Independent and Joint‐GWAS for growth traits inEucalyptusby assembling genome‐wide data for 3373 individuals across four breeding populations
| Autor: | Bárbara S. F. Müller, Janeo Eustáquio de Almeida Filho, Aurélio Mendes Aguiar, Alexandre Alves Missiaggia, Orzenil B. Silva-Junior, Dario Grattapaglia, Leandro G. Neves, Elizabete Keiko Takahashi, Bruno Marco de Lima, Carla Garcia, Matias Kirst, Salvador A. Gezan |
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| Přispěvatelé: | BÁRBARA S. F. MULLER, UNB, ORZENIL BONFIM DA SILVA JUNIOR, Cenargen, LEANDRO G. NEVES, RAPID GENOMICS LLC, USA, DARIO GRATTAPAGLIA, Cenargen., JANEO E. DE ALMEIDA FILHO, UENF, BRUNO M. LIMA, FIBRIA S.A. TECHNOLOGY CENTER, CARLA C. GARCIA, INTERNATIONAL PAPER OF BRAZIL, ALEXANDRE MISSIAGGIA, FIBRIA S.A. TECHNOLOGY CENTER, AURELIO M. AGUIAR, FIBRIA S.A. TECHNOLOGY CENTER, ELIZABETE TAKAHASHI, CELULOSE NIPO-BRASILEIRA (CENIBRA) S.A., MATIAS KIRST, UNIVERSITY OF FLORIDA, USA, SALVADOR A. GEZAN, UNIVERSITY OF FLORIDA, USA |
| Rok vydání: | 2018 |
| Předmět: |
musculoskeletal diseases
0106 biological sciences 0301 basic medicine Physiology Population Inheritance Patterns Single-nucleotide polymorphism Genome-wide association study Plant Science Biology Polymorphism Single Nucleotide 01 natural sciences Genome Linkage Disequilibrium 03 medical and health sciences Quantitative Trait Heritable High-throughput SNP genotyping Joint-GWAS Regional heritability mapping (RHM) SNP education Genetic association Principal Component Analysis Eucalyptus education.field_of_study Genome-wide association study (GWAS) Heritability Plant Breeding Meta-analysis 030104 developmental biology Evolutionary biology Tree breeding Relatedness Genome Plant Genome-Wide Association Study 010606 plant biology & botany |
| Zdroj: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice) Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
| ISSN: | 1469-8137 0028-646X |
| DOI: | 10.1111/nph.15449 |
| Popis: | Genome-wide association studies (GWAS) in plants typically suffer from limited statistical power. An alternative to the logistical and cost challenge of increasing sample sizes is to gain power by meta-analysis using information from independent studies. We carried out GWAS for growth traits with six single-marker models and regional heritability mapping (RHM) in four Eucalyptus breeding populations independently and by Joint-GWAS, using gene and segment-based models, with data for 3373 individuals genotyped with a communal EUChip60KSNP platform. While single-single nucleotide polymorphism (SNP) GWAS hardly detected significant associations at high-stringency in each population, gene-based Joint-GWAS revealed nine genes significantly associated with tree height. Associations detected using single-SNP GWAS, RHM and Joint-GWAS set-based models explained on average 3-20% of the phenotypic variance. Whole-genome regression, conversely, captured 64-89% of the pedigree-based heritability in all populations. Several associations independently detected for the same SNPs in different populations provided unprecedented GWAS validation results in forest trees. Rare and common associations were discovered in eight genes involved in cell wall biosynthesis and lignification. With the increasing adoption of genomic prediction of complex phenotypes using shared SNPs and much larger tree breeding populations, Joint-GWAS approaches should provide increasing power to pinpoint discrete associations potentially useful toward tree breeding and molecular applications. |
| Databáze: | OpenAIRE |
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