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Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

Calleja-Rodriguez, Ainhoa and Chen, Zhiqiang and Suontama, Mari and Pan, Jin and Wu, Harry (2021). Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris. Frontiers in Plant Science. 12 , 666820
[Research article]

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Abstract

Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive x additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.

Authors/Creators:Calleja-Rodriguez, Ainhoa and Chen, Zhiqiang and Suontama, Mari and Pan, Jin and Wu, Harry
Title:Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris
Series Name/Journal:Frontiers in Plant Science
Year of publishing :2021
Volume:12
Article number:666820
Number of Pages:16
Publisher:FRONTIERS MEDIA SA
ISSN:1664-462X
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
Keywords:scots pine (Pinus sylvestris L), genomic prediction, nonadditive effects, dominance, epistasis, response to selection, genetic gain
URN:NBN:urn:nbn:se:slu:epsilon-p-113304
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113304
Additional ID:
Type of IDID
DOI10.3389/fpls.2021.666820
Web of Science (WoS)000680569500001
ID Code:25154
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:02 Sep 2021 11:26
Metadata Last Modified:02 Sep 2021 11:31

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