Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle.

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270-730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle.

Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems.

Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from -0.009 to 0.029. A low (-0.12-0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (<4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5-1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.

Variability analyses of the maternal lineage of horses and donkeys.

Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will contribute to the understanding of the current population structure and diversity of breeds/ecotypes of horses and donkeys raised in the Brazil. We analyzed 310 D-loop sequences representing 41 breeds/ecotypes of Equus caballus and Equus asinus, including 14 native horse breeds/ecotypes, 3 native donkey breeds/ecotypes and 24 cosmopolite horse breeds. The results revealed that the breeds are well structured genetically and that they comprise different groups. A total of 80 and 14 haplotypes were identified for horses and donkeys, respectively. Most of the horse mtDNA haplotypes were shared by many breeds, whereas donkey mtDNA haplotypes seemed to be more group-especif. Some groups presented a low intrabreed distance and/or a low haplotype/nucleotide diversity such as Lavradeiro, Crioulo, Piquira and Percheron horses and Brazilian donkey. Thus, specific actions must be designed for each population. The different levels of genetic diversity provided important information for conservation resource management of adapted groups as well as for mating orientation of breed associations. Some autochthonous ecotypes require attention because of their low genetic variability.