Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle

Authors: UTSUNOMIYA, YURI - Universidade Estadual Paulista (UNESP); DO CARMO, ADRIANA - Universidade Estadual Paulista (UNESP); NEVES, HAROLDO - Universidade Estadual Paulista (UNESP); CARVALHEIRO, ROBERTO - Universidade Estadual Paulista (UNESP); MATOS, MARCIA - Universidade Estadual Paulista (UNESP); ZAVAREZ, LUDMILLA - Universidade Estadual Paulista (UNESP); RAUSCHKOLB KATSUDA I, PIER KENJI ITO - Universidade Estadual Paulista (UNESP); PEREZ OBRIEN, ANA - University Of Natural Resources & Applied Life Sciences - Austria; SOLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria; PORTO NETO, LAERCIO - Commonwealth Scientific And Industrial Research Organisation (CSIRO); SCHENKEL, FLAVIO - University Of Guelph; MCEWAN, JOHN - Agresearch; Cole, John; DA SILVA, MARCOS V.G.B. - Embrapa National Research Center; Van Tassell, Curtis - Curt; Sonstegard, Tad; GARCIA, JOSE FERNANDO - Sao Paulo State University (UNESP)

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2014
Publication Date: 2/18/2014
Publication URL: http://handle.nal.usda.gov/10113/58872
Citation: Utsunomiya, Y.T., Do Carmo, A.S., Neves, H.H., Carvalheiro, R., Matos, M.C., Zavarez, L.B., Rauschkolb Katsuda I, P., Perez Obrien, A.M., Solkner, J., Porto Neto, L.R., Schenkel, F.S., Mcewan, J., Cole, J.B., Da Silva, M., Van Tassell, C.P., Sonstegard, T.S., Garcia, J. 2014. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle. PLoS One. 9(2):e88561.

Interpretive Summary: Using a high density single nucleotide polymorphism assay (over 777,000 SNP), we identified chromosome regions affecting scrotal circumference (SC) in Nellore cattle (humped Bos indicus cattle). Although this type of cattle is highly adapted to tropical conditions, it is not as precocious as the Bos taurus species, making the improvement of reproductive performance an impending challenge in cattle production systems around the world. We chose to study SC, because it is a major selection criterion to improve precocity and fertility in beef herds. The characterization of genomic regions affecting SC can contribute to the identification of predictive markers for reproductive performance and uncover molecular mechanisms underlying bovine reproductive biology. Using 861 Nellore progeny-tested bulls, we found chromosome segments that explain 4% of the variance in this trait. A signal on chromosome 14 near the PLAG1 gene underscores the importance of how genetic variation in this region affects both cattle body size and fertility. Overall, our findings contribute to linking reproductive phenotypes to gene functions, and offer new insights on the molecular biology of male fertility.

Technical Abstract: The reproductive performance of bulls has a high impact on the beef cattle industry. Scrotal circumference (SC) is the most recorded reproductive trait in beef herds, and is used as a major selection criterion to improve precocity and fertility. The characterization of genomic regions affecting SC can contribute to the identification of diagnostic markers for reproductive performance and uncover molecular mechanisms underlying complex aspects of bovine reproductive biology. In this paper, we report a genome-wide scan for chromosome segments explaining differences in SC, using data of 861 Nellore bulls (Bos indicus) genotyped for over 777,000 single nucleotide polymorphisms. Loci that excel from the genome background were identified on chromosomes 4, 6, 7, 10, 14, 18 and 21. The majority of these regions were previously found to be associated with reproductive and body size traits in cattle. The signal on chromosome 14 replicates the pleiotropic quantitative trait locus encompassing PLAG1 that affects male fertility in cattle and stature in several species. Based on intensive literature mining, SP4, MAGEL2, SH3RF2, PDE5A and SNAI2 are proposed as novel candidate genes for SC, as they affect growth and testicular size in other animal models. These findings contribute to linking reproductive phenotypes to gene functions, and may offer new insights on the molecular biology of male fertility.