Genomics-Enabled Management of Genetic Resources in Radiata Pine

Jaroslav Klápště,Natalie J Graham,Heidi S Dungey,Grahame T Stovold,Mark Paget,Ahmed Ismael,Gancho T Slavov

doi:10.3390/f13020282

Jaroslav Klápště, Natalie J Graham + Show 5 more

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https://doi.org/10.3390/f13020282

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Journal: Forests	Publication Date: Feb 10, 2022
Citations: 6	License type: CC BY 4.0

Affiliation: Scion, Livestock Improvement Corporation

Abstract

Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) data for 4430 tree genotypes and single-nucleotide polymorphism (SNP) data for 2446 tree genotypes. Pedigree reconstruction was performed using a combination of maximum likelihood parentage assignment and matching based on identity-by-state (IBS) similarity. In addition, we used best linear unbiased prediction (BLUP) methods to predict phenotypes using SNP markers (GBLUP), recorded pedigree information (ABLUP), and single-step “blended” BLUP (HBLUP) combining SNP and pedigree information. We substantially improved the accuracy of pedigree records, resolving the inconsistent parental information of 506 tree genotypes. This led to substantially increased predictive ability (i.e., by up to 87%) in HBLUP analyses compared to a baseline from ABLUP. Genomic prediction was possible across populations and within previously untested families with moderately large training populations (N = 800–1200 tree genotypes) and using as few as 2000–5000 SNP markers. HBLUP was generally more effective than traditional ABLUP approaches, particularly after dealing appropriately with pedigree uncertainties. Our study provides evidence that genome-wide marker data can significantly enhance tree improvement. The operational implementation of genomic selection has started in radiata pine breeding in New Zealand, but further reductions in DNA extraction and genotyping costs may be required to realise the full potential of this approach.

Highlights

Introduction iationsDespite the increasing appreciation of deforestation as a major environmental threat, global rates of forest loss have not decreased and continue to be largely driven by anthropogenic changes in land use [1,2,3]
We focused on two phenotypic traits, both of which are part of the breeding objective for radiata pine in New Zealand: diameter at breast height (DBH), which was measured using a diameter tape at tree height of 1.4 m, and wood density (WD), which was estimated through the maximum moisture content method [28]
The second set consisted of first-degree relatives based on pedigree information that appeared unrelated based on single-nucleotide polymorphism (SNP) (IBS < 0.85)

Summary

Introduction

Despite the increasing appreciation of deforestation as a major environmental threat, global rates of forest loss have not decreased and continue to be largely driven by anthropogenic changes in land use [1,2,3]. This trend will likely be exacerbated by projected human population growth and climate change, both of which are expected to further aggravate the looming environmental crisis and put significant pressure on the long-term sustainability of natural renewable resources such as wood fibre [4]. Climate change is further increasing this complexity, and assisted migration is increasingly recognised as a potentially effective climate change adaptation tool at the population level [9,10,11,12], while the importance of within-population adaptive genetic variation is appreciated [13]

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