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

Bibliographische Detailangaben
Veröffentlicht in:	The New phytologist. - 1979. - 221(2019), 2 vom: 01. Jan., Seite 818-833
1. Verfasser:	Müller, Bárbara S F (VerfasserIn)
Weitere Verfasser:	de Almeida Filho, Janeo E, Lima, Bruno M, Garcia, Carla C, Missiaggia, Alexandre, Aguiar, Aurelio M, Takahashi, Elizabete, Kirst, Matias, Gezan, Salvador A, Silva-Junior, Orzenil B, Neves, Leandro G, Grattapaglia, Dario
Format:	Online-Aufsatz
Sprache:	English
Veröffentlicht:	2019
Zugriff auf das übergeordnete Werk:	The New phytologist
Schlagworte:	Journal Article Research Support, Non-U.S. Gov't Eucalyptus Joint-GWAS genome-wide association study (GWAS) high-throughput SNP genotyping meta-analysis regional heritability mapping (RHM) relatedness

Beschreibung
Zusammenfassung:	© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust. 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
Beschreibung:	Date Completed 14.01.2020 Date Revised 30.09.2020 published: Print-Electronic Citation Status MEDLINE
ISSN:	1469-8137
DOI:	10.1111/nph.15449