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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus

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Author(s):
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Aguiar, Tamiris Sayuri [1, 2] ; Pintor Torrecilha, Rafaela Beatriz [1, 2] ; Milanesi, Marco [1, 3, 4, 5] ; Harth Utsunomiya, Adam Taiti [1, 3] ; Trigo, Beatriz Batista [1, 3] ; Tijjani, Abdulfatai [6] ; Musa, Hassan Hussein [7] ; Lopes, Flavia Lombardi [3] ; Ajmone-Marsan, Paolo [4, 5] ; Carvalheiro, Roberto [8] ; de Rezende Neves, Haroldo Henrique [9] ; do Carmo, Adriana Santana [10] ; Hanotte, Olivier [6, 11] ; Sonstegard, Tad Stewart [12] ; Garcia, Jose Fernando [1, 3, 2] ; Utsunomiya, Yuri Tani [1, 3]
Total Authors: 16
Affiliation:
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[1] IAEA, Collaborating Ctr Anim Genom & Bioinformat, Aracatuba - Brazil
[2] Sao Paulo State Univ, Dept Preventhe Vet Med & Anim Reprod, Sch Agr & Veterinarian Sci, Jaboticabal - Brazil
[3] Sao Paulo State Univ, Dept Support Prod & Anim Hlth, Sch Vet Med, Aracatuba - Brazil
[4] Univ Cattolica Sacro Cuore, Dept Anim Sci Food & Nutr, Piacenza - Italy
[5] Univ Cattolica Sacro Cuore, Ancient DNA Res Ctr BioDNA, Piacenza - Italy
[6] Univ Nottingham, Cells Organisms & Mol Genet, Sch Life Sci, Nottingham - England
[7] Univ Khartoum, Fac Med Lab Sci, Khartoum - Sudan
[8] Sao Paulo State Univ, Sch Agr & Veterinarian Sci, Dept Anim Sci, Jaboticabal - Brazil
[9] GenSys Consultores Associados, Porto Alegre, RS - Brazil
[10] Univ Fed Goias, Escola Vet & Zootecnia, Goiania, Go - Brazil
[11] Int Livestock Res Inst, LiveGene CTLGH, Addis Ababa - Ethiopia
[12] Recombinetics Inc, St Paul, MN - USA
Total Affiliations: 12
Document type: Journal article
Source: FRONTIERS IN GENETICS; v. 9, DEC 7 2018.
Web of Science Citations: 1
Abstract

Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 x 10(-9)) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a similar to 6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding. (AU)

FAPESP's process: 10/52030-2 - Genome wide association study for reproductive traits in zebu bulls (Bos indicus) using high-density SNP chip
Grantee:José Fernando Garcia
Support type: Regular Research Grants
FAPESP's process: 17/08373-1 - Detection of deleterious alleles through absence of homozygous haplotypes in dogs
Grantee:Rafaela Beatriz Pintor Torrecilha
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 16/07531-0 - Comparison of methods for admixture and heterosis mapping in crossbred cattle populations
Grantee:Yuri Tani Utsunomiya
Support type: Scholarships abroad - Research Internship - Doctorate
FAPESP's process: 14/01095-8 - Use of next generation sequencing for the fine mapping of loci explaining variance in scrotal circumference in Nellore cattle
Grantee:Yuri Tani Utsunomiya
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 16/05787-7 - Combining high-density SNP genotypes and next generation sequence data to map disadvantageous genetic variants in Nellore cattle
Grantee:Marco Milanesi
Support type: Scholarships in Brazil - Post-Doctorate