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Independent and Joint‐<scp>GWAS</scp>for growth traits inEucalyptusby assembling genome‐wide data for 3373 individuals across four breeding populations
- Source :
- Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice), Empresa Brasileira de Pesquisa Agropecuária (Embrapa), instacron:EMBRAPA
- Publication Year :
- 2018
- Publisher :
- Wiley, 2018.
-
Abstract
- 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.
- Subjects :
- 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
Subjects
Details
- ISSN :
- 14698137 and 0028646X
- Volume :
- 221
- Database :
- OpenAIRE
- Journal :
- New Phytologist
- Accession number :
- edsair.doi.dedup.....23a1a21efed06ffe683b597153bad3dd