Single Nucleotide Polymorphism in the Promoter Region of BovineInterleukin 8 Gene and its Association with Milk Production Traits andSomatic Cell Score of Holstein Cattle in Iran

Muhaghegh-Dolatabady, M.

doi:10.15171/ijb.1016

Cited by 5 publications

(2 citation statements)

References 24 publications

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“…Recently, rSNPs are gaining attention in life sciences and animal breeding since they can be causal for specific traits and diseases and could, hence, serve as new targets for breeding. For this reason, several studies investigated the critical role of rSNPs in agriculturally important species, such as cattle [ 17 , 18 , 19 , 20 , 21 , 22 , 23 ], pig [ 24 , 25 , 26 ], and chicken [ 27 , 28 , 29 ]. As these studies were focused on the regulatory role of SNPs for a single trait of interest, they were highly case-specific.…”

Section: Introductionmentioning

confidence: 99%

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

Klees

Heinrich

Schmitt

et al. 2021

Biology

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Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.

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Section: Introductionmentioning

confidence: 99%

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

Klees

Heinrich

Schmitt

et al. 2021

Biology

View full text Add to dashboard Cite

show abstract

“…Recently, rSNPs are gaining attention in life sciences and animal breeding since they can be causal for specific traits and diseases and could, hence, serve as new targets for breeding. For this reason, several studies investigated the critical role of rSNPs in agriculturally important species, such as cattle [39,[79][80][81][82][83][84], pig [42,85,86], and chicken [40,41,87]. As these studies were focused on the regulatory role of SNPs for a single trait of interest, they were highly case-specific.…”

Section: Introductionmentioning

confidence: 99%

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

Wilhelmi

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Transcriptional regulation of gene expression in higher organisms is fundamental for numerous biological processes. These processes are mainly controlled by a special class of regulatory proteins, the transcription factors (TFs), and their combinatorial interplay. Various genetic programs, such as environmental adaptation, tissue development, or disease control, are governed by the binding of TFs to short DNA motifs, called transcription factor binding sites (TFBS), in the regulatory regions of their target genes. Single nucleotide polymorphisms (SNPs) located in promoter regions can alter TFBSs leading to a change in the binding affinity of TFs and, thus, affect gene expression. Such SNPs are referred to as regulatory SNPs (rSNPs). In recent years, rSNPs have come into the focus of research, and the underlying mechanisms resulting in a differential gene expression have been studied for many specific traits and diseases mainly in humans or model organisms, but also in agricultural species. However, these studies mostly concentrate on single regulatory variants and do not include systematic analyses. Thus, there is still a lack of such comprehensive analyses and genome-wide collections of rSNPs, and to date, only few tools and databases are available for livestock or crop species. In this work, I developed a pipeline for the detection of rSNPs and created the databases agReg-SNPdb and agReg-SNPdb-Plants, storing genome-wide collections of rSNPs and their predicted effects on TF binding for agricultural animal and plant species, respectively. agReg-SNPdb includes seven livestock and domestic species, namely cattle, pig, chicken, sheep, horse, goat, and dog and agReg-SNPdb-Plants includes 13 crop species and subspecies, namely African rice, Asian rice (with its subspecies Indica and Japonica), barley, bread wheat, durum wheat, grape, maize, rapeseed, sorghum, sunflower, tomato, and wild rice. Out of all species stored in agReg-SNPdb-Plants, rapeseed holds a special role. In contrast to the remaining species, where I used the data from Ensembl Plants as basis, in rapeseed, to date, there is no genome-wide collection of SNPs available. Therefore, I used a previously published data set based on different resequenced Brassica napus L. cultivars for the identification of rSNPs in agReg-SNPdb-Plants. Based on this data set, I investigated the regulatory mechanisms in two cultivars, namely Zhongshuang11 (ZS11), a so-called double-low accession with low content of erucic acid and glucosinolate, which is characterized by high oil content, and Zhongyou821 (ZY821), a so-called double-high accession with high content of erucic acid and glucosinolate, which is characterized by low oil content. In this way, I demonstrate the application of rSNPs together with multi-omics data to perform a systematic analysis of the complex interplay between rSNPs, TFs, and differentially expressed genes (DEGs) in four tissues (flower, leaf, stem, and root) which are underlying the oil content and -quality in rapeseed. viii Es hat mir großen Spaß ...

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Sequence Characterization in 3′-Flanking Region of Bovine TNF-α: Association with Milk Production Traits and Somatic Cell Score in Holstein Cattle of Iran

Muhaghegh-Dolatabady

Rezaei

2018

ijbiotech

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Single Nucleotide Polymorphism in the Promoter Region of BovineInterleukin 8 Gene and its Association with Milk Production Traits andSomatic Cell Score of Holstein Cattle in Iran

Cited by 5 publications

References 24 publications

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

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

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

Sequence Characterization in 3′-Flanking Region of Bovine TNF-α: Association with Milk Production Traits and Somatic Cell Score in Holstein Cattle of Iran

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