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Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
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Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
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Kuluev BR, Baymiev AK, Gerashchenkov GA, Chemeris DA, Zubov VV, Kuluev AR, Baymiev AK, Chemeris AV. Random Priming PCR Strategies for Identification of Multilocus DNA Polymorphism in Eukaryotes. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541805006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Burger NFV, Venter E, Botha AM. Profiling Diuraphis noxia (Hemiptera: Aphididae) Transcript Expression of the Biotypes SA1 and SAM Feeding on Various Triticum aestivum Varieties. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:692-701. [PMID: 28334389 DOI: 10.1093/jee/tow313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 06/06/2023]
Abstract
The intimate relationship between an aphid and its host is mediated by the composition of the secreted saliva. In the present study, aphid heads were sampled and transcript profiling conducted after aphids were fed on their preference host and transferred to a variety of preference and nonpreference hosts. It was found that the virulent Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae) biotype SAM was able to selectively up-regulate more transcripts when confronted with feeding on a variety of hosts, than was the case with the less virulent D. noxia biotype SA1, suggesting increased genomic regulation when coping with a stressful environment. Collectively, the observed transcriptomic changes are supported by previous findings that host changes induce significant changes in the proteome of phytophagous hemipterans, unlike in many other entomophagous generalist species. The current data suggest that highly specialized hemipterans may be able to counter plant defenses with inducible salivary transcripts with resulting protein biosynthesis, as demonstrated here.
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Affiliation(s)
- N F V Burger
- Genetics Department, Stellenbosch University, Private Bag X1, Matieland 7601, South Africa ( ; )
- Genetics Department, University of Pretoria, Hillcrest, Pretoria, South Africa
| | - E Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - A-M Botha
- Genetics Department, Stellenbosch University, Private Bag X1, Matieland 7601, South Africa (; )
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4
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Fransz P, Linc G, Lee C, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:159-178. [PMID: 27436134 PMCID: PMC5113708 DOI: 10.1111/tpj.13262] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 05/02/2023]
Abstract
Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.
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Affiliation(s)
- Paul Fransz
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
| | - Gabriella Linc
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Centre for Agricultural ResearchHungarian Academy of SciencesAgricultural InstituteMartonvásárHungary
| | - Cheng‐Ruei Lee
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - Hoda Ali
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address: Department of Genetics and CytologyNational Research CenterCairoEgypt
| | - Janny Peters
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Peter van Dam
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
- Present address: Department of Molecular Plant PathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Xianwen Ji
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
| | - Mateusz Kuzak
- MAD, Dutch Genomics Service & Support ProviderSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Netherlands eScience CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Tom Gerats
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Ingo Schubert
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | - Vincent Colot
- Unité de Recherche en Génomique Végétale (URGV)INRA/CNRS/UEVE 2 Rue Gaston CrémieuxEvry Cedex91057France
- Present address: Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - Rob Martienssen
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkNY11724USA
| | - Maarten Koornneef
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
- Max Planck Institute for Plant Breeding ResearchKöln50829Germany
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Hans de Jong
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
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5
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Oberholster PJ, Hill L, Jappie S, Truter JC, Botha AM. Applying genotoxicology tools to identify environmental stressors in support of river management. CHEMOSPHERE 2016; 144:319-329. [PMID: 26372886 DOI: 10.1016/j.chemosphere.2015.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 06/05/2023]
Abstract
Although bioassay approaches are useful for identifying chemicals of potential concern, they provide little understanding of the mechanisms of chemical toxicity. Without this understanding, it is difficult to address some of the key challenges that currently face aquatic ecotoxicology. To overcome this, the toxicity potential of the water samples was assessed and surviving organisms (Physa acuta) were used for protein activity measurements and gene expression profiling by making use of complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis. From the data it was evident that the impacts of specific pollutants (e.g. sewage) on organisms at the cellular level could be identified, and that the expressed stressor genes can be used as bioindicators/markers/genetic signatures or fingerprints during identification of point source pollution. From an ecosystem management point of view these insights could assist with the forecasting and reduction of environmental risks on catchment level by implementing suitable management interventions.
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Affiliation(s)
- Paul J Oberholster
- Council for Scientific and Industrial Research, Stellenbosch, 7601, South Africa; Botany and Zoology Department, Stellenbosch University, Stellenbosch, 7601, South Africa
| | - Liesl Hill
- Genetics Department, Stellenbosch University, Stellenbosch, 7601, South Africa; Council for Scientific and Industrial Research, Pretoria, 2000, South Africa
| | - Shaamiela Jappie
- Genetics Department, Stellenbosch University, Stellenbosch, 7601, South Africa
| | - Johannes C Truter
- Botany and Zoology Department, Stellenbosch University, Stellenbosch, 7601, South Africa
| | - Anna-Maria Botha
- Genetics Department, Stellenbosch University, Stellenbosch, 7601, South Africa.
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6
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Identification of Nine Pathotype-Specific Genes Conferring Resistance to Fusiform Rust in Loblolly Pine (Pinus taeda L.). FORESTS 2015. [DOI: 10.3390/f6082739] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Botha AM, van Eck L, Burger NFV, Swanevelder ZH. Near-isogenic lines of Triticum aestivum with distinct modes of resistance exhibit dissimilar transcriptional regulation during Diuraphis noxia feeding. Biol Open 2014; 3:1116-26. [PMID: 25361582 PMCID: PMC4232770 DOI: 10.1242/bio.201410280] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 10/09/2014] [Indexed: 01/04/2023] Open
Abstract
Russian wheat aphid (Diuraphis noxia, Kurdjumov) feeding on susceptible Triticum aestivum L. leads to leaf rolling, chlorosis and plant death - symptoms not present in resistant lines. Although the effects of several D. noxia (Dn) resistance genes are known, none have been isolated or characterized. Wheat varieties expressing different Dn genes exhibit distinct modes of D. noxia resistance, such as antibiosis (Dn1), tolerance (Dn2), and antixenosis (Dn5). However, the mechanism whereby feeding aphids are perceived, and how subsequent transcriptional responses are partitioned into resistance categories, remains unclear. Here we report on downstream events in near-isogenic wheat lines containing different Dn genes after D. noxia biotype SA1 feeding. Transcripts involved in stress, signal transduction, photosynthesis, metabolism and gene regulation were differentially regulated during D. noxia feeding. Expression analyses using RT-qPCR and RNA hybridization, as well as enzyme activity profiling, provide evidence that the timing and intensity of pathways induced are critical in the development of particular modes of resistance. Pathways involved include the generation of kinase signalling cascades that lead to a sustained oxidative burst, and a hypersensitive response that is active during antibiosis. Tolerance is a passive resistance mechanism that acts through repair or de novo synthesis of photosystem proteins. Results further suggest that ethylene-mediated pathways are possibly involved in generating volatile compounds and cell wall fortification during the antixenosic response.
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Affiliation(s)
- Anna-Maria Botha
- Department of Genetics, Stellenbosch University, Stellenbosch 7601, South Africa
| | - Leon van Eck
- Department of Genetics, Stellenbosch University, Stellenbosch 7601, South Africa University of Minnesota, Saint Paul, Minneapolis, MN 55455-0213, USA
| | - N Francois V Burger
- Department of Genetics, Stellenbosch University, Stellenbosch 7601, South Africa
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Theim TJ, Shirk RY, Givnish TJ. Spatial genetic structure in four understory Psychotria species (Rubiaceae) and implications for tropical forest diversity. AMERICAN JOURNAL OF BOTANY 2014; 101:1189-1199. [PMID: 25002460 DOI: 10.3732/ajb.1300460] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
• Premise of the study: Tropical forests are the most species-rich terrestrial communities on Earth, and understory trees and shrubs comprise a large fraction of their plant species diversity, especially at high rainfalls. The mechanisms responsible for generating such high levels of diversity remain unknown. One hypothesis is that fleshy-fruited understory species should have limited seed dispersal due to the sedentary nature of their avian dispersers, resulting in restricted gene flow, population differentiation at small spatial scales, and ultimately, high rates of allopatric speciation.• Methods: We sampled four species of the hyperdiverse tropical shrub genus Psychotria (Rubiaceae) on Barro Colorado Island (BCI) and two nearby sites in Panama. We genotyped each species with AFLPs, assessed genetic differentiation among populations, and determined patterns of fine-scale spatial genetic structure in the BCI population. Measures of spatial autocorrelation and population density were used to estimate the dispersal distance parameter σ.• Key results: Regionally, ΦPT values ranged from 0.13 to 0.28, reflecting local population differentiation and suggesting that Lake Gatun/Rio Chagres has posed a relatively strong barrier to gene flow. Fine-scale spatial genetic structure on BCI was stronger than in most canopy trees, and estimated distances of gene flow were unusually low for endozoochorous tropical woody plants, with dispersal distance σ = 9-113 m.• Conclusions: These results demonstrate comparatively limited gene flow in bird-dispersed understory species, supporting a hypothesized mechanism for generating high levels of plant species diversity in tropical rain forests, in one of the largest genera of flowering plants on Earth.
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Affiliation(s)
- Terra J Theim
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - Rebecca Y Shirk
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
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9
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Wu JC, Chen CH, Fu JW, Yang HC. Electrophoresis-enhanced detection of deoxyribonucleic acids on a membrane-based lateral flow strip using avian influenza H5 genetic sequence as the model. SENSORS 2014; 14:4399-415. [PMID: 24603637 PMCID: PMC4003949 DOI: 10.3390/s140304399] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/14/2014] [Accepted: 02/28/2014] [Indexed: 12/13/2022]
Abstract
This study reports a simple strategy to detect a deoxyribonucleic acid (DNA) on a membrane-based lateral flow (MBLF) strip without tedious gel preparation, gel electrophoresis, and EtBr-staining processes. The method also enhances the detection signal of the genetic sample. A direct electric field was applied over two ends of the MBLF strips to induce an electrophoresis of DNAs through the strips. The signal enhancement was demonstrated by the detection of the H5 subtype of avian influenza virus (H5 AIV). This approach showed an excellent selectivity of H5 AIV from other two control species, Arabidopsis thaliana and human PSMA5. It also showed an effective signal repeatability and sensitivity over a series of analyte concentrations. Its detection limit could be enhanced, from 40 ng to 0.1 ng by applying 12 V. The nano-gold particles for the color development were labeled on the capture antibody, and UV-VIS and TEM were used to check if the labeling was successful. This detection strategy could be further developed to apply on the detection of drug-allergic genes at clinics or detection of infectious substances at incident sites by a simple manipulation with an aid of a mini-PCR machine and auxiliary kits.
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Affiliation(s)
- Jui-Chuang Wu
- Department of Chemical Engineering, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan.
| | - Chih-Hung Chen
- Department of Chemical Engineering, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan.
| | - Ja-Wei Fu
- Department of Chemical Engineering, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan.
| | - Huan-Ching Yang
- Department of Chemical Engineering, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan.
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10
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Diggle MA, Clarke SC. Molecular methods for the detection and characterization ofNeisseria meningitidis. Expert Rev Mol Diagn 2014; 6:79-87. [PMID: 16359269 DOI: 10.1586/14737159.6.1.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Neisseria meningitidis remains a common global cause of morbidity and mortality. The laboratory confirmation of meningococcal disease is, therefore, very important for individual patient management and for public health management. Through surveillance schemes, it provides long-term epidemiologic data that can be used to inform vaccine policy. Traditional methods, such as latex agglutination and the enzyme-linked immunosorbent assay, are still used, but molecular methods are now also established. In this review, molecular methods for the laboratory confirmation and characterization of meningococci are described. PCR is an invaluable tool in modern biology and can be used to predict the group, type and subtype of meningococci. It is now also used in a fluorescence-based format for increased sensitivity and specificity. The method also provides the amplified DNA for other techniques, such as multilocus sequence typing. Other methods for the discrimination of meningococci have also played and continue to play an important part in epidemiology. For example, pulsed-field gel electrophoresis is highly discriminatory, whilst multilocus enzyme electrophoresis provided the basis for the description of global meningococcal clones and formed the foundation for multilocus sequence typing. Other less commonly used methods, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and pyrosequencing, may increasingly find their way into microbiology reference laboratories. Nevertheless, nucleotide sequencing and laboratory automation have aided the introduction of many methods and provide data that are digitally based and, therefore, highly accurate and portable.
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Affiliation(s)
- Mathew A Diggle
- Stobhill Hospital, Scottish Meningococcus & Pneumococcus Reference Laboratory, Glasgow, UK
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11
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Gonthier L, Blassiau C, Mörchen M, Cadalen T, Poiret M, Hendriks T, Quillet MC. High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2103-21. [PMID: 23689744 DOI: 10.1007/s00122-013-2122-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/08/2013] [Indexed: 05/14/2023]
Abstract
High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.
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Affiliation(s)
- Lucy Gonthier
- Université de Lille, UMR INRA-Lille 1 1281, Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d'Ascq, France
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12
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Henss JM, Moeller JR, Theim TJ, Givnish TJ. Spatial scales of genetic structure and gene flow in Calochortus albus (Liliaceae). Ecol Evol 2013; 3:1461-70. [PMID: 23789059 PMCID: PMC3686183 DOI: 10.1002/ece3.566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 12/27/2022] Open
Abstract
Calochortus (Liliaceae) displays high species richness, restriction of many individual taxa to narrow ranges, geographic coherence of individual clades, and parallel adaptive radiations in different regions. Here we test the first part of a hypothesis that all of these patterns may reflect gene flow at small geographic scales. We use amplified fragment length polymorphism variation to quantify the geographic scales of spatial genetic structure and apparent gene flow in Calochortus albus, a widespread member of the genus, at Henry Coe State Park in the Coast Ranges south of San Francisco Bay. Analyses of 254 mapped individuals spaced 0.001–14.4 km apart show a highly significant decline in genetic identity with ln distance, implying a root-mean-square distance of gene flow σ of 5–43 m. STRUCTURE analysis implies the existence of 2–4 clusters over the study area, with frequent reversals among clusters over short distances (<200 m) and a relatively high frequency of admixture within individuals at most sampling sites. While the intensity of spatial genetic structure in C. albus is weak, as measured by the Sp statistic, that appears to reflect low genetic identity of adjacent plants, which might reflect repeated colonizations at small spatial scales or density-dependent mortality of individual genotypes by natural enemies. Small spatial scales of gene flow and spatial genetic structure should permit, under a variety of conditions, genetic differentiation within species at such scales, setting the stage ultimately for speciation and adaptive radiation as such scales as well.
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Affiliation(s)
- Jillian M Henss
- Department of Entomology, University of Wisconsin-Madison Madison, Wisconsin, 53706
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13
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Steane DA, Nicolle D, Sansaloni CP, Petroli CD, Carling J, Kilian A, Myburg AA, Grattapaglia D, Vaillancourt RE. Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping. Mol Phylogenet Evol 2011; 59:206-24. [PMID: 21310251 DOI: 10.1016/j.ympev.2011.02.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 02/01/2011] [Accepted: 02/02/2011] [Indexed: 11/30/2022]
Abstract
A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.
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Affiliation(s)
- Dorothy A Steane
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia.
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Iturritxa E, Ganley RJ, Wright J, Heppe E, Steenkamp ET, Gordon TR, Wingfield MJ. A genetically homogenous population of Fusarium circinatum causes pitch canker of Pinus radiata in the Basque Country, Spain. Fungal Biol 2011; 115:288-95. [PMID: 21354535 DOI: 10.1016/j.funbio.2010.12.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 11/17/2022]
Abstract
Pitch canker, caused by Fusarium circinatum, is a destructive disease of Pinus species and has recently been shown to represent a substantial threat to natural and commercial forests in northern Spain. The genetic diversity of F. circinatum in the Basque Country of Spain was assessed by characterising 96 isolates based on vegetative compatibility groups (VCGs), mating type assays, polymorphic DNA-markers and amplified fragment length polymorphism (AFLP) analyses. For this purpose, F. circinatum isolates were collected from diseased Pinus radiata as well as from insects associated with this host. Overall, a low level of diversity was detected in the population. The isolates represented only two VCGs and they were all of the same mating type. AFLP analyses revealed three genotypes and polymorphic DNA-markers specific for F. circinatum showed nine genotypes. The most common genotypes represented 97% of all isolates for AFLP analysis and 68% of isolates for the polymorphic DNA-marker sets. Over all, this indicates that pitch canker in the Basque Country of Spain is caused by a clonally propagating population of F. circinatum, typical of a recently introduced pathogen.
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15
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Lima LJR, Kamphuis HJ, Nout MJR, Zwietering MH. Microbiota of cocoa powder with particular reference to aerobic thermoresistant spore-formers. Food Microbiol 2010; 28:573-82. [PMID: 21356467 DOI: 10.1016/j.fm.2010.11.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/17/2010] [Accepted: 11/18/2010] [Indexed: 10/18/2022]
Abstract
The microbiological criteria of commercial cocoa powder are defined in guidelines instituted by the cocoa industry. Twenty-five commercial samples were collected with the aim of assessing the compliance with the microbiological quality guidelines and investigating the occurrence and properties of aerobic Thermoresistant Spores (ThrS). Seventeen samples complied with the guidelines, but one was positive for Salmonella, five for Enterobacteriaceae and two had mould levels just exceeding the maximum admissible level. The treatment of the cocoa powder suspensions from 100 °C to 170 °C for 10 min, revealed the presence of ThrS in 36% of the samples. In total 61 ThrS strains were isolated, of which the majority belonged to the Bacillus subtilis complex (65.6%). Strains resporulation and spore crops inactivation at 110 °C for 5 min showed a wide diversity of heat-resistance capacities. Amplified fragment length polymorphism analysis revealed not only a large intraspecies diversity, but also different clusters of heat-resistant spore-forming strains. The heat-resistance of spores of six B. subtilis complex strains was further examined by determination of their D and z-values. We concluded that B. subtilis complex spores, in particular those from strain M112, were the most heat-resistant and these may survive subsequent preservation treatments, being potentially problematic in food products, such as chocolate milk.
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Affiliation(s)
- Lídia J R Lima
- Laboratory of Food Microbiology, Wageningen University, P.O. box 8129, 6700 EV Wageningen, The Netherlands
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16
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Reeves PA, Richards CM. Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus). Syst Biol 2010; 60:45-59. [PMID: 21088008 DOI: 10.1093/sysbio/syq056] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is an emerging consensus that the intent of most species concepts is to identify evolutionarily distinct lineages. However, the criteria used to identify lineages differ among concepts depending on the perceived importance of various attributes of evolving populations. We have examined five different species criteria to ask whether the three taxonomic varieties of Humulus lupulus (hops) native to North America are distinct lineages. Three criteria (monophyly, absence of genetic intermediates, and diagnosability) focus on evolutionary patterns and two (intrinsic reproductive isolation and niche specialization) consider evolutionary processes. Phylogenetic analysis of amplified fragment length polymorphism (AFLP) data under a relaxed molecular clock, a stochastic Dollo substitution model, and parsimony identified all varieties as monophyletic, thus they satisfy the monophyly criterion for species delimitation. Principal coordinate analysis and a Bayesian assignment procedure revealed deep genetic subdivisions and little admixture between varieties, indicating an absence of genetic intermediates and compliance with the genotypic cluster species criterion. Diagnostic morphological and AFLP characters were found for all varieties, thus they meet the diagnosability criterion. Natural history information suggests that reproductive isolating barriers may have evolved in var. pubescens, potentially qualifying it as a species under a criterion of intrinsic reproductive isolation. Environmental niche modeling showed that the preferred habitat of var. neomexicanus is climatically unique, suggesting niche specialization and thus compliance with an ecological species criterion. Isolation by distance coupled with imperfect sampling can lead to erroneous lineage identification using some species criteria. Compliance with complementary pattern- and process-oriented criteria provides powerful corroboration for a species hypothesis and mitigates the necessity for comprehensive sampling of the entire species range, a practical impossibility in many systems. We hypothesize that var. pubescens maintains its genetic identity, despite substantial niche overlap with var. lupuloides, via the evolution of partial reproductive isolating mechanisms. Variety neomexicanus, conversely, will likely persist as a distinct lineage, regardless of limited gene flow with vars. lupuloides and pubescens because of ecological isolation--adaptation to the unique conditions of the Rocky Mountain cordillera. Thus, we support recognition of vars. neomexicanus and pubescens as species, but delay making a recommendation for var. lupuloides until sampling of genetic variation is complete or a stable biological process can be identified to explain its observed genetic divergence.
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Affiliation(s)
- Patrick A Reeves
- United States Department of Agriculture, Agricultural Research Service, National Center for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
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17
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Molecular Characterization of Fusarium globosum Strains from South African Maize and Japanese Wheat. Mycopathologia 2010; 170:237-49. [DOI: 10.1007/s11046-010-9318-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
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18
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Emshwiller E, Theim T, Grau A, Nina V, Terrazas F. Origins of domestication and polyploidy in oca (Oxalis tuberosa; Oxalidaceae). 3. AFLP data of oca and four wild, tuber-bearing taxa. AMERICAN JOURNAL OF BOTANY 2009; 96:1839-1848. [PMID: 21622305 DOI: 10.3732/ajb.0800359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Many crops are polyploids, and it can be challenging to untangle the often complicated history of their origins of domestication and origins of polyploidy. To complement other studies of the origins of polyploidy of the octoploid tuber crop oca (Oxalis tuberosa) that used DNA sequence data and phylogenetic methods, we here compared AFLP data for oca with four wild, tuber-bearing Oxalis taxa found in different regions of the central Andes. Results confirmed the divergence of two use-categories of cultivated oca that indigenous farmers use for different purposes, suggesting the possibility that they might have had separate origins of domestication. Despite previous results with nuclear-encoded, chloroplast-expressed glutamine synthetase suggesting that O. picchensis might be a progenitor of oca, AFLP data of this species, as well as different populations of wild, tuber-bearing Oxalis found in Lima Department, Peru, were relatively divergent from O. tuberosa. Results from all analytical methods suggested that the unnamed wild, tuber-bearing Oxalis found in Bolivia and O. chicligastensis in NW Argentina are the best candidates as the genome donors for polyploid O. tuberosa, but the results were somewhat equivocal about which of these two taxa is the more strongly supported as oca's progenitor.
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Affiliation(s)
- Eve Emshwiller
- University of Wisconsin-Madison, Botany Department/Birge Hall, 430 Lincoln Drive, Madison, Wisconsin 53706-1381 USA
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19
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van der Nest MA, Slippers B, Steenkamp ET, De Vos L, Van Zyl K, Stenlid J, Wingfield MJ, Wingfield BD. Genetic linkage map for Amylostereum areolatum reveals an association between vegetative growth and sexual and self-recognition. Fungal Genet Biol 2009; 46:632-41. [PMID: 19523529 DOI: 10.1016/j.fgb.2009.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Amylostereum areolatum is a filamentous fungus that grows through tip extension, branching and hyphal fusion. In the homokaryotic phase, the hyphae of different individuals are capable of fusing followed by heterokaryon formation, only if they have dissimilar allelic specificities at their mating-type (mat) loci. In turn, hyphal fusion between heterokaryons persists only when they share the same alleles at all of their heterokaryon incompatibility (het) loci. In this study we present the first genetic linkage map for A. areolatum, onto which the mat and het loci, as well as quantitative trait loci (QTLs) for mycelial growth rate are mapped. The recognition loci (mat-A and het-A) are positioned near QTLs associated with mycelial growth, suggesting that the genetic determinants influencing recognition and growth rate in A. areolatum are closely associated. This was confirmed when isolates associated with specific mat and het loci displayed significantly different mycelial growth rates. Although the link between growth and sexual recognition has previously been observed in other fungi, this is the first time that an association between growth and self-recognition has been shown.
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Affiliation(s)
- M A van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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20
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Zaayman D, Lapitan NLV, Botha AM. Dissimilar molecular defense responses are elicited in Triticum aestivum after infestation by different Diuraphis noxia biotypes. PHYSIOLOGIA PLANTARUM 2009; 136:209-222. [PMID: 19453509 DOI: 10.1111/j.1399-3054.2009.01232.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
For sustainable solutions to the problem of insect infestation, the study of molecular plant-insect interactions is integral to resistance breeding strategies. This also holds true in the case of wheat (Triticum aestivum), where the Russian wheat aphid (Diuraphis noxia, Kurdjumov, RWA) is responsible for significant crop losses in most major wheat producing countries around the world. Our study is focused on gaining a greater understanding of the resistance mechanisms activated by the RWA resistance gene Dn7 by comparing responses following infestation with three different aphid biotypes (RWA-SA, RWA-US1 and RWA-US2). This consisted of analyzing the resistant wheat line 94M370 (containing Dn7) and its susceptible counterpart (Gamtoos) on a transcriptional level with complementary DNA-amplified fragment length polymorphisms (cDNA-AFLPs) using 17 primer combinations, as well as quantitative reverse transcription polymerase chain reaction (qRT-PCR) of 10 differentially expressed transcripts. The results of this expression profile analysis suggest that Dn7 activates similar responses against the two US aphid biotypes, which differ noticeably from the response following infestation with a South African aphid biotype. This is consistent with recent research showing limited molecular variations between the two US aphid biotypes (approximately 0.12%), compared with a distinctly different South African biotype. We therefore conclude that Dn7 recognizes and interacts in a highly specific manner with different aphid's putative eliciting agents, which in turn activates specific defense pathways unique to that interaction.
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Affiliation(s)
- Dewald Zaayman
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hillcrest, Pretoria, South Africa
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21
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Kamisugi Y, von Stackelberg M, Lang D, Care M, Reski R, Rensing SA, Cuming AC. A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:855-66. [PMID: 18657236 PMCID: PMC2667646 DOI: 10.1111/j.1365-313x.2008.03637.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The moss Physcomitrella patens is a model for the study of plant cell biology and, by virtue of its basal position in land plant phylogeny, for comparative analysis of the evolution of plant gene function and development. It is ideally suited for 'reverse genetic' analysis by virtue of its outstanding ability to undertake targeted transgene integration by homologous recombination. However, gene identification through mutagenesis and map-based cloning has hitherto not been possible, due to the lack of a genetic linkage map. Using molecular markers [amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR)] we have generated genetic linkage maps for Physcomitrella. One hundred and seventy-nine gene-specific SSR markers were mapped in 46 linkage groups, and 1574 polymorphic AFLP markers were identified. Integrating the SSR- and AFLP-based maps generated 31 linkage groups comprising 1420 markers. Anchorage of the integrated linkage map with gene-specific SSR markers coupled with computational prediction of AFLP loci has enabled its correspondence with the newly sequenced Physcomitrella genome. The generation of a linkage map densely populated with molecular markers and anchored to the genome sequence now provides a resource for forward genetic interrogation of the organism and for the development of a pipeline for the map-based cloning of Physcomitrella genes. This will radically enhance the potential of Physcomitrella for determining how gene function has evolved for the acquisition of complex developmental strategies within the plant kingdom.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds UniversityLeeds LS2 9JT, UK
| | - Mark von Stackelberg
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Matthew Care
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds UniversityLeeds LS2 9JT, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1D-79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), Faculty of Biology, Schaenzlestrasse 1D-79104 Freiburg, Germany
| | - Stefan A Rensing
- Freiburg Initiative for Systems Biology (FRISYS), Faculty of Biology, Schaenzlestrasse 1D-79104 Freiburg, Germany
- * For correspondence (fax +44 113 3433144; e-mail ; fax +49 761 203 6945; e-mail )
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds UniversityLeeds LS2 9JT, UK
- * For correspondence (fax +44 113 3433144; e-mail ; fax +49 761 203 6945; e-mail )
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22
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Liu S, Xu L, Jia Z, Xu Y, Yang Q, Fei Z, Lu X, Chen H, Huang S. Genetic association of ETHYLENE-INSENSITIVE3-like sequence with the sex-determining M locus in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:927-933. [PMID: 18629467 DOI: 10.1007/s00122-008-0832-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2007] [Accepted: 06/21/2008] [Indexed: 05/26/2023]
Abstract
Cucumber (Cucumis sativus L.) has served as the model system for sex expression in flowering plants and its sex type is predominantly controlled by two genetic loci, F and M. Ethylene is the major plant hormone that regulates sex expression in cucumber. The current model predicts that ethylene serves as both a promoter of femaleness via the F locus and an inhibitor of the male sex via the M locus. In support of this model, genetic, genomic, and transcript analyses indicate that the F gene encodes a key enzyme in ethylene biosynthesis. In this study, we discovered that the M locus co-segregates with an ETHYLENE-INSENSITIVE3 (EIN3)-like genomic sequence in an F2 population of 96 individuals. This genetic association agrees with the prediction that the M locus is involved in ethylene signaling, thus providing another line of evidence in favor of the model. In addition, we generated an amplified fragment length polymorphism (AFLP) map of the M locus, which was delimited into a genetic interval of 2.5 cM. The genetic association and the local map will assist the molecular isolation of the M gene using the combination of positional cloning and candidate gene approach.
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Affiliation(s)
- Shiqiang Liu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
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23
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Kepiro J, McClung A, Chen M, Yeater K, Fjellstrom R. Mapping QTLs for milling yield and grain characteristics in a tropical japonica long grain cross. J Cereal Sci 2008. [DOI: 10.1016/j.jcs.2007.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Stergiopoulos I, De Kock MJD, Lindhout P, De Wit PJGM. Allelic variation in the effector genes of the tomato pathogen Cladosporium fulvum reveals different modes of adaptive evolution. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1271-83. [PMID: 17918629 DOI: 10.1094/mpmi-20-10-1271] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The allelic variation in four avirulence (Avr) and four extracellular protein (Ecp)-encoding genes of the tomato pathogen Cladosporium fulvum was analyzed for a worldwide collection of strains. The majority of polymorphisms observed in the Avr genes are deletions, point mutations, or insertions of transposon-like elements that are associated with transitions from avirulence to virulence, indicating adaptive evolution of the Avr genes to the cognate C. fulvum resistance genes that are deployed in commercial tomato lines. Large differences in types of polymorphisms between the Avr genes were observed, especially between Avr2 (indels) and Avr4 (amino-acid substitutions), indicating that selection pressure favors different types of adaptation. In contrast, only a limited number of polymorphisms were observed in the Ecp genes, which mostly involved synonymous modifications. A haplotype network based on the polymorphisms observed in the effector genes revealed a complex pattern of evolution marked by reticulations that suggests the occurrence of genetic recombination in this presumed asexual fungus. This, as well as the identification of strains with identical polymorphisms in Avr and Ecp genes but with opposite mating-type genes, suggests that development of complex races can be the combined result of positive selection and genetic recombination.
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Affiliation(s)
- Ioannis Stergiopoulos
- Laboratory of Phytopathology, Wageningen University & Research Centre, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
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25
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Ellis T, Evans DA, Martin CRH, Hartley JA. A 96-well DNase I footprinting screen for drug-DNA interactions. Nucleic Acids Res 2007; 35:e89. [PMID: 17586817 PMCID: PMC1919508 DOI: 10.1093/nar/gkm467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The established protocol for DNase I footprinting has been modified to allow multiple parallel reactions to be rapidly performed in 96-well microtitre plates. By scrutinizing every aspect of the traditional method and making appropriate modifications it has been possible to considerably reduce the time, risk of sample loss and complexity of footprinting, whilst dramatically increasing the yield of data (30-fold). A semi-automated analysis system has also been developed to present footprinting data as an estimate of the binding affinity of each tested compound to any base pair in the assessed DNA sequence, giving an intuitive ‘one compound–one line’ scheme. Here, we demonstrate the screening capabilities of the 96-well assay and the subsequent data analysis using a series of six pyrrolobenzodiazepine-polypyrrole compounds and human Topoisomerase II alpha promoter DNA. The dramatic increase in throughput, quantified data and decreased handling time allow, for the first time, DNase I footprinting to be used as a screening tool to assess DNA-binding agents.
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Affiliation(s)
- Tom Ellis
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - David A. Evans
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - Christopher R. H. Martin
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
| | - John A. Hartley
- Spirogen Ltd, London Bioscience Innovation Centre, 2 Royal College Street, London, NW1 0NH and Cancer Research UK Drug-DNA Interactions Research Group, Department of Oncology, University College London, 91 Riding House Street, London W1W 7BS, UK
- *To whom correspondence should be addressed. +44 (0)20 7679 9326+44 (0)20 7436 2956
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26
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Huang CW, Cheng YS, Rouvier R, Yang KT, Wu CP, Huang MC. AFLP fingerprinting for paternity testing in ducks. Br Poult Sci 2007; 48:323-30. [PMID: 17578695 DOI: 10.1080/00071660701370459] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
1. The accuracy and reproducibility of AFLP fingerprinting was investigated in the duck (Anas Platyrhynchos), using a multicolour fluorescent labeling technique. The fluorescent labelling fragments were separated on a capillary electrophoresis-base ABI PRISM 3100 Genetic Analyzer. 2. A total of 337 AFLP peaks with 103 of them being polymorphic markers were generated by 16 sets consisting of EcoRI/TaqI primer pair combinations. The number and size range of AFLP polymorphisms detected per primer pair varied from 3 to 11 and 58 to 290 bp, respectively. About 30.6% (103/337) of AFLP peaks were detected polymorphisms, with an average of 6.4 polymorphic markers per primer pair. 3. The clear polymorphic peaks were amplified with EcoR+AC/Taq+AC primer combinations. The AFLP peaks showed high reproducibility. From the family testing, we found that the fingerprints of all the offspring were derived from one or other parent. Therefore, we conclude that AFLP fingerprinting might be a suitable method for duck paternity testing.
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Affiliation(s)
- C-W Huang
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
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27
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Abstract
The AFLP technique is a powerful DNA fingerprinting technology applicable to any organism without the need for prior sequence knowledge. The protocol involves the selective PCR amplification of restriction fragments of a total digest of genomic DNA, typically obtained with a mix of two restriction enzymes. Two limited sets of AFLP primers are sufficient to generate a large number of different primer combinations (PCs), each of which will yield unique fingerprints. Visualization of AFLP fingerprints after gel electrophoresis of AFLP products is described using either a conventional autoradiography platform or an automated LI-COR system. The AFLP technology has been used predominantly for assessing the degree of variability among plant cultivars, establishing linkage groups in crosses and saturating genomic regions with markers for gene landing efforts. AFLP fragments may also be used as physical markers to determine the overlap and positions of genomic clones and to integrate genetic and physical maps. Crucial characteristics of the AFLP technology are its robustness, reliability and quantitative nature. This latter feature has been exploited for co-dominant scoring of AFLP markers in sample collections such as F2 or back-cross populations using appropriate AFLP scoring software. This protocol can be completed in 2-3 d.
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Affiliation(s)
- Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium.
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28
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Finkers R, van Heusden AW, Meijer-Dekens F, van Kan JAL, Maris P, Lindhout P. The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1071-80. [PMID: 17273845 PMCID: PMC1913174 DOI: 10.1007/s00122-006-0500-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 12/22/2006] [Indexed: 05/04/2023]
Abstract
Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus has been identified in accessions of wild relatives of tomato such as Solanum habrochaites LYC4. In a previous F(2) mapping study, three QTLs conferring resistance to B. cinerea (Rbcq1, Rbcq2 and Rbcq4a) were identified. As it was probable that this study had not identified all QTLs involved in resistance we developed an introgression line (IL) population (n = 30), each containing a S. habrochaites introgression in the S. lycopersicum cv. Moneymaker genetic background. On average each IL contained 5.2% of the S. habrochaites genome and together the lines provide an estimated coverage of 95%. The level of susceptibility to B. cinerea for each of the ILs was assessed in a greenhouse trial and compared to the susceptible parent S. lycopersicum cv. Moneymaker. The effect of the three previously identified loci could be confirmed and seven additional loci were detected. Some ILs contains multiple QTLs and the increased resistance to B. cinerea in these ILs is in line with a completely additive model. We conclude that this set of QTLs offers good perspectives for breeding of B. cinerea resistant cultivars and that screening an IL population is more sensitive for detection of QTLs conferring resistance to B. cinerea than the analysis in an F(2) population.
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MESH Headings
- Botrytis/classification
- Botrytis/pathogenicity
- Chromosome Mapping
- Chromosomes, Plant
- Crosses, Genetic
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Genetic Markers
- Genetics, Population
- Genome, Plant
- Heterozygote
- Homozygote
- Immunity, Innate/genetics
- Models, Genetic
- Nucleic Acid Amplification Techniques
- Polymorphism, Genetic
- Quantitative Trait Loci
- Recombination, Genetic
- Seeds/genetics
- Software
- Solanum/classification
- Solanum/genetics
- Solanum/immunology
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Affiliation(s)
- Richard Finkers
- Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands.
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29
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De Vos L, Myburg AA, Wingfield MJ, Desjardins AE, Gordon TR, Wingfield BD. Complete genetic linkage maps from an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Fungal Genet Biol 2007; 44:701-14. [PMID: 17418597 DOI: 10.1016/j.fgb.2007.02.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 01/22/2007] [Accepted: 02/17/2007] [Indexed: 11/20/2022]
Abstract
The Gibberella fujikuroi complex includes many plant pathogens of agricultural crops and trees, all of which have anamorphs assigned to the genus Fusarium. In this study, an interspecific hybrid cross between Gibberella circinata and Gibberella subglutinans was used to compile a genetic linkage map. A framework map was constructed using a total of 578 AFLP markers together with the mating type (MAT-1 and MAT-2) genes and the histone (H3) gene. Twelve major linkage groups were identified (n=12). Fifty percent of the markers showed significant deviation from the expected 1:1 transmission ratio in a haploid F(1) cross (P <0.05). The transmission of the markers on the linkage map was biased towards alleles of the G. subglutinans parent, with an estimated 60% of the genome of F(1) individuals contributed by this parent. This map will serve as a powerful tool to study the genetic architecture of interspecific differentiation and pathogenicity in the two parental genomes.
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Affiliation(s)
- L De Vos
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0001, South Africa.
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30
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Brady C, Venter S, Cleenwerck I, Vancanneyt M, Swings J, Coutinho T. A FAFLP system for the improved identification of plant-pathogenic and plant-associated species of the genus Pantoea. Syst Appl Microbiol 2007; 30:413-7. [PMID: 17321713 DOI: 10.1016/j.syapm.2007.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Indexed: 11/19/2022]
Abstract
The majority of Pantoea species are either plant-pathogenic or plant-associated and cause a wide variety of symptoms on a range of hosts. Identification of Pantoea species is difficult due to minor differences in phenotypic characteristics between them and related Enterobacteriaceae. Fluorescent amplified fragment length polymorphism (FAFLP) analysis was investigated for use as a rapid, molecular-based identification technique to the species level of the genus Pantoea. Following analysis of the band patterns generated by FAFLP, seven distinct clusters were observed, one for each validly published species of the genus. FAFLP has proven to be a rapid, reproducible identification technique for all species of the genus Pantoea.
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Affiliation(s)
- Carrie Brady
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
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Finkers R, van den Berg P, van Berloo R, ten Have A, van Heusden AW, van Kan JAL, Lindhout P. Three QTLs for Botrytis cinerea resistance in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:585-93. [PMID: 17136515 DOI: 10.1007/s00122-006-0458-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 11/04/2006] [Indexed: 05/12/2023]
Abstract
Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus was identified in accessions of wild relatives of tomato such as S. habrochaites LYC4. In order to identify loci involved in quantitative resistance (QTLs) to B. cinerea, a population of 174 F(2) plants was made originating from a cross between S. lycopersicum cv. Moneymaker and S. habrochaites LYC4. The population was genotyped and tested for susceptibility to grey mold using a stem bioassay. Rbcq1, a QTL reducing lesion growth (LG) and Rbcq2, a QTL reducing disease incidence (DI) were identified. Rbcq1 is located on Chromosome 1 and explained 12% of the total phenotypic variation while Rbcq2 is located on Chromosome 2 and explained 15% of the total phenotypic variation. Both QTL effects were confirmed by assessing disease resistance in two BC(2)S(1) progenies segregating for either of the two QTLs. One additional QTL, Rbcq4 on Chromosome 4 reducing DI, was identified in one of the BC(2)S(1) progenies. F(2) individuals, homozygous for the Rbcq2 and Rbcq4 alleles of S. habrochaites showed a reduction of DI by 48%. QTLs from S. habrochaites LYC4 offer good perspectives for breeding B. cinerea resistant tomato cultivars.
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Affiliation(s)
- Richard Finkers
- Graduate school Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University, PO box 386, 6700 AJ, Wageningen, The Netherlands.
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Kato CY, Mayer RT. An improved, high-throughput method for detection of bluetongue virus RNA in Culicoides midges utilizing infrared-dye-labeled primers for reverse transcriptase PCR. J Virol Methods 2006; 140:140-7. [PMID: 17187871 DOI: 10.1016/j.jviromet.2006.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 11/06/2006] [Accepted: 11/08/2006] [Indexed: 01/27/2023]
Abstract
A new rapid (less than 6h from insect-to-results) high-throughput assay that is sensitive and specific for detecting BTV RNA in Culicoides biting midges is reported. Homogenization and extraction of nucleic acids from individual Culicoides specimens were performed in a 96-well plate format using specialized beads in a homogenization buffer compatible with cell culture and RNA extraction. A portion of homogenate (10%) from each specimen was retained for confirmatory infectious virus isolation, while the remaining 90% was used for RNA extraction. The RNA was used in a single step reverse transcriptase PCR (RT-PCR) reaction with infrared (IR)-dye-labeled primers. The RT-PCR products were visualized in agarose gels with an infrared scanner. The adaptation of IR-dye-labeled primers in combination with a one step RT-PCR resulted in a detection limit of 0.5 pfu of purified BTV RNA. All 24 serotypes of BTV prototype strains and none of the 8 serotypes of the closely related epizootic hemorrhagic disease virus (EHDV) prototype strains were detected.
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Affiliation(s)
- Cecilia Y Kato
- U.S. Department of Agriculture, Agricultural Research Service, Arthropod-Borne Animal Diseases Research Laboratory, College of Agriculture D3354, 1000 East University Avenue, Laramie, WY 82072, USA.
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BIAN YL, Yazaki S, Inoue M, CAI HW. QTLs for Sugar Content of Stalk in Sweet Sorghum (Sorghum bicolor L. Moench). ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1671-2927(06)60118-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Trybush S, Hanley S, Cho KH, Jahodová Š, Grimmer M, Emelianov I, Bayon C, Karp A. Getting the most out of fluorescent amplified fragment length polymorphism. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-096] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amplified fragment length polymorphism (AFLP™) is one of the most widely applied molecular marker detection systems used today. Among the reasons for its popularity are its reproducibility, capacity to generate large numbers of data points in a single assay, and “off-the-shelf” universal applicability. The original AFLP protocol was developed using radioactive detection. The transfer of this technique to fluorescent detection on automated DNA fragment analysers not only removed the undesirable requirement for radioactivity but also provided the possibility for increased effectiveness and detection throughput. Unfortunately, a number of problems are frequently encountered with fluorescent AFLPs, particularly failure to amplify high molecular-weight fragments and generation of nonuniform peak distributions. Here, we describe an improved generic protocol for fluorescent AFLPs achieved mainly thorough optimization of the multiplexed selective amplification reaction. This improved protocol gives increased production of valuable high molecular-weight markers and uniform peak intensities, facilitating unambiguous scoring. The protocol has been successfully applied, without further optimization, to species of Salix and Populus (Salicaceae), Melampsora (Melampsoraceae, rust fungi) and Heracleum (Apiaceae), as well as sugar beet ( Beta vulgaris L. subsp. vulgaris , Amaranthaceae), the endangered species Ranunculus kadzunensis Makino (Ranunculaceae), and to Aphidius ervi Haliday (Braconidae), a parasitoid wasp.
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Affiliation(s)
- Sviatlana Trybush
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Steven Hanley
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Kang-Hyun Cho
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Šárka Jahodová
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Michael Grimmer
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Igor Emelianov
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Carlos Bayon
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
| | - Angela Karp
- Plant and Invertebrate Ecology Division, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Broom's Barn, Higham, Bury St. Edmunds, Suffolk, IP28 6NP, UK
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Groenewald S, Van Den Berg N, Marasas WFO, Viljoen A. The application of high-throughput AFLP's in assessing genetic diversity in Fusarium oxysporum f. sp. cubense. ACTA ACUST UNITED AC 2006; 110:297-305. [PMID: 16483757 DOI: 10.1016/j.mycres.2005.10.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 09/16/2005] [Accepted: 10/15/2005] [Indexed: 10/25/2022]
Abstract
Fusarium oxysporum f. sp. cubense (Foc) is responsible for fusarium wilt of bananas. The pathogen consists of several variants that are divided into three races and 21 vegetative compatibility groups (VCGs). Several DNA-based techniques have previously been used to analyse the worldwide population of Foc, sometimes yielding results that were not always consistent. In this study, the high-resolution genotyping method of AFLP is introduced as a potentially effective molecular tool to investigate diversity in Foc at a genome-wide level. The population selected for this study included Foc isolates representing different VCGs and races, isolates of F. oxysporum f. sp. dianthi, a putatively non-pathogenic biological control strain F. oxysporum (Fo47), and F. circinatum. High-throughput AFLP analysis was attained using five different infrared dye-labelled primer combinations using a two-dye model 4200s LI-COR automated DNA analyser. An average of approx. 100 polymorphic loci were scored for each primer pair using the SAGA(MX) automated AFLP analysis software. Data generated from five primer pair combinations were combined and subjected to distance analysis, which included the use of neighbour-joining and a bootstrap of 1000 replicates. A tree inferred from AFLP distance analysis revealed the polyphyletic nature of the Foc isolates, and seven genotypic groups could be identified. The results indicate that AFLP is a powerful tool to perform detailed analysis of genetic diversity in the banana pathogen Foc.
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Affiliation(s)
- Susan Groenewald
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
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Kayodé APP, Linnemann AR, Hounhouigan JD, Nout MJR, van Boekel MAJS. Genetic and environmental impact on iron, zinc, and phytate in food sorghum grown in Benin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:256-62. [PMID: 16390208 DOI: 10.1021/jf0521404] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Seventy-six farmers' varieties of sorghum from Benin were distinguished by amplified fragment length polymorphism (AFLP) and clustered into 45 distinct genotypes. The genotype clusters were evaluated for their Fe, Zn, and phytate concentrations to assess the impact of genetic and environmental effects on the composition of the grains and to identify farmers' varieties with high potential Fe and Zn availability. The Fe concentration of the grains ranged from 30 to 113 mg/kg with an average of 58 mg/kg. The Zn concentration ranged from 11 to 44 mg/kg with an average of 25 mg/kg. The phytate concentration of the grain ranged from 0.4 to 3.5% with a mean of 1.2%. The grain-Fe and grain-Zn did not show consistent linkage to genetic variation, but varied significantly across field locations, suggesting a predominant environmental impact. The phytate concentration of the grains appeared to be environmentally as well as genetically determined. No varieties provide adequate Zn to meet nutritional requirements of sorghum consumers. The most promising varieties for Fe supply were tokogbessenou, mahi swan, biodahu, saï maï, mare dobi, sakarabokuru, and chabicouma, as they showed a [phytate]/[Fe] ratio of <14, which is the critical value above which Fe availability is strongly impaired. These varieties could therefore be recommended for the preparation of food products such as dibou, in which processing methods have only a slight diminishing effect on phytate levels. Further research is needed to test these varieties for the stability of [phytate]/[Fe] molar ratio across various environmental conditions.
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Affiliation(s)
- A P Polycarpe Kayodé
- Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, 01 B.P. 526, Cotonou, Bénin
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37
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Pelgas B, Bousquet J, Beauseigle S, Isabel N. A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1466-88. [PMID: 16215729 DOI: 10.1007/s00122-005-0068-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 07/04/2005] [Indexed: 05/04/2023]
Abstract
Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.
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Affiliation(s)
- Betty Pelgas
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre de recherche en biologie forestière, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, QC, G1K 7P4, Canada
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38
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Miura Y, Ding C, Ozaki R, Hirata M, Fujimori M, Takahashi W, Cai H, Mizuno K. Development of EST-derived CAPS and AFLP markers linked to a gene for resistance to ryegrass blast (Pyricularia sp.) in Italian ryegrass (Lolium multiflorum Lam.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:811-8. [PMID: 16025307 DOI: 10.1007/s00122-005-0001-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 05/12/2005] [Indexed: 05/03/2023]
Abstract
Ryegrass blast, also called gray leaf spot, is caused by the fungus Pyricularia sp. It is one of the most serious diseases of Italian ryegrass (Lolium multiflorum Lam.) in Japan. We analyzed segregation of resistance in an F(1) population from a cross between a resistant and a susceptible cultivar. The disease severity distribution in the F(1) population suggested that resistance was controlled by a major gene (Lm Pi1). Analysis of amplified fragment length polymorphisms with bulked segregant analysis identified several markers tightly linked to Lm Pi1. To identify other markers linked to Lm Pi1, we used expressed sequence tag-cleaved amplified polymorphic sequence (EST-CAPS) markers mapped in a reference population of Italian ryegrass. Of the 30 EST-CAPS markers screened, one marker, p 56, flanking the Lm Pi1 locus was found. The restriction pattern of p 56 amplification showed a unique fragment corresponding to the resistant allele at the Lm Pi1 locus. A linkage map constructed from the reference population showed that the Lm Pi1 locus was located in linkage group 5 of Italian ryegrass. Genotype results obtained from resistant and susceptible cultivars indicate that the p 56 marker is useful for introduction of the Lm Pi1 gene into susceptible germ plasm in order to develop ryegrass cultivars with enhanced resistance to ryegrass blast.
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Affiliation(s)
- Yuichi Miura
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed Association, 388-5 Higashiakada, Nasushiobara, Tochigi 329-2742, Japan.
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Vasemägi A, Primmer CR. Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Mol Ecol 2005; 14:3623-42. [PMID: 16202085 DOI: 10.1111/j.1365-294x.2005.02690.x] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Strategies for the identification of functional genetic variation underlying phenotypic traits of ecological and evolutionary importance have received considerable attention in the literature recently. This paper aims to bring together and compare the relative strengths and limitations of various potentially useful research strategies for dissecting functionally important genetic variation in a wide range of organisms. We briefly explore the relative strengths and limitations of traditional and emerging approaches and evaluate their potential use in free-living populations. While it is likely that much of the progress in functional genetic analyses will rely on progress in traditional model species, it is clear that with prudent choices of methods and appropriate sampling designs, much headway can be also made in a diverse range of species. We suggest that combining research approaches targeting different functional and biological levels can potentially increase understanding the genetic basis of ecological and evolutionary processes both in model and non-model organisms.
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Affiliation(s)
- A Vasemägi
- Department of Biology, University of Turku, Finland
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40
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Hegarty MJ, Hiscock SJ. Hybrid speciation in plants: new insights from molecular studies. THE NEW PHYTOLOGIST 2005; 165:411-23. [PMID: 15720652 DOI: 10.1111/j.1469-8137.2004.01253.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Abrupt speciation through interspecific hybridisation is an important mechanism in angiosperm evolution. Flowering plants therefore offer excellent opportunities for studying genetic processes associated with hybrid speciation. Novel molecular approaches are now available to examine these processes at the level of both genome organization and gene expression - transcriptomics. Here, we present an overview of the molecular technologies currently used to study hybrid speciation and how they are providing new insights into this mode of speciation in flowering plants. We begin with an introduction to hybrid speciation in plants, followed by a review of techniques, such as isozymes and other markers, which have been used to study hybrid species in the past. We then review advances in molecular techniques that have the potential to be applied to studies of hybrid species, followed by an overview of the main genomic and transcriptomic changes suspected, or known, to occur in newly formed hybrids, together with commentary on the application of advanced molecular tools to studying these changes.
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Affiliation(s)
- Matthew J Hegarty
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
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41
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Myburg AA, Vogl C, Griffin AR, Sederoff RR, Whetten RW. Genetics of postzygotic isolation in Eucalyptus: whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E. globulus. Genetics 2004; 166:1405-18. [PMID: 15082559 PMCID: PMC1470765 DOI: 10.1534/genetics.166.3.1405] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of hybrid fitness characters can provide valuable insights into the nature and evolution of postzygotic reproductive barriers in diverged species. We determined the genome-wide distribution of barriers to introgression in an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and E. globulus (Labill.). Two interspecific backcross families (N = 186) were used to construct comparative, single-tree, genetic linkage maps of an F(1) hybrid individual and two backcross parents. A total of 1354 testcross AFLP marker loci were evaluated in the three parental maps and a substantial proportion (27.7% average) exhibited transmission ratio distortion (alpha = 0.05). The distorted markers were located in distinct regions of the parental maps and marker alleles within each region were all biased toward either of the two parental species. We used a Bayesian approach to estimate the position and effect of transmission ratio distorting loci (TRDLs) in the distorted regions of each parental linkage map. The relative viability of TRDL alleles ranged from 0.20 to 0.72. Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterospecific interactions affect introgression rates in this wide interspecific pedigree.
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Affiliation(s)
- Alexander A Myburg
- Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695, USA.
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Schmidt H, Niessen L, Vogel RF. AFLP analysis of Fusarium species in the section Sporotrichiella—evidence for Fusarium langsethiae as a new species. Int J Food Microbiol 2004; 95:297-304. [PMID: 15337594 DOI: 10.1016/j.ijfoodmicro.2003.12.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Amplified fragment length polymorphism (AFLP) was applied to compare 100 isolates of Fusarium poae, Fusarium sporotrichioides, and Fusarium langsethiae. Comparison of fingerprints revealed several markers specific for each group of isolates. Cluster analysis showed a clear separation of F. poae from F. sporotrichioides and F. langsethiae. F. langsethiae isolates formed a rather homogeneous group separated from F. sporotrichioides. The AFLP data obtained support F. langsethiae as a new Fusarium species, for the time being in the section Sporotrichiella.
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Affiliation(s)
- Holger Schmidt
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Weihenstephaner Steig 16, Freising D-85350, Germany
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Inoue M, Gao Z, Hirata M, Fujimori M, Cai H. Construction of a high-density linkage map of Italian ryegrass (Lolium multiflorum Lam) using restriction fragment length polymorphism, amplified fragment length polymorphism, and telomeric repeat associated sequence markers. Genome 2004; 47:57-65. [PMID: 15060602 DOI: 10.1139/g03-097] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To construct a high-density molecular linkage map of Italian ryegrass (Lolium multiflorum Lam), we used a two-way pseudo-testcross F1 population consisting of 82 individuals to analyze three types of markers: restriction fragment length polymorphism markers, which we detected by using genomic probes from Italian ryegrass as well as heterologous anchor probes from other species belonging to the Poaceae family, amplified fragment length polymorphism markers, which we detected by using PstI/MseI primer combinations, and telomeric repeat associated sequence markers. Of the restriction fragment length polymorphism probes that we generated from a PstI genomic library, 74% (239 of 323) of randomly selected probes detected hybridization patterns consistent with single-copy or low-copy genetic locus status in the screening. The 385 (mostly restriction fragment length polymorphism) markers that we selected from the 1226 original markers were grouped into seven linkage groups. The maps cover 1244.4 cM, with an average of 3.7 cM between markers. This information will prove useful for gene targeting, quantitative trait loci mapping, and marker-assisted selection in Italian ryegrass.
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Affiliation(s)
- Maiko Inoue
- Japan Grassland Farming and Forage Seed Association, Forage Crop Research Institute, Tochigi, Japan
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44
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Myburg AA, Griffin AR, Sederoff RR, Whetten RW. Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach. THEORETICAL AND APPLIED GENETICS 2003; 107:1028-42. [PMID: 12838392 DOI: 10.1007/s00122-003-1347-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2003] [Accepted: 05/12/2003] [Indexed: 05/22/2023]
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45
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Komulainen P, Brown GR, Mikkonen M, Karhu A, García-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:667-678. [PMID: 12827250 DOI: 10.1007/s00122-003-1312-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 03/10/2003] [Indexed: 05/24/2023]
Abstract
A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F(1) progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.
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Affiliation(s)
- P Komulainen
- Department of Biology, University of Oulu, FIN-90014 University of Oulu, Finland
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Cai HW, Gao ZS, Yuyama N, Ogawa N. Identification of AFLP markers closely linked to the rhm gene for resistance to Southern Corn Leaf Blight in maize by using bulked segregant analysis. Mol Genet Genomics 2003; 269:299-303. [PMID: 12684877 DOI: 10.1007/s00438-003-0837-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2002] [Accepted: 02/13/2003] [Indexed: 10/26/2022]
Abstract
Southern Corn Leaf Blight (SCLB) is an important disease in warm-temperate and tropical corn-producing areas throughout the world. We applied a combination of the amplified fragment length polymorphism (AFLP) technique and bulked segregant analysis (BSA) to a large F2 population in order to identify molecular markers linked to the rhm gene for resistance to SCLB. One co-dominant AFLP marker, p7m36, was mapped to a position 1.0 cM from rhm, and we converted this marker to an STS (sequence-tagged site) marker. Combined with the previously identified agrP144, this new marker may be useful for map-based cloning of the rhm gene and marker-assisted selection for rhm.
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Affiliation(s)
- H-w Cai
- Forage Crop Research Institute, Japan Grassland Farming and Forage Seed Association, 388-5 Higashiakata, Nishinasuno, Tochigi 329-2742, Japan.
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