Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design

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Calleja-Rodriguez , A , Li , Z , Hallingbäck , H R , Sillanpää , M J , Wu , H X , Abrahamsson , S & Garcia-Gil , M R 2019 , ' Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design ' , Journal of Theoretical Biology , vol. 462 , pp. 283-292 . https://doi.org/10.1016/j.jtbi.2018.11.007

Title: Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
Author: Calleja-Rodriguez, Ainhoa; Li, Zitong; Hallingbäck, Henrik R.; Sillanpää, Mikko J.; Wu, Harry X.; Abrahamsson, Sara; Garcia-Gil, Maria Rosario
Contributor organization: Organismal and Evolutionary Biology Research Programme
Date: 2019-02-07
Language: eng
Number of pages: 10
Belongs to series: Journal of Theoretical Biology
ISSN: 0022-5193
DOI: https://doi.org/10.1016/j.jtbi.2018.11.007
URI: http://hdl.handle.net/10138/327989
Abstract: In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F-2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G x E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.
Subject: Scots pine
Quantitative trait locus
LASSO
Adaptive traits
CONTROLLING ADAPTIVE TRAITS
GENOME-WIDE ASSOCIATION
COASTAL DOUGLAS-FIR
AUTUMN COLD-HARDINESS
POPULATION-SIZE
WOOD PROPERTIES
ABSCISIC-ACID
HEIGHT GROWTH
QTL DETECTION
ABI3 GENE
4112 Forestry
1172 Environmental sciences
Peer reviewed: Yes
Rights: cc_by_nc_nd
Usage restriction: openAccess
Self-archived version: publishedVersion


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