Combining high-density SNP genotypes and next generation sequence data to map disadvantageous genetic variants in Nellore cattle

• Grant number: 16/05787-7
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: June 01, 2017
• End date: May 31, 2019
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Animal Reproduction
• Principal Investigator: José Fernando Garcia
• Grantee: Marco Milanesi
• Host Institution: Faculdade de Medicina Veterinária (FMVA). Universidade Estadual Paulista (UNESP). Campus de Araçatuba. Araçatuba , SP, Brazil

Abstract

All animal species carry a genetic load of disadvantageous allelic variants. Those that are lethal occur only in the heterozygous state while those non-lethal can reduce the fitness of homozygous individuals for the variant. The long-term destiny of these mutations in outbred species is to decrease in frequency, due to negative selection, and disappear. However, in livestock populations they could be kept or even increase in frequency, when occurring in linkage with favourable alleles or carried by important sires. This proposal aims to detect these disadvantageous variants in Nellore cattle, the most important beef breed in Brazil. Inbreeding or fertility problems are not commonly reported in the Nellore population although there are real chances to have them increased in the future, due to artificial selction. The general objective of this research proposal is to build knowledge and anticipate possible problems caused by disadvantageous variants by implementing actions to avoid their spreading. High- density SNP genotyping data will be use to identify loss-of-homozygosity haplotypes. The characterization of them will be conducted using public information (i.e. previous research results, gene function information, associations with genetic diseases) and putative causative variants database of potential disadvantageous sequence variants (coding and noncoding conserved sequences) and structural variants, which will be created using the complete sequence data from twenty four key Nellore bulls. (AU)

Scientific publications

(11)

(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)

PALOMBO, V; MILANESI, M.; SGORLON, S.; CAPOMACCIO, S.; MELE, M.; NICOLAZZI, E.; AJMONE-MARSAN, P.; PILLA, F.; STEFANON, B.; D'ANDREA, M.. Genome-wide association study of milk fatty acid composition in Italian Simmental and Italian Holstein cows using single nucleotide polymorphism arrays. JOURNAL OF DAIRY SCIENCE, v. 101, n. 12, p. 11004-11019, DEC 2018. (16/05787-7)

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)

BEATRIZ BATISTA TRIGO; FERNANDA MULLER DE OLIVEIRA-ROVAI; MARCO MILANESI; PIER KENJI RAUSCHKOLB KATSUDA ITO; YURI TANI UTSUNOMIYA; FLÁVIA LOMBARDI LOPES; SILVANA DE CÁSSIA PAULAN; CÁRIS MARONI NUNES. Avaliação in silico e in vitro de iniciadores para a diferenciação molecular de espécies de Leishmania. Revista Brasileira de Parasitologia Veterinária, v. 30, n. 1, 2021-03-12. (16/05787-7)

PALOMBO, VALENTINO; MILANESI, MARCO; SFERRA, GABRIELLA; CAPOMACCIO, STEFANO; SGORLON, SANDY; D'ANDREA, MARIASILVIA. PANEV: an R package for a pathway-based network visualization. BMC Bioinformatics, v. 21, n. 1, FEB 6 2020. (16/05787-7)

MESZAROS, GABOR; MILANESI, MARCO; AJMONE-MARSAN, PAOLO; UTSUNOMIYA, YURI TANI. Editorial: Haplotype Analysis Applied to Livestock Genomics. FRONTIERS IN GENETICS, v. 12, p. 2-pg., 2021-05-18. (16/05787-7)

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)

TORRECILHA, R. B. P.; MILANESI, M.; GALLANA, M.; FALBO, A. -K.; REICHLER, I. M.; HUG, P.; JAGANNATHAN, V.; TRIGO, B. B.; PAULAN, S. C.; BRUNO, D. B.; et al. Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs. ANIMAL GENETICS, v. 51, n. 1, p. 78-86, FEB 2020. (17/08373-1, 16/05787-7)

COLLI, LICIA; MILANESI, MARCO; TALENTI, ANDREA; BERTOLINI, FRANCESCA; CHEN, MINHUI; CRISA, ALESSANDRA; DALY, KEVIN GERARD; DEL CORVO, MARCELLO; GULDBRANDTSEN, BERNT; LENSTRA, JOHANNES A.; et al. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes. GENETICS SELECTION EVOLUTION, v. 50, NOV 19 2018. (16/05787-7)

VAJANA, ELIA; BARBATO, MARIO; COLLI, LICIA; MILANESI, MARCO; ROCHAT, ESTELLE; FABRIZI, ENRICO; MUKASA, CHRISTOPHER; DEL CORVO, MARCELLO; MASEMBE, CHARLES; MUWANIKA, VINCENT B.; et al. Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever. FRONTIERS IN GENETICS, v. 9, OCT 3 2018. (16/05787-7)

COLLI, LICIA; MILANESI, MARCO; VAJANA, ELIA; IAMARTINO, DANIELA; BOMBA, LORENZO; PUGLISI, FRANCESCO; DEL CORVO, MARCELLO; NICOLAZZI, EZEQUIEL L.; AHMED, SAHAR S. E.; HERRERA, JESUS R. V.; et al. New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data. FRONTIERS IN GENETICS, v. 9, MAR 2 2018. (16/05787-7)

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)