Genome wide association study for reproductive traits in zebu bulls (Bos indicus) using high-density SNP chip

• Grant number: 10/52030-2
• Support Opportunities: Regular Research Grants
• Start date: February 01, 2011
• End date: September 30, 2013
• Field of knowledge: Agronomical Sciences - Veterinary Medicine
• Principal Investigator: José Fernando Garcia
• Grantee: José Fernando Garcia
• Host Institution: Faculdade de Medicina Veterinária (FMVA). Universidade Estadual Paulista (UNESP). Campus de Araçatuba. Araçatuba , SP, Brazil

Abstract

Several studies in quantitative genetics and functional genomics have demonstrated that the Genome Wide Association Study (GWAS) allows the identification of molecular markers useful in animal selection, enhancing the genetic gain in breeding programs. This technique allows the identification of genetic markers associated with specific phenotypes, such as semen quality and sperm cryotolerance, useful for early, efficient and reliable selection, thereby increasing productivity and profitability of livestock systems. The use of advanced molecular tools, such as SNP chip, has maximized the benefits of marker assisted selection, allowing uniform coverage of the genome for thousands of markers simultaneously, providing dense and highly informative genomic maps. Taking into consideration the current need of the beef production chain to shorten production cycles by selecting superior animals with better reproductive performance at early age, this project proposes the identification of molecular markers associated with semen quality and sperm cryotolerance in zebu sires using the high-density (HD) SNP chip technology. (AU)

Scientific publications

(17)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

PORTO-NETO, LAERCIO R.; SONSTEGARD, TAD S.; LIU, GEORGE E.; BICKHART, DEREK M.; DA SILVA, MARCOS V. B.; MACHADO, MARCO A.; UTSUNOMIYA, YURI T.; GARCIA, JOSE F.; GONDRO, CEDRIC; VAN TASSELL, CURTIS P.. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics, v. 14, DEC 13 2013. (10/52030-2)

UTSUNOMIYA, YURI TANI; MILANESI, MARCO; HARTH UTSUNOMIYA, ADAM TAITI; PINTOR TORRECILHA, RAFAELA BEATRIZ; KIM, EUI-SOO; COSTA, MARCIO SILVA; AGUIAR, TAMIRIS SAYURI; SCHROEDER, STEVEN; DO CARMO, ADRIANA SANTANA; CARVALHEIRO, ROBERTO; et al. A PLAG1 mutation contributed to stature recovery in modern cattle. SCIENTIFIC REPORTS, v. 7, DEC 7 2017. (10/52030-2, 16/07531-0, 14/01095-8)

AGUIAR, TAMIRIS SAYURI; PINTOR TORRECILHA, RAFAELA BEATRIZ; MILANESI, MARCO; HARTH UTSUNOMIYA, ADAM TAITI; TRIGO, BEATRIZ BATISTA; TIJJANI, ABDULFATAI; MUSA, HASSAN HUSSEIN; LOPES, FLAVIA LOMBARDI; AJMONE-MARSAN, PAOLO; CARVALHEIRO, ROBERTO; et al. Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus. FRONTIERS IN GENETICS, v. 9, DEC 7 2018. (14/01095-8, 16/07531-0, 16/05787-7, 10/52030-2, 17/08373-1)

NEVES, HAROLDO H. R.; CARVALHEIRO, ROBERTO; PEREZ O'BRIEN, ANA M.; UTSUNOMIYA, YURI T.; DO CARMO, ADRIANA S.; SCHENKEL, FLAVIO S.; SOELKNER, JOHANN; MCEWAN, JOHN C.; VAN TASSELL, CURTIS P.; COLE, JOHN B.; et al. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. GENETICS SELECTION EVOLUTION, v. 46, FEB 27 2014. (10/52030-2, 11/16643-2, 10/06185-4)

UTSUNOMIYA, YURI T.; DO CARMO, ADRIANA S.; CARVALHEIRO, ROBERTO; NEVES, HAROLDO H. R.; MATOS, MARCIA C.; ZAVAREZ, LUDMILLA B.; O'BRIEN, ANA M. PEREZ; SOELKNER, JOHANN; MCEWAN, JOHN C.; COLE, JOHN B.; et al. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC GENETICS, v. 14, JUN 13 2013. (10/52030-2, 11/16643-2)

O'BRIEN, ANA M. PEREZ; MESZAROS, GABOR; UTSUNOMIYA, YURI T.; SONSTEGARD, TAD S.; GARCIA, J. FERNANDO; VAN TASSELL, CURTIS P.; CARVALHEIRO, ROBERTO; DA SILVA, MARCOS V. B.; SOLKNER, JOHANN. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. LIVESTOCK SCIENCE, v. 166, p. 12-pg., 2014-08-01. (11/16643-2, 10/52030-2)

O'BRIEN, ANA M. PEREZ; MESZAROS, GABOR; UTSUNOMIYA, YURI T.; SONSTEGARD, TAD S.; GARCIA, J. FERNANDO; VAN TASSELL, CURTIS P.; CARVALHEIRO, ROBERTO; DA SILVA, MARCOS V. B.; SOLKNER, JOHANN. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. LIVESTOCK SCIENCE, v. 166, n. SI, p. 121-132, AUG 2014. (10/52030-2, 11/16643-2)

BOISON, S. A.; NEVES, H. H. R.; PEREZ O'BRIEN, A. M.; UTSUNOMIYA, Y. T.; CARVALHEIRO, R.; DA SILVA, M. V. G. B.; SOELKNER, J.; GARCIA, J. F.. Imputation of non-genotyped individuals using genotyped progeny in Nellore, a Bos indicus cattle breed. LIVESTOCK SCIENCE, v. 166, n. SI, p. 176-189, AUG 2014. (10/52030-2, 11/16643-2)

UTSUNOMIYA, Y. T.; FORTUNATO, A. A. A. D.; MILANESI, M.; TRIGO, B. B.; ALVES, N. F.; SONSTEGARD, T. S.; GARCIA, J. F.. Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle. ANIMAL GENETICS, v. 53, n. 1, DEC 2021. (10/52030-2)

O'BRIEN, ANA M. PEREZ; UTSUNOMIYA, YURI T.; MESZAROS, GABOR; BICKHART, DEREK M.; LIU, GEORGE E.; VAN TASSELL, CURTIS P.; SONSTEGARD, TAD S.; DA SILVA, MARCOS V. B.; GARCIA, JOSE FERNANDO; SOELKNER, JOHANN. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. GENETICS SELECTION EVOLUTION, v. 46, MAR 4 2014. (10/52030-2, 11/16643-2)

O'BRIEN, ANA M. PEREZ; HOELER, DANIELA; BOISON, SOLOMON A.; MILANESI, MARCO; BOMBA, LORENZO; UTSUNOMIYA, YURI T.; CARVALHEIRO, ROBERTO; NEVES, HAROLDO H. R.; DA SILVA, MARCOS V. B.; VANTASSELL, CURTIS P.; et al. Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. GENETICS SELECTION EVOLUTION, v. 47, APR 17 2015. (10/52030-2, 14/01095-8)

UTSUNOMIYA, ADAM T. H.; SANTOS, DANIEL J. A.; BOISON, SOLOMON A.; UTSUNOMIYA, YURI T.; MILANESI, MARCO; BICKHART, DEREK M.; AJMONE-MARSAN, PAOLO; SOELKNER, JOHANN; GARCIA, JOSE F.; DA FONSECA, RICARDO; et al. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics, v. 17, SEP 5 2016. (10/52030-2, 14/01095-8)

UTSUNOMIYA, YURI T.; CARMO, ADRIANA S.; NEVES, HAROLDO H. R.; CARVALHEIRO, ROBERTO; MATOS, MARCIA C.; ZAVAREZ, LUDMILLA B.; ITO, PIER K. R. K.; O'BRIEN, ANA M. PEREZ; SOELKNER, JOHANN; PORTO-NETO, LAERCIO R.; et al. Genome-Wide Mapping of Loci Explaining Variance in Scrotal Circumference in Nellore Cattle. PLoS One, v. 9, n. 2, FEB 18 2014. (10/52030-2, 11/16643-2)

UTSUNOMIYA, YURI TANI; O'BRIEN, ANA MARIA PEREZ; SONSTEGARD, TAD STEWART; VAN TASSELL, CURTIS PAUL; DO CARMO, ADRIANA SANTANA; MESZAROS, GABOR; SOELKNER, JOHANN; GARCIA, JOSE FERNANDO. Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods. PLoS One, v. 8, n. 5, MAY 16 2013. (10/52030-2, 11/16643-2)

TRIGO, BEATRIZ B.; UTSUNOMIYA, ADAM T. H.; FORTUNATO, ALVARO A. A. D.; MILANESI, MARCO; TORRECILHA, RAFAELA B. P.; LAMB, HARRISON; NGUYEN, LOAN; ROSS, ELIZABETH M.; HAYES, BEN; PADULA, ROMULO C. M.; et al. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. GENETICS SELECTION EVOLUTION, v. 53, n. 1, APR 28 2021. (10/52030-2, 16/05787-7)

BOISON, S. A.; NEVES, H. H. R.; PEREZ O'BRIEN, A. M.; UTSUNOMIYA, Y. T.; CARVALHEIRO, R.; DA SILVA, M. V. G. B.; SOELKNER, J.; GARCIA, J. F.. Imputation of non-genotyped individuals using genotyped progeny in Nellore, a Bos indicus cattle breed. LIVESTOCK SCIENCE, v. 166, p. 14-pg., 2014-08-01. (11/16643-2, 10/52030-2)

UTSUNOMIYA, YURI TANI; PINTOR TORRECILHA, RAFAELA BEATRIZ; MILANESI, MARCO; PAULAN, SILVANA DE CASSIA; HARTH UTSUNOMIYA, ADAM TAITI; GARCIA, JOSE FERNANDO. Hornless Nellore cattle (Bos indicus) carrying a novel 110 kbp duplication variant of the polled locus. ANIMAL GENETICS, v. 50, n. 2, p. 2-pg., 2019-04-01. (16/05787-7, 10/52030-2, 17/08373-1)