Navegando por Autor "Fonseca, Pablo Augusto Souza"
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Item Identifcation and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr.(2021) Matosinho, Carolina Guimarães Ramos; Cruz, Izinara Rosse da; Fonseca, Pablo Augusto Souza; Oliveira, Francislon Silva de; Santos, Fausto Gonçalves dos; Araújo, Flávio Marcos Gomes de; Salim, Anna Christina de Matos; Lopes, Beatriz Cordenonsi; Arbex, Wagner Antonio; Machado, Marco Antônio; Peixoto, Maria Gabriela Campolina Diniz; Verneque, Rui da Silva; Martins, Marta Fonseca; Silva, Marcos Vinicius Gualberto Barbosa da; Oliveira, Guilherme; Pires, Douglas Eduardo Valente; Carvalho, Maria Raquel SantosWhole genome sequencing of bovine breeds has allowed identifcation of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identifed genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted efects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcrip- tion factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identifed in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identifed. LALBA Ile60Val was predicted to afect protein stability and fexibility, by reducing the number the disulfde bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly afect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn afect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of afecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identifcation of potentially functional variants for milk protein genes.Item Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows.(2023) Matosinho, Carolina Guimarães Ramos; Fonseca, Pablo Augusto Souza; Peixoto, Maria Gabriela Campolina Diniz; Cruz, Izinara Rosse da; Lopes, Fernando César Ferraz; Zózimo, Thalía Rodrigues de Souza; Vercesi Filho, Aníbal Eugênio; Bruneli, Frank Angelo Tomita; Carvalho, Maria Raquel Santos; Gama, Marco Antonio SundfeldIndividual variation in milk fatty acid (FA) composition has been partially attrib- uted to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of SCD1 variants was predicted using bioinformatics tools. Milk and blood samples were collected from 312 cows distributed in 10 herds from five states of Brazil. SCD1 variants were identified through target sequencing, and milk FA composi- tion was determined by gas chromatography. Phenotypic variation in milk FA composition fell within the range reported for taurine breeds, with SCD18 index showing the lowest variation among the DI. Fourteen SCD1 variants were identi- fied, six of which not previously described. Regarding the A293V polymorphism, all cows were homozygous for the C allele (coding for alanine), whereas all gen- otypes were detected for the second SNP affecting the 293 codon (G>A), with compelling evidence for functional effects. Significant associations (based on raw p-values) were found between this SNP and C12:0, cis-9, trans-11 CLA and short- chain FA, and between another SNP (rs523411937) and C15:0 and odd-chain lin- ear FA. A new SNP on Chr26:21277069 was associated with trans-11 C18:1, cis-9, trans-11 CLA, C18:3 n-3 and n-3 FA. These findings indicate that SCD1 polymor- phisms also contributes to the phenotypic variation in milk FA composition of Gir cows, with potential use in their breeding programmes.