A genome-wide search of meat productivity candidate genes in Russian Meat Merino breed

Q4 Biochemistry, Genetics and Molecular Biology

Animal Gene Pub Date : 2023-03-01 DOI:10.1016/j.angen.2023.200146

Alexander Krivoruchko , Alexander Surov , Anastasiya Kanibolotskaya , Peter Sheludko , Natalia Likhovid , Olesya Yatsyk , Andrey Likhovid

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Abstract

A genome-wide associations study (GWAS) of single nucleotide polymorphisms (SNP) with indicators of meat productivity in Russian Meat Merino was carried out. A new approach is based on the selection of animals for research considered with known productivity genes (MSTN, MYOD1, etc.). Animal genotyping was performed using Ovine Infinium HD BeadChip 600 K (Illumina, USA). As a result, 20 SNPs significantly associated with the body measurements and ultrasound parameters of the animals were identified. Around these SNPs, 14 candidate genes were discovered. Investigated parameters of phenotype can be associated with structural disorders in these genes. Most SNPs were located in the intergenic space, two polymorphisms were located in the Upstream and Downstream regions. One SNP was localized in the intron, two are in the exon of genes. Two substitutions were next to the long non-coding RNA and micro-RNA. The following candidate genes were annotated: ASB3, THADA, PRPS1L1, Ccdc130, MTHFS, RALGAPA1, MEIS1, AKIRIN1, GRXCR1, Lrig1, ANKS1B, CFI, KRAB, and SLCO2B1. These genes are involved in some metabolic processes of cell proliferation and differentiation, function of neurons and immune system. Further research should be oriented to study the structure of these genes and use discovered SNPs as new molecular markers in breeding.

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俄罗斯美利奴肉品系生产能力候选基因的全基因组搜索

对俄罗斯美利奴肉品的单核苷酸多态性（SNP）与肉品生产指标进行了全基因组关联研究（GWAS）。一种新的方法是基于选择具有已知生产力基因（MSTN、MYOD1等）的动物进行研究。使用Ovine Infinium HD BeadChip 600K（Illumina，USA）进行动物基因分型。结果，鉴定出20个与动物的身体测量和超声参数显著相关的SNP。围绕这些SNPs，发现了14个候选基因。研究的表型参数可能与这些基因的结构紊乱有关。大多数SNPs位于基因间空间，两个多态性位于上游和下游区域。一个SNP位于内含子中，两个位于基因外显子中。在长的非编码RNA和微小RNA旁边有两个取代。对以下候选基因进行了注释：ASB3、THADA、PRPS1L1、Ccdc130、MTHFS、RALGAPA1、MEIS1、AKIRIN1、GRXCR1、Lrig1、ANKS1B、CFI、KRAB和SLCO2B1。这些基因参与细胞增殖和分化、神经元功能和免疫系统的一些代谢过程。进一步的研究应该着眼于研究这些基因的结构，并将发现的SNPs作为育种中的新分子标记。

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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.