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De Ollas C, Morillón R, Fotopoulos V, Puértolas J, Ollitrault P, Gómez-Cadenas A, Arbona V. Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:427. [PMID: 31057569 PMCID: PMC6477659 DOI: 10.3389/fpls.2019.00427] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Raphaël Morillón
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, France
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Jaime Puértolas
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San-Giuliano, France
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
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Yurkevich OY, Kirov IV, Bolsheva NL, Rachinskaya OA, Grushetskaya ZE, Zoschuk SA, Samatadze TE, Bogdanova MV, Lemesh VA, Amosova AV, Muravenko OV. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase ( CesA) Genes in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1467. [PMID: 28878799 PMCID: PMC5572355 DOI: 10.3389/fpls.2017.01467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/07/2017] [Indexed: 05/07/2023]
Abstract
Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.
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Affiliation(s)
- Olga Y. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga A. Rachinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Zoya E. Grushetskaya
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Svyatoslav A. Zoschuk
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Marina V. Bogdanova
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Valentina A. Lemesh
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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Borneman AR, Schmidt SA, Pretorius IS. At the cutting-edge of grape and wine biotechnology. Trends Genet 2013; 29:263-71. [DOI: 10.1016/j.tig.2012.10.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/24/2012] [Accepted: 10/26/2012] [Indexed: 11/29/2022]
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Appels R, Barrero R, Bellgard M. Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals. Funct Integr Genomics 2013; 13:1-9. [PMID: 23494190 PMCID: PMC3605488 DOI: 10.1007/s10142-013-0319-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/02/2013] [Accepted: 03/03/2013] [Indexed: 11/27/2022]
Abstract
Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.
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Affiliation(s)
- R. Appels
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - R. Barrero
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
| | - M. Bellgard
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150 Australia
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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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Riaz S, Hu R, Walker MA. A framework genetic map of Muscadinia rotundifolia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1195-1210. [PMID: 22688272 DOI: 10.1007/s00122-012-1906-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 05/25/2012] [Indexed: 06/01/2023]
Abstract
This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n = 20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879 cM on 18 chromosomes. The average distance between the markers was 4.1 cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841 cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088 cM, which represented 66 % of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome.
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Affiliation(s)
- S Riaz
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
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Bertazzon N, Raiola A, Castiglioni C, Gardiman M, Angelini E, Borgo M, Ferrari S. Transient silencing of the grapevine gene VvPGIP1 by agroinfiltration with a construct for RNA interference. PLANT CELL REPORTS 2012; 31:133-43. [PMID: 21932028 DOI: 10.1007/s00299-011-1147-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/29/2011] [Accepted: 08/31/2011] [Indexed: 05/23/2023]
Abstract
Grapevine is an economically important crop, and the recent completion of its genome makes it possible to study the function of specific genes through reverse genetics. However, the analysis of gene function by RNA interference (RNAi) in grapevine is difficult, because the generation of stable transgenic plants has low efficiency and is time consuming. Recently, transient expression of genes in grapevine leaves has been obtained by Agrobacterium tumefaciens infiltration (agroinfiltration). We therefore tested the possibility to silence grapevine genes by agroinfiltration of RNAi constructs. A construct to express a double strand RNA (dsRNA) corresponding to the defense-related gene VvPGIP1, encoding a polygalacturonase-inhibiting protein (PGIP), was obtained and transiently expressed by agroinfiltration in leaves of grapevine plants grown in vitro. Expression of VvPGIP1 and accumulation of PGIP activity were strongly induced by infiltration with control bacteria, but not with bacteria carrying the dsRNA construct, indicating that the gene was efficiently silenced. In contrast, expression of another defense-related gene, VST1, encoding a stilbene synthase, was unaffected by the dsRNA construct. We have therefore demonstrated the possibility of transient down-regulation of grapevine genes by agroinfiltration of constructs for the expression of dsRNA. This system can be employed to evaluate the effectiveness of constructs that can be subsequently used to generate stable RNAi transgenic plants.
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Affiliation(s)
- Nadia Bertazzon
- CRA-VIT Centro di ricerca per la viticoltura, Conegliano, TV, Italy
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de Boer JM, Borm TJA, Jesse T, Brugmans B, Wiggers-Perebolte L, de Leeuw L, Tang X, Bryan GJ, Bakker J, van Eck HJ, Visser RGF. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome. BMC Genomics 2011; 12:594. [PMID: 22142254 PMCID: PMC3261212 DOI: 10.1186/1471-2164-12-594] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 12/05/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). RESULTS First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. CONCLUSIONS The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalstesteeg 1, 6708 PD Wageningen, The Netherlands.
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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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Tillett RL, Ergül A, Albion RL, Schlauch KA, Cramer GR, Cushman JC. Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets. BMC PLANT BIOLOGY 2011; 11:86. [PMID: 21592389 PMCID: PMC3224124 DOI: 10.1186/1471-2229-11-86] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 05/18/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses. RESULTS A total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, short-term, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues. CONCLUSIONS The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods.
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Affiliation(s)
- Richard L Tillett
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Ali Ergül
- Biotechnology Institute, Ankara University, Merkez Laboratuvari, Rektorluk Binasi Arkasi, 06100 Ankara, Turkey
| | - Rebecca L Albion
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Karen A Schlauch
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Grant R Cramer
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
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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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