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Wang J, Zhang L, Wang J, Hao Y, Xiao Q, Teng J, Shen S, Zhang Y, Feng Y, Bao S, Li Y, Yan Z, Wei C, Wang L, Wang J. Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow. BMC PLANT BIOLOGY 2022; 22:298. [PMID: 35710333 PMCID: PMC9205023 DOI: 10.1186/s12870-022-03684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. RESULTS Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. CONCLUSIONS Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.
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Affiliation(s)
- Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Lan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jiaqi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanan Hao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yu Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zimo Yan
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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Bdeir R, Muchero W, Yordanov Y, Tuskan GA, Busov V, Gailing O. Quantitative trait locus mapping of Populus bark features and stem diameter. BMC PLANT BIOLOGY 2017; 17:224. [PMID: 29179673 PMCID: PMC5704590 DOI: 10.1186/s12870-017-1166-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/10/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Bark plays important roles in photosynthate transport and storage, along with physical and chemical protection. Bark texture varies extensively among species, from smooth to fissured to deeply furrowed, but its genetic control is unknown. This study sought to determine the main genomic regions associated with natural variation in bark features and stem diameter. Quantitative trait loci (QTL) were mapped using an interspecific pseudo-backcross pedigree (Populus trichocarpa x P. deltoides and P. deltoides) for bark texture, bark thickness and diameter collected across three years, two sites and three biological replicates per site. RESULTS QTL specific to bark texture were highly reproducible in shared intervals across sites, years and replicates. Significant positive correlations and co-localization between trait QTL suggest pleiotropic regulators or closely linked genes. A list of candidate genes with related putative function, location close to QTL maxima and with the highest expression level in the phloem, xylem and cambium was identified. CONCLUSION Candidate genes for bark texture included an ortholog of Arabidopsis ANAC104 (PopNAC128), which plays a role in lignified fiber cell and ray development, as well as Pinin and Fasciclin (PopFLA) genes with a role in cell adhesion, cell shape and migration. The results presented in this study provide a basis for future genomic characterization of genes found within the QTL for bark texture, bark thickness and diameter in order to better understand stem and bark development in Populus and other woody perennial plants. The QTL mapping approach identified a list of prime candidate genes for further validation using functional genomics or forward genetics approaches.
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Affiliation(s)
- Roba Bdeir
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Yordan Yordanov
- Departement of Biology, Eastern Illinois University, 600 Lincoln Ave, Charleston, IL 61920 USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 USA
| | - Victor Busov
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931 USA
- Present address: Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
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Mousavi M, Tong C, Liu F, Tao S, Wu J, Li H, Shi J. De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies. BMC Genomics 2016; 17:656. [PMID: 27538483 PMCID: PMC4991039 DOI: 10.1186/s12864-016-3003-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/09/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands of genetic markers for linkage mapping across many individuals, and can be applied in species with or without a reference genome. Although several analytical tools are available for RAD-seq data, alternative strategies are necessary for improving the marker quality and hence the genetic mapping accuracy. RESULTS We demonstrate a strategy for constructing dense genetic linkage maps in hybrid forest trees by combining RAD-seq and whole-genome sequencing technologies. We performed RAD-seq of 150 progeny and whole-genome sequencing of the two parents in an F1 hybrid population of Populus deltoides × P. simonii. Two rough references were assembled from the whole-genome sequencing reads of the two parents separately. Based on the parental reference sequences, 3442 high-quality single nucleotide polymorphisms (SNPs) were identified that segregate in the ratio of 1:1. The maternal linkage map of P. deltoides was constructed with 2012 SNPs, containing 19 linkage groups and spanning 4067.16 cM of the genome with an average distance of 2.04 cM between adjacent markers, while the male map of P. simonii consisted of 1430 SNPs and the same number of linkage groups with a total length of 4356.04 cM and an average interval distance of 3.09 cM. Collinearity between the parental linkage maps and the reference genome of P. trichocarpa was also investigated. Compared with the result on the basis of the existing reference genome, our strategy identified more high-quality SNPs and generated parental linkage groups that nicely match the karyotype of Populus. CONCLUSIONS The strategy of simultaneously using RAD and whole-genome sequencing technologies can be applied to constructing high-density genetic maps in forest trees regardless of whether a reference genome exists. The two parental linkage maps constructed here provide more accurate genetic resources for unraveling quantitative trait loci and accelerating molecular breeding programs, as well as for comparative genomics in Populus.
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Affiliation(s)
- Mohaddeseh Mousavi
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Chunfa Tong
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Fenxiang Liu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Shentong Tao
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Jiyan Wu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Huogen Li
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Jisen Shi
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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Foster AJ, Pelletier G, Tanguay P, Séguin A. Transcriptome Analysis of Poplar during Leaf Spot Infection with Sphaerulina spp. PLoS One 2015; 10:e0138162. [PMID: 26378446 PMCID: PMC4575021 DOI: 10.1371/journal.pone.0138162] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/25/2015] [Indexed: 12/12/2022] Open
Abstract
Diseases of poplar caused by the native fungal pathogen Sphaerulina musiva and related species are of growing concern, particularly with the increasing interest in intensive poplar plantations to meet growing energy demands. Sphaerulina musiva is able to cause infection on leaves, resulting in defoliation and canker formation on stems. To gain a greater understanding of the different responses of poplar species to infection caused by the naturally co-evolved Sphaerulina species, RNA-seq was conducted on leaves of Populus deltoides, P. balsamifera and P. tremuloides infected with S. musiva, S. populicola and a new undescribed species, Ston1, respectively. The experiment was designed to contain the pathogen in a laboratory environment, while replicating disease development in commercial plantations. Following inoculation, trees were monitored for disease symptoms, pathogen growth and host responses. Genes involved in phenylpropanoid, terpenoid and flavonoid biosynthesis were generally upregulated in P. balsamifera and P. tremuloides, while cell wall modification appears to play an important role in the defense of P. deltoides. Poplar defensive genes were expressed early in P. balsamifera and P. tremuloides, but their expression was delayed in P. deltoides, which correlated with the rate of disease symptoms development. Also, severe infection in P. balsamifera led to leaf abscission. This data gives an insight into the large differences in timing and expression of genes between poplar species being attacked by their associated Sphaerulina pathogen.
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Affiliation(s)
- Adam J. Foster
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Canada
| | - Gervais Pelletier
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Canada
| | - Armand Séguin
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Canada
- * E-mail:
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Fichot R, Brignolas F, Cochard H, Ceulemans R. Vulnerability to drought-induced cavitation in poplars: synthesis and future opportunities. PLANT, CELL & ENVIRONMENT 2015; 38:1233-51. [PMID: 25444560 DOI: 10.1111/pce.12491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 11/12/2014] [Indexed: 05/04/2023]
Abstract
Vulnerability to drought-induced cavitation is a key trait of plant water relations. Here, we summarize the available literature on vulnerability to drought-induced cavitation in poplars (Populus spp.), a genus of agronomic, ecological and scientific importance. Vulnerability curves and vulnerability parameters (including the water potential inducing 50% loss in hydraulic conductivity, P50) were collected from 37 studies published between 1991 and 2014, covering a range of 10 species and 12 interspecific hybrid crosses. Results of our meta-analysis confirm that poplars are among the most vulnerable woody species to drought-induced cavitation (mean P50 = -1.44 and -1.55 MPa across pure species and hybrids, respectively). Yet, significant variation occurs among species (P50 range: 1.43 MPa) and among hybrid crosses (P50 range: 1.12 MPa), within species and hybrid crosses (max. P50 range reported: 0.8 MPa) as well as in response to environmental factors including nitrogen fertilization, irradiance, temperature and drought (max. P50 range reported: 0.75 MPa). Potential implications and gaps in knowledge are discussed in the context of poplar cultivation, species adaptation and climate modifications. We suggest that poplars represent a valuable model for studies on drought-induced cavitation, especially to elucidate the genetic and molecular basis of cavitation resistance in Angiosperms.
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Affiliation(s)
- Régis Fichot
- INRA, LBLGC, EA 1207, University of Orléans, Orléans, F-45067, France
| | - Franck Brignolas
- INRA, LBLGC, EA 1207, University of Orléans, Orléans, F-45067, France
| | - Hervé Cochard
- UMR547 PIAF, INRA, Clermont-Ferrand, F-63100, France
- UMR547 PIAF, Clermont Université, Université Blaise-Pascal, Clermont-Ferrand, F-63000, France
| | - Reinhart Ceulemans
- Department of Biology, Centre of Excellence, Plant and Vegetation Ecology (PLECO), University of Antwerp, Wilrijk, B-2610, Belgium
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de Boer JM, Datema E, Tang X, Borm TJA, Bakker EH, van Eck HJ, van Ham RCHJ, de Jong H, Visser RGF, Bachem CWB. Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin. BMC Genomics 2015; 16:374. [PMID: 25958312 PMCID: PMC4470070 DOI: 10.1186/s12864-015-1578-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/24/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned. RESULTS For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1-3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5. CONCLUSIONS Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands.
| | - Erwin Datema
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Xiaomin Tang
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Department of Biology, Colorado State University, Fort Collins, USA.
| | - Theo J A Borm
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Erin H Bakker
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Herman J van Eck
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Roeland C H J van Ham
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Christian W B Bachem
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo MC. Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Funct Integr Genomics 2014; 14:59-73. [PMID: 24610029 PMCID: PMC4273598 DOI: 10.1007/s10142-014-0363-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/27/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.
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Affiliation(s)
- Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Reyazul Rouf Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Yuqin Hu
- University of California, Davis, USA
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Canada
| | | | - Oscar Riera-Lizarazu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Dow AgroSciences, Pullman, USA
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Lischer HE, Excoffier L, Heckel G. Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles. Mol Biol Evol 2013; 31:817-31. [DOI: 10.1093/molbev/mst271] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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DeWoody J, Viger M, Lakatos F, Tuba K, Taylor G, Smulders MJM. Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree. PLoS One 2013; 8:e79925. [PMID: 24260320 PMCID: PMC3833894 DOI: 10.1371/journal.pone.0079925] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 09/30/2013] [Indexed: 12/27/2022] Open
Abstract
Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree.
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Affiliation(s)
- Jennifer DeWoody
- Centre for Biological Sciences, Life Sciences, University of Southampton, Southampton, United Kingdom
- Current address: USDA Forest Service, National Forest Genetics Lab, 2480 Carson Road, Placerville, California, United States of America
| | - Maud Viger
- Centre for Biological Sciences, Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ferenc Lakatos
- Institute of Silviculture and Forest Protection, University of West-Hungary, Sopron, Hungary
| | - Katalin Tuba
- Institute of Silviculture and Forest Protection, University of West-Hungary, Sopron, Hungary
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences, University of Southampton, Southampton, United Kingdom
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Perdereau AC, Douglas GC, Hodkinson TR, Kelleher CT. High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:114. [PMID: 23924375 PMCID: PMC3750764 DOI: 10.1186/1754-6834-6-114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/02/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation. RESULTS Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix. CONCLUSIONS The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes.
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Affiliation(s)
- Aude C Perdereau
- Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland
- Botany Building, School of Natural Sciences, Trinity College Dublin, Dublin, D2, Ireland
- Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin, D2, Ireland
| | - Gerry C Douglas
- Teagasc, Agriculture and Food Development Authority, Kinsealy Research Centre, Malahide Road, Dublin, D17, Ireland
| | - Trevor R Hodkinson
- Botany Building, School of Natural Sciences, Trinity College Dublin, Dublin, D2, Ireland
- Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin, D2, Ireland
| | - Colin T Kelleher
- DBN Plant Molecular Laboratory, National Botanic Gardens, Glasnevin, Dublin, D9, Ireland
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11
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Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biol 2013; 14:120. [PMID: 23796049 PMCID: PMC3706761 DOI: 10.1186/gb-2013-14-6-120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the dominant species in much of the earth's terrestrial ecosystems.
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12
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Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1783-95. [PMID: 22890805 PMCID: PMC3493668 DOI: 10.1007/s00122-012-1953-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/21/2012] [Indexed: 05/06/2023]
Abstract
Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.
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Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
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13
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Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. THE NEW PHYTOLOGIST 2012; 196:713-725. [PMID: 22861491 DOI: 10.1111/j.1469-8137.2012.04258.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
• Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
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Affiliation(s)
- Gancho T Slavov
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Mindie F Lipphardt
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | | | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Len A Pennacchio
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lee E Gunter
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kelly Vining
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Kyle R Pomraning
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | | | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-1606, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yousry A El-Kassaby
- Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Dan Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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14
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Zhao L, Yuanda L, Caiping C, Xiangchao T, Xiangdong C, Wei Z, Hao D, Xiuhua G, Wangzhen G. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information. BMC Genomics 2012; 13:539. [PMID: 23046547 PMCID: PMC3557173 DOI: 10.1186/1471-2164-13-539] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 09/23/2012] [Indexed: 01/02/2023] Open
Abstract
Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium.
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Affiliation(s)
- Liang Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China
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15
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Abstract
In recent years, the number of sequencing data of plant whole genome have been increasing rapidly and the whole genome sequencing has been also performed widely in woody plants. However, there are a set of obstacles in investigating the whole genome sequencing in woody plants, which include larger genome, complex genome structure, limitations of assembly, annotation, functional analysis, and restriction of the funds for scientific research. Therefore, to promote the efficiency of the whole genome sequencing in woody plants, the development and defect of this field should be analyzed. The three-generation sequencing technologies (i.e., Sanger sequencing, synthesis sequencing, and single molecule sequencing) were compared in our studies. The progress mainly focused on the whole genome sequencing in four woody plants (Populus, Grapevine, Papaya, and Apple), and the application of sequencing results also was analyzed. The future of whole genome sequencing research in woody plants, consisting of material selection, establishment of genetic map and physical map, selection of sequencing technology, bioinformatic analysis, and application of sequencing results, was discussed.
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16
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Lopez D, Bronner G, Brunel N, Auguin D, Bourgerie S, Brignolas F, Carpin S, Tournaire-Roux C, Maurel C, Fumanal B, Martin F, Sakr S, Label P, Julien JL, Gousset-Dupont A, Venisse JS. Insights into Populus XIP aquaporins: evolutionary expansion, protein functionality, and environmental regulation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2217-30. [PMID: 22223812 DOI: 10.1093/jxb/err404] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A novel category of major intrinsic proteins which share weak similarities with previously identified aquaporin subfamilies was recently identified in land plants, and named X (for unrecognized) intrinsic proteins (XIPs). Because XIPs are still ranked as uncharacterized proteins, their further molecular characterization is required. Herein, a systematic fine-scale analysis of XIP sequences found in flowering plant databases revealed that XIPs are found in at least five groups. The phylogenetic relationship of these five groups with the phylogenetic organization of angiosperms revealed an original pattern of evolution for the XIP subfamily through distinct angiosperm taxon-specific clades. Of all flowering plant having XIPs, the genus Populus encompasses the broadest panel and the highest polymorphism of XIP isoforms, with nine PtXIP sequences distributed within three XIP groups. Comprehensive PtXIP gene expression patterns showed that only two isoforms (PtXIP2;1 and PtXIP3;2) were transcribed in vegetative tissues. However, their patterns are contrasted, PtXIP2;1 was ubiquitously accumulated whereas PtXIP3;2 was predominantly detected in wood and to a lesser extent in roots. Furthermore, only PtXIP2;1 exhibited a differential expression in leaves and stems of drought-, salicylic acid-, or wounding-challenged plants. Unexpectedly, the PtXIPs displayed different abilities to alter water transport upon expression in Xenopus laevis oocytes. PtXIP2;1 and PtXIP3;3 transported water while other PtXIPs did not.
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Affiliation(s)
- D Lopez
- Université Blaise Pascal UMRA 547 PIAF, Clermont-Ferrand, France
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17
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Wu J, Gu YQ, Hu Y, You FM, Dandekar AM, Leslie CA, Aradhya M, Dvorak J, Luo MC. Characterizing the walnut genome through analyses of BAC end sequences. PLANT MOLECULAR BIOLOGY 2012; 78:95-107. [PMID: 22101470 DOI: 10.1007/s11103-011-9849-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/29/2011] [Indexed: 05/31/2023]
Abstract
Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots of J. regia cv. Chandler using the HindIII and MboI cloning sites. A total of 48,218 high-quality BAC end sequences (BESs) were generated, with an accumulated sequence length of 31.2 Mb, representing approximately 5.1% of the walnut genome. Analysis of repeat DNA content in BESs revealed that approximately 15.42% of the genome consists of known repetitive DNA, while walnut-unique repetitive DNA identified in this study constitutes 13.5% of the genome. Among the walnut-unique repetitive DNA, Julia SINE and JrTRIM elements represent the first identified walnut short interspersed element (SINE) and terminal-repeat retrotransposon in miniature (TRIM) element, respectively; both types of elements are abundant in the genome. As in other species, these SINEs and TRIM elements could be exploited for developing repeat DNA-based molecular markers in walnut. Simple sequence repeats (SSR) from BESs were analyzed and found to be more abundant in BESs than in expressed sequence tags. The density of SSR in the walnut genome analyzed was also slightly higher than that in poplar and papaya. Sequence analysis of BESs indicated that approximately 11.5% of the walnut genome represents a coding sequence. This study is an initial characterization of the walnut genome and provides the largest genomic resource currently available; as such, it will be a valuable tool in studies aimed at genetically improving walnut.
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Affiliation(s)
- Jiajie Wu
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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18
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Bresson A, Jorge V, Dowkiw A, Guerin V, Bourgait I, Tuskan GA, Schmutz J, Chalhoub B, Bastien C, Faivre Rampant P. Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar. THE NEW PHYTOLOGIST 2011; 192:151-163. [PMID: 21658182 DOI: 10.1111/j.1469-8137.2011.03786.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
• R(US) is a major dominant gene controlling quantitative resistance, inherited from Populus trichocarpa, whereas R(1) is a gene governing qualitative resistance, inherited from P. deltoides. • Here, we report a reiterative process of concomitant fine-scale genetic and physical mapping guided by the P. trichocarpa genome sequence. The high-resolution linkage maps were developed using a P. deltoides × P. trichocarpa progeny of 1415 individuals. R(US) and R(1) were mapped in a peritelomeric region of chromosome 19. Markers closely linked to R(US) were used to screen a bacterial artificial chromosome (BAC) library constructed from the P. trichocarpa parent, heterozygous at the locus R(US) . • Two local physical maps were developed, one encompassing the R(US) allele and the other spanning r(US) . The alignment of the two haplophysical maps showed structural differences between haplotypes. The genetic and physical maps were anchored to the genome sequence, revealing genome sequence misassembly. Finally, the R(US) locus was localized within a 0.8-cM interval, whereas R(1) was localized upstream of R(US) within a 1.1-cM interval. • The alignment of the genetic and physical maps with the local reorder of the chromosome 19 sequence indicated that R(US) and R(1) belonged to a genomic region rich in nucleotide-binding site leucine-rich repeat (NBS-LRR) and serine threonine kinase (STK) genes.
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Affiliation(s)
- Aloïs Bresson
- INRA, UMR1165, UMR INRA/Université de Evry: Unité de Recherche en Génomique Végétale, Centre de Recherche de Versailles-Grignon, Evry Cedex, 91057, France
| | - Véronique Jorge
- INRA, UR0588, Unité de Recherche Amélioration, Génétique et Physiologie Forestières, Centre de Recherche d'Orléans, Orléans Cedex 2, 45075, France
| | - Arnaud Dowkiw
- INRA, UR0588, Unité de Recherche Amélioration, Génétique et Physiologie Forestières, Centre de Recherche d'Orléans, Orléans Cedex 2, 45075, France
| | - Vanina Guerin
- INRA, UR0588, Unité de Recherche Amélioration, Génétique et Physiologie Forestières, Centre de Recherche d'Orléans, Orléans Cedex 2, 45075, France
| | - Isabelle Bourgait
- INRA, UR0588, Unité de Recherche Amélioration, Génétique et Physiologie Forestières, Centre de Recherche d'Orléans, Orléans Cedex 2, 45075, France
| | - Gerald A Tuskan
- Oak Ridge National Laboratory, PO Box 2008, MS-6422, Bldg. 1062, Rm 215, Oak Ridge, TN 37831-6422, USA
| | - Jeremy Schmutz
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 3508-2908, USA
| | - Boulos Chalhoub
- INRA, UMR1165, UMR INRA/Université de Evry: Unité de Recherche en Génomique Végétale, Centre de Recherche de Versailles-Grignon, Evry Cedex, 91057, France
| | - Catherine Bastien
- INRA, UR0588, Unité de Recherche Amélioration, Génétique et Physiologie Forestières, Centre de Recherche d'Orléans, Orléans Cedex 2, 45075, France
| | - Patricia Faivre Rampant
- INRA, UMR1165, UMR INRA/Université de Evry: Unité de Recherche en Génomique Végétale, Centre de Recherche de Versailles-Grignon, Evry Cedex, 91057, France
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Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever JE, Korban SS. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5117-30. [PMID: 21743103 PMCID: PMC3193016 DOI: 10.1093/jxb/err215] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143 cM, with an average density of 2.5 cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421 Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97 kb to 4.0 Mb, with an average of 995 kb. The average physical length of anchored contigs on each linkage group was ∼24.8 Mb, ranging from 17.0 Mb to 37.73 Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple.
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Affiliation(s)
- Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, 430074, PR China
| | - Danman Zheng
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Sornkanok Vimolmangkang
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Muhammad A. Khan
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Jonathan E. Beever
- Department of Animal Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA
- To whom correspondence should be addressed. E-mail:
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20
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Ragupathy R, Rathinavelu R, Cloutier S. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 2011; 12:217. [PMID: 21554714 PMCID: PMC3113786 DOI: 10.1186/1471-2164-12-217] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/09/2011] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. RESULTS The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. CONCLUSION The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.
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Affiliation(s)
- Raja Ragupathy
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada
| | - Rajkumar Rathinavelu
- Genomics & Bioinformatics Division, ITC Research & Development Centre, Bangalore, India
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB, R3T 2M9, Canada
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB, R3T 2N2, Canada
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21
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Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K. Crop genome sequencing: lessons and rationales. TRENDS IN PLANT SCIENCE 2011; 16:77-88. [PMID: 21081278 DOI: 10.1016/j.tplants.2010.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/09/2010] [Accepted: 10/16/2010] [Indexed: 05/06/2023]
Abstract
2010 marks the 10th anniversary of the completion of the first plant genome sequence (Arabidopsis thaliana). Triggered by advancements in sequencing technologies, many crop genome sequences have been produced, with eight published since 2008. To date, however, only the rice (Oryza sativa) genome sequence has been finished to a quality level similar to that of the Arabidopsis sequence. This trend to produce draft genomes could affect the ability of researchers to address biological questions of speciation and recent evolution or to link sequence variation accurately to phenotypes. Here, we review the current crop genome sequencing activities, discuss how variability in sequence quality impacts utility for different studies and provide a perspective for a paradigm shift in selecting crops for sequencing in the future.
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Affiliation(s)
- Catherine Feuillet
- Institut National de la Recherche Agronomique-Université Blaise Pascal-UMR1095-Domaine de Crouel, 63100 Clermont-Ferrand, France.
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22
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Echt CS, Saha S, Krutovsky KV, Wimalanathan K, Erpelding JE, Liang C, Nelson CD. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genet 2011; 12:17. [PMID: 21269494 PMCID: PMC3038140 DOI: 10.1186/1471-2156-12-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 01/26/2011] [Indexed: 12/21/2022] Open
Abstract
Background Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda.
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Affiliation(s)
- Craig S Echt
- Southern Institute of Forest Genetics, Southern Research Station, USDA Forest Service, Saucier, MS 39574, USA.
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Yin T, Zhang X, Gunter L, Priya R, Sykes R, Davis M, Wullschleger SD, Tuskan GA. Differential detection of genetic Loci underlying stem and root lignin content in Populus. PLoS One 2010; 5:e14021. [PMID: 21151641 PMCID: PMC2999904 DOI: 10.1371/journal.pone.0014021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Accepted: 08/20/2010] [Indexed: 01/16/2023] Open
Abstract
In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.
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Affiliation(s)
- Tongming Yin
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- The Key Lab of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, China
| | - Xinye Zhang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
| | - Lee Gunter
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
| | - Ranjan Priya
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
| | - Robert Sykes
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, Colorado, United States of America
| | - Mark Davis
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, Colorado, United States of America
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Gerald A. Tuskan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bioenergy Science Center, Oak Ridge, Tennessee, United States of America
- * E-mail:
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Fang GC, Blackmon BP, Henry DC, Staton ME, Saski CA, Hodges SA, Tomkins JP, Luo H. Genomic tools development for Aquilegia: construction of a BAC-based physical map. BMC Genomics 2010; 11:621. [PMID: 21059242 PMCID: PMC3091760 DOI: 10.1186/1471-2164-11-621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 11/08/2010] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance. RESULTS BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (Vitis vinifera) than to rice and Arabidopsis in the transcriptomes. CONCLUSIONS The A. formosa BAC-based genomic resources provide valuable tools to study Aquilegia genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology.
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Affiliation(s)
- Guang-Chen Fang
- Department of Genetics and Biochemistry, Clemson University, SC 29634, USA
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Neilson KA, Gammulla CG, Mirzaei M, Imin N, Haynes PA. Proteomic analysis of temperature stress in plants. Proteomics 2010; 10:828-45. [PMID: 19953552 DOI: 10.1002/pmic.200900538] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this review we examine current approaches used for proteomic analysis of temperature stress in plants. Rapid advances in this field in recent years are discussed, including metabolic, chemical and isotopic labeling, and label-free quantitative techniques. These are compared and contrasted with well-established methods such as 2-DE approaches. Examples of applications of various methods are presented, and technical difficulties and limitations of each are also considered. Results of previous studies are examined in detail, and commonly occurring temperature stress response proteins are collated. We conclude that technical advances, and improvements in genome sequence availability, will have an ever increasing impact on our understanding of molecular mechanisms of stress response in plants.
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Affiliation(s)
- Karlie A Neilson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
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[A review of the genomic and gene cloning studies in trees]. YI CHUAN = HEREDITAS 2010; 32:677-84. [PMID: 20650848 DOI: 10.3724/sp.j.1005.2010.00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Supported by the Department of Energy (DOE) of U.S., the first tree genome, black cottonwood (Populus trichocarpa), has been completely sequenced and publicly release. This is the milestone that indicates the beginning of post-genome era for forest trees. Identification and cloning genes underlying important traits are one of the main tasks for the post-genome-era tree genomic studies. Recently, great achievements have been made in cloning genes coordinating important domestication traits in some crops, such as rice, tomato, maize and so on. Molecular breeding has been applied in the practical breeding programs for many crops. By contrast, molecular studies in trees are lagging behind. Trees possess some characteristics that make them as difficult organisms for studying on locating and cloning of genes. With the advances in techniques, given also the fast growth of tree genomic resources, great achievements are desirable in cloning unknown genes from trees, which will facilitate tree improvement programs by means of molecular breeding. In this paper, the author reviewed the progress in tree genomic and gene cloning studies, and prospected the future achievements in order to provide a useful reference for researchers working in this area.
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Baurens FC, Bocs S, Rouard M, Matsumoto T, Miller RNG, Rodier-Goud M, MBéguié-A-MBéguié D, Yahiaoui N. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC PLANT BIOLOGY 2010; 10:149. [PMID: 20637079 PMCID: PMC3017797 DOI: 10.1186/1471-2229-10-149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 07/16/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). RESULTS Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. CONCLUSIONS A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.
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Affiliation(s)
| | - Stéphanie Bocs
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, F-34397 Montpellier Cedex 5, France
| | - Takashi Matsumoto
- Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences (NIAS)/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan
| | - Robert NG Miller
- Postgraduate program in Genomic Science and Biotechnology, Universidade Católica de Brasília, SGAN 916, Módulo B, CEP 70.790-160, Brasília, DF, Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Asa Norte, Brasília, Brazil
| | | | | | - Nabila Yahiaoui
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics 2010; 11:204. [PMID: 20346114 PMCID: PMC2865496 DOI: 10.1186/1471-2164-11-204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 03/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. RESULTS We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. CONCLUSIONS We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.
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Affiliation(s)
- Simone Scalabrin
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli, Via J Linussio 51, 33100 Udine, Italy
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Cheung KH, Mei L, Mak DOD, Hayashi I, Iwatsubo T, Kang DE, Foskett JK. Gain-of-function enhancement of IP3 receptor modal gating by familial Alzheimer's disease-linked presenilin mutants in human cells and mouse neurons. Sci Signal 2010; 3:ra22. [PMID: 20332427 DOI: 10.1126/scisignal.2000818] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Familial Alzheimer's disease (FAD) is caused by mutations in amyloid precursor protein or presenilins (PS1 and PS2). Many FAD-linked PS mutations affect intracellular calcium (Ca(2+)) homeostasis by mechanisms proximal to and independent of amyloid production, although the molecular details are controversial. We found that several FAD-causing PS mutants enhance gating of the inositol trisphosphate receptor (IP(3)R) Ca(2+) release channel by a gain-of-function effect that mirrored the genetics of FAD and was independent of secretase activity. In contrast, wild-type PS or PS mutants that cause frontotemporal dementia had no such effect. FAD-causing PS mutants altered the modes in which the IP(3)R channel gated. Recordings of endogenous IP(3)R in lymphoblasts derived from individuals with FAD or cortical neurons of asymptomatic PS1-AD mice revealed that they were more likely than IP(3)R in cells with wild-type PS to dwell in a high open-probability burst mode, resulting in enhanced Ca(2+) signaling. These results indicate that exaggerated Ca(2+) signaling through IP(3)R-PS interaction is a disease-specific and robust proximal mechanism in FAD.
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Affiliation(s)
- King-Ho Cheung
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Yuan HM, Li KL, Ni RJ, Guo WD, Shen Z, Yang CP, Wang BC, Liu GF, Guo CH, Jiang J. A systemic proteomic analysis of Populus chloroplast by using shotgun method. Mol Biol Rep 2010; 38:3045-54. [DOI: 10.1007/s11033-010-9971-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
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Yu Q, Tong E, Skelton RL, Bowers JE, Jones MR, Murray JE, Hou S, Guan P, Acob RA, Luo MC, Moore PH, Alam M, Paterson AH, Ming R. A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics 2009; 10:371. [PMID: 19664231 PMCID: PMC3224731 DOI: 10.1186/1471-2164-10-371] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 08/07/2009] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly. RESULTS The physical map consists of 963 contigs, representing 9.4x genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes. CONCLUSION A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly, and is a valuable resource for comparative genomics and map-based cloning of agronomically and economically important genes and for sex chromosome research.
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Affiliation(s)
- Qingyi Yu
- Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA
| | - Eric Tong
- Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA
| | - Rachel L Skelton
- Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA
| | - John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Meghan R Jones
- Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA
| | - Jan E Murray
- Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shaobin Hou
- Center for Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI 96822, USA
| | - Peizhu Guan
- Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
| | - Ricelle A Acob
- Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Paul H Moore
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Maqsudul Alam
- Center for Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI 96822, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Ray Ming
- Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Drost DR, Novaes E, Boaventura-Novaes C, Benedict CI, Brown RS, Yin T, Tuskan GA, Kirst M. A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:1054-67. [PMID: 19220791 DOI: 10.1111/j.1365-313x.2009.03828.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.
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Affiliation(s)
- Derek R Drost
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
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Scalabrin S, Morgante M, Policriti A. Automated FingerPrint Background removal: FPB. BMC Bioinformatics 2009; 10:127. [PMID: 19405935 PMCID: PMC2689866 DOI: 10.1186/1471-2105-10-127] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 04/30/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The construction of a whole-genome physical map has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project. Its usefulness has been proved for whole-genome shotgun projects as a post-assembly validation and recently it has also been used in the assembly step to constrain on BACs positions. Fingerprinting is usually the method of choice for construction of physical maps. A clone fingerprint is composed of true peaks representing real fragments and background peaks, mainly composed of E. coli genomic DNA, partial digestions, star activity by-products, and machine background. High-throughput fingerprinting leads to the production of thousands of BAC clone fingerprints per day. That is why background peaks removal has become an important issue and needs to be automatized, especially in capillary electrophoresis based fingerprints. RESULTS At the moment, the only tools available for such a task are GenoProfiler and its descendant FPMiner. The large variation in the quality of fingerprints that is usually present in large fingerprinting projects represents a major difficulty in the correct removal of background peaks that has only been partially addressed by the methods so far adopted that all require a long manual optimization of parameters. Thus, we implemented a new data-independent tool, FPB (FingerPrint Background removal), suitable for large scale projects as well as mapping of few clones. CONCLUSION FPB is freely available at http://www.appliedgenomics.org/tools.php. FPB was used to remove the background from all fingerprints of three grapevine physical map projects. The first project consists of about 50,000 fingerprints, the second one consists of about 70,000 fingerprints, and the third one consists of about 45,000 fingerprints. In all cases a successful assembly was built.
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Affiliation(s)
- Simone Scalabrin
- Istituto di Genomica Applicata (IGA), via J, Linussio 51, I-33100 Udine, Italy.
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Kondou Y, Higuchi M, Takahashi S, Sakurai T, Ichikawa T, Kuroda H, Yoshizumi T, Tsumoto Y, Horii Y, Kawashima M, Hasegawa Y, Kuriyama T, Matsui K, Kusano M, Albinsky D, Takahashi H, Nakamura Y, Suzuki M, Sakakibara H, Kojima M, Akiyama K, Kurotani A, Seki M, Fujita M, Enju A, Yokotani N, Saitou T, Ashidate K, Fujimoto N, Ishikawa Y, Mori Y, Nanba R, Takata K, Uno K, Sugano S, Natsuki J, Dubouzet JG, Maeda S, Ohtake M, Mori M, Oda K, Takatsuji H, Hirochika H, Matsui M. Systematic approaches to using the FOX hunting system to identify useful rice genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:883-94. [PMID: 18980645 DOI: 10.1111/j.1365-313x.2008.03733.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ectopic gene expression, or the gain-of-function approach, has the advantage that once the function of a gene is known the gene can be transferred to many different plants by transformation. We previously reported a method, called FOX hunting, that involves ectopic expression of Arabidopsis full-length cDNAs in Arabidopsis to systematically generate gain-of-function mutants. This technology is most beneficial for generating a heterologous gene resource for analysis of useful plant gene functions. As an initial model we generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt tolerance, UV signaling, high light tolerance, and heat stress tolerance. Some of the mutant phenotypes displayed by rice FOX Arabidopsis lines resulted from the expression of rice genes that had no homologs in Arabidopsis. This result demonstrated that rice fl-cDNAs could be used to introduce new gene functions in Arabidopsis. Furthermore, these findings showed that rice gene function could be analyzed by employing Arabidopsis as a heterologous host. This technology provides a framework for the analysis of plant gene function in a heterologous host and of plant improvement by using heterologous gene resources.
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SLAVOV GT, LEONARDI S, BURCZYK J, ADAMS WT, STRAUSS SH, DIFAZIO SP. Extensive pollen flow in two ecologically contrasting populations ofPopulus trichocarpa. Mol Ecol 2009; 18:357-73. [DOI: 10.1111/j.1365-294x.2008.04016.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dohm JC, Lange C, Reinhardt R, Himmelbauer H. Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:14-26. [PMID: 18764921 DOI: 10.1111/j.1365-313x.2008.03665.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We characterized two overlapping sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) clones representing different haplotypes. A total of 254 kbp of the genomic sequence was determined, of which the two BACs share 92 kbp. Eleven of 15 genes discovered in the sequenced interval locate to the overlap region. The haplotypes differ in exons by 1% (nucleotide level) and in non-coding regions by 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.
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Affiliation(s)
- Juliane C Dohm
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin, Germany
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Moroldo M, Paillard S, Marconi R, Fabrice L, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M, Adam-Blondon AF. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance. BMC PLANT BIOLOGY 2008; 8:66. [PMID: 18554400 PMCID: PMC2442077 DOI: 10.1186/1471-2229-8-66] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 06/13/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. RESULTS The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. CONCLUSION Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.
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Affiliation(s)
- Marco Moroldo
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Sophie Paillard
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
- UMR118, INRA-Agrocampus, University of Rennes, Amélioration des Plantes et Biotechnologies Végétales, F-35650 Le Rheu, France
| | - Raffaella Marconi
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
| | - Legeai Fabrice
- Unité de Recherche Génomique-Info, URGI, Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France
| | - Aurelie Canaguier
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Corinne Cruaud
- Gnoscope, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
| | | | - Cecile Guichard
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Veronique Brunaud
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Isabelle Le Clainche
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Simone Scalabrin
- Dipartimento di Scienze Matematiche, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Raffaele Testolin
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Gabriele Di Gaspero
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
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Neale DB, Ingvarsson PK. Population, quantitative and comparative genomics of adaptation in forest trees. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:149-55. [PMID: 18262830 DOI: 10.1016/j.pbi.2007.12.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 12/11/2007] [Accepted: 12/19/2007] [Indexed: 05/25/2023]
Abstract
High-throughput DNA sequencing and genotyping technologies have enabled a new generation of research in plant genetics where combined quantitative and population genetic approaches can be used to better understand the relationship between naturally occurring genotypic and phenotypic diversity. Forest trees are highly amenable to such studies because of their combined undomesticated and partially domesticated state. Forest geneticists are using association genetics to dissect complex adaptive traits and discover the underlying genes. In parallel, they are using resequencing of candidate genes and modern population genetics methods to discover genes under natural selection. This combined approach is identifying the most important genes that determine patterns of complex trait adaptation observed in many tree populations.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, Mail Stop 6 and Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Davis, CA 95616, USA.
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Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Duchaussoy F, Meyers BC, Boerjan W, Martin F. Genome-wide identification of NBS resistance genes in Populus trichocarpa. PLANT MOLECULAR BIOLOGY 2008; 66:619-36. [PMID: 18247136 DOI: 10.1007/s11103-008-9293-9] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 01/11/2008] [Indexed: 05/04/2023]
Abstract
As the largest class of disease resistance R genes, the genes encoding nucleotide binding site and leucine-rich repeat proteins ("NBS-LRR genes") play a critical role in defending plants from a multitude of pathogens and pests. The diversity of NBS-LRR genes was examined in the Populus trichocarpa draft genome sequence. The NBS class of genes in this perennial tree is large and diverse, comprised of approximately 400 genes, at least twice the complement of Arabidopsis. The NBS family can be divided into multiple subfamilies with distinct domain organizations. It includes 119 Coiled-Coil-NBS-LRR genes, 64 TIR-NBS-LRR genes, 34 BED-finger-NBS-LRR, and both truncated and unusual NBS- and NBS-LRR-containing genes. The transcripts of only 34 NBS-LRR genes were detected in rust-infected and non-infected leaves using a whole-genome oligoarray. None showed an altered expression two days post inoculation.
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Affiliation(s)
- Annegret Kohler
- Unité Mixte de Recherche INRA/UHP 1136 Interactions Arbres/Microorganismes, Institut National de la Recherche Agronomique, Centre de Recherches de Nancy, 54280 Champenoux, France.
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Yin T, Difazio SP, Gunter LE, Zhang X, Sewell MM, Woolbright SA, Allan GJ, Kelleher CT, Douglas CJ, Wang M, Tuskan GA. Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res 2008; 18:422-30. [PMID: 18256239 DOI: 10.1101/gr.7076308] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The genus Populus consists of dioecious woody species with largely unknown genetic mechanisms for gender determination. We have discovered genetic and genomic features in the peritelomeric region of chromosome XIX that suggest this region of the Populus genome is in the process of developing characteristics of a sex chromosome. We have identified a gender-associated locus that consistently maps to this region. Furthermore, comparison of genetic maps across multiple Populus families reveals consistently distorted segregation within this region. We have intensively characterized this region using an F(1) interspecific cross involving the female genotype that was used for genome sequencing. This region shows suppressed recombination and high divergence between the alternate haplotypes, as revealed by dense map-based genome assembly using microsatellite markers. The suppressed recombination, distorted segregation, and haplotype divergence were observed only for the maternal parent in this cross. Furthermore, the progeny of this cross showed a strongly male-biased sex ratio, in agreement with Haldane's rule that postulates that the heterogametic sex is more likely to be absent, rare, or sterile in interspecific crosses. Together, these results support the role of chromosome XIX in sex determination and suggest that sex determination in Populus occurs through a ZW system in which the female is the heterogametic gender.
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Affiliation(s)
- Tongming Yin
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA, Bohlmann J. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics 2008; 9:57. [PMID: 18230180 PMCID: PMC2270264 DOI: 10.1186/1471-2164-9-57] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 01/29/2008] [Indexed: 11/30/2022] Open
Abstract
Background The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions. Results As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa × P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in poplar leaves attacked by forest tent caterpillars. Conclusion This study has generated a high-quality FLcDNA resource for poplar and the third largest FLcDNA collection published to date for any plant species. We successfully used the FLcDNA sequences to reassess gene prediction in the poplar genome sequence, perform comparative sequence annotation, and identify differentially expressed transcripts associated with defense against insects. The FLcDNA sequences will be essential to the ongoing curation and annotation of the poplar genome, in particular for targeting gaps in the current genome assembly and further improvement of gene predictions. The physical FLcDNA clones will serve as useful reagents for functional genomics research in areas such as analysis of gene functions in defense against insects and perennial growth. Sequences from this study have been deposited in NCBI GenBank under the accession numbers EF144175 to EF148838.
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Affiliation(s)
- Steven G Ralph
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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Philippe RN, Bohlmann J. Poplar defense against insect herbivoresThis review is one of a selection of papers published in the Special Issue on Poplar Research in Canada. ACTA ACUST UNITED AC 2007. [DOI: 10.1139/b07-109] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The availability of a poplar ( Populus trichocarpa Torr & A. Gray, black cottonwood) genome sequence is enabling new research approaches in angiosperm tree biology. Much of the recent genomics research in poplars has been on wood formation, growth and development, resistance to abiotic stress and pathogens, motivated, at least in part, by the fact that poplars provide an important system for large-scale, short-rotation plantation forestry in the Northern Hemisphere. To sustain productivity and ecosystem health of natural and planted poplar forests it is of critical importance to also develop a better understanding of the molecular mechanisms of defense and resistance of poplars against insect pests. Previous research has established a solid foundation of the chemical ecology of poplar defense against insects. This review summarizes some of the relevant literature on defense against insect herbivores in poplars with an emphasis on molecular, biochemical, and emerging genomic research in this important field within forest biotechnology and chemical ecology. Following a general introduction, we provide a brief overview of some of the most relevant insect pests of poplars; we then describe some of the general defense strategies of poplars along with selected examples of their activities. We conclude with a summary of emerging results and perspectives from recent advances in genomics research on poplar defense against insects.
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Affiliation(s)
- Ryan N. Philippe
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
- Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Johnson LA, Douglas CJ. Populus trichocarpa MONOPTEROS/AUXIN RESPONSE FACTOR5(ARF5) genes: comparative structure, sub-functionalization, andPopulus–ArabidopsismicrosyntenyThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada. ACTA ACUST UNITED AC 2007. [DOI: 10.1139/b07-065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The genome of Populus (poplar) has been shaped by a whole genome duplication event specific to the salicoid lineage. The MONOPTEROS (MP)/AUXIN RESPONSE FACTOR5 (ARF5) transcription factor plays a key role in auxin-mediated morphogenesis and vascular development in Arabidopsis , and may play a similar role in secondary xylem development in Populus. We used EST and genome sequence information to identify and characterize two duplicated Populus MP genes, PoptrMP1 and PoptrMP2. PoptrMP1 and PoptrMP2 DNA binding and other domains are highly conserved relative to Arabidopsis MP, while the glutamine-rich middle domains are divergent. The two PoptrMP genes are located on duplicated regions of linkage groups II and V. Comparative analysis of the surrounding genes in both the Populus and Arabidopsis genomes revealed a high degree of conservation of gene content and order extending over 11 genes in the immediate vicinity, but also specific changes to genomic regions surrounding each MP locus, providing insights into genome evolution. Expression studies showed that PoptrMP1 and PoptrMP2 have overlapping but distinct expression patterns, suggesting that subfunctionalization of the duplicated genes has occurred, with PoptrMP1 specialized for expression in developing secondary xylem. Transgenic Populus lines overexpressing PoptrMP1 exhibited a 2–4 fold increase in expression of a Populus AtHB8 homolog, a proposed MP target gene, confirming conservation of this regulatory module.
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Affiliation(s)
- Lee A. Johnson
- Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Carl J. Douglas
- Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
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Abstract
With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.
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Affiliation(s)
- Stefan Jansson
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, SE-901 87 Umeå, Sweden.
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