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Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species

Thistlethwaite, Frances R. and El-Dien, Omnia Gamal and Ratcliffe, Blaise and Klapste, Jaroslav and Porth, Ilga and Chen, Charles and Stoehr, Michael U. and Ingvarsson, Pär and El-Kassaby, Yousry A. (2020). Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species. PLoS ONE. 15 , e0232201 , 1-14
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Abstract

Background The presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with similar to 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesiiMirb. (Franco)) and Interior spruce (Picea glauca(Moench) Voss xPicea engelmanniiParry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200-50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F(1)families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada.
Results As marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000-15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size.
Conclusions Although possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits.

Authors/Creators:Thistlethwaite, Frances R. and El-Dien, Omnia Gamal and Ratcliffe, Blaise and Klapste, Jaroslav and Porth, Ilga and Chen, Charles and Stoehr, Michael U. and Ingvarsson, Pär and El-Kassaby, Yousry A.
Title:Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species
Year of publishing :2020
Volume:15
Article number:e0232201
Number of Pages:14
Publisher:PLoS
ISSN:1932-6203
Language:English
Publication Type:Journal 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
URN:NBN:urn:nbn:se:slu:epsilon-p-106930
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-106930
Additional ID:
Type of IDID
DOI10.1371/journal.pone.0232201
Web of Science (WoS)000542969500029
ID Code:17337
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:28 Aug 2020 08:01
Metadata Last Modified:28 Aug 2020 08:01

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