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 type: Scholarships in Brazil - Doctorate
• Effective date (Start): May 01, 2014
• Effective date (End): December 20, 2017
• Field of knowledge: Agronomical Sciences - Veterinary Medicine
• Principal Investigator: José Fernando Garcia
• Grantee: Yuri Tani Utsunomiya
• Home 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

(13)

(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; DE REZENDE NEVES, HAROLDO HENRIQUE; DO CARMO, ADRIANA SANTANA; HANOTTE, OLIVIER; SONSTEGARD, TAD STEWART; GARCIA, JOSE FERNANDO; UTSUNOMIYA, YURI TANI. Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus. FRONTIERS IN GENETICS, v. 9, DEC 7 2018. Web of Science Citations: 1.

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.; SILVEIRA, FERNANDO T.; MARCONDES, MARY; NUNES, CARIS M.; LAURENTI, MARCIA D. Canine leishmaniasis: Genome-wide analysis and antibody response to Lutzomyia longipalpis saliva. PLoS One, v. 13, n. 5 MAY 9 2018. Web of Science Citations: 0.

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; SUN, JIAJIE; CRESPO, EDWARD; AMATI, NORMAN; COLE, JOHN B.; NULL, DANIEL J.; GARCIA, JOSE F.; REVERTER, ANTONIO; BARENDSE, WILLIAM; SONSTEGARD, TAD S. Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor. FRONTIERS IN GENETICS, v. 9, FEB 23 2018. Web of Science Citations: 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. Web of Science Citations: 0.

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; REZENDE NEVES, HAROLDO HENRIQUE; MOROZINI PADULA, ROMULO CLAUDIO; SUSSAI, THAYLA SOUZA; ZAVAREZ, LUDMILLA BALBO; CIPRIANO, RAFAEL SILVA; THEODORO CAMINHAS, MARIA MARGARETH; HAMBRECHT, GEORGE; COLLI, LICIA; EUFEMI, ELISA; AJMONE-MARSAN, PAOLO; CESANA, DENEB; SANNAZARO, MARCO; BUORA, MAURIZIO; MORGANTE, MICHELE; LIU, GEORGE; BICKHART, DEREK; VAN TASSELL, CURTIS PAUL; SOLKNER, JOHANN; SONSTEGARD, TAD STEWART; GARCIA, JOSE FERNANDO. A PLAG1 mutation contributed to stature recovery in modern cattle. SCIENTIFIC REPORTS, v. 7, DEC 7 2017. Web of Science Citations: 9.

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.; LAURENTI, MARCIA D. 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. Web of Science Citations: 2.

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.; NUNES, C. M.; CIARLINI, P. C. 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. Web of Science Citations: 5.

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. Web of Science Citations: 7.

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; DA SILVA, MARCOS V. G. B. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics, v. 17, SEP 5 2016. Web of Science Citations: 12.

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; CONTRERAS-CASTILLO, CARMEN J.; GARCIA, JOSE F. Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth. PLoS One, v. 11, n. 7 JUL 13 2016. Web of Science Citations: 5.

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.; SCHNABEL, ROBERT D.; SONSTEGARD, TAD S.; GARCIA, JOSE F.; NUNES, CARIS M. 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. Web of Science Citations: 13.

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. Web of Science Citations: 5.

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.; SONSTEGARD, TAD S.; MESZAROS, GABOR; AJMONE-MARSAN, PAOLO; GARCIA, FERNANDO; SOELKNER, JOHANN. Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations. GENETICS SELECTION EVOLUTION, v. 47, APR 17 2015. Web of Science Citations: 13.

Academic Publications

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

UTSUNOMIYA, Yuri Tani. Sobre a origem e dispersão da mutação do gene PLAG1 em bovinos. 2017. Doctoral Thesis - Universidade Estadual Paulista "Júlio de Mesquita Filho" Faculdade de Ciências Agrárias e Veterinárias..