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

Calleja-Rodriguez, Ainhoa and Li, Zitong and Hallingbäck, Henrik and Sillanpää, Mikko J. and Wu, Harry and Abrahamsson, Sara and Garcia Gil, Rosario (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. 462, 283-292
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Official URL: http://dx.doi.org/10.1016/j.jtbi.2018.11.007

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 F2-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 × 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.

Authors/Creators:Calleja-Rodriguez, Ainhoa and Li, Zitong and Hallingbäck, Henrik and Sillanpää, Mikko J. and Wu, Harry and Abrahamsson, Sara and Garcia Gil, Rosario
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
Series/Journal:Journal of theoretical biology (0022-5193)
Year of publishing :2019
Volume:462
Page range:283-292
Number of Pages:10
Publisher:Elsevier
ISSN:0022-5193
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
Keywords:Scots pine, Quantitative trait locus, LASSO, Adaptive traits, (Pinus sylvestris L.
URN:NBN:urn:nbn:se:slu:epsilon-e-5133
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-5133
Additional ID:
Type of IDID
DOIUNSPECIFIED
ID Code:15778
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
S - Faculty of Forest Sciences
Department:(NL, NJ) > Department of Plant Biology (from 140101)
(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:11 Dec 2018 08:06
Metadata Last Modified:11 Dec 2018 08:06

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