Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations.

Autor: Müller BSF; Molecular Biology Program, Cell Biology Department, Biological Sciences Institute, University of Brasília, Campus Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.; EMBRAPA Genetic Resources and Biotechnology - EPqB, Brasília, DF, 70770-910, Brazil., de Almeida Filho JE; Plant Breeding Laboratory, State University of North Fluminense 'Darcy Ribeiro', Campos dos Goytacazes, RJ, 28013-602, Brazil., Lima BM; FIBRIA S.A. Technology Center, Jacareí, SP, 12340-010, Brazil., Garcia CC; International Paper of Brazil, Rodovia SP 340 KM 171, Mogi Guaçu, SP, 13840-970, Brazil., Missiaggia A; FIBRIA S.A. Technology Center, Jacareí, SP, 12340-010, Brazil., Aguiar AM; FIBRIA S.A. Technology Center, Jacareí, SP, 12340-010, Brazil., Takahashi E; Celulose Nipo-Brasileira (CENIBRA) S.A., Belo Oriente, MG, 35196-000, Brazil., Kirst M; School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA., Gezan SA; School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA., Silva-Junior OB; EMBRAPA Genetic Resources and Biotechnology - EPqB, Brasília, DF, 70770-910, Brazil.; Genomic Sciences and Biotechnology Program, SGAN, Catholic University of Brasília, 916 modulo B, Brasília, DF, 70790-160, Brazil., Neves LG; RAPiD Genomics LLC, Gainesville, FL, 32601, USA., Grattapaglia D; Molecular Biology Program, Cell Biology Department, Biological Sciences Institute, University of Brasília, Campus Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.; EMBRAPA Genetic Resources and Biotechnology - EPqB, Brasília, DF, 70770-910, Brazil.; Genomic Sciences and Biotechnology Program, SGAN, Catholic University of Brasília, 916 modulo B, Brasília, DF, 70790-160, Brazil.
Jazyk: angličtina
Zdroj: The New phytologist [New Phytol] 2019 Jan; Vol. 221 (2), pp. 818-833. Date of Electronic Publication: 2018 Sep 25.
DOI: 10.1111/nph.15449
Abstrakt: 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.
(© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)
Databáze: MEDLINE
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