amount of genetic material, and hence play a crucial role in the expression of a phenotype. Compared to SNPs in the exonic regions, predicting the consequences of SNPs in the promoter regions is not as straightforward [3,[6][7][8]. Such consequences could be the disruption or creation of one or more transcription factor binding sites (TFBSs), which can have a major impact on the level of gene transcription.…”

Section: Introductionmentioning

confidence: 99%

“…In our previous studies, we addressed this limited knowledge and created a pipeline for the systematic detection of rSNPs, which we applied to different agriculturally important species such as rapeseed [3], faba bean [7], and various animal species [6]. By creating the database agReg-SNPdb [6], we have provided genome-wide collections of rSNPs for seven different animal species (cattle, pig, chicken, sheep, horse, goat, and dog). In order to extend the available information on rSNPs to additional plant species, we present in this study the database agReg-SNPdb-Plants, which can be considered as an extension of agReg-SNPdb.…”

Section: Introductionmentioning

confidence: 99%

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agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species

Klees

Heinrich

Schmitt

et al. 2022

Biology

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Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (Brassica napus, Helianthus annuus, Hordeum vulgare, Oryza glaberrima, Oryza glumipatula, Oryza sativa Indica, Oryza sativa Japonica, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Triticum turgidum, Vitis vinifera, and Zea mays). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise.

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agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species

Cited by 10 publications

References 62 publications

A novel candidate gene CLN8 regulates fat deposition in avian

A novel candidate gene CLN8 regulates fat deposition in avian

A novel candidate gene CLN8 regulates fat deposition in avian

agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species

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