Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes

Authors: ZAVAREZ, LUDMILLA - Universidade Estadual Paulista (UNESP); UTSUNOMIYA, YURI - Universidade Estadual Paulista (UNESP); CARMO, ADRIANA - Universidade Estadual Paulista (UNESP); NEVES, HAROLDO - Universidade Estadual Paulista (UNESP); CARVALHEIRO, ROBERTO - Universidade Estadual Paulista (UNESP); FERENCAKOVIC, MAJA - University Of Zagreb; PÉREZ O’BRIEN, ANA - University Of Natural Resources & Applied Life Sciences - Austria; CURIK, INO - University Of Zagreb; Cole, John; Van Tassell, Curtis - Curt; SILVA, MARCOS - Embrapa; Sonstegard, Tad; SÖLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria; GARCIA, JOSE - Universidade Estadual Paulista (UNESP)

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2015
Publication Date: 1/29/2015
Publication URL: https://handle.nal.usda.gov/10113/60883
Citation: Zavarez, L.B., Utsunomiya, Y.T., Carmo, A.S., Neves, H.H., Carvalheiro, R., Ferencakovic, M., Pérez O’Brien, A.M., Curik, I., Cole, J.B., Van Tassell, C.P., Silva, M.V., Sonstegard, T.S., Sölkner, J., Garcia, J.F. 2015. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Frontiers in Genetics. 6:5.

Interpretive Summary: Genetic diversity is important because livestock with low levels of diversity often have reduced productivity, health, and fertility compared to other animals. Diversity has commonly been measured using coefficients of inbreeding, but runs of homozygosity based on high-density DNA marker information can help provide a more nuanced overview than pedigree information alone. In this study, genetic diversity in Nellore beef cattle was measured using rons of homozygosity, and several regions of the genome that have changed in response to artificial selection for body weight, carcass composition, and fertility were identified.

Technical Abstract: The use of relatively low number of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, conservation of genetic resources and maintenance of the sustainability of the breeding schemes. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore (Bos indicus) cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH was 8.31%, indicating low genome-wide autozygosity. In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of the Nellore breeding program. Three signatures of selection, based on common ROH for infectious diseases resistance and fertility, were described in chromosomes 4, 7 and 12, and these regions should be subject of future investigation.