1
|
Fehrer J, Slavíková R, Paštová L, Josefiová J, Mráz P, Chrtek J, Bertrand YJK. Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae). FRONTIERS IN PLANT SCIENCE 2021; 12:647375. [PMID: 33777082 PMCID: PMC7994888 DOI: 10.3389/fpls.2021.647375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 05/14/2023]
Abstract
Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.
Collapse
Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Judith Fehrer,
| | - Renáta Slavíková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | | | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Patrik Mráz
- Department of Botany, Charles University, Prague, Czechia
| | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Charles University, Prague, Czechia
| | | |
Collapse
|
2
|
Zagorski D, Hartmann M, Bertrand YJK, Paštová L, Slavíková R, Josefiová J, Fehrer J. Characterization and Dynamics of Repeatomes in Closely Related Species of Hieracium (Asteraceae) and Their Synthetic and Apomictic Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:591053. [PMID: 33224172 PMCID: PMC7667050 DOI: 10.3389/fpls.2020.591053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/09/2020] [Indexed: 05/05/2023]
Abstract
The repetitive content of the plant genome (repeatome) often represents its largest fraction and is frequently correlated with its size. Transposable elements (TEs), the main component of the repeatome, are an important driver in the genome diversification due to their fast-evolving nature. Hybridization and polyploidization events are hypothesized to induce massive bursts of TEs resulting, among other effects, in an increase of copy number and genome size. Little is known about the repeatome dynamics following hybridization and polyploidization in plants that reproduce by apomixis (asexual reproduction via seeds). To address this, we analyzed the repeatomes of two diploid parental species, Hieracium intybaceum and H. prenanthoides (sexual), their diploid F1 synthetic and their natural triploid hybrids (H. pallidiflorum and H. picroides, apomictic). Using low-coverage next-generation sequencing (NGS) and a graph-based clustering approach, we detected high overall similarity across all major repeatome categories between the parental species, despite their large phylogenetic distance. Medium and highly abundant repetitive elements comprise ∼70% of Hieracium genomes; most prevalent were Ty3/Gypsy chromovirus Tekay and Ty1/Copia Maximus-SIRE elements. No TE bursts were detected, neither in synthetic nor in natural hybrids, as TE abundance generally followed theoretical expectations based on parental genome dosage. Slight over- and under-representation of TE cluster abundances reflected individual differences in genome size. However, in comparative analyses, apomicts displayed an overabundance of pararetrovirus clusters not observed in synthetic hybrids. Substantial deviations were detected in rDNAs and satellite repeats, but these patterns were sample specific. rDNA and satellite repeats (three of them were newly developed as cytogenetic markers) were localized on chromosomes by fluorescence in situ hybridization (FISH). In a few cases, low-abundant repeats (5S rDNA and certain satellites) showed some discrepancy between NGS data and FISH results, which is due partly to the bias of low-coverage sequencing and partly to low amounts of the satellite repeats or their sequence divergence. Overall, satellite DNA (including rDNA) was markedly affected by hybridization, but independent of the ploidy or reproductive mode of the progeny, whereas bursts of TEs did not play an important role in the evolutionary history of Hieracium.
Collapse
|
3
|
Bartaula R, Melo ATO, Kingan S, Jin Y, Hale I. Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid. BMC PLANT BIOLOGY 2019; 19:319. [PMID: 31311507 PMCID: PMC6636152 DOI: 10.1186/s12870-019-1893-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/19/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Non-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis (Pg)], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen's alternate host, barberry (Berberis spp.), to overcome this challenge. RESULTS In this study, an interspecific mapping population derived from a cross between Pg-resistant Berberis thunbergii (Bt) and Pg-susceptible B. vulgaris was developed to investigate the Pg-NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance. CONCLUSIONS Foundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg-NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg-NHR in the alternate host of one of agriculture's most devastating pathogens.
Collapse
Affiliation(s)
- Radhika Bartaula
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824 USA
| | - Arthur T. O. Melo
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | | | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108 USA
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| |
Collapse
|
4
|
Butler JB, Vaillancourt RE, Potts BM, Lee DJ, King GJ, Baten A, Shepherd M, Freeman JS. Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement. BMC Genomics 2017; 18:397. [PMID: 28532390 PMCID: PMC5441008 DOI: 10.1186/s12864-017-3782-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/10/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. RESULTS We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. CONCLUSIONS These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.
Collapse
Affiliation(s)
- J B Butler
- School of Biological Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - R E Vaillancourt
- School of Biological Science and ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - B M Potts
- School of Biological Science and ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - D J Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD, 4558, Australia
| | - G J King
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - A Baten
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - M Shepherd
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - J S Freeman
- School of Biological Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
| |
Collapse
|
5
|
Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing. Sci Rep 2016; 6:24070. [PMID: 27040179 PMCID: PMC4819198 DOI: 10.1038/srep24070] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/07/2016] [Indexed: 11/08/2022] Open
Abstract
Salvia miltiorrhiza is an important medicinal crop in traditional Chinese medicine (TCM). Knowledge of its genetic foundation is limited because sufficient molecular markers have not been developed, and therefore a high-density genetic linkage map is incomplete. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-throughput strategy for large-scale SNP (Single Nucleotide Polymorphisms) discovery and genotyping based on next generation sequencing (NGS). In this study, genomic DNA extracted from two parents and their 96 F1 individuals was subjected to high-throughput sequencing and SLAF library construction. A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. The final linkage map consists of 5,164 SLAFs in 8 linkage groups (LGs) and spans 1,516.43 cM, with an average distance of 0.29 cM between adjacent markers. The results will not only provide a platform for mapping quantitative trait loci but also offer a critical new tool for S. miltiorrhiza biotechnology and comparative genomics as well as a valuable reference for TCM studies.
Collapse
|
6
|
Bartholomé J, Mandrou E, Mabiala A, Jenkins J, Nabihoudine I, Klopp C, Schmutz J, Plomion C, Gion JM. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. THE NEW PHYTOLOGIST 2015; 206:1283-96. [PMID: 25385325 DOI: 10.1111/nph.13150] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/29/2014] [Indexed: 05/21/2023]
Abstract
Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.
Collapse
Affiliation(s)
- Jérôme Bartholomé
- CIRAD, UMR AGAP, F-33612, Cestas, France
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| | - Eric Mandrou
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Ibouniyamine Nabihoudine
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Christophe Klopp
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| | - Jean-Marc Gion
- CIRAD, UMR AGAP, F-33612, Cestas, France
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| |
Collapse
|
7
|
Cao PB, Azar S, SanClemente H, Mounet F, Dunand C, Marque G, Marque C, Teulières C. Genome-wide analysis of the AP2/ERF family in Eucalyptus grandis: an intriguing over-representation of stress-responsive DREB1/CBF genes. PLoS One 2015; 10:e0121041. [PMID: 25849589 DOI: 10.1371/journal.pone.0121041] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/11/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The AP2/ERF family includes a large number of developmentally and physiologically important transcription factors sharing an AP2 DNA-binding domain. Among them DREB1/CBF and DREB2 factors are known as master regulators respectively of cold and heat/osmotic stress responses. EXPERIMENTAL APPROACHES The manual annotation of AP2/ERF family from Eucalyptus grandis, Malus, Populus and Vitis genomes allowed a complete phylogenetic study for comparing the structure of this family in woody species and the model Arabidopsis thaliana. Expression profiles of the whole groups of EgrDREB1 and EgrDREB2 were investigated through RNAseq database survey and RT-qPCR analyses. RESULTS The structure and the size of the AP2/ERF family show a global conservation for the plant species under comparison. In addition to an expansion of the ERF subfamily, the tree genomes mainly differ with respect to the group representation within the subfamilies. With regard to the E. grandis DREB subfamily, an obvious feature is the presence of 17 DREB1/CBF genes, the maximum reported to date for dicotyledons. In contrast, only six DREB2 have been identified, which is similar to the other plants species under study, except for Malus. All the DREB1/CBF and DREB2 genes from E. grandis are expressed in at least one condition and all are heat-responsive. Regulation by cold and drought depends on the genes but is not specific of one group; DREB1/CBF group is more cold-inducible than DREB2 which is mainly drought responsive. CONCLUSION These features suggest that the dramatic expansion of the DREB1/CBF group might be related to the adaptation of this evergreen tree to climate changes when it expanded in Australia.
Collapse
Affiliation(s)
- P B Cao
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - S Azar
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - H SanClemente
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - F Mounet
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - C Dunand
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - G Marque
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - C Marque
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| | - C Teulières
- Université de Toulouse, UPS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France; CNRS, UMR 5546, LRSV, 24 Chemin de Borde Rouge, Auzeville, BP 42617 31326, Castanet-Tolosan, France
| |
Collapse
|
8
|
Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One 2015; 10:e0116528. [PMID: 25602379 PMCID: PMC4300219 DOI: 10.1371/journal.pone.0116528] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
Collapse
Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
- * E-mail:
| | - Veeramuthu Dharanishanthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
| | - Ishangi Agarwal
- Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
| |
Collapse
|
9
|
Abstract
In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F1 population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.
Collapse
Affiliation(s)
- Dawei Wang
- College of Forestry, Northwest A and F University, Yangling, Shaanxi 712100, People's Republic of China.
| | | | | | | | | |
Collapse
|
10
|
Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 2012; 7:e44684. [PMID: 22984541 PMCID: PMC3439404 DOI: 10.1371/journal.pone.0044684] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
Collapse
|
11
|
Hudson CJ, Freeman JS, Kullan ARK, Petroli CD, Sansaloni CP, Kilian A, Detering F, Grattapaglia D, Potts BM, Myburg AA, Vaillancourt RE. A reference linkage map for Eucalyptus. BMC Genomics 2012; 13:240. [PMID: 22702473 PMCID: PMC3436727 DOI: 10.1186/1471-2164-13-240] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 06/04/2012] [Indexed: 01/26/2023] Open
Abstract
Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.
Collapse
Affiliation(s)
- Corey J Hudson
- School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Abril N, Gion JM, Kerner R, Müller-Starck G, Cerrillo RMN, Plomion C, Renaut J, Valledor L, Jorrin-Novo JV. Proteomics research on forest trees, the most recalcitrant and orphan plant species. PHYTOCHEMISTRY 2011; 72:1219-42. [PMID: 21353265 DOI: 10.1016/j.phytochem.2011.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 12/27/2010] [Accepted: 01/06/2011] [Indexed: 05/06/2023]
Abstract
The contribution of proteomics to the knowledge of forest tree (the most recalcitrant and almost forgotten plant species) biology is being reviewed and discussed, based on the author's own research work and papers published up to November 2010. This review is organized in four introductory sections starting with the definition of forest trees (1), the description of the environmental and economic importance (2) and its derived current priorities and research lines for breeding and conservation (3) including forest tree genomics (4). These precede the main body of this review: a general overview to proteomics (5) for introducing the forest tree proteomics section (6). Proteomics, defined as scientific discipline or experimental approach, it will be discussed both from a conceptual and methodological point of view, commenting on realities, challenges and limitations. Proteomics research in woody plants is limited to a reduced number of genera, including Pinus, Picea, Populus, Eucalyptus, and Fagus, mainly using first-generation approaches, e.g., those based on two-dimensional electrophoresis coupled to mass spectrometry. This area joins the own limitations of the technique and the difficulty and recalcitrance of the plant species as an experimental system. Furthermore, it contributes to a deeper knowledge of some biological processes, namely growth, development, organogenesis, and responses to stresses, as it is also used in the characterization and cataloguing of natural populations and biodiversity (proteotyping) and in assisting breeding programmes.
Collapse
Affiliation(s)
- Nieves Abril
- Dpt. of Biochemistry and Molecular Biology, ETSIAM, University of Cordoba, Campus de Rabanales, Ed. Severo Ochoa, Cordoba, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Kang BY, Major JE, Rajora OP. A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid. Genome 2011; 54:128-43. [PMID: 21326369 DOI: 10.1139/g10-099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.
Collapse
Affiliation(s)
- Bum-Yong Kang
- Forest Genetics and Biotechnology Group, Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4J1, Canada
| | | | | |
Collapse
|
14
|
Sansaloni CP, Petroli CD, Carling J, Hudson CJ, Steane DA, Myburg AA, Grattapaglia D, Vaillancourt RE, Kilian A. A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus. PLANT METHODS 2010; 6:16. [PMID: 20587069 PMCID: PMC2903579 DOI: 10.1186/1746-4811-6-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/30/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. FINDINGS After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56%) were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. CONCLUSIONS This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees and thus provide high genome coverage. This array will also provide a high-throughput platform for population genetics and phylogenetics in Eucalyptus. The transferability of DArT across species and pedigrees is particularly valuable for a large genus such as Eucalyptus and will facilitate the transfer of information between different studies. Furthermore, the DArT marker array will provide a high-resolution link between phenotypes in populations and the Eucalyptus reference genome, which will soon be completed.
Collapse
Affiliation(s)
- Carolina P Sansaloni
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910 Brasilia, Brazil
- Dep. Cell Biology, Universidade de Brasilia - 70910-900 Brasília - DF, Brazil
| | - César D Petroli
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910 Brasilia, Brazil
- Dep. Cell Biology, Universidade de Brasilia - 70910-900 Brasília - DF, Brazil
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, ACT 2600, Australia
| | - Corey J Hudson
- School of Plant Science and Cooperative Research Centre for Forestry, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Dorothy A Steane
- School of Plant Science and Cooperative Research Centre for Forestry, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Dario Grattapaglia
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology - EPqB, 70770-910 Brasilia, Brazil
- Dep. Cell Biology, Universidade de Brasilia - 70910-900 Brasília - DF, Brazil
- Genomic Sciences Program - Universidade Católica de Brasília - SGAN, 916 modulo B, 70790-160 Brasília - DF, Brazil
| | - René E Vaillancourt
- School of Plant Science and Cooperative Research Centre for Forestry, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, ACT 2600, Australia
| |
Collapse
|
15
|
Construction of Genetic Linkage Map in Peanut ( Arachis hypogaea L.) Cultivars. ZUOWU XUEBAO 2009. [DOI: 10.3724/sp.j.1006.2009.00395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Gong L, Pachner M, Kalai K, Lelley T. SSR-based genetic linkage map of Cucurbita moschata and its synteny with Cucurbita pepo. Genome 2009; 51:878-87. [PMID: 18956020 DOI: 10.1139/g08-072] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The first SSR-based genetic linkage map of Cucurbita moschata was created by integrating the maps of two F2 populations with one common parent developed from the crosses Waltham Butternut (WB) x Nigerian Local (NL) and ZHOU (a hull-less type) x WB. The integrated C. moschata map comprises 205 SSR markers and two morphological traits (Gr and n). The map is composed of 27 linkage groups with a marker density of 7 cM. Comparing the C. moschata map with the published Cucurbita pepo map, we found a high level of macrosynteny. Seventy-two of 76 common SSR markers between C. moschata and C. pepo were located in homologous linkage groups. These markers in general have conserved orders and similar genetic distances; they represent orthologous loci. A reference map based on these SSRs was obtained. No major chromosomal rearrangement between the two species could be detected at present, although four SSR markers were mapped in nonhomologous linkage groups. The comparative alignment of SSR markers did not provide any indication of a possible ancient polyploid origin of the species. The comparative mapping of C. moschata and C. pepo reported here will be useful for further studies on Cucurbit evolution, gene isolation, and breeding work.
Collapse
Affiliation(s)
- L Gong
- University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | | | | | | |
Collapse
|
17
|
HONG YB, LIANG XQ, CHEN XP, LIU HY, ZHOU GY, LI SX, WEN SJ. Construction of Genetic Linkage Map Based on SSR Markers in Peanut (Arachis hypogaea L.). ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1671-2927(08)60130-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
Grattapaglia D, Kirst M. Eucalyptus applied genomics: from gene sequences to breeding tools. THE NEW PHYTOLOGIST 2008; 179:911-929. [PMID: 18537893 DOI: 10.1111/j.1469-8137.2008.02503.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.
Collapse
Affiliation(s)
- Dario Grattapaglia
- Plant Genetics Laboratory, Embrapa - Genetic Resources and Biotechnology, Parque Estação Biológica, Brasília 70770-970 DF, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília - SGAN 916 módulo B, Brasília 70790-160 DF, Brazil
| | - Matias Kirst
- School of Forest Resources and Conservation, Graduate Program in Plant Molecular and Cellular Biology, and University of Florida Genetics Institute, University of Florida, PO Box 110410, Gainesville, FL 32611, USA
| |
Collapse
|
19
|
De Vos L, Myburg AA, Wingfield MJ, Desjardins AE, Gordon TR, Wingfield BD. Complete genetic linkage maps from an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Fungal Genet Biol 2007; 44:701-14. [PMID: 17418597 DOI: 10.1016/j.fgb.2007.02.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 01/22/2007] [Accepted: 02/17/2007] [Indexed: 11/20/2022]
Abstract
The Gibberella fujikuroi complex includes many plant pathogens of agricultural crops and trees, all of which have anamorphs assigned to the genus Fusarium. In this study, an interspecific hybrid cross between Gibberella circinata and Gibberella subglutinans was used to compile a genetic linkage map. A framework map was constructed using a total of 578 AFLP markers together with the mating type (MAT-1 and MAT-2) genes and the histone (H3) gene. Twelve major linkage groups were identified (n=12). Fifty percent of the markers showed significant deviation from the expected 1:1 transmission ratio in a haploid F(1) cross (P <0.05). The transmission of the markers on the linkage map was biased towards alleles of the G. subglutinans parent, with an estimated 60% of the genome of F(1) individuals contributed by this parent. This map will serve as a powerful tool to study the genetic architecture of interspecific differentiation and pathogenicity in the two parental genomes.
Collapse
Affiliation(s)
- L De Vos
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0001, South Africa.
| | | | | | | | | | | |
Collapse
|
20
|
Abstract
For whole-genome analysis in a basal chordate (protochordate), we used F1 pseudo-testcross mapping strategy and amplified fragment length polymorphism (AFLP) markers to construct primary linkage maps of the ascidian tunicate Ciona intestinalis. Two genetic maps consisted of 14 linkage groups, in agreement with the haploid chromosome number, and contained 276 and 125 AFLP loci derived from crosses between British and Neapolitan individuals. The two maps covered 4218.9 and 2086.9 cM, respectively, with an average marker interval of 16.1 and 18.9 cM. We observed a high recombinant ratio, ranging from 25 to 49 kb/cM, which can explain the high degree of polymorphism in this species. Some AFLP markers were converted to sequence tagged sites (STSs) by sequence determination, in order to create anchor markers for the fragmental physical map. Our recombination tools provide basic knowledge of genetic status and whole genome organization, and genetic markers to assist positional cloning in C. intestinalis.
Collapse
Affiliation(s)
- Shungo Kano
- Laboratory of Biochemistry and Molecular Biology, Stazione Zoologica A. Dohrn, Naples 80121, Italy.
| | | | | |
Collapse
|
21
|
Brondani RPV, Williams ER, Brondani C, Grattapaglia D. A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC PLANT BIOLOGY 2006; 6:20. [PMID: 16995939 PMCID: PMC1599733 DOI: 10.1186/1471-2229-6-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 09/22/2006] [Indexed: 05/11/2023]
Abstract
BACKGROUND Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs) in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. RESULTS The consensus map covers approximately 90% of the recombining genome of Eucalyptus, involves 234 mapped EMBRA loci on 11 linkage groups, an observed length of 1,568 cM and a mean distance between markers of 8.4 cM. A compilation of all microsatellite linkage information published in Eucalyptus allowed us to establish the homology among linkage groups between this consensus map and other maps published for E. globulus. Comparative mapping analyses also resulted in the linkage group assignment of other 41 microsatellites derived from other Eucalyptus species as well as candidate genes and QTLs for wood and flowering traits published in the literature. This report significantly increases the availability of microsatellite markers and mapping information for species of Eucalyptus and corroborates the high conservation of microsatellite flanking sequences and locus ordering between species of the genus. CONCLUSION This work represents an important step forward for Eucalyptus comparative genomics, opening stimulating perspectives for evolutionary studies and molecular breeding applications. The generalized use of an increasingly larger set of interspecific transferable markers and consensus mapping information, will allow faster and more detailed investigations of QTL synteny among species, validation of expression-QTL across variable genetic backgrounds and positioning of a growing number of candidate genes co-localized with QTLs, to be tested in association mapping experiments.
Collapse
Affiliation(s)
- Rosana PV Brondani
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 DF Brasilia, Brazil
- Department of Cell Biology, Universidade de Brasília UnB, DF, Brasília
- EMBRAPA Arroz e Feijão, CP 179, Goiânia GO 74001-970, Brazil
| | - Emlyn R Williams
- CSIRO Forestry and Forest Products, POBox E4008, Kingston ACT 2604, Australia
| | - Claudio Brondani
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 DF Brasilia, Brazil
- EMBRAPA Arroz e Feijão, CP 179, Goiânia GO 74001-970, Brazil
| | - Dario Grattapaglia
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 DF Brasilia, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Catolica de Brasília, 70790-160 DF Brasilia, Brazil
| |
Collapse
|
22
|
Poke FS, Vaillancourt RE, Potts BM, Reid JB. Genomic research in Eucalyptus. Genetica 2005; 125:79-101. [PMID: 16175457 DOI: 10.1007/s10709-005-5082-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 04/05/2005] [Indexed: 11/25/2022]
Abstract
Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.
Collapse
Affiliation(s)
- Fiona S Poke
- Cooperative Research Centre for Sustainable Production Forestry and School of Plant Science, University of Tasmania, Churchill Avenue, Private Bag 55, Hobart, Tasmania 7001, Australia.
| | | | | | | |
Collapse
|
23
|
Pelgas B, Bousquet J, Beauseigle S, Isabel N. A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1466-88. [PMID: 16215729 DOI: 10.1007/s00122-005-0068-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 07/04/2005] [Indexed: 05/04/2023]
Abstract
Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.
Collapse
Affiliation(s)
- Betty Pelgas
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre de recherche en biologie forestière, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, QC, G1K 7P4, Canada
| | | | | | | |
Collapse
|
24
|
Kirst M, Basten CJ, Myburg AA, Zeng ZB, Sederoff RR. Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid. Genetics 2005; 169:2295-303. [PMID: 15687266 PMCID: PMC1449597 DOI: 10.1534/genetics.104.039198] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species diversity may have evolved by differential regulation of a similar set of genes. To analyze and compare the genetic architecture of transcript regulation in different genetic backgrounds of Eucalyptus, microarrays were used to examine variation in mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population [E. grandis x F(1) hybrid (E. grandis x E. globulus)]. Least-squares mean estimates of transcript levels were generated for 2608 genes in 91 interspecific backcross progeny. The quantitative measurements of variation in transcript abundance for specific genes were mapped as expression QTL (eQTL) in two single-tree genetic linkage maps (F(1) hybrid paternal and E. grandis maternal). EQTL were identified for 1067 genes in the two maps, of which 811 were located in the F(1) hybrid paternal map, and 451 in the E. grandis maternal map. EQTL for 195 genes mapped to both parental maps, the majority of which localized to nonhomologous linkage groups, suggesting trans-regulation by different loci in the two genetic backgrounds. For 821 genes, a single eQTL that explained up to 70% of the transcript-level variation was identified. Hotspots with colocalized eQTL were identified in both maps and typically contained genes associated with specific metabolic and regulatory pathways, suggesting coordinated genetic regulation.
Collapse
Affiliation(s)
- Matias Kirst
- Forest Biotechnology Group, North Carolina State University, Raleigh, 27695, USA
| | | | | | | | | |
Collapse
|
25
|
Barbosa-da-Silva A, Wanderley-Nogueira AC, Silva RR, Berlarmino LC, Soares-Cavalcanti NM, Benko-Iseppon AM. In silico survey of resistance (R) genes in Eucalyptus transcriptome. Genet Mol Biol 2005. [DOI: 10.1590/s1415-47572005000400011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
26
|
Myburg AA, Vogl C, Griffin AR, Sederoff RR, Whetten RW. Genetics of postzygotic isolation in Eucalyptus: whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E. globulus. Genetics 2004; 166:1405-18. [PMID: 15082559 PMCID: PMC1470765 DOI: 10.1534/genetics.166.3.1405] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of hybrid fitness characters can provide valuable insights into the nature and evolution of postzygotic reproductive barriers in diverged species. We determined the genome-wide distribution of barriers to introgression in an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and E. globulus (Labill.). Two interspecific backcross families (N = 186) were used to construct comparative, single-tree, genetic linkage maps of an F(1) hybrid individual and two backcross parents. A total of 1354 testcross AFLP marker loci were evaluated in the three parental maps and a substantial proportion (27.7% average) exhibited transmission ratio distortion (alpha = 0.05). The distorted markers were located in distinct regions of the parental maps and marker alleles within each region were all biased toward either of the two parental species. We used a Bayesian approach to estimate the position and effect of transmission ratio distorting loci (TRDLs) in the distorted regions of each parental linkage map. The relative viability of TRDL alleles ranged from 0.20 to 0.72. Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterospecific interactions affect introgression rates in this wide interspecific pedigree.
Collapse
Affiliation(s)
- Alexander A Myburg
- Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695, USA.
| | | | | | | | | |
Collapse
|
27
|
Kirst M, Myburg AA, De León JPG, Kirst ME, Scott J, Sederoff R. Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus. PLANT PHYSIOLOGY 2004; 135:2368-78. [PMID: 15299141 PMCID: PMC520804 DOI: 10.1104/pp.103.037960] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 04/18/2004] [Accepted: 05/03/2004] [Indexed: 05/18/2023]
Abstract
Phenotypic, genotypic, and transcript level (microarray) data from an interspecific backcross population of Eucalyptus grandis and Eucalyptus globulus were integrated to dissect the genetic and metabolic network underlying growth variation. Transcript abundance, measured for 2,608 genes in the differentiating xylem of a 91 (E. grandis x E. globulus) x E. grandis backcross progeny was correlated with diameter variation, revealing coordinated down-regulation of genes encoding enzymes of the lignin biosynthesis and associated methylation pathways in fast growing individuals. Lignin analysis of wood samples confirmed the content and quality predicted by the transcript levels measured on the microarrays. Quantitative trait locus (QTL) analysis of transcript levels of lignin-related genes showed that their mRNA abundance is regulated by two genetic loci, demonstrating coordinated genetic control over lignin biosynthesis. These two loci colocalize with QTLs for growth, suggesting that the same genomic regions are regulating growth, and lignin content and composition in the progeny. Genetic mapping of the lignin genes revealed that most of the key biosynthetic genes do not colocalize with growth and transcript level QTLs, with the exception of the locus encoding the enzyme S-adenosylmethionine synthase. This study illustrates the power of integrating quantitative analysis of gene expression data and genetic map information to discover genetic and metabolic networks regulating complex biological traits. (Sequence data for this article have been deposited with the EMBL/GenBank data libraries under accession numbers CB 967505 to CB 968059; CD 667988 to CD 670002; CD 670004; CD 670097; CD 670101 to CD 670112; and CD 670114 to CD 670137.)
Collapse
Affiliation(s)
- Matias Kirst
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA.
| | | | | | | | | | | |
Collapse
|
28
|
Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J. Identification of genes preferentially expressed during wood formation in Eucalyptus. PLANT MOLECULAR BIOLOGY 2004; 55:263-280. [PMID: 15604680 DOI: 10.1007/s11103-004-0621-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Wood is the most abundant biological resource on earth and it is also an important raw material for a major global industry with rapidly increasing demand. The genus Eucalyptus includes the most widely used tree species for industrial plantation, mainly for making pulp and paper. With the aim of identifying major genes involved in wood formation in Eucalyptus , we have developed a targeted approach of functional genomics based on the isolation of xylem preferentially expressed genes by subtractive PCR. Transcript profiling using cDNA arrays and analysis of variance (ANOVA) were used to identify differentially expressed ESTs between secondary xylem and leaves. Real-time RT-PCR was performed to confirm the differential expression of representative EST. Of 224 independent EST sequences obtained, 81% were preferentially expressed in xylem. One-third of the ESTs exhibiting homologies with proteins of known function fell into two main classes highlighting the importance of the auxin signalling through ubiquitin-dependent proteolysis on one hand, and of the enzymes involved in cell wall biosynthesis and remodelling, on the other. The functions of the genes represented by the remaining 61% of ESTs should be of great interest for future research. This systematic analysis of genes involved in wood formation in Eucalyptus provides valuable insights into the molecular mechanisms involved in secondary xylem differentiation as well as new candidate-genes for wood quality improvement.
Collapse
Affiliation(s)
- Etienne Paux
- UMR UPS/CNRS 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP17, Auzeville Tolosane, 31326 Castanet Tolosan, France
| | | | | | | | | |
Collapse
|