Genomic regions associated with coat color in Gir cattle.

Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.

Variability in the PRDM9 gene in Sindhi cattle.

BACKGROUND: Sindhi is a dual-purpose breed adapted to tropical environments. However, this breed has the smallest total population among indicine breeds in Brazil and the smallest effective number. In addition, the inbreeding coefficient is higher than 6.25% in ~ 60% of the population. Therefore, alternatives to increase genetic diversity are important. Within this context, the PRDM9 gene is particularly interesting since it is involved in meiotic recombination events, consequently enhancing genetic variability in the population by increasing the number of circulating haplotypes. Each allele of the gene induces recombination at a different hotspot. The larger the number of circulating alleles, the higher the recombination rate and the greater the genetic variability. METHODS: The aim of this study was to characterize alleles of the PRDM9 gene in Sindhi cattle. The region of the zinc finger domains of the gene was amplified by PCR, genotyped, and sequenced for allele identification in 50 Sindhi animals. RESULTS: Three alleles (A-cattle1, B-cattle14, and C-cattle19) and six genotypes (AA, BB, CC, AB, AC, and BC) were identified. CONCLUSION: The allele variation of the PRDM9 gene in the Sindhi breed enables to guide the mating of animals with different genotypes/alleles and to promote genetic variability by recombination if there is intralocus variability.

Genomic association using principal components of morphometric traits in horses: identification of genes related to bone growth.

The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HPC for 15 linear measurements as the explanatory variable in order to identify associated genomic regions and to elucidate the biological mechanisms linked to this index in Campolina horses. For GWAS, weighted single-step GBLUP was applied to HPC. The eight genomic windows that explained the highest proportion of additive genetic variance were identified. The sum of the additive variance explained by the eight windows was 95.89%. Genes involved in bone and cartilage development were identified (SPRY2, COL9A2, MIR30C, HEYL, BMP8B, LTBP1, FAM98A, and CRIM1). They represent potential positional candidates for the HPC of the linear measurements evaluated. The HPC is an efficient alternative to reduce the 15 usually measured traits in Campolina horses. Moreover, candidate genes inserted in region that explained high additive variance of the HPC were identified and might be fine-mapped for searching putative mutation/markers.

Genetic origin of donkeys in Brazil.

INTRODUCTION: The genetic groups of native donkeys in Brazil are characterized by adaptation to the local environment. However, the donkey population in the country is declining, mainly because of agricultural mechanization and transportation that has led to the abandonment and the consequent indiscriminate slaughter of these animals. There are three local genetic groups of distinct geographic and temporal formation. However, analyses of their origin, phylogenetic relationship, and population structure are scarce. Within this context, molecular markers such as the mitochondrial control region (D-loop) are useful for these analyses. MATERIAL AND METHODS: This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino, and Pêga). RESULTS AND DISCUSSION: We detected five mitochondrial haplotypes with 19 polymorphic sites, two of them exclusively found in the Nordestino donkey; this group is in fact more distant from the others. Phylogenetic analysis indicates maternal contributions of two clades (Nubian and Somali) to the formation of the genetic groups of donkeys, a fact that explains the high diversity, structure, and distances of the groups, reported here for the first time. CONCLUSION : This analysis contributes production and conservation of native donkey breeds. It also gives clues about the formation of the Iberian breeds from which Brazilian donkeys originated.

The effect of mitochondrial DNA polymorphisms on cattle reproduction.

The aim of this study was to identify SNPs located in mitochondrial DNA that are associated with reproductive traits in beef cows. A total of 1999 Nelore females genotyped with the high-density Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) were used to study the association of mitochondrial DNA variants with reproductive traits using a single-step procedure. In a preliminary analysis, the present results indicate a small participation of the mitogenome in the expression of reproductive traits in beef cattle. However, possible difficulties related to the biological characteristics of mitochondrial DNA and its inheritance, genotyping, and annotation of the phenotypes studied may also explain the results.

Water buffaloes (Bubalus bubalis) only have A2A2 genotype for beta-casein.

Beta-casein is a milk protein that has two variants: A1 and A2. Some individuals have difficulties digesting beta-casein A1, which can cause gastrointestinal disorders. A2 milk has emerged as an alternative. This milk only contains beta-casein A2 and is obtained from females carrying the A2A2 genotype of the gene. In cattle, allele and genotype frequencies vary according to breed and marker-assisted selection is performed to obtain A2A2 animals and the consequent production of A2 milk that is easier to digest. This study aimed to evaluate the alleles of beta-casein in buffaloes. A total of 657 buffaloes of four different breeds were genotyped and all animals carried the A2A2 genotype, i.e., allele A1 does not exist in the buffalo species. Thus, all milk products of buffaloes are naturally A2. This result adds value to products derived from buffalo milk.