1. Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus
- Author
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S. C. M. Niciura, Karina Santos de Oliveira, Tainã Figueiredo Cardoso, Marcela Maria de Souza, Juliana Afonso, Luciana Correia de Almeida Regitano, Adhemar Zerlotini, Jennifer Jessica Bruscadin, M. I. P. Rocha, Luiz Lehmann Coutinho, JENNIFER JESSICA BRUSCADIN, UFSCAR, MARCELA MARIA DE SOUZA, IOWA STATE UNIVERSITY, KARINA SANTOS DE OLIVEIRA, UFSCAR, MARINA IBELLI PEREIRA ROCHA, UFSCAR, JULIANA AFONSO, ESALQ/USP, TAINÃ FIGUEIREDO CARDOSO, ADHEMAR ZERLOTINI NETO, CNPTIA, LUIZ LEHMANN COUTINHO, ESALQ/USP, SIMONE CRISTINA MEO NICIURA, CPPSE, and LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE.
- Subjects
Genomic imprinting ,Gene Expression ,Linkage Disequilibrium ,Allele-specific expression ,Polimorfismo de nucleotídeo único ,Genetics ,education.field_of_study ,Multidisciplinary ,Allelic expression ,Genome ,Gado Nelore ,Functional genomics ,Genomics ,Phenotype ,Reduced representation bisulfite sequencing ,Expressão alélica ,Medicine ,Imprint genômico ,Biotechnology ,Genetic Markers ,Quantitative trait loci ,Heterozygote ,Meat ,Genotype ,Science ,Population ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,MiRNA binding ,Loci de característica quantitativa ,Biology ,Methylation ,Polymorphism, Single Nucleotide ,Article ,Animals ,Allele ,education ,Muscle, Skeletal ,Gene ,Alleles ,Animal breeding ,Animal biotechnology ,Bos Indicus ,Binding Sites ,DNA Methylation ,Single nucleotide polymorphism ,Gene regulation ,DNA binding site ,MicroRNAs ,Gene Expression Regulation ,Expression quantitative trait loci ,Cattle ,Genome-Wide Association Study - Abstract
Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes. Made available in DSpace on 2021-08-17T12:02:54Z (GMT). No. of bitstreams: 1 MuscleAlleleSpecific.pdf: 13183203 bytes, checksum: a634e71a998500cd0f7dd0ad1e644846 (MD5) Previous issue date: 2021 Article number: 7321.
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- 2021