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Archtecture and Dissection of F2 Population and Girolando Breed Genome

PAMELA ITAJARA OTTO.
Tese em Inglês | VETTESES | ID: vtt-212264

Resumo

Livestock production is one of the most important activities of Brazilian agribusiness. Milk production has taken a prominent position in this sector, with continuous growth over the last decades. Most of the milk in Brazil is produced in systems relying on grazing mainly located in tropical and subtropical regions, which favors parasite infections in dairy cattle. Among the parasites that affect cattle, ticks are the main cause of economic losses in tropical and subtropical regions around the world. The bovine tick, Rhipicephalus (Boophilus) microplus, promotes several losses in bovine production. In parallel, gastrointestinal nematodes infections are the biggest problem on livestock production, especially in ruminants, in which the infections are usually subclinical, what makes difficult the diagnosis of this parasitosis and aggravates the losses caused by this parasite. Such parasite infections and also heat stress, bring, large losses in dairy industry. In these circumstances, an alternative to overcome parasite infections and heat stress in dairy production systems is the use of crossing or synthetic breeds containing some portion of Bos indicus genetics. To meet these requirements, the Girolando breed was created aiming to produce milk sustainably in tropical and subtropical regions. Despite of its relevance in dairy production, Girolando Breed still lack information about its genomic architecture and genomic data regarding important traits for production and adaptive. GWAS studies was the first step in our process to find causal variants in our work. Post-GWAS studies, such as ontology terms enrichment and gene-transcription factors networks, were used to identify most likely candidate genes. By the BOA approach we assigned breed-of-origin of alleles in the crossbred animals. In this context, our overall aims were 1) to identify genetic markers and haplotypes associated with tick counts, variation of rectal temperature and averages of last measurements for fecal egg count (AVFEC) in Gir x Holstein crossbred cattle, as well as for 305-days milk yield in Girolando breed; 2) to identify candidate genes for the four evaluated traits using the ontology terms enrichment and gene-transcription factors networks; 3) To infer the breed origin of marker alleles located on the candidate genes identified for adaptive traits in F2 population, to check if there is a prevalence of alleles from a certain breed in animals groups; 4) To investigate whether estimated SNP-specific variance for 305MY is affected by the breed of origin. The results of this thesis showed the genetic variability for the evaluated traits, which makes the use of genetic selection promising for the improvement of them. Results from GWAS approaches pinpointed relevant QTL regions for four traits in several Bos taurus chromosomes. The post-GWAS analyses increased the biological understanding of evaluated traits and allowed us to identify the TREM1, TREM2, TREML1, CD83, MYO5A and PRSS16 candidate genes for tick counts, the LIF, OSM, TXNRD2 and DGCR8 candidate genes for variation of rectal temperature, and finally the LEP, CLOCK, CASR, LRRC4, DOCK1, SLC15A2 and SND1 candidate genes for the 305MY. Based in the literature review we identified the MYOD1 and CALCB candidate genes for AVFEC. According to the origin of alleles analysis we observed that most of resistant animals for tick infestation showed two alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Holstein breed alleles could be associated to higher response to heat stress effects and to AVFEC resistance. For the seven candidate genes identified for 305MY in Girolando cattle, the SNP variances were different depending upon the breed-of-origin, while the alleles coming from the Gir breed-of-origin showed the highest genetic variance. The present study was shown a rich information resource to add more pieces to the intricate nature of Girolando Cattle, providing better biological comprehension of its nature and physiology of production under tropical conditions.
Livestock production is one of the most important activities of Brazilian agribusiness. Milk production has taken a prominent position in this sector, with continuous growth over the last decades. Most of the milk in Brazil is produced in systems relying on grazing mainly located in tropical and subtropical regions, which favors parasite infections in dairy cattle. Among the parasites that affect cattle, ticks are the main cause of economic losses in tropical and subtropical regions around the world. The bovine tick, Rhipicephalus (Boophilus) microplus, promotes several losses in bovine production. In parallel, gastrointestinal nematodes infections are the biggest problem on livestock production, especially in ruminants, in which the infections are usually subclinical, what makes difficult the diagnosis of this parasitosis and aggravates the losses caused by this parasite. Such parasite infections and also heat stress, bring, large losses in dairy industry. In these circumstances, an alternative to overcome parasite infections and heat stress in dairy production systems is the use of crossing or synthetic breeds containing some portion of Bos indicus genetics. To meet these requirements, the Girolando breed was created aiming to produce milk sustainably in tropical and subtropical regions. Despite of its relevance in dairy production, Girolando Breed still lack information about its genomic architecture and genomic data regarding important traits for production and adaptive. GWAS studies was the first step in our process to find causal variants in our work. Post-GWAS studies, such as ontology terms enrichment and gene-transcription factors networks, were used to identify most likely candidate genes. By the BOA approach we assigned breed-of-origin of alleles in the crossbred animals. In this context, our overall aims were 1) to identify genetic markers and haplotypes associated with tick counts, variation of rectal temperature and averages of last measurements for fecal egg count (AVFEC) in Gir x Holstein crossbred cattle, as well as for 305-days milk yield in Girolando breed; 2) to identify candidate genes for the four evaluated traits using the ontology terms enrichment and gene-transcription factors networks; 3) To infer the breed origin of marker alleles located on the candidate genes identified for adaptive traits in F2 population, to check if there is a prevalence of alleles from a certain breed in animals groups; 4) To investigate whether estimated SNP-specific variance for 305MY is affected by the breed of origin. The results of this thesis showed the genetic variability for the evaluated traits, which makes the use of genetic selection promising for the improvement of them. Results from GWAS approaches pinpointed relevant QTL regions for four traits in several Bos taurus chromosomes. The post-GWAS analyses increased the biological understanding of evaluated traits and allowed us to identify the TREM1, TREM2, TREML1, CD83, MYO5A and PRSS16 candidate genes for tick counts, the LIF, OSM, TXNRD2 and DGCR8 candidate genes for variation of rectal temperature, and finally the LEP, CLOCK, CASR, LRRC4, DOCK1, SLC15A2 and SND1 candidate genes for the 305MY. Based in the literature review we identified the MYOD1 and CALCB candidate genes for AVFEC. According to the origin of alleles analysis we observed that most of resistant animals for tick infestation showed two alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Holstein breed alleles could be associated to higher response to heat stress effects and to AVFEC resistance. For the seven candidate genes identified for 305MY in Girolando cattle, the SNP variances were different depending upon the breed-of-origin, while the alleles coming from the Gir breed-of-origin showed the highest genetic variance. The present study was shown a rich information resource to add more pieces to the intricate nature of Girolando Cattle, providing better biological comprehension of its nature and physiology of production under tropical conditions.
Biblioteca responsável: BR68.1