New candidate genes of high productivity in North-Caucasian sheep using genome-wide association study (GWAS)

Q4 Biochemistry, Genetics and Molecular Biology Animal Gene Pub Date : 2022-03-01 DOI:10.1016/j.angen.2021.200119

Alexander Krivoruchko, Olesya Yatsyk, Anastasiya Kanibolockaya

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引用次数: 1

Abstract

Genome-wide association study (GWAS) is a powerful tool for identifying loci and individual polymorphisms associated with economically important traits in various species of productive animals. The objective of this study was a genome-wide association search in sheep of the North-Caucasian meat and wool breed to identify single nucleotide polymorphisms (SNPs) associated with a class assessment determined by a set of productive parameters. Sixty rams of the North-Caucasian sheep breed were selected based on the criteria of phenotype and assigned to one of the groups - elite (control, 50 rams) and super-elite (case, 10 rams). They were genotyped using Ovine Infinium HD BeadChip 600 K DNA array and search of SNPs associations with productivity class were conducted. Candidate genes was annotated using ENSEMBLE database. Twelve SNPs were identified that have highly significant differences in the frequency of occurrence in animals with a super-elite score. From these twelve substitutions, five are in introns, seven are located at different distances from the genes. Most of the genes located next to the detected SNPs regulate development and functions of neurons. The greatest reliability in the associations was shown by the substitutions rs410503867 (p = 2 × 10⁻¹³) and rs428223899 (p = 1.2 × 10⁻¹⁰) located on chromosomes 4 and 21. Only in animals with a super-elite score three substitutions - rs404739757, rs402746571 and rs413668028 were found, they are presented together next to NALCN gene. The studies revealed a number of new candidate genes located near of SNPs associated with a general assessment of the complex of sheep traits (DGKB, PAK1, CHL1, CTTNBP2, NALCN and NFATC2) and proposed new molecular genetic markers in the form of single nucleotide polymorphisms. We are promising to use the identified genetic markers of super-elite animals in marker-associated breeding to improve the productive qualities of some sheep breed.

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基于全基因组关联研究(GWAS)的北高加索羊高产新候选基因

全基因组关联研究(Genome-wide association study, GWAS)是一种强大的工具，用于鉴定各种生产动物物种中与重要经济性状相关的位点和个体多态性。本研究的目的是在北高加索肉羊和毛羊品种中进行全基因组关联搜索，以确定与一组生产参数确定的类别评估相关的单核苷酸多态性(snp)。选取北高加索羊品种60只公羊，根据表型标准分为精英组(对照组，50只)和超精英组(病例，10只)。使用Ovine Infinium HD BeadChip 600 K DNA阵列对它们进行基因分型，并搜索与生产力类别相关的snp。候选基因用ENSEMBLE数据库进行标注。在超级精英得分的动物中，鉴定出了12个snp，它们的出现频率具有高度显著的差异。在这12个替换中，5个位于内含子中，7个位于与基因的不同距离上。大多数位于检测到的snp旁边的基因调节神经元的发育和功能。位于4号染色体和21号染色体上的rs410503867 (p = 2 × 10−13)和rs428223899 (p = 1.2 × 10−10)的遗传关联可靠性最高。只有在具有超级精英得分的动物中，发现了三个替换位点rs404739757、rs402746571和rs413668028，它们一起出现在NALCN基因旁边。这些研究发现了一些新的候选基因位于与绵羊性状复合体总体评估相关的snp附近(DGKB、PAK1、CHL1、CTTNBP2、NALCN和NFATC2)，并提出了新的单核苷酸多态性分子遗传标记。我们希望在标记相关育种中利用鉴定的超级精英动物遗传标记来提高某些绵羊品种的生产品质。

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Animal Gene Agricultural and Biological Sciences-Insect Science

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期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.