Efficiency of RFLP, RAPD, and AFLP markers for the construction of an intraspecific map of the tomato genome

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Vera Saliba-Colombani ◽  
Mathilde Causse ◽  
Laurent Gervais ◽  
Jacqueline Philouze
Keyword(s):  
Lycopersicon Esculentum ◽  
Linkage Map ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Aflp Markers ◽  
Rflp Rapd

We have constructed a tomato genetic linkage map based on an intraspecific cross between two inbred lines of Lycopersicon esculentum and L. esculentum var. cerasiforme. The segregating population was composed of 153 recombinant inbred lines. This map is comprised of one morphological, 132 RFLP (restriction fragment length polymorphism, including 16 known-function genes), 33 RAPD (random amplified polymorphic DNA), and 211 AFLP (amplified fragment length polymorphism) loci. We compared the 3 types of markers for their polymorphism, segregation, and distribution over the genome. RFLP, RAPD, and AFLP methods revealed 8.7%, 15.8%, and 14.5% informative bands, respectively. This corresponded to polymorphism in 30% of RFLP probes, 32% of RAPD primers, and 100% of AFLP primer combinations. Less deviation from the 1:1 expected ratio was obtained with RFLP than with AFLP loci (8% and 18%, respectively). RAPD and AFLP markers were not randomly distributed over the genome. Most of them (60% and 80%, respectively) were grouped in clusters located around putative centromeric regions. This intraspecific map spans 965 cM with an average distance of 8.3 cM between markers (of the framework map). It was compared to other published interspecific maps of tomato. Despite the intraspecific origin of this map, it did not show any increase in length when compared to the high-density interspecific map of tomato. Key words: Lycopersicon esculentum, molecular linkage map, RFLP, AFLP, intraspecific cross.

Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon esculentum

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 619-630 ◽  
Author(s):  
Christie E. Williams ◽  
Dina A. St. Clair
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Lycopersicon Esculentum ◽  
Genetic Distance ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Polymorphic Loci ◽  
Restriction Fragment Length

Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to assess the variability in tomato germplasm (Lycopersicon esculentum Mill.), which included 46 accessions from the following groups: vintage cultivars, modern cultivars, South American regional cultivars, and wild L. esculentum van cerasiforme. Two L. cheesmanii accessions served as an outgroup. The 48 accessions were monomorphic at 135 of the 215 RAPDs loci and 31 of the 48 RFLP loci that were assayed. Alleles were identified that distinguished the five groups and many of the cultivars. The frequency of polymorphic loci was low in vintage cultivars, with less than 2.8% of the loci being variable within the group. In contrast, introgression of wild germplasm into modern cultivars has increased the polymorphic loci to 11.6%, whereas within the group of regional cultivars linkage drag and outcrossing may be responsible for the further increase to 20.3%. These levels of genetic variability were lower in comparison to the 24.5% polymorphic loci of cerasiforme, a group that may contain unutilized desirable traits. The small genetic distance from the vintage cultivars to several of the widely distributed regionals and cerasiformes indicated that proximity of vintage cultivars in Latin America may have resulted in intercrossing of these materials with the wilder germplasm. RAPDs appear promising for both germplasm fingerprinting and as a predictor of genetic diversity for plant breeding applications.Key words: tomato, restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), genetic distance.

scholarly journals A Genetic Linkage Map of the Model Legume Lotus japonicus and Strategies for Fast Mapping of New Loci

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1673-1683 ◽  
Author(s):  
Niels Sandal ◽  
Lene Krusell ◽  
Simona Radutoiu ◽  
Magdalena Olbryt ◽  
Andrea Pedrosa ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Lotus Japonicus ◽  
Aflp Markers ◽  
Linkage Groups ◽  
Model Legume ◽  
Group I

Abstract A genetic map for the model legume Lotus japonicus has been developed. The F2 mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa  et al. (2002, this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3.

Assessment of Genetic Diversity in 31 Species of Mangroves and their Associates through RAPD and AFLP Markers

2006 ◽  
Vol 61 (5-6) ◽  
pp. 413-420 ◽  
Author(s):  
Arup Kumar Mukherjee ◽  
Laxmikanta Acharya ◽  
Pratap Chandra Panda ◽  
Trilochan Mohapatra
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Aflp Markers ◽  
The Family ◽  
Associated Species ◽  
High Degree

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity in 31 species of mangroves and mangrove associates. Four AFLP primer combinations resulted in the amplification of 840 bands with an average of 210 bands per primer combination and 11 RAPD primers yielded 319 bands with an average of 29 bands per primer. The percentage of polymorphism detected was too high indicating the high degree of genetic variability in mangrove taxa both at inter- and intra-generic levels. In the dendrogram, species belonging to a particular family/ genus, taxa inhabiting similar habitats or having similar adaptations tended to be together. There were exceptions too; as many unrelated species of mangroves form clusters. The intrafamilial classification and inter-relationships of genera in the family Rhizophoraceae could be confirmed by molecular analysis. Both the markers RAPD and AFLP were found equally informative and useful for a better understanding of the genetic variability and genome relationships among mangroves and their associated species.

An Amplified Fragment Length Polymorphism Map of the Silkworm

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1277-1284 ◽  
Author(s):  
Yuan-De Tan ◽  
Chunling Wan ◽  
Yufang Zhu ◽  
Chen Lu ◽  
Zhonghuai Xiang ◽  
...  
Keyword(s):  
Linkage Group ◽  
Linkage Map ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Polymorphic Markers ◽  
Linkage Groups ◽  
Group 3

Abstract The silkworm (Bombyx mori L.) is a lepidopteran insect with a long history of significant agricultural value. We have constructed the first amplified fragment length polymorphism (AFLP) genetic linkage map of the silkworm B. mori at a LOD score of 2.5. The mapping AFLP markers were genotyped in 47 progeny from a backcross population of the cross no. 782 × od100. A total of 1248 (60.7%) polymorphic AFLP markers were detected with 35 PstI/TaqI primer combinations. Each of the primer combinations generated an average of 35.7 polymorphic AFLP markers. A total of 545 (44%) polymorphic markers are consistent with the expected segregation ratio of 1:1 at the significance level of P = 0.05. Of the 545 polymorphic markers, 356 were assigned to 30 linkage groups. The number of markers on linkage groups ranged from 4 to 36. There were 21 major linkage groups with 7-36 markers and 9 relatively small linkage groups with 4-6 markers. The 30 linkage groups varied in length from 37.4 to 691.0 cM. The total length of this AFLP linkage map was 6512 cM. Genetic distances between two neighboring markers on the same linkage group ranged from 0.2 to 47 cM with an average of 18.2 cM. The sex-linked gene od was located between the markers P1T3B40 and P3T3B27 at the end of group 3, indicating that AFLP linkage group 3 was the Z (sex) chromosome. This work provides an essential basic map for constructing a denser linkage map and for mapping genes underlying agronomically important traits in the silkworm B. mori L.

Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near-isogenic lines

Genome ◽  
1991 ◽  
Vol 34 (6) ◽  
pp. 1021-1027 ◽  
Author(s):  
Ilan Paran ◽  
Richard Kesseli ◽  
Richard Michelmore
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Rapd Markers ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Restriction Fragment Length

Near-isogenic lines were used to identify restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers linked to genes for resistance to downy mildew (Dm) in lettuce. Two pairs of near-isogenic lines that differed for Dm1 plus Dm3 and one pair of near-isogenic lines that differed for Dm11 were used as sources of DNA. Over 500 cDNAs and 212 arbitrary 10-mer oligonucleotide primers were screened for their ability to detect polymorphism between the near-isogenic lines. Four RFLP markers and four RAPD markers were identified as linked to the Dm1 and Dm3 region. Dm1 and Dm3 are members of a cluster of seven Dm genes. Marker CL922 was absolutely linked to Dm15 and Dm16, which are part of this cluster. Six RAPD markers were identified as linked to the Dm11 region. The use of RAPD markers allowed us to increase the density of markers in the two Dm regions in a short time. These regions were previously only sparsely populated with RFLP markers. The rapid screening and identification of tightly linked markers to the target genes demonstrated the potential of RAPD markers for saturating genetic maps.Key words: lettuce, downy mildew, near-isogenic lines, disease resistance, restriction fragment length polymorphism, random amplified polymorphic DNA.

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