Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds

This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.

Genomic Association between SNP Markers and Diseases in the "Curraleiro Pé-Duro" Cattle

Susceptibility to diseases is inherited and can be transmitted between populations. Single-nucleotide polymorphism (SNPs) in genes related to immune response is associated with diseases in cattle. This study investigated SNPs in the genomic region of cytokines in 702 samples of Curraleiro Pé-Duro cattle and associated them with the occurrence of antibodies in brucellosis, leptospirosis, neosporosis, leukosis, infectious bovine rhinotracheitis (IBR), and bovine viral diarrhea (BVD) tests. DNA samples were evaluated by the kompetitive allele-specific polymerase chain reaction (KASP) method to identify polymorphisms. The gametic phase and SNP haplotypes were determined with the help of PHASE 2.1.1 software. Haplotypes were associated with serological results against Brucella abortus, Leptospira sp., Neospora caninum, leukosis, infectious rhinotracheitis, and BVD using univariate analysis followed by logistic regression. Haplotype 2 of TLR2 was present in 70% of the animals that tested positive for N. caninum infection. Haplotypes of TLR10 and TLR6 and IL10RA were more common in seronegative animals. Haplotypes related to the gene IL10RA were associated with animals negative to all infections. Curraleiro Pé-Duro cattle presented polymorphisms related to resistance to bacterial, viral, and N. caninum infections.

PSVIII-34 Identification of copy number variants in Curraleiro Pé Duro breed

Locally adapted cattle herds such as Curraleiro Pé Duro (CDP) are rustic and adapted to the tropics and are able to survive in extreme environmental conditions such as the Brazilian Semi-Arid region. The study aimed to identify copy number variants (CNVs) possibly related to CPD adaptive traits. A total of 126 CPD animals were genotyped using the Illumina Bovine50K Genotyping BeadChip (Illumina Inc., San Diego, CA). To reduce false positives, the LRR of each SNP was adjusted for the GC content of 1 Mb window surrounding the SNP and PennCNV software was applied to 29 autosomes to detect CNVs. All samples with standard deviation of LRR > 0.30, standard deviation of BAF > 0.001, wave factor > 0.05, samples with > 150 CNVs and CNVs presenting length < 50kb were discarded for downstream analysis. BEDtools suite was used to map CNVs onto genes using the BioMart tool (Bos taurus UMD 3.1 assembly). Gene lists were mapped onto curated biological process and gene categories using the PANTHER classification system. 635 CNVs were identified after quality control of the autosomal chromosomes (51 deletions and 584 insertions). The CNVs length ranged from 50.6 kb (BTA20) up to 1,362 kb (BTA7) with a mean and median of 179.4 kb and 148.8 kb, respectively, corresponding to 0.03% of the bovine genome. The CNVs identified were overlapping with 339 genes, which we can highlight GRIK2 (BTA9:48476204), PCDH18 (BTA17:20336068), IGF2 (BTA4:32077891) previously reported in the literature as involved with flight time (temperament), rectal temperature and reproduction, respectively. The functional enrichment analysis demonstrated that the main enriched pathways (P < 0.05) were regulation of biogenesis (GO:0071840) and catalytic activities (GO 0005198). The CNVs identified as potentially related to adaptive traits may be used to select animals of higher adaptive value to a tropical environment.