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| Author(s): |
Tatiane Cristina Seleguim Chud
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Institution: | Universidade Estadual Paulista (Unesp) |
| Defense date: | 2018-02-23 |
| Advisor: | Danísio Prado Munari; Marcos Vinícius Gualberto Barbosa da Silva; Fernando Sebastián Baldi Rey |
| Abstract | |
The advances of the genomic technologies has enabled to identify a high number of chromosomal structural variations in human and domestic animal genomes, such as copy number variation (CNV). In animal breeding, CNVs may assist to understand genetic variability of the economic important traits due most of the CNVs influence gene expression with specific biological functions. To identify possible CNVs linked to health, reproductive and productive traits in dairy cattle, the objective of this work was to detect and to describe CNVs in Girolando cattle (Gir x Holstein), to identify breed-specific CNV regions in Girolando from Gir and Holstein, and to investigate the population differentiation among the breeds using the copy number located on regions within annotated genes. In chapter 2, the CNV detection using single-nucleotidepolymorphism (SNP) panel was carried out on 1.607 females genotyped with the medium-density SNP panel (50K SNP) and 280 bulls genotyped with high-density panel (HD SNP) using Hidden Markov model implemented by PennCNV software. CNV calling also was perform using read-depth method applied on next-generation sequencing (NGS) data from two bulls resenquenced. A total of 203 and 213 CNVs candidate’s regions were picked using 50K e HD panels, respectively. Deletions and duplications related to parasite resistance, to disease susceptibility, and to reproductive efficiency was observed mainly located on chromosome BTA 5 and BTA 17. The detection and characterization of the CNVs in composite dairy cattle breed demonstrated better understanding of the traits, such disease resistance and reproductive efficiency. In chapter 3, the CNV calling was carried out on three Girolando bulls, 14 Gir bulls, and five Holstein bulls resequenced using the “readdepth” method implemented by CNVnator software. The VST statistic was calculated for the average of the copy number in regions located near annotated genes. Genes linked to fertility (MEPCE, ASB3) and disease susceptibility (HLX, MIR-455) were mapped on specific regions shared between Girolando and the pure-breeds (Gir ans Holstein). VST values ranged from -0.37 to 0.98. The genes AOX1, SLBP, TACC3 and PRAME, showed high VST, indicating high level of the population differentiation for the copy number located on the regions near of these genes. We found CNVR regions in Girolando specific from Gir and Holstein. The population differentiation study evidenced positive selection in genome of the Gir and Girolando animals for traits related to the adaptability of the breeds in tropical environmental may have originated from the domestication process. (AU) | |
| FAPESP's process: | 15/08939-0 - Identification of copy number variations in Girolando cattle |
| Grantee: | Tatiane Cristina Seleguim Chud |
| Support Opportunities: | Scholarships in Brazil - Doctorate |