Genome-wide structural variations in Brazilian Senepol cattle, a tropically adapted taurine breed

Abstract

This study aimed to identify structural variations in the form of runs of homozygosity (ROH) and copy number variants (CNVs) in the genome of the Brazilian Senepol cattle and to better explore the potential biological functions of the genes located within such regions. A total of 140 animals were genotyped with the GeneSeek® Genomic Profiler™ Bovine 50 K. Autosomal ROH and CNVs were detected after appropriated quality control. A total of 5,531 ROH were identified, with an average number of 40.37 per animal and an average length of 5.09 Mb. BTA1 had the greatest number of ROH per chromosome (n = 458), while BTA20 displayed the greatest fraction of the chromosome covered with ROH (22.06%). A total of 181 CNVs were identified, with an average length size of 184.67 kb, with values ranging from 26.61 to 334.48 kb. A total of 16 CNV regions (CNVRs) were seen distributed among eleven autosomes, and the largest number of CNVRs (n = 4) was described on BTA12. Autozygosity islands were identified using an outlier approach, and none of them overlapped with CNVRs. Our study revealed that the limited genetic basis together with the narrow number of imported animals to disseminate the breed might have strongly contributed to the low effective population size and the high genomic autozygosity proportion described in this population. The functional enrichment analysis revealed several significant terms (p<0.05) within the autozygosity islands and CNVRs closely linked to molecular and immune response mechanisms. The average FROH of different lengths were low to in the studied population, however, the autozygotic proportion in the genome indicates moderate to high inbreeding levels. The results exposed the need of implementing mating programs to control the increase of inbreeding and coancestry in Brazilian Senepol cattle. In these sense, Senepol breeders should apply selection and mating strategies to minimize the occurrence of long ROH in the offspring, as well as import of new genetic material to avoid the loss of genetic diversity. This study revealed the existence of overlapped regions between CNVRs and ROH throughout the genome of the Senepol cattle, that contributes to a better understanding of the functional role of genomic structural variations in taurine cattle adapted to tropical regions.