Dispersion and domestication shaped the genome of bread wheat
Paul J. Berkman
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
CSIRO Plant Industry, St Lucia, QLD, Australia
Search for more papers by this authorPaul Visendi
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorHong C. Lee
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorJiri Stiller
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
CSIRO Plant Industry, St Lucia, QLD, Australia
Search for more papers by this authorSahana Manoli
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorMichał T. Lorenc
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorKaitao Lai
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorJacqueline Batley
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorDelphine Fleury
Australian Centre for Plant Functional Genomics, University of Adelaide, Glen Osmond, SA, Australia
Search for more papers by this authorHana Šimková
Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech, Republic
Search for more papers by this authorMarie Kubaláková
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
Search for more papers by this authorSong Weining
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
Search for more papers by this authorJaroslav Doležel
Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech, Republic
Search for more papers by this authorCorresponding Author
David Edwards
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Correspondence (Tel +61 0 7 3346 7084; fax +61 0 7 3365 1176; email [email protected])Search for more papers by this authorPaul J. Berkman
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
CSIRO Plant Industry, St Lucia, QLD, Australia
Search for more papers by this authorPaul Visendi
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorHong C. Lee
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorJiri Stiller
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
CSIRO Plant Industry, St Lucia, QLD, Australia
Search for more papers by this authorSahana Manoli
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorMichał T. Lorenc
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorKaitao Lai
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorJacqueline Batley
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Search for more papers by this authorDelphine Fleury
Australian Centre for Plant Functional Genomics, University of Adelaide, Glen Osmond, SA, Australia
Search for more papers by this authorHana Šimková
Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech, Republic
Search for more papers by this authorMarie Kubaláková
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
Search for more papers by this authorSong Weining
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
Search for more papers by this authorJaroslav Doležel
Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech, Republic
Search for more papers by this authorCorresponding Author
David Edwards
School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
Correspondence (Tel +61 0 7 3346 7084; fax +61 0 7 3365 1176; email [email protected])Search for more papers by this authorAbstract
Summary
Despite the international significance of wheat, its large and complex genome hinders genome sequencing efforts. To assess the impact of selection on this genome, we have assembled genomic regions representing genes for chromosomes 7A, 7B and 7D. We demonstrate that the dispersion of wheat to new environments has shaped the modern wheat genome. Most genes are conserved between the three homoeologous chromosomes. We found differential gene loss that supports current theories on the evolution of wheat, with greater loss observed in the A and B genomes compared with the D. Analysis of intervarietal polymorphisms identified fewer polymorphisms in the D genome, supporting the hypothesis of early gene flow between the tetraploid and hexaploid. The enrichment for genes on the D genome that confer environmental adaptation may be associated with dispersion following wheat domestication. Our results demonstrate the value of applying next-generation sequencing technologies to assemble gene-rich regions of complex genomes and investigate polyploid genome evolution. We anticipate the genome-wide application of this reduced-complexity syntenic assembly approach will accelerate crop improvement efforts not only in wheat, but also in other polyploid crops of significance.
Supporting Information
| Filename | Description |
|---|---|
| pbi12044-sup-0001-FigS1-S3.pptxapplication/, 8.5 MB | Figure S1 Network image produced by STRING representing the scale of gene networking on 7A (A), 7B (B), and 7D (C). Figure S2 Histogram displaying the number of bin-mapped EST sequences across all wheat chromosomes that have aligned to the assemblies of 7A (red), 7B (blue), and 7D (green). Figure S3 CMap image representing the comparison of genetic markers from A. tauschii against the 7D syntenic build. |
| pbi12044-sup-0002-TableS1-S6.xlsxMS Excel, 675.3 KB | Table S1 Full summary of Syntenic Build statistics. Table S2 GenomeZipper of wheat group 7 chromosomes against B. distachyon, O. sativa, and S. bicolor in both syntenic (A) and nonsyntenic (B) regions. Table S3 STRING GO terms enrichment analysis with all group 7 genes used as the background. Table S4 Table listing chromosome-arm specific bin-mapped EST RBB alignment results for contigs assembled from each chromosome arm. Table S5 Read mapping statistics for Illumina 100 bp paired-end reads from 4 Australian varieties (Gladius, Drysdale, Excalibur, RAC875). TableS6 SNPs called between 4 Australian wheat cultivars (Gladius, Drysdale, Excalibur, RAC875). |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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