Identificação e análise funcional de genes associados às características produtivas e reprodutivas em zebuínos leiteiros

Abstract

The Brazilian cattle herd is composed of 218.2 million animals (in 2020). The country is the first largest producer of cattle in the world and the fifth largest producer of bovine milk in the world. The Brazilian herd is made up of representatives of taurine (Bos taurus), zebu (Bos indicus) and crossbred breeds. Zebu cattle constitute the largest part of the national herd with more than 165 million animals, including beef and dairy cattle. Among the dairy zebu cattle, the Guzerá and Gir breeds are of great importance for the national agricultural scenario. Due to the selection of animals for productive efficiency, an increase in cases of reproductive problems has been reported in the literature. The present work had as general objective to investigate the genetic-molecular basis of production and reproductive traits in the main zebu breeds selected for milk in the state of Minas Gerais. Four studies were carried out: Study 1 - Development of a flowchart for in silico classification of genetic variants regarding the potential functional repercussion and identification and in silico analysis of variants shared between the Gir and Guzerá breeds in the milk protein genes (CSN1S1, CSN1S2, CSN2, CSN3, LALBA, LGB and LTF). The results of this study are already published (Matosinho et al., 2021, https://link.springer.com/article/10.1007%2Fs11250-021-02970-2). Study 2 - Identification and in silico analysis of variants identified in each of the breeds, Gir and Guzerá, in the milk protein genes (CSN1S1, CSN1S2, CSN2, CSN3, LALBA, LGB and LTF). Complete genome sequencing data from six individuals were used, three of each race, Gir and Guzerá. Seventy-one genetic variants (64 SNVs and 7 INDELs) shared between Guzerá and Gir breeds were studied. Using a pipeline developed by the research group to classify genetic variants in terms of potential functional repercussion, using Bioinformatics tools, 13 of the 71 variants were considered potentially functional. Among the exclusive variants in each breed, 433 SNVs and nine INDELs were identified in the Gir breed and 91 SNVs and eight INDELs in the Guzerá breed, with 63 and 17 variants being considered potentially functional in each breed, respectively. Study 3 - Identification of genetic variants in SCD1, DGAT1 and LTF genes, prediction of their functional impact and studies of association with the fatty acid profile of individual Gir's milk. A target sequencing was performed for the genes stearoyl CoA desaturase 1 (SCD1), diacylglycerol acyltransferase 1 (DGAT1) and lactoferrin (LTF), aiming at the discovery of genetic variants in these genes, for the Gir and Guzerá breeds. An association study with the milk fatty acid profile of the genotyped variants was developed. Study 4 - Genome resequencing, identification and in silico analysis of variants in a bull with subfertility in the Gyr breed. To identify potentially deleterious genetic variants, a complete genome sequencing of a bull of the Gir breed, with gonadal hypoplasia and sperm abnormalities, was performed. After sequencing, mapping was performed against the reference (ARS-UCD1.2) and variants were identified and classified as to potential pathogenicity. The ASGR2, CNGB1, DNAH3, and FKBP1A genes present potentially pathogenic variants and may be related to reproductive problems.