Use of next generation sequencing for the fine mapping of loci explaining variance in scrotal circumference in Nellore cattle

• Grant number: 14/01095-8
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: May 01, 2014
• End date: December 20, 2017
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Animal Reproduction
• Principal Investigator: José Fernando Garcia
• Grantee: Yuri Tani Utsunomiya
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated scholarship(s): 16/07531-0 - Comparison of methods for admixture and heterosis mapping in crossbred cattle populations, BE.EP.DR

Abstract

The reproductive performance of bulls has a major impact on the beef industry, affecting generation intervals, the rate of genetic change, and the amount of product that can be sent to the market. Scrotal circumference evaluated at yearling (SC) is the most recorded reproductive trait in beef cattle, 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 of reproductive performance and unravel molecular mechanisms involved in bovine reproductive biology. Recently, the candidate performed a genome-wide mapping of chromosome segments explaining differences in SC in 861 Nellore bulls (Bos indicus), using data from over 777,000 single nucleotide polymorphism (SNP) markers. 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, including humans. New candidate genes have been proposed for SC from this study, which affect growth and testicular size in other animal models. This project aims at the refinement of these loci using next-generation sequencing (next generation sequencing - NGS) data, aiming at investigating the putative causality of SNPs, copy number variants, insertions and deletions found in these regions.

Scientific publications

(15)

(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)

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)

UTSUNOMIYA, YURI T.; MILANESI, MARCO; UTSUNOMIYA, ADAM T. H.; AJMONE-MARSAN, PAOLO; GARCIA, JOSE F.. GHap: an R package for genome-wide haplotyping. Bioinformatics, v. 32, n. 18, p. 2861-2862, SEP 15 2016. (14/01095-8)

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)

PEREIRA, ANIRENE G. T.; UTSUNOMIYA, YURI T.; MILANESI, MARCO; TORRECILHA, RAFAELA B. P.; CARMO, ADRIANA S.; NEVES, HAROLDO H. R.; CARVALHEIRO, ROBERTO; AJMONE-MARSAN, PAOLO; SONSTEGARD, TAD S.; SOLKNER, JOHANN; et al. Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth. PLoS One, v. 11, n. 7, JUL 13 2016. (13/02552-0, 14/01095-8)

BATISTA, LUIS F. S.; UTSUNOMIYA, YURI T.; SILVA, THAIS B. F.; DIAS, RAISSA A.; TOMOKANE, THAISE Y.; PACHECO, ACACIO D.; DA MATTA, VANIA L. R.; SILVEIRA, FERNANDO T.; MARCONDES, MARY; NUNES, CARIS M.; et al. Genome-Wide Association Study of Cell-Mediated Response in Dogs Naturally Infected by Leishmania infantum. Infection and Immunity, v. 84, n. 12, p. 3629-3637, DEC 2016. (12/50285-9, 12/05847-9, 14/01095-8)

UTSUNOMIYA, YURI T.; RIBEIRO, ERICA S.; QUINTAL, AMANDA P. N.; SANGALLI, JULIANO R.; GAZOLA, VALQUIRIA R.; PAULA, HENRIQUE B.; TRINCONI, CRISTIANA M.; LIMA, VALERIA M. F.; PERRI, SILVIA H. V.; TAYLOR, JEREMY F.; et al. Genome-Wide Scan for Visceral Leishmaniasis in Mixed-Breed Dogs Identifies Candidate Genes Involved in T Helper Cells and Macrophage Signaling. PLoS One, v. 10, n. 9, SEP 8 2015. (14/01095-8)

HARTATI, HARTATI; UTSUNOMIYA, YURI TANI; SONSTEGARD, TAD STEWART; GARCIA, JOSE FERNANDO; JAKARIA, JAKARIA; MULADNO, MULADNO. Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle. BMC GENETICS, v. 16, JUL 4 2015. (14/01095-8)

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)

BATISTA, LUIS F. S.; UTSUNOMIYA, YURI T.; SILVA, THAIS B. F.; CARNEIRO, MARIANA M.; PAIVA, JOYR S. F.; SILVA, RAFAELA B.; TOMOKANE, THAISE Y.; ROSSI, CLAUDIO N.; PACHECO, ACACIO D.; TORRECILHA, RAFAELA B. P.; et al. Canine leishmaniasis: Genome-wide analysis and antibody response to Lutzomyia longipalpis saliva. PLoS One, v. 13, n. 5, MAY 9 2018. (12/05847-9, 14/01095-8, 12/50285-9)

PORTO-NETO, LAERCIO R.; BICKHART, DEREK M.; LANDAETA-HERNANDEZ, ANTONIO J.; UTSUNOMIYA, YURI T.; PAGAN, MELVIN; JIMENEZ, ESBAL; HANSEN, PETER J.; DIKMEN, SERDAL; SCHROEDER, STEVEN G.; KIM, EUI-SOO; et al. Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor. FRONTIERS IN GENETICS, v. 9, FEB 23 2018. (14/01095-8)

TORRECILHA, R. B. P.; UTSUNOMIYA, Y. T.; BOSCO, A. M.; ALMEIDA, B. F.; PEREIRA, P. P.; NARCISO, L. G.; PEREIRA, D. C. M.; BAPTISTIOLLI, L.; CALVO-BADO, L.; COURTENAY, O.; et al. Correlations between peripheral parasite load and common clinical and laboratory alterations in dogs with visceral leishmaniasis. PREVENTIVE VETERINARY MEDICINE, v. 132, p. 83-87, SEP 15 2016. (14/01095-8)

KHAYATZADEH, N.; MESZAROS, G.; UTSUNOMIYA, Y. T.; SCHMITZ-HSU, F.; SEEFRIED, F.; SCHNYDER, U.; FERENCAKOVIC, M.; GARCIA, J. F.; CURIK, I.; SOELKNER, J.. Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed. JOURNAL OF ANIMAL BREEDING AND GENETICS, v. 135, n. 1, p. 45-53, FEB 2018. (16/07531-0, 14/01095-8)

KHAYATZADEH, N.; MESZAROS, G.; UTSUNOMIYA, Y. T.; SCHMITZ-HSU, F.; SEEFRIED, F.; SCHNYDER, U.; FERENCAKOVIC, M.; GARCIA, J. F.; CURIK, I; SOELKNER, J.. Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls. JOURNAL OF DAIRY SCIENCE, v. 102, n. 12, p. 11217-11224, DEC 2019. (16/07531-0, 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)

BATISTA, LUIS F. S.; TORRECILHA, RAFAELA B. P.; SILVA, RAFAELA B.; UTSUNOMIYA, YURI T.; SILVA, THAIS B. F.; TOMOKANE, THAISE Y.; PACHECO, ACACIO D.; BOSCO, ANELISE M.; PAULAN, SILVANA C.; ROSSI, CLAUDIO N.; et al. Chromosomal segments may explain the antibody response cooperation for canine leishmaniasis pathogenesis. Veterinary Parasitology, v. 288, DEC 2020. (12/05847-9, 14/01095-8, 12/50285-9)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

UTSUNOMIYA, Yuri Tani. On the origin and spread of the bovine PLAG1 mutation. 2017. Doctoral Thesis - Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal Jaboticabal.