dc.contributor.author |
Mostert-O’Neill, Marja
|
|
dc.contributor.author |
Tate, Hannah
|
|
dc.contributor.author |
Reynolds, Sharon Melissa
|
|
dc.contributor.author |
Mphahlele, M.M. (Makobatjatji)
|
|
dc.contributor.author |
Van den Berg, Gert
|
|
dc.contributor.author |
Verryn, Steve D.
|
|
dc.contributor.author |
Acosta, Juan J.
|
|
dc.contributor.author |
Borevitz, Justin O.
|
|
dc.contributor.author |
Myburg, Alexander Andrew
|
|
dc.date.accessioned |
2023-09-29T10:11:38Z |
|
dc.date.available |
2023-09-29T10:11:38Z |
|
dc.date.issued |
2022-09 |
|
dc.description |
DATA AVAILABILITY : The genomic data generated and analysed in this study are available online via the Dryad archives under accession https://doi. org/10.5061/dryad.h18931zj6. |
en_US |
dc.description |
SUPPLEMENTARY MATERIAL : FIG. S1. Population structure in relation to wild Eucalyptus grandis and other species in section Latoangulatae based on principal component analysis, discriminant analysis of principal components and sparse nonnegative matrix factorization. FIG. S2. Breeding Eucalyptus grandis population structure for all breeding samples, those excluding introgressed, and those excluding infused individuals in relation to the wild progenitor populations based on principal component analysis, sparse nonnegative matrix factorization and discriminant analysis of principal components analyses. FIG. S3. Population differentiation FST estimates among breeding Eucalyptus grandis, wild E. grandis and other species in section Latoangulatae. FIG. S4. Chloroplast (cp) haplotype network based on 24 cp single nucleotide polymorphisms. FIG. S5. Marker-specific Hardy–Weinberg equilibrium signed R values of wild vs breeding populations. FIG. S6. Genomic outliers and linkage disequilibrium plots per chromosome. FIG. S7. Breeding population linkage disequilibrium decay over genomic distance in kb. FIG. S8 Outlier detection by pcadapt scan. |
en_US |
dc.description |
TABLE S1. Ancestry assignment of chromosomal segments. |
en_US |
dc.description |
TABLE S2. Cluster assignment of samples using discriminant analysis of principal components to identify genetically infused breeding individuals. TABLE S3. Summary statistics of genetic diversity using hierfstat v.0.04-22. TABLE S4. Wilcoxon signed rank test P-values supporting the alternative hypothesis that the mean of the outliers was greater than the mean of the rest of the single nucleotide polymorphisms. TABLE S5. Gene Ontology enrichment analysis for genes in linkage disequilibrium with outlier single nucleotide polymorphisms (SNPs) before excluding organellar-targeting SNPs. |
en_US |
dc.description |
TABLE S6. Blastn against the organellar genomes. |
en_US |
dc.description |
TABLE S7. Marker statistics of single nucleotide polymorphisms with multigenome targets. Please note: Wiley Blackwell are not responsible for the content or functionality of any Supporting Information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office. |
en_US |
dc.description.abstract |
From its origins in Australia, Eucalyptus grandis has spread to every continent, except
Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as
South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its
infancy, representing a unique opportunity to interrogate the genomic consequences of artificial
selection early in the domestication process.
To determine how a century of artificial selection has changed the genome of E. grandis,
we generated single nucleotide polymorphism genotypes for 1080 individuals from three
advanced South African breeding programmes using the EUChip60K chip, and investigated
population structure and genome-wide differentiation patterns relative to wild progenitors.
Breeding and wild populations appeared genetically distinct. We found genomic evidence
of evolutionary processes known to have occurred in other plant domesticates, including
interspecific introgression and intraspecific infusion from wild material. Furthermore, we
found genomic regions with increased linkage disequilibrium and genetic differentiation,
putatively representing early soft sweeps of selection.
This is, to our knowledge, the first study of genomic signatures of domestication in a timber
species looking beyond the first few generations of cultivation. Our findings highlight the
importance of intra- and interspecific hybridization during early domestication. |
en_US |
dc.description.department |
Biochemistry |
en_US |
dc.description.department |
Forestry and Agricultural Biotechnology Institute (FABI) |
en_US |
dc.description.department |
Genetics |
en_US |
dc.description.department |
Microbiology and Plant Pathology |
en_US |
dc.description.librarian |
am2023 |
en_US |
dc.description.sponsorship |
The Department of Science and Innovation and Technology Innovation Agency (DSI/TIA, Strategic Grant-Eucalyptus Genomics Platform), the Forestry Sector Innovation Fund (FSIF Eucalyptus Genome Diversity Atlas grant), National Research Foundation (NRF) of South Africa, the Technology and Human Resources for Industry Programme and by the Forest Molecular Genetics (FMG) Industry Consortium at the University of Pretoria. |
en_US |
dc.description.uri |
www.newphytologist.com |
en_US |
dc.identifier.citation |
Mostert-O’Neill, M.M., Tate, H., Reynolds, S.M. et al. 2022, 'Genomic consequences of artificial selection during early domestication of a wood fibre crop', New Phytologist, vol. 235, pp. 1944-1956. DOI : 10.1111/nph.18297. |
en_US |
dc.identifier.issn |
0028-646X (print) |
|
dc.identifier.issn |
1469-8137 (online) |
|
dc.identifier.other |
10.1111/nph.18297 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/92610 |
|
dc.language.iso |
en |
en_US |
dc.publisher |
Wiley |
en_US |
dc.rights |
© 2022 New Phytologist Foundation.
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License. |
en_US |
dc.subject |
Artificial selection |
en_US |
dc.subject |
Domestication |
en_US |
dc.subject |
Eucalypt |
en_US |
dc.subject |
Forestry |
en_US |
dc.subject |
Population genomics |
en_US |
dc.subject |
Selection signatures |
en_US |
dc.subject |
SDG-15: Life on land |
en_US |
dc.title |
Genomic consequences of artificial selection during early domestication of a wood fibre crop |
en_US |
dc.type |
Article |
en_US |