1
|
van de Wiel CCM, Schaart JG, Lotz LAP, Smulders MJM. Correction to: New traits in crops produced by genome editing techniques based on deletions. Plant Biotechnol Rep 2018; 12:375. [PMID: 31186814 PMCID: PMC6244920 DOI: 10.1007/s11816-018-0498-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
[This corrects the article DOI: 10.1007/s11816-017-0425-z.].
Collapse
Affiliation(s)
| | - J. G. Schaart
- Wageningen University and Research, Wageningen, The Netherlands
| | - L. A. P. Lotz
- Wageningen University and Research, Wageningen, The Netherlands
| | | |
Collapse
|
2
|
Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 2018; 4:473-484. [PMID: 29892093 DOI: 10.1101/254102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/27/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Collapse
Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
3
|
Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 2018; 4:473-484. [PMID: 29892093 PMCID: PMC6786968 DOI: 10.1038/s41477-018-0166-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/18/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Collapse
Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
4
|
van de Wiel CCM, Schaart JG, Lotz LAP, Smulders MJM. New traits in crops produced by genome editing techniques based on deletions. Plant Biotechnol Rep 2017; 11:1-8. [PMID: 28386301 PMCID: PMC5360818 DOI: 10.1007/s11816-017-0425-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 01/23/2017] [Indexed: 05/21/2023]
Abstract
One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.
Collapse
Affiliation(s)
| | - J. G. Schaart
- Wageningen University and Research, Wageningen, The Netherlands
| | - L. A. P. Lotz
- Wageningen University and Research, Wageningen, The Netherlands
| | | |
Collapse
|
5
|
Dubois AEJ, Pagliarani G, Brouwer RM, Kollen BJ, Dragsted LO, Eriksen FD, Callesen O, Gilissen LJWJ, Krens FA, Visser RGF, Smulders MJM, Vlieg-Boerstra BJ, Flokstra-de Blok BJ, van de Weg WE. First successful reduction of clinical allergenicity of food by genetic modification: Mal d 1-silenced apples cause fewer allergy symptoms than the wild-type cultivar. Allergy 2015; 70:1406-12. [PMID: 26138410 DOI: 10.1111/all.12684] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Genetic modification of allergenic foods such as apple has the potential to reduce their clinical allergenicity, but this has never been studied by oral challenges in allergic individuals. METHODS We performed oral food challenges in 21 apple-allergic individuals with Elstar apples which had undergone gene silencing of the major allergen of apple, Mal d 1, by RNA interference. Downregulation of Mal d 1 gene expression in the apples was verified by qRT-PCR. Clinical responses to the genetically modified apples were compared to those seen with the wild-type Elstar using a visual analogue scale (VAS). RESULTS Gene silencing produced two genetically modified apple lines expressing Mal d 1.02 and other Mal d 1 gene mRNA levels which were extensively downregulated, that is only 0.1-16.4% (e-DR1) and 0.2-9.9% (e-DR2) of those of the wild-type Elstar, respectively. Challenges with these downregulated apple lines produced significantly less intense maximal symptoms to the first dose (Vmax1) than with Elstar (Vmax1 Elstar 3.0 mm vs 0.0 mm for e-DR1, P = 0.017 and 0.0 mm for e-DR2, P = 0.043), as well as significantly less intense mean symptoms per dose (meanV/d) than with Elstar (meanV/d Elstar 2.2 mm vs 0.2 mm for e-DR1, P = 0.017 and 0.0 mm for e-DR2, P = 0.043). Only one subject (5%) remained symptom-free when challenged with the Elstar apple, whereas 43% did so with e-DR1 and 63% with e-DR2. CONCLUSION These data show that mRNA silencing of Mal d 1 results in a marked reduction of Mal d 1 gene expression in the fruit and reduction of symptoms when these apples are ingested by allergic subjects. Approximately half of the subjects developed no symptoms whatsoever, and virtually all subjects wished to consume the apple again in the future.
Collapse
Affiliation(s)
- A. E. J. Dubois
- Department of Pediatric Pulmonology and Pediatric Allergy, and GRIAC Research Institute; Beatrix Children's Hospital; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - G. Pagliarani
- Wageningen UR Plant Breeding; Wageningen University and Research Centre; Wageningen The Netherlands
| | - R. M. Brouwer
- Department of Pediatric Pulmonology and Pediatric Allergy, and GRIAC Research Institute; Beatrix Children's Hospital; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - B. J. Kollen
- Department of General Practice, and GRIAC Research Institute; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - L. O. Dragsted
- Department of Nutrition, Exercise and Sports; University of Copenhagen; Frederiksberg Denmark
| | - F. D. Eriksen
- Technical University of Denmark; National Food Institute, Toxicology and Risk Assessment; Søborg Denmark
| | - O. Callesen
- Department of Horticulture; Faculty of Agricultural Sciences; University of Aarhus; Årslev Denmark
| | - L. J. W. J. Gilissen
- Bioscience; Wageningen University and Research Centre; Wageningen The Netherlands
- Allergy Consortium Wageningen; Wageningen University and Research Centre; Wageningen The Netherlands
| | - F. A. Krens
- Wageningen UR Plant Breeding; Wageningen University and Research Centre; Wageningen The Netherlands
| | - R. G. F. Visser
- Allergy Consortium Wageningen; Wageningen University and Research Centre; Wageningen The Netherlands
| | - M. J. M. Smulders
- Wageningen UR Plant Breeding; Wageningen University and Research Centre; Wageningen The Netherlands
- Allergy Consortium Wageningen; Wageningen University and Research Centre; Wageningen The Netherlands
| | - B. J. Vlieg-Boerstra
- Department of Pediatric Pulmonology and Pediatric Allergy, and GRIAC Research Institute; Beatrix Children's Hospital; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - B. J. Flokstra-de Blok
- Department of General Practice, and GRIAC Research Institute; University Medical Center Groningen; University of Groningen; Groningen The Netherlands
| | - W. E. van de Weg
- Wageningen UR Plant Breeding; Wageningen University and Research Centre; Wageningen The Netherlands
- Allergy Consortium Wageningen; Wageningen University and Research Centre; Wageningen The Netherlands
| |
Collapse
|
6
|
Addisalem AB, Esselink GD, Bongers F, Smulders MJM. Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests. AoB Plants 2015; 7:plu086. [PMID: 25573702 PMCID: PMC4433549 DOI: 10.1093/aobpla/plu086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/08/2014] [Indexed: 06/01/2023]
Abstract
Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2-12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin.
Collapse
Affiliation(s)
- A B Addisalem
- Wageningen UR Plant Breeding, Wageningen University and Research Center, PO Box 386, NL-6700 AJ Wageningen, The Netherlands Center for Ecosystem Studies, Forest Ecology and Forest Management Group, Wageningen University and Research Center, PO Box 47, NL-6700 AA Wageningen, The Netherlands Wondo Genet College of Forestry and Natural Resources, PO Box 128, Shashemene, Ethiopia
| | - G Danny Esselink
- Wageningen UR Plant Breeding, Wageningen University and Research Center, PO Box 386, NL-6700 AJ Wageningen, The Netherlands
| | - F Bongers
- Center for Ecosystem Studies, Forest Ecology and Forest Management Group, Wageningen University and Research Center, PO Box 47, NL-6700 AA Wageningen, The Netherlands
| | - M J M Smulders
- Wageningen UR Plant Breeding, Wageningen University and Research Center, PO Box 386, NL-6700 AJ Wageningen, The Netherlands
| |
Collapse
|
7
|
Vukosavljev M, Esselink GD, van ’t Westende WPC, Cox P, Visser RGF, Arens P, Smulders MJM. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals. Mol Ecol Resour 2014; 15:17-27. [DOI: 10.1111/1755-0998.12289] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 11/26/2022]
Affiliation(s)
- M. Vukosavljev
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
- C.T. de Wit Graduate School for Production Ecology and Resource Conservation (PE&RC); Wageningen the Netherlands
| | - G. D. Esselink
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - W. P. C. van ’t Westende
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - P. Cox
- Roath BV; Eindhoven the Netherlands
| | - R. G. F. Visser
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - P. Arens
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - M. J. M. Smulders
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| |
Collapse
|
8
|
Cornille A, Giraud T, Bellard C, Tellier A, Le Cam B, Smulders MJM, Kleinschmit J, Roldan-Ruiz I, Gladieux P. Postglacial recolonization history of the European crabapple (Malus sylvestrisMill.), a wild contributor to the domesticated apple. Mol Ecol 2013; 22:2249-63. [DOI: 10.1111/mec.12231] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 11/27/2022]
Affiliation(s)
- A. Cornille
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
| | - T. Giraud
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
| | - C. Bellard
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
| | - A. Tellier
- Section of Population Genetics; Center of Life and Food Sciences Weihenstephan; Technische Universität München; 85354 Freising Deutschland
| | - B. Le Cam
- INRA; IRHS; PRES UNAM; SFR QUASAV; Rue G. Morel F-49071 Beaucouzé France
| | - M. J. M. Smulders
- Plant Research International; Wageningen UR Plant Breeding; PO Box 16 6700 AA Wageningen The Netherlands
| | - J. Kleinschmit
- Department of Forest Genetic Resources; Northwest German Forest Research Institute; Professor-Oelkers Str. 6, 34346 Hann. Münden Germany
| | - I. Roldan-Ruiz
- ILVO; Plant-Growth and Development; Caritasstraat 21 9090 Melle Belgium
| | - P. Gladieux
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720-3102 USA
| |
Collapse
|
9
|
Ghahramanzadeh R, Esselink G, Kodde LP, Duistermaat H, van Valkenburg JLCH, Marashi SH, Smulders MJM, van de Wiel CCM. Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding. Mol Ecol Resour 2012; 13:21-31. [PMID: 23039943 DOI: 10.1111/1755-0998.12020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/08/2012] [Accepted: 08/16/2012] [Indexed: 11/29/2022]
Abstract
Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics.
Collapse
Affiliation(s)
- R Ghahramanzadeh
- Wageningen UR Plant Breeding, Wageningen, NL-6700 AA, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Koning-Boucoiran CFS, Gitonga VW, Yan Z, Dolstra O, van der Linden CG, van der Schoot J, Uenk GE, Verlinden K, Smulders MJM, Krens FA, Maliepaard C. The mode of inheritance in tetraploid cut roses. Theor Appl Genet 2012; 125:591-607. [PMID: 22526522 PMCID: PMC3397129 DOI: 10.1007/s00122-012-1855-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 03/21/2012] [Indexed: 05/18/2023]
Abstract
Tetraploid hybrid tea roses (Rosa hybrida) represent most of the commercial cultivars of cut roses and form the basis for breeding programmes. Due to intensive interspecific hybridizations, modern cut roses are complex tetraploids for which the mode of inheritance is not exactly known. The segregation patterns of molecular markers in a tetraploid mapping population of 184 genotypes, an F(1) progeny from a cross of two heterozygous parents, were investigated for disomic and tetrasomic inheritance. The possible occurrence of double reduction was studied as well. We can exclude disomic inheritance, but while our observations are more in line with a tetrasomic inheritance, we cannot exclude that there is a mixture of both inheritance modes. Two novel parental tetraploid linkage maps were constructed using markers known from literature, combined with newly generated markers. Comparison with the integrated consensus diploid map (ICM) of Spiller et al. (Theor Appl Genet 122:489-500, 2010) allowed assigning numbers to each of the linkage groups of both maps and including small linkage groups. So far, the possibility of using marker-assisted selection in breeding of tetraploid cut roses and of other species with a tetrasomic or partly tetrasomic inheritance, is still limited due to the difficulties in establishing marker-trait associations. We used these tetraploid linkage maps to determine associations between markers, two morphological traits and powdery mildew resistance. The knowledge on inheritance and marker-trait associations in tetraploid cut roses will be of direct use to cut rose breeding.
Collapse
Affiliation(s)
- C F S Koning-Boucoiran
- Wageningen University and Research Centre, Plant Breeding, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Aggarwal RK, Allainguillaume J, Bajay MM, Barthwal S, Bertolino P, Chauhan P, Consuegra S, Croxford A, Dalton DL, den Belder E, Díaz-Ferguson E, Douglas MR, Drees M, Elderson J, Esselink GD, Fernández-Manjarrés JF, Frascaria-Lacoste N, Gäbler-Schwarz S, Garcia de Leaniz C, Ginwal HS, Goodisman MAD, Guo B, Hamilton MB, Hayes PK, Hong Y, Kajita T, Kalinowski ST, Keller L, Koop BF, Kotzé A, Lalremruata A, Leese F, Li C, Liew WY, Martinelli S, Matthews EA, Medlin LK, Messmer AM, Meyer EI, Monteiro M, Moyer GR, Nelson RJ, Nguyen TTT, Omoto C, Ono J, Pavinato VAC, Pearcy M, Pinheiro JB, Power LD, Rawat A, Reusch TBH, Sanderson D, Sannier J, Sathe S, Sheridan CK, Smulders MJM, Sukganah A, Takayama K, Tamura M, Tateishi Y, Vanhaecke D, Vu NV, Wickneswari R, Williams AS, Wimp GM, Witte V, Zucchi MI. Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010. Mol Ecol Resour 2011; 11:219-22. [PMID: 21429127 DOI: 10.1111/j.1755-0998.2010.02944.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.
Collapse
Affiliation(s)
-
- Centre for Cellular and Molecular Biology (CSIR), Hyderabad 500007, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Bryce M, Drews O, Schenk MF, Menzel A, Estrella N, Weichenmeier I, Smulders MJM, Buters J, Ring J, Görg A, Behrendt H, Traidl-Hoffmann C. Impact of urbanization on the proteome of birch pollen and its chemotactic activity on human granulocytes. Int Arch Allergy Immunol 2009; 151:46-55. [PMID: 19672096 DOI: 10.1159/000232570] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 03/27/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Epidemiologic studies reveal a dramatic increase in allergies in the last decades. Air pollution is considered to be one of the factors responsible for this augmentation. The aim of this study was to analyze the impact of urbanization on birch pollen. The birch pollen proteome was investigated in order to identify differences in protein abundance between pollen from rural and urban areas. The allergenicity of birch pollen from both areas was evaluated by assessing its chemotactic potency as well as its protein and allergen contents. METHODS Difference gel electrophoresis (DIGE) was used to analyze the pollen proteome. The chemotactic activity of aqueous pollen extracts was determined by migration assays of human neutrophils. RESULTS DIGE revealed 26 differences in protein spot intensity between pollen from urban and rural areas. One of these proteins was identified by de novo sequencing as the 14-3-3 protein, which resembles a stress-induced factor in other plant species. Furthermore, extracts from pollen collected in urban areas had higher chemotactic activity on human neutrophils compared to pollen from rural sites. CONCLUSIONS The present study points to an impact of air pollution on allergen carrier proteome and release of chemotactic substances. The increment in proinflammatory substances such as pollen-associated lipid mediators might contribute to the described urban-rural gradient of allergy prevalence. Furthermore, our study suggests that allergenicity is determined by more than the sole allergen content.
Collapse
Affiliation(s)
- M Bryce
- Division of Environmental Dermatology and Allergy, Helmholtz Center Munich/TUM, ZAUM - Center of Allergy and Environment, Technische Universität, Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Riba M, Mayol M, Giles BE, Ronce O, Imbert E, Van Der Velde M, Chauvet S, Ericson L, Bijlsma R, Vosman B, Smulders MJM, Olivieri I. Darwin's wind hypothesis: does it work for plant dispersal in fragmented habitats? New Phytol 2009; 183:667-677. [PMID: 19659587 DOI: 10.1111/j.1469-8137.2009.02948.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Using the wind-dispersed plant Mycelis muralis, we examined how landscape fragmentation affects variation in seed traits contributing to dispersal. Inverse terminal velocity (Vt(-1)) of field-collected achenes was used as a proxy for individual seed dispersal ability. We related this measure to different metrics of landscape connectivity, at two spatial scales: in a detailed analysis of eight landscapes in Spain and along a latitudinal gradient using 29 landscapes across three European regions. In the highly patchy Spanish landscapes, seed Vt(-1)increased significantly with increasing connectivity. A common garden experiment suggested that differences in Vt(-1) may be in part genetically based. The Vt(-1) was also found to increase with landscape occupancy, a coarser measure of connectivity, on a much broader (European) scale. Finally, Vt(-1)was found to increase along a south-north latitudinal gradient. Our results for M. muralis are consistent with 'Darwin's wind dispersal hypothesis' that high cost of dispersal may select for lower dispersal ability in fragmented landscapes, as well as with the 'leading edge hypothesis' that most recently colonized populations harbour more dispersive phenotypes.
Collapse
Affiliation(s)
- Miquel Riba
- CREAF (Center for Ecological Research and Forestry Applications), Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Maria Mayol
- CREAF (Center for Ecological Research and Forestry Applications), Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Barbara E Giles
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Ophélie Ronce
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| | - Eric Imbert
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| | - Marco Van Der Velde
- Animal Ecology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, PO Box 14, NL-9750 AA Haren, The Netherlands
| | - Stéphanie Chauvet
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
- Association Tela Botanica, Institut de Botanique, 163 Rue Auguste Broussonnet, F-34090 Montpellier, France
| | - Lars Ericson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - R Bijlsma
- Population and Conservation Genetics, Theoretical Biology, University of Groningen, PO Box 14, NL-9750 AA Haren, The Netherlands
| | - Ben Vosman
- Plant Research International, Wageningen UR, PO Box 16, NL-6700 AA Wageningen, The Netherlands
| | - M J M Smulders
- Plant Research International, Wageningen UR, PO Box 16, NL-6700 AA Wageningen, The Netherlands
| | - Isabelle Olivieri
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| |
Collapse
|
14
|
Schroeder H, Arens P, Smulders MJM. Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L. (Lepidoptera, Tortricidae). Mol Ecol Resour 2009; 9:809-11. [PMID: 21564751 DOI: 10.1111/j.1755-0998.2008.02249.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy-Weinberg equilibrium. The other two were linked to the Z-chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies.
Collapse
Affiliation(s)
- H Schroeder
- Institute for Forest Genetics, Johann Heinrich von Thuenen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany Plant Research International, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | | | | |
Collapse
|
15
|
VAN DE Wiel CCM, VAN DER Schoot J, VAN Valkenburg JLCH, Duistermaat H, Smulders MJM. DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoides L.f.), from non-invasive relatives. Mol Ecol Resour 2009; 9:1086-91. [PMID: 21564846 DOI: 10.1111/j.1755-0998.2009.02547.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Floating pennywort (Hydrocotyle ranunculoides L.f.), a member of the plant family Araliaceae originating from North America, is an example of an invasive aquatic species posing serious problems to the management of waterways outside of its original distribution area in Australia and Western Europe. As a consequence, its import was banned in the Netherlands. It can be difficult to distinguish H. ranunculoides from other species of the genus on a morphological basis. In this regard, DNA barcoding may become a good alternative once this could be performed on a routine basis. In this study, we show that it is possible to distinguish H. ranunculoides from a series of closely related congeners by using a single plastid DNA sequence, trnH-psbA.
Collapse
Affiliation(s)
- C C M VAN DE Wiel
- Wageningen UR Plant Breeding, PO Box 16, NL-6700 AA Wageningen, The Netherlands.
| | | | | | | | | |
Collapse
|
16
|
Van Herpen TWJM, Riley M, Sparks C, Jones HD, Gritsch C, Dekking EH, Hamer RJ, Bosch D, Salentijn EMJ, Smulders MJM, Shewry PR, Gilissen LJWJ. Detailed analysis of the expression of an alpha-gliadin promoter and the deposition of alpha-gliadin protein during wheat grain development. Ann Bot 2008; 102:331-42. [PMID: 18621967 PMCID: PMC2701793 DOI: 10.1093/aob/mcn114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/22/2008] [Accepted: 06/09/2008] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Alpha-gliadin proteins are important for the industrial quality of bread wheat flour, but they also contain many epitopes that can trigger celiac (coeliac) disease (CD). The B-genome-encoded alpha-gliadin genes, however, contain very few epitopes. Controlling alpha-gliadin gene expression in wheat requires knowledge on the processes of expression and deposition of alpha-gliadin protein during wheat grain development. METHODS A 592-bp fragment of the promotor of a B-genome-encoded alpha-gliadin gene driving the expression of a GUS reporter gene was transformed into wheat. A large number of transgenic lines were used for data collection. GUS staining was used to determine GUS expression during wheat kernel development, and immunogold labelling and tissue printing followed by staining with an alpha-gliadin-specific antibody was used to detect alpha-gliadin protein deposited in developing wheat kernels. The promoter sequence was screened for regulatory motifs and compared to other available alpha-gliadin promoter sequences. KEY RESULTS GUS expression was detected primarily in the cells of the starchy endosperm, notably in the subaleurone layer but also in the aleurone layer. The alpha-gliadin promoter was active from 11 days after anthesis (DAA) until maturity, with an expression similar to that of a 326-bp low molecular weight (LMW) subunit gene promoter reported previously. An alpha-gliadin-specific antibody detected alpha-gliadin protein in protein bodies in the starchy endosperm and in the subaleurone layer but, in contrast to the promoter activity, no alpha-gliadin was detected in the aleurone cell layer. Sequence comparison showed differences in regulatory elements between the promoters of alpha-gliadin genes originating from different genomes (A and B) of bread wheat both in the region used here and upstream. CONCLUSIONS The results suggest that additional regulator elements upstream of the promoter region used may specifically repress expression in the aleurone cell layer. Observed differences in expression regulator motifs between the alpha-gliadin genes on the different genomes (A and B) of bread wheat leads to a better understanding how alpha-gliadin expression can be controlled.
Collapse
Affiliation(s)
- T. W. J. M. Van Herpen
- Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
- Allergy Consortium Wageningen, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
| | - M. Riley
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - C. Sparks
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - H. D. Jones
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - C. Gritsch
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - E. H. Dekking
- Leiden University Medical Center, Albinusdreef 2, E3-Q, P.O. Box 9600, NL-2300 RC Leiden, The Netherlands
| | - R. J. Hamer
- Laboratory for Food Chemistry, Wageningen University, Bomenweg 2, NL-6700 EV Wageningen, The Netherlands
| | - D. Bosch
- Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
| | - E. M. J. Salentijn
- Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
| | - M. J. M. Smulders
- Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
- Allergy Consortium Wageningen, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
| | - P. R. Shewry
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - L. J. W. J. Gilissen
- Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
- Allergy Consortium Wageningen, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands
| |
Collapse
|
17
|
Dormann CF, Schweiger O, Arens P, Augenstein I, Aviron S, Bailey D, Baudry J, Billeter R, Bugter R, Bukácek R, Burel F, Cerny M, Cock RD, De Blust G, DeFilippi R, Diekötter T, Dirksen J, Durka W, Edwards PJ, Frenzel M, Hamersky R, Hendrickx F, Herzog F, Klotz S, Koolstra B, Lausch A, Le Coeur D, Liira J, Maelfait JP, Opdam P, Roubalova M, Schermann-Legionnet A, Schermann N, Schmidt T, Smulders MJM, Speelmans M, Simova P, Verboom J, van Wingerden W, Zobel M. Prediction uncertainty of environmental change effects on temperate European biodiversity. Ecol Lett 2007; 11:235-44. [PMID: 18070098 DOI: 10.1111/j.1461-0248.2007.01142.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Observed patterns of species richness at landscape scale (gamma diversity) cannot always be attributed to a specific set of explanatory variables, but rather different alternative explanatory statistical models of similar quality may exist. Therefore predictions of the effects of environmental change (such as in climate or land cover) on biodiversity may differ considerably, depending on the chosen set of explanatory variables. Here we use multimodel prediction to evaluate effects of climate, land-use intensity and landscape structure on species richness in each of seven groups of organisms (plants, birds, spiders, wild bees, ground beetles, true bugs and hoverflies) in temperate Europe. We contrast this approach with traditional best-model predictions, which we show, using cross-validation, to have inferior prediction accuracy. Multimodel inference changed the importance of some environmental variables in comparison with the best model, and accordingly gave deviating predictions for environmental change effects. Overall, prediction uncertainty for the multimodel approach was only slightly higher than that of the best model, and absolute changes in predicted species richness were also comparable. Richness predictions varied generally more for the impact of climate change than for land-use change at the coarse scale of our study. Overall, our study indicates that the uncertainty introduced to environmental change predictions through uncertainty in model selection both qualitatively and quantitatively affects species richness projections.
Collapse
Affiliation(s)
- Carsten F Dormann
- Computational Landscape Ecology, UFZ Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Chaerani R, Smulders MJM, van der Linden CG, Vosman B, Stam P, Voorrips RE. QTL identification for early blight resistance (Alternaria solani) in a Solanum lycopersicum x S. arcanum cross. Theor Appl Genet 2007; 114:439-50. [PMID: 17093974 DOI: 10.1007/s00122-006-0442-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Accepted: 10/21/2006] [Indexed: 05/12/2023]
Abstract
Alternaria solani (Ellis and Martin) Sorauer, the causal agent of early blight (EB) disease, infects aerial parts of tomato at both seedling and adult plant stages. Resistant cultivars would facilitate a sustainable EB management. EB resistance is a quantitatively expressed character, a fact that has hampered effective breeding. In order to identify and estimate the effect of genes conditioning resistance to EB, a quantitative trait loci (QTL) mapping study was performed in F2 and F3 populations derived from the cross between the susceptible Solanum lycopersicum (syn. Lycopersicon esculentum) cv. 'Solentos' and the resistant Solanum arcanum (syn. Lycopersicon peruvianum) LA2157 and genotyped with AFLP, microsatellite and SNP markers. Two evaluation criteria of resistance were used: measurements of EB lesion growth on the F2 plants in glasshouse tests and visual ratings of EB severity on foliage of the F3 lines in a field test. A total of six QTL regions were mapped on chromosomes 1, 2, 5-7, and 9 with LOD scores ranging from 3.4 to 17.5. Three EB QTL also confer resistance to stem lesions in the field, which has not been reported before. All QTL displayed significant additive gene action; in some cases a dominance effect was found. Additive x additive epistatic interactions were detected between one pair of QTL. For two QTL, the susceptible parent contributed resistance alleles to both EB and stem lesion resistance. Three of the QTL showed an effect in all tests despite methodological and environmental differences.
Collapse
Affiliation(s)
- R Chaerani
- Plant Research International, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
19
|
Mix C, Arens PFP, Rengelink R, Smulders MJM, Van Groenendael JM, Ouborg NJ. Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape. Mol Ecol 2006; 15:1749-58. [PMID: 16689895 DOI: 10.1111/j.1365-294x.2006.02887.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P < 0.01). A significant isolation-by-distance pattern was found when all populations were simultaneously analysed (r = 0.24, P = 0.013). Isolation by distance was (marginally) significant at the small scale (r = 0.32, P = 0.06), whereas nonsignificant at the large spatial scale (r = -0.05, P = 0.66). A maximization-of-explained-variance procedure resulted in a threshold distance of 3.5 km above which populations were effectively genetically isolated. An additional partial exclusion Bayesian-based assignment test showed that overall 32.3% of the individuals were assigned to their population of origin, 48% were assigned to another population in the area and 19.7% were not assigned. Together, these results suggest high levels of gene flow. Seed dispersal contributes to the observed gene flow up to several hundred metres, which is higher than previously modelled using aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.
Collapse
Affiliation(s)
- C Mix
- Department of Ecology, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
| | | | | | | | | | | |
Collapse
|
20
|
Arens P, Bijlsma RJ, van't Westende W, van Os B, Smulders MJM, Vosman B. Genetic structure in populations of an ancient woodland sedge, Carex sylvatica Hudson, at a regional and local scale. Plant Biol (Stuttg) 2005; 7:387-96. [PMID: 16025411 DOI: 10.1055/s-2005-865644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Wood sedge (Carex sylvatica) is a well-known ancient woodland species with a long-term persistent seed bank and a caespitose growth habit. All thirteen isolated Carex sylvatica populations in the Dutch Rhine floodplain (including the river branches Waal and IJssel) were mapped in detail and analysed for genetic variation at a large number of AFLP loci and one microsatellite locus. Across all populations, only 40 % of the sampled individuals (n=216) represented a unique genotype. A high number of the studied patches (spatial clusters of tussocks, 2-10 m in diameter) within populations contained only one or a few genotypes. Identical plants (tussocks) were also found 20-500 m apart and in one case even 1000 m apart. Observed heterozygosity levels (H(O)=0.029) were low, indicating low levels of gene flow, which is in agreement with the selfing nature of other caespitose sedges. Although the number of genotypes in populations is low, these genotypes are genetically very distinct and variation within populations accounted for 55% of the total variation. The absence of a correlation between genetic and geographic distances among populations, and the scattered distribution of genotypes among patches within woodlands, support our hypothesis of rare establishments and subsequent local dispersal within woodlands in this forest floor species, which may benefit from and partly depend on human land use and forest management activities.
Collapse
Affiliation(s)
- P Arens
- Department of Biodiversity and Breeding, Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA Wageningen, The Netherlands.
| | | | | | | | | | | |
Collapse
|
21
|
Adin A, Weber JC, Sotelo Montes C, Vidaurre H, Vosman B, Smulders MJM. Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management. Theor Appl Genet 2004; 108:1564-1573. [PMID: 14985969 DOI: 10.1007/s00122-003-1581-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Accepted: 12/12/2003] [Indexed: 05/24/2023]
Abstract
Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.
Collapse
Affiliation(s)
- A Adin
- Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
22
|
Chauvet S, van der Velde M, Imbert E, Guillemin ML, Mayol M, Riba M, Smulders MJM, Vosman B, Ericson L, Bijlsma R, Giles BE. Past and current gene flow in the selfing, wind-dispersed species Mycelis muralis in western Europe. Mol Ecol 2004; 13:1391-407. [PMID: 15140085 DOI: 10.1111/j.1365-294x.2004.02166.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The distribution of genetic diversity in Mycelis muralis, or wall lettuce, was investigated at a European scale using 12 microsatellite markers to infer historical and contemporary forces from genetic patterns. Mycelis muralis has the potential for long-distance seed dispersal by wind, is mainly self-pollinated, and has patchily distributed populations, some of which may show metapopulation dynamics. A total of 359 individuals were sampled from 17 populations located in three regions, designated southern Europe (Spain and France), the Netherlands, and Sweden. At this within-region scale, contemporary evolutionary forces (selfing and metapopulation dynamics) are responsible for high differentiation between populations (0.34 < F(ST) < 0.60) but, contrary to expectation, levels of within-population diversity, estimated by Nei's unbiased expected heterozygosity (H(E)) (0.24 < H(E) < 0.68) or analyses of molecular variance (50% of the variation found within-populations), were not low. We suggest that the latter results, which are unusual in selfing species, arise from efficient seed dispersal that counteracts population turnover and thus maintains genetic diversity within populations. At the European scale, northern regions showed lower allelic richness (A = 2.38) than populations from southern Europe (A = 3.34). In light of postglacial colonization hypotheses, these results suggest that rare alleles may have been lost during recolonization northwards. Our results further suggest that mutation has contributed to genetic differentiation between southern and northern Europe, and that Sweden may have been colonized by dispersers originating from at least two different refugia.
Collapse
Affiliation(s)
- S Chauvet
- Umeå University, Department of Ecology and Environmental Science, 901 87 Umeå, Sweden.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Storme V, Vanden Broeck A, Ivens B, Halfmaerten D, Van Slycken J, Castiglione S, Grassi F, Fossati T, Cottrell JE, Tabbener HE, Lefèvre F, Saintagne C, Fluch S, Krystufek V, Burg K, Bordács S, Borovics A, Gebhardt K, Vornam B, Pohl A, Alba N, Agúndez D, Maestro C, Notivol E, Bovenschen J, van Dam BC, van der Schoot J, Vosman B, Boerjan W, Smulders MJM. Ex-situ conservation of Black poplar in Europe: genetic diversity in nine gene bank collections and their value for nature development. Theor Appl Genet 2004; 108:969-81. [PMID: 15067382 DOI: 10.1007/s00122-003-1523-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 10/27/2003] [Indexed: 05/11/2023]
Abstract
Populus nigra L. is a pioneer tree species of riparian ecosystems that is threatened with extinction because of the loss of its natural habitat. To evaluate the existing genetic diversity of P. nigra within ex-situ collections, we analyzed 675 P. nigra L. accessions from nine European gene banks with three amplified fragment length polymorphism (AFLP) and five microsatellite [or simple sequence repeat (SSR)] primer combinations, and 11 isozyme systems. With isozyme analysis, hybrids could be detected, and only 3% were found in the gene bank collection. AFLP and SSR analyses revealed effectively that 26% of the accessions were duplicated and that the level of clonal duplication varied from 0% in the French gene bank collection up to 78% in the Belgian gene bank collection. SSR analysis was preferred because AFLP was technically more demanding and more prone to scoring errors. To assess the genetic diversity, we grouped material from the gene banks according to topography of the location from which the accessions were originally collected (river system or regions separated by mountains). Genetic diversity was expressed in terms of the following parameters: percentage of polymorphic loci, observed and effective number of alleles, and Nei's expected heterozygosity or gene diversity (for AFLP). Genetic diversity varied from region to region and depended, to some extent, on the marker system used. The most unique alleles were identified in the Danube region (Austria), the Rhône region (France), Italy, the Rijn region (The Netherlands), and the Ebro region (Spain). In general, the diversity was largest in the material collected from the regions in Southern Europe. Dendrograms and principal component analysis resulted in a clustering according to topography. Material from the same river systems, but from different countries, clustered together. The genetic differentiation among the regions (F(st)/G(st)) was moderate.
Collapse
Affiliation(s)
- V Storme
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Smulders MJM, Noordijk Y, Rus-Kortekaas W, Bredemeijer GMM, Vosman B. Microsatellite genotyping of carnation varieties. Theor Appl Genet 2003; 106:1191-1195. [PMID: 12748769 DOI: 10.1007/s00122-002-1166-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2002] [Accepted: 09/23/2002] [Indexed: 05/24/2023]
Abstract
A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluorescence-based approach. In a set of 82 cultivars, the markers amplified 4-16 alleles each. The effective number of alleles varied from 1.9 to 6.0. For the eight best scorable markers, heterozygosity was between 0.51 and 0.99. The markers were able to distinguish all cultivars with a unique combination of alleles, except for sport mutants, which were readily grouped together with the original cultivar. In addition, one group of three and one group of six cultivars each had the same combination of 'allelic peaks'. The cluster of three varieties concerned original cultivars and their mutants. The cluster of six consisted of four mutants from the same cultivar and two other varieties.
Collapse
Affiliation(s)
- M J M Smulders
- Plant Research International, P.O. Box 16, 6700 AA Wageningen, The Netherlands.
| | | | | | | | | |
Collapse
|
25
|
Pastorelli R, Smulders MJM, VAN’T Westende WPC, Vosman B, Giannini R, Vettori C, Vendramin GG. Characterization of microsatellite markers inFagus sylvaticaL. andFagus orientalisLipsky. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1471-8286.2003.00355.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Esselink GD, Smulders MJM, Vosman B. Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet 2003; 106:277-86. [PMID: 12582853 DOI: 10.1007/s00122-002-1122-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2002] [Accepted: 07/01/2002] [Indexed: 05/18/2023]
Abstract
In this study a DNA fingerprinting protocol was developed for the identification of rose varieties based on the variability of microsatellites. Microsatellites were isolated from Rosa hybrida L. using enriched small insert libraries. In total 24 polymorphic sequenced tagged microsatellite site (STMS) markers with easily scorable allele profiles, from six different linkage groups, were used to characterize 46 Hybrid Tea varieties and 30 rootstock varieties belonging to different species (Rosa canina L., Rosa indica Thory., Rosa chinensis Jacq., Rosa rubiginosa L., and Rosa rubrifolia glauca Pour.). Clones and known flower color mutants were identified as being identical, all other varieties were differentiated by a unique pattern with as few as three STMS markers. The high discriminating power of the loci suggests that a selection of the most-robust STMS markers may be able to differentiate any two varieties within rootstocks or Hybrid Teas except for mutants. The selected STMS markers will be useful as a tool for reference collection management, for assessing essential derivation of varieties and illegal propagation.
Collapse
Affiliation(s)
- G D Esselink
- Department of Biodiversity and Identity, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands
| | | | | |
Collapse
|
27
|
Abstract
With the aim of finding genes involved in the floral transition of woody species four MADS box genes containing cDNAs from apple (Malus domestica) have been isolated. Three genes were isolated from vegetative tissue of apple, but were homologues of known genes that specify floral organ identity. MdMADS13 is an AP3-like B class MADS box gene, and was mainly expressed in petals and stamens as demonstrated by Northern blot analysis. MdMADS14 and -15 are AGAMOUS-like genes. They differed slightly in expression patterns on Northern blots, with MdMADS15 mRNA levels equally high in stamens and carpels, but MdMADS14 preferably expressed in carpels. MdMADS14 is likely to be the apple orthologue of one of the Arabidopsis thaliana SHATTERPROOF genes, and MdMADS15 closely resembled the Arabidopsis AGAMOUS gene. It has been shown with RT-PCR that the three floral apple MADS box genes are expressed in vegetative tissues of adult as well as juvenile trees, albeit at low levels. MdMADS12 is an AP1-like gene that is expressed at similar levels in leaves, vegetative shoots, and floral tissues, and that may be involved in the transition from the juvenile to the adult stage.
Collapse
MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Gene Expression Regulation, Plant
- MADS Domain Proteins/genetics
- Malus/genetics
- Molecular Sequence Data
- Phylogeny
- Plant Shoots/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
Collapse
Affiliation(s)
- C G van der Linden
- Plant Research International BV, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 16, 6700 AA Wageningen, The Netherlands.
| | | | | |
Collapse
|
28
|
|
29
|
Abstract
Using repeats found in sequences from Dianthus species present in the EMBL database, primers for STMS (sequence-tagged microsatellite site) analysis were developed and tested. Five loci were polymorphic and amplified products of sufficient quality in nearly all of the 26 Dianthus species tested, except MS-DINGSTA, which amplified in only one-third of the species. Loci MS-DINMADSBOX and MS-DCDIA30 produced allele series that were mostly two nucleotides (the repeat unit) apart. MS-DCAMCRBSY and MS-DINCARACC also amplified regular series of alleles, but more than two fragments per individual were detected in a number of species. Both loci code for a member of the ACC synthase gene family. The observation that the loci amplified across a wide range of Dianthus species may imply that the different species within the genus are relatively closely related. Alternatively, it may indicate that the regions selected for primer design (some of which are in coding regions) are well conserved. These microsatellites will be useful for the measurement of genetic diversity in natural populations of Dianthus species and the identification of carnation varieties. Key words: SSR, simple sequence repeat, identification, STMS, sequence-tagged microsatellite site.
Collapse
|