Pinus radiata genome reveals a downward demographic trajectory and opportunities for genomics-assisted breeding Article Swipe
Shane Sturrock
,
Tancred Frickey
,
Jules S. Freeman
,
Jakob B. Butler
,
Steffi Fritsche
,
Paloma Gea
,
Natalie J. Graham
,
Lucy Macdonald
,
Céline Mercier
,
Mark Paget
,
Leonardo Rippel Salgado
,
Frances C. Sussmilch
,
Emily Telfer
,
Phillip Wilcox
,
Heidi S. Dungey
,
Gancho T. Slavov
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/g3journal/jkaf125
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/g3journal/jkaf125
Pinus radiata D. Don is one of the most widely planted exotic conifers. It is also a threatened species because native populations are small, disjunct, and challenged by pests and pathogens, deforestation, and climate maladaptation. Genomic tools can both enhance genetic improvement in operational breeding programs, and support conservation efforts. Using PacBio long-read sequencing, we assembled 20.6 Gbp of the large and complex P. radiata genome into 305,330 scaffolds, achieving a scaffold N50 of 196.22 kbp, which corresponds to 89% of its estimated genome size. Gene annotation, based on transcriptome data with a 97.9% BUSCO score, yielded 86,039 gene models. Linkage maps were used to anchor 7,952 contigs totaling 1.79 Gbp (approximately 9% of the assembly) across 12 pseudomolecules, which included c. 26% of the predicted genes. Genome resequencing (5.2×) of 40 trees, from 4 native populations and a major Australasian breeding population, uncovered c. 608.3 M SNPs which were used for population genomic analyses. A key finding of these analyses was the slower-than-expected decay of linkage disequilibrium (i.e. r2 > 0.2 up to 30 kb for SNPs with minor allele frequencies ≥ 0.10), suggesting recent drastic reductions of effective population size. Our findings indicate that genomic prediction could use fewer markers than the ca. 30 k that are currently employed. Additionally, this study highlights the potential for Southern Hemisphere breeding programs as ex situ conservation resources and established a foundation for functional characterization of the P. radiata genome.
Related Topics
Concepts
Biology
Genome
Population
Population genomics
Linkage disequilibrium
Genomics
Tree breeding
Threatened species
Effective population size
Genome size
Evolutionary biology
Pinus radiata
Radiata
Genetics
Single-nucleotide polymorphism
Genetic variation
Ecology
Gene
Botany
Woody plant
Genotype
Sociology
Demography
Vigna
Habitat
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/g3journal/jkaf125
- OA Status
- gold
- Cited By
- 2
- References
- 54
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4411071311
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4411071311Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/g3journal/jkaf125Digital Object Identifier
- Title
-
Pinus radiata genome reveals a downward demographic trajectory and opportunities for genomics-assisted breedingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-06-05Full publication date if available
- Authors
-
Shane Sturrock, Tancred Frickey, Jules S. Freeman, Jakob B. Butler, Steffi Fritsche, Paloma Gea, Natalie J. Graham, Lucy Macdonald, Céline Mercier, Mark Paget, Leonardo Rippel Salgado, Frances C. Sussmilch, Emily Telfer, Phillip Wilcox, Heidi S. Dungey, Gancho T. SlavovList of authors in order
- Landing page
-
https://doi.org/10.1093/g3journal/jkaf125Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.1093/g3journal/jkaf125Direct OA link when available
- Concepts
-
Biology, Genome, Population, Population genomics, Linkage disequilibrium, Genomics, Tree breeding, Threatened species, Effective population size, Genome size, Evolutionary biology, Pinus radiata, Radiata, Genetics, Single-nucleotide polymorphism, Genetic variation, Ecology, Gene, Botany, Woody plant, Genotype, Sociology, Demography, Vigna, HabitatTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 2Per-year citation counts (last 5 years)
- References (count)
-
54Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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