Identification of CNVs in the Nelore genome and its association with meat tenderness

• Ano de defesa: 2015
• Autor(a) principal: Silva, Vinicius Henrique da
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Genome-wide; Integração; Integration; Pangenômico; RNA-seq; SNP-chip
• Link de acesso: http://www.teses.usp.br/teses/disponiveis/11/11139/tde-22042015-134017/

The Nelore breed represents the vast majority of Brazilian Zebuine cattle (Bos taurus indicus). The great adaptability of the Nelore breed to Brazilian tropical climate, however, is not associated with meat tenderness (MT). It is known that MT is influenced by several environmental factors, but also genetic composition. In the first chapter, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® Bovine High Density SNP-chip data for a Nelore population of 723 males including 30 sires. We detected >2600 CNV regions (CNVRs) representing ≈6.5% of the Bos taurus genome. The CNVR size was 65 kb on average, ranging from 5 kb to 4.3 Mb. A total of 1155 CNVRs (43.6%) overlapped 2750 genes. They are enriched for important functions such as immune response, olfactory reception and processes involving guanosine triphosphate (GTP). The GTP processes have known influence in skeletal muscle physiology and morphology. Quantitative trait loci for MT, partly specific for Nelore, overlapped a substantial fraction of CNVRs and two CNVRs were found proximal to glutathione metabolism genes that are associated with MT as well. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). We selected 9 CNVRs that overlapped regions associated with MT and we validated them in all 30 sires by qPCR. There was identified many genomic regions of structural variation in Nelore with important implications on the MT phenotype. In the second chapter, a total of 34 animals of the population were subjected to transcriptome analysis and meat tenderness (MT) phenotyping. We identified 170 CNV fragments (CNVFs) residing in 20 CNVRs, which occurred in different frequencies between animals with tougher and softer meat genetic potential. A considerable fraction of the identified CNVFs affected gene expression of the MT genes, which play important roles in glycogen metabolism, connective tissue turnover, membrane transporters and glutathione pathways. We also detected that several CNVRs substantially influenced the expression of overlapped and nearby genes, where the increase or decrease of copy number correlated well with the change in gene expression. Among them are two CNVRs at chromosomes 12 and 23, which are in the vicinity of previously described QTLs for MT in Nelore breed. Several CNVFs, which are more frequent in animals with genetic potential for softer or tougher MT, showed significant differences in gene expression. Those regions are linked to important biological functions with highly relevant influences on MT and skeletal muscle physiology.