A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum × Lycopersicon hirsutum cross

A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); OI-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, I-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with other molecular linkage maps of tomato, including the high density L. esculentum × Lycopersicon pennellii map, indicated that the lengths of the maps and linear order of RFLP markers were in good agreement, though certain chromosomal regions were less consistent than others in terms of the frequency of recombination. The present map provides a basis for identification and mapping of genes and QTLs for disease resistance and other desirable traits in PI126445 and other L. hirsutum accessions, and will be useful for marker-assisted selection and map-based gene cloning in tomato.Key words: disease resistance, genetic marker, molecular map, quantitative trait locus (QTL), restriction fragment length polymorphism (RFLP), RGAs.

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Physical mapping of restriction fragment length polymorphism (RFLP) markers in homoeologous groups 1 and 3 chromosomes of wheat by in situ hybridization

Genome ◽

10.1139/g01-001 ◽

2001 ◽

Vol 44 (3) ◽

pp. 401-412 ◽

Cited By ~ 10

Author(s):

X -F. Ma ◽

K Ross ◽

J P Gustafson

Keyword(s):

In Situ Hybridization ◽

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Physical Mapping ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Markers ◽

Restriction Fragment Length

Using wheat ditelosomic lines and in situ hybridization of biotin-labelled DNA probes, 18 restriction fragment length polymorphism (RFLP) markers were physically located on homoeologous groups 1 and 3 chromosomes of wheat. Most of the markers hybridized to chromosome arms in a physical order concordant with the genetic maps. A majority of the markers studied were clustered in non-C-banded, distal euchromatic areas, indicating the presence of recombination hot spots and cold spots in those regions. However, on 1BS the markers were well dispersed, which could be due to the abundance of heterochromatin throughout the arm. An inversion between Xpsr653 and Xpsr953 was observed on 1AL. One new Xpsr688 locus, approximately 2026% from the centromere, was found on 1AS and 1BS. The physical location of Xpsr170 on group 3 chromosomes probably represents an alternative to the loci on the genetic map. Finally, Xpsr313 was mapped to two physical loci on 1DL. Five markers were located to bins consistent with the deletion-based physical maps.Key words: wheat, physical mapping, in situ hybridization.

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Restriction Fragment Length Polymorphism Assessment of the Heterogeneous Nature of Maize Population GT-MAS:gk and Field Evaluation of Resistance to Aflatoxin Production by Aspergillus flavus

Journal of Food Protection ◽

10.4315/0362-028x-65.1.167 ◽

2002 ◽

Vol 65 (1) ◽

pp. 167-171 ◽

Cited By ~ 10

Author(s):

B. Z. GUO ◽

A. BUTRON ◽

H. LI ◽

N. W. WIDSTROM ◽

R. E. LYNCH

Keyword(s):

Cluster Analysis ◽

Restriction Fragment Length Polymorphism ◽

Length Polymorphism ◽

Fragment Length Polymorphism ◽

Field Evaluation ◽

Aflatoxin Production ◽

Inbred Lines ◽

Rflp Markers ◽

Maize Population ◽

Restriction Fragment Length

Aflatoxin, produced by Aspergillus flavus, is one of the most toxic and carcinogenic substances known and contaminates many agricultural commodities such as corn, peanuts, cottonseed, and tree nuts. The challenge to breeders/plant pathologists is to identify lines that have resistance to aflatoxin production. Maize population GT-MAS:gk has been identified and released as a germplasm with resistance to aflatoxin contamination. In the present study, we assessed genetic divergence in the GT-MAS:gk population using restriction fragment length polymorphism (RFLP) DNA markers to survey 11 selfed inbred lines and conducted field evaluations for the dissimilarities in aflatoxin production among these inbred lines in comparison with a sister population, GT-MAS:pw,nf. The 11 selfed inbred lines were assayed for DNA polymorphism using 113 RFLP markers in 10 linkage groups covering 1,518.2 centimorgans (cM; unit of gene or chromosome size). Considerable variation among the inbreds was detected with RFLP markers, of which 42 probe-enzyme combinations gave 102 polymorphic bands. Cluster analysis based on genetic similarities revealed associations and variations among the tested lines. Three polymorphic groups were distinguished by cluster analysis. Two years of field evaluation data showed that aflatoxin concentrations among the lines were significantly different in both years (P < 0.001). Maturity data were also different. Thus, this study demonstrates that the maize population GT-MAS:gk is heterogeneous and that individuals may be different in resistance to A. flavus infection and aflatoxin production. Therefore, the most resistant lines should be inbred to increase homogeneity, and resistance should be confirmed through progeny testing.

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New restriction fragment length polymorphism (RFLP) markers forAspergillus fumigatus

FEMS Immunology & Medical Microbiology ◽

10.1111/j.1574-695x.2001.tb01580.x ◽

2001 ◽

Vol 31 (1) ◽

pp. 15-19 ◽

Cited By ~ 12

Author(s):

Camile Pizeta Semighini ◽

Guillaume Delmas ◽

Steven Park ◽

Donald Amstrong ◽

David Perlin ◽

...

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Markers ◽

Restriction Fragment Length

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Identification of X chromosomal restriction fragment length polymorphism markers and their use in a gene localization study in Drosophila virilis and D. littoralis

Genome ◽

10.1139/g01-006 ◽

2001 ◽

Vol 44 (2) ◽

pp. 242-248 ◽

Cited By ~ 7

Author(s):

Seliina Päällysaho ◽

Susanna Huttunen ◽

Anneli Hoikkala

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Drosophila Virilis ◽

Rflp Markers ◽

Male Courtship ◽

Restriction Fragment Length

We have identified six restriction fragment length polymorphism (RFLP) markers based on unique gene sequences on the X chromosome of Drosophila virilis and D. littoralis. The markers were localized by in situ hybridization on larval polytene chromosomes, and the conjugation of the X chromosomes of the two species was studied in salivary glands of interspecific hybrid female larvae. The gene arrangement of D. virilis and D. littoralis appeared to be very different at the proximal end of the X chromosome preventing recombination between RFLP markers located in this area. Simple quantitative trait loci (QTL) analysis showed that five of our marker genes (including nonA and Dmca1A, previously found to affect male courtship song in D. melanogaster) are linked with a gene(s) having a major effect on species differences in the male courtship song between D. virilis and D. littoralis. This shows that the song gene(s) may be located inside a large X-chromosomal inversion in D. littoralis (as previously suggested), but that it may also be located on an area between this inversion and the centromere, close to nonA and Dmca1A. Localization of this gene or gene complex will be continued with the aid of our newly identified RFLP markers by making interspecific crosses between D. virilis group species with more similar X chromosomes.Key words: restriction fragment length polymorphism (RFLP), in situ hybridization, Drosophila virilis.

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RESTRICTION FRAGMENT LENGTH POLYMORPHISM IN GENETICALLY RELATED ROSE CULTIVARS

HortScience ◽

10.21273/hortsci.27.6.574d ◽

1992 ◽

Vol 27 (6) ◽

pp. 574d-574

Author(s):

Sriyani Rajapakse ◽

Albert Abbott ◽

John Kelly ◽

Robert Ballard

Keyword(s):

Escherichia Coli ◽

Restriction Fragment Length Polymorphism ◽

Dna Fingerprinting ◽

Genomic Dna ◽

Genetic Relatedness ◽

Fragment Length Polymorphism ◽

Restriction Enzymes ◽

Rflp Markers ◽

High Degree ◽

Restriction Fragment Length

The feasibility of using RFLP to distinguish genetically related Hybrid Tea rose cultivars for DNA `fingerprinting' was examined with a group of cultivars related to `Peace'. The following cultivars used in this study, `Chicago Peace', `Flaming Peace', `Climbing Peace' and `Lucky Piece', were derived from bud mutations (sports) of `Peace'. We also investigated two additional cultivars, `Perfume Delight' and `Garden Party', in which one of the parents for each was `Peace'. Genomic rose DNA probes, cloned in pUC8 plasmid of Escherichia coli, were hybridized with genomic DNA of these cultivars digested with different restriction enzymes. Although polymorphisms were observed among these related cultivars, only a few probe/enzyme combinations screened produced RFLPs due to the high degree of genetic relatedness of these cultivars. We have identified probes that can distinguish all of these related rose cultivars. This study demonstrates that RFLP markers can be used effectively in DNA `fingerprinting' of genetically related rose cultivars, eventhough the level of detectable polymorphism is quite low.

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Single Cystosorus Isolate Production and Restriction Fragment Length Polymorphism Characterization of the Obligate Biotroph Spongospora subterranea f. sp. subterranea

Phytopathology ◽

10.1094/phyto-96-1157 ◽

2006 ◽

Vol 96 (10) ◽

pp. 1157-1163 ◽

Cited By ~ 8

Author(s):

Xinshun Qu ◽

Barbara J. Christ

Keyword(s):

North America ◽

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Markers ◽

Spongospora Subterranea ◽

Geographic Locations ◽

Restriction Fragment Length

Spongospora subterranea f. sp. subterranea causes powdery scab in potatoes and is distributed worldwide. Genetic studies of this pathogen have been hampered due, in part, to its obligate parasitism and the lack of molecular markers for this pathogen. In this investigation, a single cystosorus inoculation technique was developed to produce large amounts of S. subterranea f. sp. subterranea plasmodia or zoosporangia in eastern black nightshade (Solanum ptycanthum) roots from which DNA was extracted. Cryopreservation of zoosporangia was used for long-term storage of the isolates. S. subterranea f. sp. subterranea-specific restriction fragment length polymorphism (RFLP) markers were developed from randomly amplified polymorphic DNA (RAPD) fragments. Cystosori of S. subterranea f. sp. subterranea were used for RAPD assays and putative pathogen-specific RAPD fragments were cloned and sequenced. The fragments were screened for specificity by Southern hybridization and subsequent DNA sequence BLAST search. Four polymorphic S. subterranea f. sp. subterranea-specific probes containing repetitive elements, and one containing single copy DNA were identified. These RFLP probes were then used to analyze 24 single cystosorus isolates derived from eight geographic locations in the United States and Canada. Genetic variation was recorded among, but not within, geographic locations. Cluster analysis separated the isolates into two major groups: group I included isolates originating from western North America, with the exception of those from Colorado, and group II included isolates originating from eastern North America and from Colorado. The techniques developed in this study, i.e., production of single cystosorus isolates of S. subterranea f. sp. subterranea and development of RFLP markers for this pathogen, provide methods to further study the genetic structure of S. subterranea f. sp. subterranea.

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