Genome-Wide Mapping of Loci Explaining Variance in Scrotal Circumference in Nellore Cattle

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Abstract

The reproductive performance of bulls has a high impact on the beef cattle industry. Scrotal circumference (SC) is the most recorded reproductive trait in beef herds, 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 for reproductive performance and uncover molecular mechanisms underlying complex aspects of bovine reproductive biology. In this paper, we report a genome-wide scan for chromosome segments explaining differences in SC, using data of 861 Nellore bulls ( Bos indicus) genotyped for over 777,000 single nucleotide polymorphisms. 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. Based on intensive literature mining, SP4, MAGEL2, SH3RF2, PDE5A and SNAI2 are proposed as novel candidate genes for SC, as they affect growth and testicular size in other animal models. These findings contribute to linking reproductive phenotypes to gene functions, and may offer new insights on the molecular biology of male fertility.

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Most cited references 24

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Family-based association tests for genomewide association scans.

Wei-Min Chen, Gonçalo R Abecasis (2007)

With millions of single-nucleotide polymorphisms (SNPs) identified and characterized, genomewide association studies have begun to identify susceptibility genes for complex traits and diseases. These studies involve the characterization and analysis of very-high-resolution SNP genotype data for hundreds or thousands of individuals. We describe a computationally efficient approach to testing association between SNPs and quantitative phenotypes, which can be applied to whole-genome association scans. In addition to observed genotypes, our approach allows estimation of missing genotypes, resulting in substantial increases in power when genotyping resources are limited. We estimate missing genotypes probabilistically using the Lander-Green or Elston-Stewart algorithms and combine high-resolution SNP genotypes for a subset of individuals in each pedigree with sparser marker data for the remaining individuals. We show that power is increased whenever phenotype information for ungenotyped individuals is included in analyses and that high-density genotyping of just three carefully selected individuals in a nuclear family can recover >90% of the information available if every individual were genotyped, for a fraction of the cost and experimental effort. To aid in study design, we evaluate the power of strategies that genotype different subsets of individuals in each pedigree and make recommendations about which individuals should be genotyped at a high density. To illustrate our method, we performed genomewide association analysis for 27 gene-expression phenotypes in 3-generation families (Centre d'Etude du Polymorphisme Humain pedigrees), in which genotypes for ~860,000 SNPs in 90 grandparents and parents are complemented by genotypes for ~6,700 SNPs in a total of 168 individuals. In addition to increasing the evidence of association at 15 previously identified cis-acting associated alleles, our genotype-inference algorithm allowed us to identify associated alleles at 4 cis-acting loci that were missed when analysis was restricted to individuals with the high-density SNP data. Our genotype-inference algorithm and the proposed association tests are implemented in software that is available for free.

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Copy number variation of individual cattle genomes using next-generation sequencing.

Maria Francesca Cardone, Derek Bickhart, T Sonstegard … (2012)

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ~55.6-Mbp sequence--476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, χ(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

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BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma.

Sarah J. Fletcher, I Kubonishi, Christopher C. French … (2003)

The poorly differentiated carcinoma with t(15;19)(q13, p13.1) is characterized by its highly aggressive, invariably lethal clinical course. The chromosome 19 translocation breakpoint targets the BRD4 double bromodomain-containing gene, which functions in regulation of cell cycle progression. Herein we demonstrate that BRD4 is fused with nearly the entire transcript of the novel 15q13 gene, NUT (nuclear protein in testis), forming a 6.4-kb fusion oncogene, BRD4-NUT. NUT, like BRD4, is predicted to encode a nuclear protein but, unlike the ubiquitous BRD4 transcript, is expressed only in testis. These findings establish a model to elucidate the oncogenic consequences of unscheduled NUT expression and altered BRD4 function. Very few fusion oncogenes have been identified in epithelial tumors, and BRD4-NUT is the first fusion oncogene mechanism identified in a highly lethal form of carcinoma.

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Author and article information

Contributors

Zhanjiang Liu: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2014

Publication date (Electronic): 18 February 2014

Volume: 9

Issue: 2

Electronic Location Identifier: e88561

Affiliations

[1 ]Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil

[2 ]Departamento de Zootecnia, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil

[3 ]GenSys Consultores Associados, Porto Alegre, Rio Grande do Sul, Brazil

[4 ]Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil

[5 ]Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria

[6 ]CSIRO - Commonwealth Scientific and Industrial Research Organization, Food Futures Flagship, Brisbane, Queensland, Australia

[7 ]Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada

[8 ]Centre for Reproduction and Genomics, AgResearch, Invermay, Mosgiel, Otago, New Zealand

[9 ]Animal Improvement Programs Laboratory, ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Beltsville, Maryland, United States of America

[10 ]Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil

[11 ]Bovine Functional Genomics Laboratory, ARS-USDA - Agricultural Research Service - United States Department of Agriculture, Beltsville, Maryland, United States of America

Auburn University, United States of America

Author notes

* E-mail: jfgarcia@ 123456fmva.unesp.br

Competing Interests: Roberto Carvalheiro is affiliated to GenSys Consultores Associados. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.

Conceived and designed the experiments: JFG TSS JS JM JBC CPVT FSS MVGBS LRPN. Performed the experiments: ASC YTU HHRN RC MCM LBZ PKRKI AMPO. Analyzed the data: YTU. Contributed reagents/materials/analysis tools: JFG TSS JS JM JBC CPVT FSS MVGBS LRPN RC HHRN ASC YTU. Wrote the paper: YTU. Coordinated the study: JFG. All authors read, approved and contributed to edit the final manuscript.

Article

Publisher ID: PONE-D-13-44134

DOI: 10.1371/journal.pone.0088561

PMC ID: 3928245

SO-VID: 2f9c735e-73a7-4ab3-8a1c-be79a20fb9cb

License:

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

History

Date received : 28 October 2013

Date accepted : 7 January 2014

Page count

Pages: 9

Funding

This research was supported by: National Counsel of Technological and Scientific Development (CNPq - http://www.cnpq.br/) (process 560922/2010-8 and 483590/2010-0); and São Paulo Research Foundation (FAPESP - http://www.fapesp.br/) (process 2011/16643-2 and 2010/52030-2).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Genome-Wide Mapping of Loci Explaining Variance in Scrotal Circumference in Nellore Cattle

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Genome Integrity

Most cited references 24

Family-based association tests for genomewide association scans.

Copy number variation of individual cattle genomes using next-generation sequencing.

BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma.

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