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Sheeja TE, Kumar IPV, Giridhari A, Minoo D, Rajesh MK, Babu KN. Amplified Fragment Length Polymorphism: Applications and Recent Developments. Methods Mol Biol 2021; 2222:187-218. [PMID: 33301096 DOI: 10.1007/978-1-0716-0997-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species. Genomics 2020; 112:1554-1564. [DOI: 10.1016/j.ygeno.2019.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
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Veselá P, Volařík D, Mráček J. Optimization of AFLP for extremely large genomes over 70 Gb. Mol Ecol Resour 2016; 16:933-45. [PMID: 26849414 DOI: 10.1111/1755-0998.12506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/23/2016] [Indexed: 11/29/2022]
Abstract
Here, we present an improved amplified fragment length polymorphism (AFLP) protocol using restriction enzymes (AscI and SbfI) that recognize 8-base pair sequences to provide alternative optimization suitable for species with a genome size over 70 Gb. This cost-effective optimization massively reduces the number of amplified fragments using only +3 selective bases per primer during selective amplification. We demonstrate the effects of the number of fragments and genome size on the appearance of nonidentical comigrating fragments (size homoplasy), which has a negative impact on the informative value of AFLP genotypes. We also present various reaction conditions and their effects on reproducibility and the band intensity of the extremely large genome of Viscum album. The reproducibility of this octo-cutter protocol was calculated using several species with genome sizes ranging from 1 Gb (Carex panicea) to 76 Gb (V. album). The improved protocol also succeeded in detecting high intraspecific variability in species with large genomes (V. album, Galanthus nivalis and Pinus pumila).
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Affiliation(s)
- Petra Veselá
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Daniel Volařík
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Jaroslav Mráček
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
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Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:385-394. [PMID: 26332657 DOI: 10.1111/tpj.13006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.
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Affiliation(s)
- Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Miroslava Karafiátová
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
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Vdovychenko ZV, Sytnyk KS, Stupak IY, Spyrydonov VG, Melnychuk SD, Melnychuk MD, Parii MF. Molecular-genetic polymorphism of barley varieties (Hordeum vulgare L.) detected by the AFLP-method. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714020108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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El Rabey HA, Al-Malki AL, Abulnaja KO, Ebrahim MK, Kumosani T, Khan JA. Phylogeny of ten species of the genus Hordeum L. as revealed by AFLP markers and seed storage protein electrophoresis. Mol Biol Rep 2013; 41:365-72. [PMID: 24242674 DOI: 10.1007/s11033-013-2870-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
Abstract
The phylogenetic relationships of 60 accessions representing ten species of the genus Hordeum were investigated based on AFLP markers and seed storage protein SDS-PAGE electrophoresis. A total of 339 AFLP polymorphic markers were scored as a result of fingerprinting the studied taxa using seven AFLP primer combinations, whereas 46 polymorphic protein bands resulted from the water soluble and water non-soluble seed storage protein electrophoresis. The phylogenetic tree deduced from AFLP analysis is concordant in a large extent with that deduced from seed storage protein electrophoresis. The studied taxa were clustered according to their genome type into two main groups representing the Old and New World's species. Inside each group the species were clustered according to their genome type. Highly significant cophenetic correlation coefficient was obtained between both AFLP (0.96) and seed storage protein (0.89) indicating the reliability of the results.
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Affiliation(s)
- Haddad A El Rabey
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia,
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Duan LX, Chen TL, Li M, Chen M, Zhou YQ, Cui GH, Zhao AH, Jia W, Huang LQ, Qi X. Use of the metabolomics approach to characterize Chinese medicinal material Huangqi. MOLECULAR PLANT 2012; 5:376-86. [PMID: 22138859 DOI: 10.1093/mp/ssr093] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Integration of the genetic and metabolic fingerprinting can provide a new approach to differentiate similar Traditional Chinese Medical (TCM) materials. Two leguminous plants, Mojia Huangqi and Menggu Huangqi, are important medical herbs and share great similarities in morphology, chemical constituent, and genomic DNA sequence. The taxonomy of Mojia Huangqi and Menggu Huangqi has been debated for more than 50 years and discrimination of TCM materials directly affects the pharmacological and clinical effects. AFLP based genetic fingerprinting and GC-TOF/MS-based metabolic fingerprinting were used to successfully discriminate the two species. The results of AFLP supported the opinion that Menggu Huangqi was a variant of Mojia Huangqi. The metabolic fingerprinting showed growth locations have greater impacts on the metabolite composition and quantity than the genotypes (cultivated versus wild) in Menggu Huangqi. The difference of some soluble sugars, fatty acids, proline, and polyamine reflected plant adaptation to different growth environments. Using multivariate and univariate statistical analysis, three AFLP markers and eight metabolites were identified as candidate DNA and metabolic markers to distinguish the two herb materials. The correlation network between AFLP markers and metabolites revealed a complex correlation network, which indicated the special metabolic pathways and the regulation networks of Huangqi.
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Affiliation(s)
- Li-Xin Duan
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun Xiangshan Road, Beijing 100093, China
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Barbieri M, Marcel TC, Niks RE, Francia E, Pasquariello M, Mazzamurro V, Garvin DF, Pecchioni N. QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L. Genome 2012; 55:152-63. [PMID: 22321152 DOI: 10.1139/g2012-001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass-pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F(2) population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F(2), resistance was quantified in F(2)-derived F(3) families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.
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Affiliation(s)
- Mirko Barbieri
- Dipartimento di Scienze Agrarie e degli Alimenti, Università di Modena e Reggio Emilia, Italy
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Joshi GP, Nasuda S, Endo TR. Dissection and cytological mapping of barley chromosome 2H in the genetic background of common wheat. Genes Genet Syst 2011; 86:231-48. [DOI: 10.1266/ggs.86.231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Giri Prasad Joshi
- Laboratory of plant genetics, Graduate School of Agriculture, Kyoto University
| | - Shuhei Nasuda
- Laboratory of plant genetics, Graduate School of Agriculture, Kyoto University
| | - Takashi R. Endo
- Laboratory of plant genetics, Graduate School of Agriculture, Kyoto University
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Sakai K, Nasuda S, Sato K, Endo TR. Dissection of barley chromosome 3H in common wheat and a comparison of 3H physical and genetic maps. Genes Genet Syst 2009; 84:25-34. [PMID: 19420798 DOI: 10.1266/ggs.84.25] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We used the gametocidal system to dissect a barley chromosome 3H added to common wheat. The gametocidal system induced chromosomal structural changes in the 3H addition line of common wheat, and we cytologically screened for rearranged chromosomes involving the 3H chromosome by in situ hybridization (FISH/GISH). We established 50 common wheat lines carrying single rearranged (or dissected) 3H chromosomes of independent origin. The dissected 3H chromosomes were either deletions or translocations with wheat chromosomes, and their breakpoints were in the centromere/the long arm/the short arm in a rough ratio of 1:2:2. We used these so-called 3H dissection lines to map 36 EST markers that were polymorphic between euploid common wheat and the 3H addition line and that had been used for the construction of a 3H genetic map. We conducted PCR analysis to detect the EST markers in the dissection lines. The results of the PCR analysis, which mostly corresponded to the retained or lost segments of the dissected 3H chromosomes, allowed us to place the 36 EST markers into 20 chromosomal regions flanked by the breakpoints of the dissected chromosomes. We compared this physical map constructed in this study with a 3H genetic map constructed using the same EST markers. The order of all EST markers was consistent between the two maps. We briefly discuss on the advantage of the physical mapping using dissection lines over genetic mapping.
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Affiliation(s)
- Kazuhiko Sakai
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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A preliminary assessment of genetic relationships among agronomically important cultivars of black pepper. BMC Genet 2007; 8:42. [PMID: 17603884 PMCID: PMC1948014 DOI: 10.1186/1471-2156-8-42] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Accepted: 06/29/2007] [Indexed: 11/18/2022] Open
Abstract
Background The impact of diseases such as Phytophthora foot rot and the replacement of unproductive cultivars by high yielding ones has brought about the disappearance of varieties in Piper species, like any other crop. Black pepper (King of spices), is a major spice crop consumed throughout the world. It is widely cultivated across various parts of the world apart from India. The different cultivars may be genetically related and could be a source of valuable genes for disease resistance and an increase in quantity and quality. Even though Western Ghats in India is believed to be the site of origin of this crop, numerous accessions from the NBPGR have not yet been evaluated. Our study aims to investigate the genetic relatedness in major cultivars of black pepper using Amplified Fragment Length Polymorphism. Results Amplified Fragment Length Polymorphic (AFLP) DNA analysis was performed in thirty popular cultivars of black pepper from National Bureau of Plant Genetic Resources (NBPGR), India. Fingerprint profiles were generated initially with, five different primer combinations, from which three primer pair combinations (EAGC/MCAA, EAGG/MCTA and EAGC/MCTG) gave consistent and scorable banding patterns. From 173 scorable markers, 158(> 90%) were polymorphic which shows there is considerable variation in the available germplasm. The dendrogram derived by unweighted pair group method analysis (UPGMA) grouped the accessions into three major clusters and four diverse cultivars with only 30% similarity. Karimunda, a widely grown and popular cultivar was unique in the fingerprint profiles obtained. Conclusion There are currently few fingerprinting studies using the valuable spice crop black pepper. We found considerable genetic variability among cultivars of black pepper. Fingerprinting analysis with AFLP proved to be an ideal tool for cultivar identification and phylogenetic studies. It shows the high level of polymorphism and the unique characterization of the major cultivars. An extensive range of similarity value between the cultivars was noted (6.01 to 98.13). Further screening of more cultivars will provide valuable information for current breeding programmes.
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Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJD, Graner A, Niks RE. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:487-500. [PMID: 17115126 DOI: 10.1007/s00122-006-0448-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 10/25/2006] [Indexed: 05/12/2023]
Abstract
A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin.
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Affiliation(s)
- T C Marcel
- Laboratory of Plant Breeding, Graduate school for Experimental Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Deniau AX, Pieper B, Ten Bookum WM, Lindhout P, Aarts MGM, Schat H. QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:907-20. [PMID: 16850314 DOI: 10.1007/s00122-006-0350-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 06/21/2006] [Indexed: 05/10/2023]
Abstract
Thlaspi caerulescens (Tc; 2n = 14) is a natural Zn, Cd and Ni hyperaccumulator species belonging to the Brassicaceae family. It shares 88% DNA identity in the coding regions with Arabidopsis thaliana (At) (Rigola et al. 2006). Although the physiology of heavy metal (hyper)accumulation has been intensively studied, the molecular genetics are still largely unexplored. We address this topic by constructing a genetic map based on AFLP markers and expressed sequence tags (ESTs). To establish a genetic map, an F(2) population of 129 individuals was generated from a cross between a plant from a Pb/Cd/Zn-contaminated site near La Calamine, Belgium, and a plant from a comparable site near Ganges (GA), France. These two accessions show different degrees of Zn and, particularly, Cd accumulation. We analyzed 181 AFLP markers (of which 4 co-dominant) and 13 co-dominant EST sequences-based markers and mapped them to seven linkage groups (LGs), presumably corresponding to the seven chromosomes of T. caerulescens. The total length of the genetic map is 496 cM with an average density of one marker every 2.5 cM. This map was used for Quantitative Trait Locus (QTL) mapping in the F(2). For Zn as well as Cd concentration in root we mapped two QTLs. Three QTLs and one QTL were mapped for Zn and Cd concentration in shoot, respectively. These QTLs explain 23.8-60.4% of the total variance of the traits measured. We found only one common locus (LG6) for Zn and Cd (concentration in root) and one common locus for shoot and root concentrations of Zn (LG1) and of Cd (LG3). For all QTLs, the GA allele increased the trait value except for two QTLs for Zn accumulation in shoot (LG1 and LG4) and one for Zn concentration in root (LG1).
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Affiliation(s)
- A X Deniau
- Ecology and Physiology of Plants, Vrije Universiteit Amsterdam, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
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van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JNAMR, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ. Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 2006; 173:1075-87. [PMID: 16582432 PMCID: PMC1526527 DOI: 10.1534/genetics.106.055871] [Citation(s) in RCA: 205] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).
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Affiliation(s)
- Hans van Os
- Laboratory of Plant Breeding, Wageningen University, The Netherlands
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Assunção AGL, Pieper B, Vromans J, Lindhout P, Aarts MGM, Schat H. Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation. THE NEW PHYTOLOGIST 2006; 170:21-32. [PMID: 16539600 DOI: 10.1111/j.1469-8137.2005.01631.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL.
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Affiliation(s)
- Ana G L Assunção
- Institute of Ecological Sciences, Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands.
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Soleimani VD, Baum BR, Johnson DA. Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:1290-1300. [PMID: 15803291 DOI: 10.1007/s00122-005-1966-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Accepted: 02/14/2005] [Indexed: 05/24/2023]
Abstract
We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69-86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.
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Affiliation(s)
- V D Soleimani
- Agriculture and Agri-Food Canada, K. W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
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Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 2005; 168:435-46. [PMID: 15454555 PMCID: PMC1448125 DOI: 10.1534/genetics.104.026831] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Associations between markers and complex quantitative traits were investigated in a collection of 146 modern two-row spring barley cultivars, representing the current commercial germ plasm in Europe. Using 236 AFLP markers, associations between markers were found for markers as far apart as 10 cM. Subsequently, for the 146 cultivars the complex traits mean yield, adaptability (Finlay-Wilkinson slope), and stability (deviations from regression) were estimated from the analysis of variety trial data. Regression of those traits on individual marker data disclosed marker-trait associations for mean yield and yield stability. Support for identified associations was obtained from association profiles, i.e., from plots of P-values against chromosome positions. In addition, many of the associated markers were located in regions where earlier QTL were found for yield and yield components. To study the oligogenic genetic base of the traits in more detail, multiple linear regression of the traits on markers was carried out, using stepwise selection. By this procedure, 18-20 markers that accounted for 40-58% of the variation were selected. Our results indicate that association mapping approaches can be a viable alternative to classical QTL approaches based on crosses between inbred lines, especially for complex traits with costly measurements.
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Affiliation(s)
- Arnold T W Kraakman
- Wageningen University, Laboratory of Plant Breeding, 6700 AJ, The Netherlands
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18
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Nasuda S, Kikkawa Y, Ashida T, Islam AKMR, Sato K, Endo TR. Chromosomal assignment and deletion mapping of barley EST markers. Genes Genet Syst 2005; 80:357-66. [PMID: 16394587 DOI: 10.1266/ggs.80.357] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
From about 10000 PCR-based EST markers of barley we chose 1421 EST markers that were demonstrated to be amplified differently by PCR between wheat (Triticum aestivum cv. Chinese Spring) and barley (Hordeum vulgare cv. Betzes). We assigned them to the seven barley chromosomes (1H to 7H) by PCR analysis using a set of wheat-barley chromosome addition lines. We successfully assigned 701 (49.3%) EST markers to the barley chromosomes: 75 to 1H, 127 to 2H, 119 to 3H, 94 to 4H, 108 to 5H, 81 to 6H and 97 to 7H. By using a set of Betzes barley telosomic addition lines of Chinese Spring, we could successfully determine the chromosome-arm (S or L) location of at least 90% of the EST markers assigned to each barley chromosome. We conducted a trial mapping using 90 EST markers assigned to 7HS (49) or 7HL (41) and 19 wheat lines carrying 7H structural changes. More EST markers were found in the distal region than in the proximal region.
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Affiliation(s)
- Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Japan
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19
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Poncet V, Hamon P, de Saint Marc MBS, Bernard T, Hamon S, Noirot M. Base Composition of Coffea AFLP Sequences and Their Conservation Within the Genus. J Hered 2004; 96:59-65. [PMID: 15601908 DOI: 10.1093/jhered/esi013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) is often used for genetic mapping and diversity analysis, but very little information is currently available on their sequence characteristics. Species-specific sequences were analyzed from a single Coffea genome (Coffea pseudozanguebariae) associated with clustered or nonclustered AFLP loci of known genetic position. Compared with the expressed sequence tag (EST) sequence composition, their AT content exhibited a bimodal distribution with AT-poor sequences corresponding mainly to putative coding sequences. AT-rich sequences, apart from the EST distribution, were usually clustered on the genetic map and might correspond to noncoding sequences. Conversion of these AFLP markers into sequence-characterized amplified region (SCAR) anchor markers allowed us to assess sequence conservation within Coffea species with respect to species relatedness.
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Affiliation(s)
- V Poncet
- UMR 1097 Diversité et Génome des Plantes Cultivées, Centre IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.
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20
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Moralejo M, Swanston JS, Muñoz P, Prada D, Elía M, Russell JR, Ramsay L, Cistué L, Codesal P, Casas AM, Romagosa I, Powell W, Molina-Cano JL. Use of new EST markers to elucidate the genetic differences in grain protein content between European and North American two-rowed malting barleys. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 110:116-125. [PMID: 15551038 DOI: 10.1007/s00122-004-1805-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Accepted: 08/24/2004] [Indexed: 05/24/2023]
Abstract
A population comprising 102 doubled haploid lines were produced from a cross between Beka, a barley cultivar widely grown in Spain, and Logan, a north American cultivar with inherently low protein content, a character considered to derive from the cultivar Karl. The intentions were to determine whether low-nitrogen malting barleys could be developed in Spain, and if genetic factors that influenced protein content were similarly expressed in widely diverse environments, i.e. northeastern Spain and eastern Scotland. An extensive map comprising 187 molecular markers was developed. Expressed sequence-tagged-derived markers were used in addition to anonymous simple sequence repeats to determine the potential for identifying candidate genes for quantitative trait loci (QTLs), and 22 such markers were mapped for the first time. There was transgressive segregation for both yield and protein content, and the gene for low protein from Logan was not expressed in the Scottish environment. In 2002, high yield was associated with earlier heading date in Spain, while late heading at the Scottish site was associated with greater lodging and lower thousand-kernel weight. These appeared to be possible pleiotropic effects of a factor detected on chromosome 2H. Using information from a consensus map, it was shown that this locus on 2H was in the region of the photoperiod response gene Eam6. A QTL explaining 18% of the variation in grain protein content was detected on chromosome 5H in a region in which a gene for nitrate reductase was previously observed. No effect on grain protein was associated with chromosome 6H, which has been suggested as the location of the low protein gene from Karl. However, it is likely that Karl contained more than one genetic factor reducing protein, and we postulate that the gene on 6H may have been lost during the breeding of Logan.
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Affiliation(s)
- M Moralejo
- Centre UdL-IRTA, Av. Rovira Roure 191, 25198 Lleida, Spain
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21
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Poorter H, van Rijn CPE, Vanhala TK, Verhoeven KJF, de Jong YEM, Stam P, Lambers H. A genetic analysis of relative growth rate and underlying components in Hordeum spontaneum. Oecologia 2004; 142:360-77. [PMID: 15655691 DOI: 10.1007/s00442-004-1705-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2004] [Accepted: 08/04/2004] [Indexed: 10/26/2022]
Abstract
Species from productive and unproductive habitats differ inherently in their relative growth rate (RGR) and a wide range of correlated quantitative traits. We investigated the genetic basis of this trait complex, and specifically assessed whether it is under the control of just one or a few genes that can act as 'master switches' by simultaneously affecting a range of traits in the complex. To address this problem, we crossed two Hordeum spontaneum lines originating from two habitats that differ in productivity. The F3 offspring, in which parental alleles are present in different combinations due to recombination and segregation, was analysed for RGR and its underlying components (leaf area ratio, unit leaf rate, photosynthesis, respiration), as well as a number of other physiological and morphological parameters. For this intra-specific comparison, we found a complex of positively and negatively correlated traits, which was quite similar to what is generally observed across species. A quantitative trait loci (QTL) analysis showed three major and one minor QTL for RGR. Most other variables of the growth-trait complex showed fewer QTLs that were typically scattered over various locations on the genome. Thus, at least in H. spontaneum, we found no evidence for regulation of the trait complex by one or two master switches.
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Affiliation(s)
- Hendrik Poorter
- Plant Ecophysiology, Utrecht University, PO Box 800.84, 3508 TB Utrecht, The Netherlands.
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22
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Yu Z, Guo X. Genetic analysis of selected strains of eastern oyster (Crassostrea virginica Gmelin) using AFLP and microsatellite markers. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2004; 6:575-586. [PMID: 15747088 DOI: 10.1007/s10126-004-3600-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Accepted: 01/14/2004] [Indexed: 05/24/2023]
Abstract
Amplified fragment length polymorphisms (AFLPs) and microsatellite markers were used to examine genetic variation and divergence in 4 selected strains (DBH, NEH, FMF, and CTS) and 1 wild population (DBW) of the eastern oyster Crassostrea virginica Gmelin. Eighty-six AFLP markers (from 3 primer pairs) and 5 microsatellite loci were used for the analysis of 30 oysters from each of the 5 populations. Microsatellite loci were considerably more variable than AFLPs. The observed heterozygosity ranged from 0.560 to 0.640 across populations for microsatellites, and from 0.186 to 0.207 for AFLPs. Both Fst and phiPT of microsatellite data and phiPT statistics of AFLP data revealed significant divergence between all pairs of populations. There was no significant reduction in heterozygosity in all 4 selected strains; however, the number of alleles per locus was considerably lower in the selected strains than in the wild population. Two strains subjected to long-term selection for disease resistance shared frequency shifts at a few loci, which deserve further analysis to determine if they are linked to disease-resistance genes.
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Affiliation(s)
- Ziniu Yu
- Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey 08349, USA
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23
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Miranda Oliveira K, Rios Laborda P, Augusto F Garcia A, Zagatto Paterniani MEAG, de Souza AP. Evaluating genetic relationships between tropical maize inbred lines by means of AFLP profiling. Hereditas 2004; 140:24-33. [PMID: 15032944 DOI: 10.1111/j.1601-5223.2004.01702.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Diversity among tropical maize inbred lines that compose breeding programs, is not well known. The lack of this information has made the arrangement of heterotic groups to be used for breeding purposes difficult. Methods of molecular analysis have been used as efficient alternatives for evaluating genetic diversity, aiming at heterotic group arrangement and acquisition of new hybrids. In this study, AFLP (amplified fragment length polymorphism) was used to investigate the genetic relationships among 96 tropical maize inbred lines from two different origins. The polymorphism level among the genotypes and the possibility of their allocation in heterotic groups were evaluated. Besides, correlations among genetic diversity and flowering time were analyzed. Nine primer combinations were used to obtain AFLP markers, producing 638 bands, 569 of which were polymorphic. Genetic similarities (GS), determined by Jaccard's similarity coefficient, varied from 0.345 to 0.891, with an average of 0.543. The dendrogram based on the GS and on the UPGMA cluster method did not separate the inbred lines in well-defined groups. Aiming at separating the lines into more accurate groups, Tocher's optimization procedure was carried out, 17 groups being identified. Association between flowering time and germplasm pools was detected. AFLP showed itself to be a robust assay, revealing a great power of detection of genetic variability in the tropical germplasm, and also demonstrated to be very useful for guiding breeding programs.
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Affiliation(s)
- Karine Miranda Oliveira
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, SP, Brasil
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24
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Prada D, Ullrich SE, Molina-Cano JL, Cistué L, Clancy JA, Romagosa I. Genetic control of dormancy in a Triumph/Morex cross in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:62-70. [PMID: 14991108 DOI: 10.1007/s00122-004-1608-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Accepted: 01/19/2004] [Indexed: 05/06/2023]
Abstract
Seed dormancy in barley ( Hordeum vulgare L.) is one of the most important parameters affecting malting. Seed dormancy is quantitatively inherited and variously influenced by the environment. The objectives of the present study were to determine the genome location and effects of quantitative trait loci (QTLs) involved in the expression of seed dormancy in a barley cross between two varieties derived from different germplasm pools. Using a doubled-haploid population of 107 lines of the cross between the malting types Triumph (two-row, dormant) and Morex (six-row, non-dormant), seed dormancy phenotypic data sets from five environments and a 147-marker linkage map were developed in order to perform QTL analyses with simple interval mapping and simplified composite interval mapping procedures. Two different types of variables were considered for seed dormancy characterization: (1) level of dormancy induced during seed development, which was indirectly measured as germination percentage at 3 days and 7 days, GP3 and GP7 respectively; (2) rate of dormancy release in the course of a period after seed harvest (after-ripening). Different mechanisms of genetic control were detected for these two types of dormancy-related traits. A major and consistent dormancy QTL near the centromere on chromosome 7(5H) was associated with the establishment of dormancy during seed development and accounted for 52% and 33% of the variability for GP3 and GP7, respectively. Two other QTLs located in the vicinity of the vrs1 locus on chromosome 2(2H) and near the long arm telomere on chromosome 7(5H) explained 9% and 19% of variation, respectively, for the rate of dormancy release during after-ripening. Likewise, seed dormancy was assessed in an F(2) population derived from the cross between two dormant types of distinct germplasm groups, Triumph (European, two-row, malt) and Steptoe (North American, six-row, feed), which showed similar but not identical genetic control for dormancy. Interestingly, there is remarkable dormancy QTL conservation in both regions on chromosome 7(5H) identified in this study and among other barley mapping populations. These widely conserved QTLs show potential as targets for selection of a moderate level of seed dormancy in breeding programs.
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Affiliation(s)
- D Prada
- Centre UdL-IRTA, Av. Alcalde Rovira Route 191, 25198 Lleida, Spain
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25
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Francia E, Rizza F, Cattivelli L, Stanca AM, Galiba G, Tóth B, Hayes PM, Skinner JS, Pecchioni N. Two loci on chromosome 5H determine low-temperature tolerance in a 'Nure' (winter) x 'Tremois' (spring) barley map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:670-680. [PMID: 14576984 DOI: 10.1007/s00122-003-1468-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Accepted: 08/18/2003] [Indexed: 05/24/2023]
Abstract
Barley ( Hordeum vulgare subsp. vulgare) is an economically important diploid model for the Triticeae; and a better understanding of low-temperature tolerance mechanisms could significantly improve the yield of fall-sown cereals. We developed a new resource for genetic analysis of winter hardiness-related traits, the 'Nure' x 'Tremois' linkage map, based on a doubled-haploid population that is segregating for low-temperature tolerance and vernalization requirement. Three measures of low-temperature tolerance and one measure of vernalization requirement were used and, for all traits, QTLs were mapped on chromosome 5H. The vernalization response QTL coincides with previous reports at the Vrn-1/Fr1 region of the Triticeae. We also found coincident QTLs at this position for all measures of low-temperature tolerance. Using Composite Interval Mapping, a second proximal set, of coincident QTLs for low-temperature tolerance, and the accumulation of two different COR proteins (COR14b and TMC-Ap3) was identified. The HvCBF4 locus, or another member of the CBF loci clustered in this region, is the candidate gene underlying this QTL. There is a CRT/DRE recognition site in the promoter of cor14b with which a CBF protein could interact. These results support the hypothesis that highly conserved regulatory factors, such as members of the CBF gene family, may regulate the stress responses of a wide range of plant species.
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Affiliation(s)
- E Francia
- Istituto Sperimentale per la Cerealicoltura, 29017, Fiorenzuola d'Arda, Italy
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26
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Two loci on chromosome 5H determine low-temperature tolerance in a 'Nure' (winter) x 'Tremois' (spring) barley map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003. [PMID: 14576984 DOI: 10.1007/s00122‐003‐1468‐9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Barley ( Hordeum vulgare subsp. vulgare) is an economically important diploid model for the Triticeae; and a better understanding of low-temperature tolerance mechanisms could significantly improve the yield of fall-sown cereals. We developed a new resource for genetic analysis of winter hardiness-related traits, the 'Nure' x 'Tremois' linkage map, based on a doubled-haploid population that is segregating for low-temperature tolerance and vernalization requirement. Three measures of low-temperature tolerance and one measure of vernalization requirement were used and, for all traits, QTLs were mapped on chromosome 5H. The vernalization response QTL coincides with previous reports at the Vrn-1/Fr1 region of the Triticeae. We also found coincident QTLs at this position for all measures of low-temperature tolerance. Using Composite Interval Mapping, a second proximal set, of coincident QTLs for low-temperature tolerance, and the accumulation of two different COR proteins (COR14b and TMC-Ap3) was identified. The HvCBF4 locus, or another member of the CBF loci clustered in this region, is the candidate gene underlying this QTL. There is a CRT/DRE recognition site in the promoter of cor14b with which a CBF protein could interact. These results support the hypothesis that highly conserved regulatory factors, such as members of the CBF gene family, may regulate the stress responses of a wide range of plant species.
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27
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Turpeinen T, Vanhala T, Nevo E, Nissilä E. AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 106:1333-1339. [PMID: 12748785 DOI: 10.1007/s00122-002-1151-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2001] [Accepted: 08/05/2002] [Indexed: 05/24/2023]
Abstract
The genetic diversity produced by the amplified fragment length polymorphism (AFLP) method was studied in 94 genotypes of wild barley, Hordeum spontaneum (C. Koch) Thell., originating from ten ecologically and geographically different locations in Israel. Eight primer pairs produced 204 discernible loci of which 189 (93%) were polymorphic. Each genotype had a unique banding profile and the genetic similarity coefficient varied between 0.74 and 0.98. The phenogram generated from these similarities by the UPGMA method did not group genotypes strictly according to their geographical origin, which pattern was also seen in the principal coordinate (PCO) plot. Genetic diversity was larger within (69%) than among (31%) populations. Associations between ecogeographical variables and the mean gene diversity were found at one primer pair. The results are discussed and compared with data obtained by the simple sequence repeat (SSR) method.
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Affiliation(s)
- T Turpeinen
- MTT Agrifood Research Finland, Plant Production Research, Crops and Biotechnology, FIN-31600 Jokioinen, Finland.
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28
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Vaz Patto MC, Rubiales D, Martín A, Hernández P, Lindhout P, Niks RE, Stam P. QTL mapping provides evidence for lack of association of the avoidance of leaf rust in Hordeum chilense with stomata density. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 106:1283-1292. [PMID: 12748780 DOI: 10.1007/s00122-003-1195-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2002] [Accepted: 10/15/2002] [Indexed: 05/24/2023]
Abstract
In cereals, rust fungi are among the most harmful pathogens. Breeders usually rely on short-lived hypersensitivity resistance. As an alternative, "avoidance" may be a more durable defence mechanism to protect plants to rust fungi. In Hordeum chilense avoidance is based on extensive wax covering of stomata, which interferes with the induction of appressorium formation by the rust fungi. High avoidance levels are associated with a higher stoma density on the abaxial leaf epidermis. The avoidance level was assessed as the percentage of germ tube/stoma encounters that did not result in appressorium differentiation by Puccinia hordei, the barley leaf rust fungus. One hundred F(2) individuals from the cross between two H. chilense accessions with contrasting levels of avoidance showed a continuous distribution for avoidance of the rust fungus and for stoma density, indicating quantitative inheritance of the traits. No significant correlation was found between avoidance and stoma density in the segregating F(2) population. In order to map quantitative trait loci (QTLs) for both traits, an improved molecular marker linkage map was constructed, based on the F(2) population. The resulting linkage map spanned 620 cM and featured a total of 437 AFLP markers, thirteen RFLPs, four SCARs, nine SSRs, one STS and two seed storage protein markers. It consisted of seven long and two shorter linkage groups, and was estimated to cover 81% of the H. chilense genome. Restricted multiple interval mapping identified two QTLs for avoidance and three QTLs for stoma density in the abaxial leaf surface. The QTLs for avoidance were mapped on chromosome 3 and 5; those for stoma density on chromosomes 1, 3 and 7. Only the two QTLs regions located on chromosome 3 (one for avoidance and the other for stoma density) overlapped. The wild barley H. chilense has a high crossability with other members of the Triticeae tribe. The knowledge on the location of the QTLs responsible for the avoidance trait is a prerequisite to transfer this favourable agronomic trait from H. chilense to cultivated cereal genomes.
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Affiliation(s)
- M C Vaz Patto
- Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, The Netherlands
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29
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KRAUSS SIEGFRIEDL. Complete exclusion of nonsires in an analysis of paternity in a natural plant population using amplified fragment length polymorphism (AFLP). Mol Ecol 2003. [DOI: 10.1046/j.1365-294x.1999.00552.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- SIEGFRIED L. KRAUSS
- Division of Botany and Zoology, The Australian National University, Canberra, ACT, 0200, Australia
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30
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Bai Y, Huang CC, van der Hulst R, Meijer-Dekens F, Bonnema G, Lindhout P. QTLs for tomato powdery mildew resistance (Oidium lycopersici) in Lycopersicon parviflorum G1.1601 co-localize with two qualitative powdery mildew resistance genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:169-76. [PMID: 12575751 DOI: 10.1094/mpmi.2003.16.2.169] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Tomato (Lycopersicon esculentum) is susceptible to the powdery mildew Oidium lycopersici, but several wild relatives such as Lycopersicon parviflorum G1.1601 are completely resistant. An F2 population from a cross of Lycopersicon esculentum cv. Moneymaker x Lycopersicon parviflorum G1.1601 was used to map the O. lycopersici resistance by using amplified fragment length polymorphism markers. The resistance was controlled by three quantitative trait loci (QTLs). Ol-qtl1 is on chromosome 6 in the same region as the Ol-1 locus, which is involved in a hypersensitive resistance response to O. lycopersici. Ol-qtl2 and Ol-qtl3 are located on chromosome 12, separated by 25 cM, in the vicinity of the Lv locus conferring resistance to another powdery mildew species, Leveillula taurica. The three QTLs, jointly explaining 68% of the phenotypic variation, were confirmed by testing F3 progenies. A set of polymerase chain reaction-based cleaved amplified polymorphic sequence and sequence characterized amplified region markers was generated for efficient monitoring of the target QTL genomic regions in marker assisted selection. The possible relationship between genes underlying major and partial resistance for tomato powdery mildew is discussed.
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Affiliation(s)
- Yuling Bai
- Laboratory of Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
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31
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Kim KS, Yeo JS, Kim JW. Assessment of genetic diversity of Korean native pig (Sus scrofa) using AFLP markers. Genes Genet Syst 2002; 77:361-8. [PMID: 12441647 DOI: 10.1266/ggs.77.361] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In order to assess the genetic diversity and genetic relationships among the six commercial pig breeds including the Korean native pig, we performed an amplified fragment length polymorphism (AFLP) analysis. Applying the three EcoRI/TagI primer combinations to 54 individual pig samples out of six breeds, a total of 186 AFLP bands were generated, 67 (36%) of which were identified as polymorphic bands. From these polymorphic bands, the three estimates (percentage of polymorphic loci, Neis heterozygosity and Shannon index) of genetic diversity, G(ST) estimates, Neis unbiased genetic distance and two indices of genetic similarity were calculated. From all the calculations of genetic diversity, the lowest genetic diversity was exhibited in the Korean native pig, and the highest in the Chinese Yanbian pig. Given the mean G(ST) value (G(ST) = 0.390) across all pigs examined, levels of apparent breed subdivision were considerable. A UPGMA tree of individuals based on Jaccards similarity index showed that the Korean native pig formed a distinct cluster from the other five pigs. In addition, the tree displayed that all the individuals except for six individuals were grouped into their breeds. Principal component analysis based on the binary data matrix of either presence or absence confirmed the distinctness of the Korean native pig from the other pigs. Our results indicate that the Korean native pig has a low level of genetic diversity and is distinct from the five pig breeds, confirming the results from previous microsatellite data. The findings also suggest that AFLP analysis may be a valuable tool for revealing genetic relationships and genetic diversity among different pig breeds.
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Affiliation(s)
- Kyung Seok Kim
- Institute of Biotechnology, Yeungnam University, Kyongsan, Korea
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32
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Arru L, Niks RE, Lindhout P, Valé G, Francia E, Pecchioni N. Genomic regions determining resistance to leaf stripe (Pyrenophora graminea) in barley. Genome 2002; 45:460-6. [PMID: 12033613 DOI: 10.1139/g02-004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Leaf stripe is a seed-borne disease of barley (Hordeum vulgare) caused by Pyrenophora graminea. Little is known about the genetics of resistance to this pathogen. In the present work, QTL analysis was applied on two recombinant inbred line (RIL) populations derived from two- and six-rowed barley genotypes with different levels of partial resistance to barley leaf stripe. Quantitative trait loci for partial resistance were identified using the composite interval mapping (CIM) method of PLABQTL software, using the putative QTL markers as cofactors. In the L94 x 'Vada' mapping population, one QTL for resistance was detected on chromosome 2H; the same location as the leaf-stripe resistance gene Rdg1 mapped earlier in 'Alf', where it confers complete resistance to the pathogen. An additional minor-effect QTL was identified by further analyses in this segregating population on chromosome 7H. In L94 x C123, two QTLs for resistance were mapped, one each on chromosomes 7H and 2H.
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Affiliation(s)
- L Arru
- Istituto Sperimentale per la Cerealicoltura Sezione di Fiorenzuola, Fiorenzuola d'Arda, PC, Italy
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33
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Affiliation(s)
- A Linacre
- Forensic Science Unit, University of Strathclyde, G1 1XW, United Kingdom
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Kim KS, Jeong HW, Park CK, Ha JH. Suitability of AFLP markers for the study of genetic relationships among Korean native dogs. Genes Genet Syst 2001; 76:243-50. [PMID: 11732633 DOI: 10.1266/ggs.76.243] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To determine the genetic relationships among domestic dog breeds, we performed both a sequence comparison of mitochondrial DNA (mtDNA) and an amplified fragment length polymorphisms (AFLP) analysis. Three of four regions of mtDNA, cytochrome b, cytochrome oxidase subunit II, and 16S rRNA genes were highly homogeneous among dog breeds, whereas the other region, the control region, showed relatively high polymorphisms with a maximum percentage difference of 3.18%. However, the control region showed extensive polymorphism even within breeds, and the relationship tree derived from the data could not clearly delimit distinct breeds. 19 EcoRI/MseI primer combinations were used to generate AFLP markers among 25 dogs from 11 breeds including three Korean native dogs. These amplification reactions allowed the detection of more than 1900 amplification products of which 408 were identified as polymorphic bands. Unrooted neighbor-joining tree based on dissimilarity values showed that the Korean native dogs were clustered together with the Asian dogs and that the Asian originated dogs were clustered separately from Western originated dogs. A consensus tree using parsimony method also showed Korean native dogs were grouped separately from the other dogs with moderate bootstrap values. Taken together, it is concluded that AFLP analysis is a more informative tool for revealing genetic relationships among dog breeds than mtDNA sequence comparison.
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Affiliation(s)
- K S Kim
- Department of Genetic Engineering, Kyungpook National University, Taegu, Korea
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Cervera MT, Storme V, Ivens B, Gusmão J, Liu BH, Hostyn V, Van Slycken J, Van Montagu M, Boerjan W. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 2001; 158:787-809. [PMID: 11404342 PMCID: PMC1461694 DOI: 10.1093/genetics/158.2.787] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.
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Affiliation(s)
- M T Cervera
- Vakgroep Moleculaire Genetica en Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, Ledeganckstraat 35, B-9000 Gent, Belgium
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36
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Serizawa N, Nasuda S, Endo TR. Barley chromosome addition lines of wheat for screening of AFLP markers on barley chromosomes. Genes Genet Syst 2001; 76:107-10. [PMID: 11434455 DOI: 10.1266/ggs.76.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We conducted AFLP (Amplified Fragment Length Polymorphism) analysis with the six wheat-barley chromosome addition lines of common wheat cultivar Chinese Spring. We analyzed the AFLP fingerprints generated by 36 combinations of selective-amplification primers to find 103 markers specific to the barley chromosomes (2.9 markers per combination on average). The numbers of AFLP markers mapped to the barley chromosomes varied (one to 16) depending of the primer combinations. Each barley chromosome had 10 to 27 AFLP markers (17.2 markers on average). We identified the chromosome arms in which these markers are located using the barley telocentric addition lines (one to 20 markers per chromosome arm). The AFLP markers were not distributed evenly among chromosomes and chromosome arms. We could not determine the chromosome-arm locations for some of the barley-specific markers, either because such markers were found in both the short- and long-arm telocentric lines, or in neither line.
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Affiliation(s)
- N Serizawa
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Japan
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Boekhout T, Theelen B, Diaz M, Fell JW, Hop WCJ, Abeln ECA, Dromer F, Meyer W. Hybrid genotypes in the pathogenic yeast Cryptococcus neoformans. MICROBIOLOGY (READING, ENGLAND) 2001; 147:891-907. [PMID: 11283285 DOI: 10.1099/00221287-147-4-891] [Citation(s) in RCA: 305] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Amplified fragment length polymorphism (AFLP) genotyping of isolates of the pathogenic fungus Cryptococcus neoformans suggested a considerable genetic divergence between the varieties C. neoformans var. neoformans and C. neoformans var. grubii on the one hand versus C. neoformans var. gattii on the other. This divergence is supported by additional phenotypic, biochemical, clinical and molecular differences. Therefore, the authors propose the existence of two species, C. neoformans (Sanfelice) Vuillemin and C. bacillisporus Kwon-Chung, which differ in geographical distribution, serotypes and ecological origin. Within each species three AFLP genotypes occur, which differ in geographical distribution and serotypes. Differences in ecological origin (AIDS patients, non-AIDS patients, animals or the environment) were found to be statistically not significant. In C. neoformans as well as in C. bacillisporus one of the genotypes represented a hybrid. The occurrence of hybridization has consequences for the reproductive biology of the species, as new genotypes with altered virulence or susceptibility to antifungal drugs may arise through the exchange of genetic material.
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Affiliation(s)
- Teun Boekhout
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands1
| | - Bart Theelen
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands1
| | - Mara Diaz
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, FL 33149, USA2
| | - Jack W Fell
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, FL 33149, USA2
| | - Wim C J Hop
- Department of Epidemiology & Biostatistics, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, The Netherlands3
| | - Edwin C A Abeln
- Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands1
| | - Françoise Dromer
- Institut Pasteur, Unité de Mycologie, Rue du Dr Roux, 75724 Paris Cedex 15, France4
| | - Wieland Meyer
- Molecular Mycology Laboratory, University of Sydney at Westmead Hospital, Westmead, NSW, Australia5
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Patto MCV, Aardse A, Buntjer J, Rubiales D, Martín A, Niks RE. Morphology and AFLP markers suggest three Hordeum chilense ecotypes that differ in avoidance to rust fungi. ACTA ACUST UNITED AC 2001. [DOI: 10.1139/b00-152] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Hordeum chilense Roem. & Schult., a high variation in the level of avoidance to infection of barley leaf rust (Puccinia hordei Otth) occurs. Probably resulting from the properties of the stomata, the rust germ tube overgrows stomata, and the infection process fails in an early stage. In the present study we tested the hypothesis that the avoidance character occurs in certain morphologically and molecularly distinct ecotypes of H. chilense. Eighty-eight H. chilense accessions were inoculated with P. hordei to assess the level of avoidance. The accessions were described for 30 morphological characters and three AFLP primer combinations. Cluster analysis using both morphological and AFLP fingerprint data suggested three distinct clusters of accessions. One of the clusters had a particularly high level of avoidance. This putative subspecific taxon was characterized by shorter and wider spikes, more erect culms, a greater number of stomata per square centimetre on the abaxial leaf side, and a shorter uppermost internode until flag leaf. All accessions clustered in this subspecific taxon were collected from humid habitats. We conclude that H. chilense consists of at least three rather well defined, morphologically and genetically distinct subspecific taxa, one of which has a very high level of avoidance to barley leaf rust.Key words: AFLP fingerprinting, diversity, Hordeum chilense, avoidance, rust fungi, Puccinia hordei.
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Abstract
A saturated genetic map of diploid oat was constructed based on a recombinant inbred (RI) population developed from a cross between Avena strigosa (Cereal Introduction, C.I. 3815) and A. wiestii (C.I. 1994). This 513-locus map includes 372 AFLP (amplified fragment length polymorphism) and 78 S-SAP (sequence-specific-amplification polymorphism) markers, 6 crown-rust resistance loci, 8 resistance-gene analogs (RGAs), one morphological marker, one RAPD (random amplified polymorphic DNA) marker, and is anchored by 45 grass-genome RFLP (restriction fragment length polymorphism) markers. This new A. strigosa × A. wiestii RI map is colinear with a diploid Avena map from an A. atlantica × A. hirtula F2 population. However, some linkage blocks were rearranged as compared to the RFLP map derived from the progenitor A. strigosa × A. wiestii F2 population. Mapping of Bare-1-like sequences via sequence-specific AFLP indicated that related retrotransposons had considerable heterogeneity and widespread distribution in the diploid Avena genome. Novel amplified fragments detected in the RI population suggested that some of these retrotransposon-like sequences are active in diploid Avena. Three markers closely linked to the Pca crown-rust resistance cluster were identified via AFLP-based bulk-segregant analysis. The derived STS (sequence-tagged-site) marker, Agx4, cosegregates with Pc85, the gene that provides resistance specificity to crown-rust isolate 202 at the end of the cluster. This framework map will be useful in gene cloning, genetic mapping of qualitative genes, and positioning QTL (quantitative trait loci) of agricultural importance.Key words: AFLP, Bare-1 retrotransposon, sequence-specific-amplification polymorphism (S-SAP), resistance-gene analog, crown-rust resistance, Pca, Gramineae, grass anchor probe.
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Savelkoul PH, Aarts HJ, de Haas J, Dijkshoorn L, Duim B, Otsen M, Rademaker JL, Schouls L, Lenstra JA. Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 1999; 37:3083-91. [PMID: 10488158 PMCID: PMC85499 DOI: 10.1128/jcm.37.10.3083-3091.1999] [Citation(s) in RCA: 265] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- P H Savelkoul
- Department of Medical Microbiology and Infection Control, University Hospital Vrije Universiteit, Amsterdam, The Netherlands.
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Ayele M, Tefera H, Assefa K, Nguyen HT. Genetic characterization of two Eragrostis species using AFLP and morphological traits. Hereditas 1999; 130:33-40. [PMID: 10364827 DOI: 10.1111/j.1601-5223.1999.00033.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal crop in Ethiopia. An experiment was conducted to investigate genetic diversity among four cultivars of tef and 14 accessions of Eragrostis pilosa using radiolabelled and silver stained amplified fragment length polymorphism. Morphological traits were also evaluated. A total of 897 markers were obtained out of which 395 were polymorphic using 11 primer combinations. Cluster analysis revealed accessions of E. pilosa which are distantly related and others closely related to tef. Our previous experience also indicates that E. pilosa is crossable with tef. Those accessions distantly related to tef could be used in a crossing program to generate a population for selection and/or genetic mapping. Such genetic mapping populations will form an important entry point towards the molecular genetic dissection of the plant genus, Eragrostis, especially in the context of comparative mapping. Knowledge gained from such study, apart from tef improvement, will also be useful for many forage and turf grass species where little molecular genetic information is available. Nine cultivars or accessions had one or more unique fragments using one or more AFLP primers indicating the potential of the technology in fingerprinting tef in a breeding or seed multiplication program. The results also showed that clusters obtained using silver staining and gamma 33P-ATP labeling were similar, suggesting that silver staining could be used as an alternative to radiolabeling at least in genetic diversity analysis. Significant genetic variation was obtained for morphological traits. Of particular interest to tef breeding was short plant stature in E. pilosa which could be transferred to tef to minimize the problem of lodging. Diversity revealed at the morphological trait level was not commensurate with that observed for AFLP. This was due to the small number of available morphological traits and their interaction with the environment.
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Affiliation(s)
- M Ayele
- Department of Plant and Soil Science, Texas Tech University, Lubbock 79409-2122, USA
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Affiliation(s)
- CJ Ridout
- Dept of Cereals Research, John Innes Centre, Norwich Research Park, Colney, Norwich, UK NR4 7UH
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Castiglioni P, Pozzi C, Heun M, Terzi V, Müller KJ, Rohde W, Salamini F. An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley. Genetics 1998; 149:2039-56. [PMID: 9691056 PMCID: PMC1460261 DOI: 10.1093/genetics/149.4.2039] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A strategy based upon AFLP markers for high-efficiency mapping of morphological mutations and DNA probes to linkage groups in barley is presented. First, 511 AFLP markers were placed on the linkage map derived from the cross Proctor x Nudinka. Second, loci controlling phenotypic traits were assigned to linkage groups by AFLP analysis, using F2 populations consisting of 30-50 mutant plants derived from crosses of the type "mutant x Proctor" and "mutant x Nudinka." To map DNA probes, 67 different wild-type barley lines were selected to generate F2 populations by crossing with Proctor and Nudinka. F2 plants that were polymorphic for a given RFLP fragment were classified into genotypic classes. Linkage of the RFLP polymorphism to 1 of the 511 AFLP loci was indicated by cosegregation. The use of the strategy is exemplified by the mapping of the mutation branched-5 to chromosome 2 and of the DNA probes Bkn2 and BM-7 to chromosomes 5 and 1, respectively. Map expansion and marker order in map regions with dense clustering of markers represented a particular problem. A discussion considering the effect of noncanonical recombinant products on these two parameters is provided.
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Affiliation(s)
- P Castiglioni
- Max-Planck-Institut für Züchtungsforschung, 50829 Cologne, Germany
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