scholarly journals (260) Development of SCAR and CAPS Markers Linked to Tomato Begomovirus Resistance Genes Introgressed from Lycopersicon chilense

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1090A-1090 ◽  
Author(s):  
Yuanfu Ji ◽  
John W. Scott
Keyword(s):  
Resistance Genes ◽  
Rapd Markers ◽  
Fragment Length Polymorphism ◽  
Rflp Markers ◽  
Randomly Amplified Polymorphic Dna ◽  
Breeding Lines ◽  
Sequence Characterized Amplified Region ◽  
Lycopersicon Chilense ◽  
Caps Markers ◽  
Leaf Curl Virus

Resistance to begomoviruses tomato mottle virus (ToMoV) and tomato yellow leaf curl virus (TYLCV) has been introgressed to tomato (Lycopersicon esculentum) from L. chilense accessions LA 1932, LA 2779, and LA 1938. Resistance genes have been mapped to three regions on chromosome 6 using randomly amplified polymorphic DNA (RAPD) markers. We call these regions 1, 2, and 3. To facilitate breeding by marker assisted selection, advanced breeding lines with resistance from the above sources were assayed for the presence of RAPD markers to determine which were most tightly linked to begomovirus resistance. The best RAPD markers were then converted to sequence characterized amplified region (SCAR) markers or cleaved amplified polymorphic sequence (CAPS) markers. In addition, selected restriction fragment length polymorphism (RFLP) markers near the three regions were converted into CAPS markers, which were tested for association with the advanced breeding lines. Only LA 2779 derivatives have the L. chilense introgression in region 1, which is near the location of the Ty-1 gene and spans across CAPS markers 32.5Cla and TG118. Two region 1 RAPD markers UBC197 and UBC621 were converted co-dominant SCAR or CAPS markers, which were present in all 16 resistant breeding lines tested. Derivatives from all three accessions have introgressions in region 2. Further assays with more markers in this region are under way to determine the lengths and locations of the introgressions. No tightly linked RAPD markers have been found for the resistance gene from LA 1932 in region 3. RFLP and CAPS markers are being used to more precisely locate the region 3 gene.

Identification of Molecular Markers Linked to Tomato Mottle Virus Resistance Genes

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 515b-515
Author(s):  
P.D. Griffiths ◽  
J.W. Scott
Keyword(s):  
Resistance Genes ◽  
Rapd Markers ◽  
Mottle Virus ◽  
Fresh Market ◽  
Arbitrary Primers ◽  
Breeding Lines ◽  
Lycopersicon Chilense ◽  
Good Repeatability ◽  
Tomato Breeding ◽  
Β Carotene

Tomato mottle virus (ToMoV) is a whitefly transmitted geminivirus threatening the Florida fresh-market tomato (Lycopersicon esculentum Mill.) industry. ToMoV resistance was identified in Lycopersicon chilense accessions LA 1932, LA 1938, LA 1969, and LA 2779, and introgressed into tomato breeding lines. Inheritance studies of populations derived from resistant accessions of LA 1932 and LA 1938 suggest that introgressed resistance is largely additive and multigenic. RAPD polymorphisms were identified using 800 arbitrary primers (decamers), and 88 polymorphisms with good repeatability were identified. Of these, 45 polymorphisms were identified in breeding lines derived from two or more of the four accessions. Analysis of segregating F2 populations has resulted in association of RAPD markers with geminivirus resistance genes, and markers have been identified that are common to different L. chilense resistance sources. Linkage of several markers to each other and to the self pruning (sp) and β-carotene (B) loci on chromosome 6 was also determined.

scholarly journals Isozyme, Randomly Amplified Polymorphic DNA (RAPD), and Restriction Fragment-length Polymorphism (RFLP) Markers Used to Deduce a Putative Parent for the `Braeburn' Apple

1996 ◽  
Vol 121 (6) ◽  
pp. 996-1001 ◽  
Author(s):  
S.E. Gardiner ◽  
H.C.M. Bassett ◽  
C. Madie ◽  
D.A.M. Noiton
Keyword(s):  
New Zealand ◽  
Fragment Length Polymorphism ◽  
Rapd Analysis ◽  
Rflp Analysis ◽  
Rare Allele ◽  
Genetic Distances ◽  
Rflp Markers ◽  
High Likelihood ◽  
Randomly Amplified Polymorphic Dna ◽  
Restriction Fragment Length

Information about a rare allele of phosphoglucomutase (PGM) that is shared by `Braeburn' and 16% of cultivars in the New Zealand Cultivar Collection was combined with historical information about cultivar distribution to select a set of 15 cultivars for a more detailed genetic analysis of their relatedness to the key New Zealand apple (Malus domestica Borkh.) `Braeburn'. DNA from all 16 cultivars was examined by RFLP analysis using 41 probe-enzyme combinations and also by RAPD analysis with 39 selected primers. The RFLP and RAPD data excluded a proposal that `Lady Hamilton' and `Braeburn' are genetically identical. All cultivars except `Lady Hamilton' were excluded as potential parents for `Braeburn' based on incompatible RFLP banding. Assessment of genetic distances between `Braeburn' and the other 15 cultivars from RFLP and RAPD data demonstrated that `Lady Hamilton' was more closely related to `Braeburn' than all others. We conclude that there is a high likelihood that `Lady Hamilton' is one of the parents of `Braeburn'.

scholarly journals Randomly Amplified Polymorphic DNA Loci from a Walnut Backcross [(Juglans hindsii × J. regia) × J. regia]

1996 ◽  
Vol 121 (3) ◽  
pp. 358-361 ◽  
Author(s):  
Keith Woeste ◽  
Gale H. McGranahan ◽  
Robert Bernatzky
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Rapd Markers ◽  
Fragment Length Polymorphism ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Backcross Population ◽  
Persian Walnut ◽  
Marker Data ◽  
Juglans Hindsii ◽  
Restriction Fragment Length

Twenty-five random decamer primers were used to evaluate the level of polymorphism between Persian walnut and the Northern California black walnut. Sixty-six randomly amplified polymorphic DNA (RAPD) markers were identified using an interspecific walnut backcross population [(Juglans hindsii × J. regia) × J. regia]. Segregation data from these polymorphisms were joined to a previously published set of restriction fragment-length polymorphism (RFLP) marker data to expand the genetic map of walnut to 107 markers in 15 linkage groups.

scholarly journals Marker-Assisted Pyramiding of Multiple Disease Resistance Genes in Coffee Genotypes (Coffea arabica)

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1763
Author(s):  
Dênia Pires de Almeida ◽  
Eveline Teixeira Caixeta ◽  
Karoliny Ferreira Moreira ◽  
Antonio Carlos Baião de Oliveira ◽  
Kátia Nogueira Pestana de Freitas ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Resistance Genes ◽  
Fragment Length Polymorphism ◽  
Caps Marker ◽  
Coffee Berry ◽  
Hemileia Vastatrix ◽  
Sequence Characterized Amplified Region ◽  
F2 Population ◽  
Coffee Leaf Rust ◽  
Multiple Disease Resistance

The use of resistant cultivars is the most effective strategy for controlling coffee leaf rust caused by the fungus Hemileia vastatrix. To assist the development of such cultivars, amplified fragment-length polymorphism (AFLP) markers linked to two loci of coffee resistance to races I and II as well as pathotype 001 of H. vastatrix were converted to sequence-characterized amplified region (SCAR) and cleaved amplified polymorphic site (CAPS) markers. In total, 2 SCAR markers and 1 CAPS marker were validated in resistant and susceptible parents as well as in 247 individuals from the F2 population. The efficiency of these markers for marker-assisted selection (MAS) was evaluated in F2:3 and backcross (BCrs2) populations genotyped with the developed markers and phenotyped with race II of H. vastatrix. The markers showed 90% efficiency in MAS. Therefore, the developed markers, together with molecular markers associated with other rust resistance genes, were used for F3:4 and BCrs3 coffee selection. The selected plants were analyzed using two markers associated with coffee berry disease (CBD) resistance, aiming for preventive breeding. MAS of F3:4 and BCrs3 individuals with all resistance loci was feasible. Our phenotypic and genotypic approaches are useful for the development of coffee genotypes with multiple genes conferring resistance to coffee leaf rust and CBD.

scholarly journals Molecular Characterization of Three Comercial Cultivars and a New Pollinator in Kiwifruit

HortScience ◽  
2006 ◽  
Vol 41 (1) ◽  
pp. 90-95 ◽  
Author(s):  
M.J. Prado ◽  
S. Romo ◽  
M. Novo ◽  
M. Rey ◽  
M.T. Herrera ◽  
...  
Keyword(s):  
Plant Material ◽  
Rapd Markers ◽  
Fragment Length Polymorphism ◽  
Molecular Techniques ◽  
Aflp Markers ◽  
Randomly Amplified Polymorphic Dna ◽  
Banding Patterns ◽  
Specific Protocol ◽  
Technical Features

We investigated the characterization of genotypes of Actinidia deliciosa (Chev.) Liang and Ferguson var. deliciosa by using isozymatic and molecular techniques [randomly amplified polymorphic DNA (RAPD), amplified fragment-length polymorphism (AFLP), standard AFLP, and modified AFLP]. Four genotypes were tested, the female cultivar `Hayward', the traditional New Zealand pollinizers `Matua' and `Tomuri', and a new pollinizer named clone A selected in a breeding program in Spain. PGI and PGM were the only isozymes that allowed us to distinguish the kiwifruit genotypes, although the accessions of `Matua' presented two different banding patterns for both isozymes. All three molecular markers differentiated between the genotypes of kiwifruit tested, although RAPD markers did not allow us to establish differences between accessions of `Matua', while both standard and modified AFLP did. These results, along with those of isozymes, support the hypothesis that the male kiwifruit genotypes present in Europe belong to different clones. None of the markers used showed differences between accessions of `Hayward', which would suggest that it is a uniform cultivar. On the other hand, clone A was a seedling derived from `Hayward' and an unknown pollinizer. The results obtained using AFLP markers strongly suggest that `Tomuri' may have been the male parent of clone A. A specific protocol for kiwifruit characterization based on a modified AFLP technique is also presented, that gave rise to the highest percentage of polymorphism while scoring the lowest number of bands. This, together with the technical features of modified AFLP markers, make them very useful for identifying propagated kiwifruit plant material in commercial nurseries.

scholarly journals Development of Sequence-characterized Amplified Region Markers for the Identification of Grapevine Cultivars

HortScience ◽  
2015 ◽  
Vol 50 (12) ◽  
pp. 1744-1750
Author(s):  
Kang Hee Cho ◽  
Jung Ho Noh ◽  
Seo Jun Park ◽  
Se Hee Kim ◽  
Dae-Hyun Kim ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Morphological Characteristics ◽  
Polymorphic Band ◽  
Group Method ◽  
Scar Markers ◽  
Randomly Amplified Polymorphic Dna ◽  
Genetic Fingerprinting ◽  
Sequence Characterized Amplified Region ◽  
Pair Group ◽  
Average Similarity

Grapevine cultivars have traditionally been identified based on the morphological characteristics, but the identification of closely related cultivars has been difficult because of their similar pedigree backgrounds. In this study, we developed DNA markers for genetic fingerprinting in 37 grapevine cultivars, including 20 cultivars bred in Korea. A total of 180 randomly amplified polymorphic DNA (RAPD) markers were obtained using 30 different primers. The number of polymorphic bands ranged from three (OPG-08 and OPU-19) to nine (OPV-01 and UBC116), with an average of six. RAPD markers were used in cluster analysis performed with the unweighted pair-group method of arithmetic averages (UPGMA). The average similarity value was 0.69 and the dendrogram clustered the 37 grapevine cultivars into five clusters. The relationships among the grapevine cultivars were consistent with the known pedigrees of the cultivars. The 50 RAPD fragments selected were sequenced for the development of sequence-characterized amplified region (SCAR) markers. As a result, 16 of 50 fragments were successfully converted into SCAR markers. A single polymorphic band, the same size as the RAPD fragments or smaller, was amplified depending on the primer combinations in the 14 SCAR markers, and codominant polymorphisms were detected using the SCAR markers G119_412 and GB17_732. Among these markers, combination of 11 SCAR markers, GG05_281, G116_319, G146_365, G119_412, GW04_463, G169_515, G116_539, GV04_618, GV01_678, GG05_689, and GB17_732, provided sufficient polymorphisms to distinguish the grapevine cultivars investigated in this study. These newly developed markers could be a fast and reliable tool for identifying grapevine cultivars.

Genetic mapping of Russian wheat aphid resistance genes Dn2 and Dn4 in wheat

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 303-306 ◽  
Author(s):  
Z -Q Ma ◽  
A Saidi ◽  
J S Quick ◽  
NLV Lapitan
Keyword(s):  
Triticum Aestivum ◽  
Restriction Fragment Length Polymorphism ◽  
Resistance Genes ◽  
Fragment Length Polymorphism ◽  
Triticum Aestivum L ◽  
Russian Wheat Aphid ◽  
Aphid Resistance ◽  
Rflp Markers ◽  
Marker Assisted Breeding ◽  
Restriction Fragment Length

To obtain markers for marker-assisted breeding of Russian wheat aphid resistance in wheat (Triticum aestivum L.), resistance genes Dn2 and Dn4 were mapped with restriction fragment length polymorphism (RFLP) markers, using populations derived from PI 62660 x 'Carson' and PI 372129 x 'Yuma'. PI 262660 and PI 372129 are the donor parents of Dn2 and Dn4, respectively. A locus detected by marker KsuA1 was linked to Dn2 at a distance of 9.8 cM on the long arm of chromosome 7D, and a locus detected by marker ABC156 was 11.6 cM away from Dn4 on the short arm of chromosome 1D.Key words: Russian wheat aphid, RFLP markers, Triticum aestivum.

scholarly journals Molecular Mapping of the Leaf Rust Resistance Gene Rph6 in Barley and Its Linkage Relationships with Rph5 and Rph7

2003 ◽  
Vol 93 (5) ◽  
pp. 604-609 ◽  
Author(s):  
Shaobin Zhong ◽  
Roger J. Effertz ◽  
Yue Jin ◽  
Jerome D. Franckowiak ◽  
Brian J. Steffenson
Keyword(s):  
Leaf Rust ◽  
Resistance Genes ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Rust Resistance ◽  
Fragment Length Polymorphism ◽  
Leaf Rust Resistance ◽  
Rflp Marker ◽  
Rflp Markers ◽  
Progeny Testing

The barley cv. Bolivia carries two leaf rust (Puccinia hordei) resistance genes, Rph2 and Rph6, and is the only known source of the latter gene. A resistant line (Bolivia-Rph6) carrying Rph6 only was obtained in the F4 generation of a cross between cv. Bolivia and the susceptible cv. Bowman via progeny testing with differential isolates of the leaf rust pathogen. Genetic analyses and bulk segregant analysis using amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers localized Rph6 on the short arm of barley chromosome 3H at a distance of 4.4 centimorgans (cM) distal from RFLP marker MWG2021 and 1.2 cM proximal from RFLP marker BCD907. The allelic relationship of Rph6 to other leaf rust resistance genes mapping to this region of chromosome 3H (namely Rph5 and Rph7) were tested using crosses among cvs. Magnif 102 (carrying Rph5), Bolivia-Rph6 (Rph6), and Cebada Capa (Rph7). Segregation analyses indicated that Rph6 is allelic to Rph5 and closely linked to Rph7. The data generated from this study will facilitate breeding for leaf rust resistance via marker-assisted selection and provide a starting point for positional gene cloning.

scholarly journals Quantitative Trait Loci for Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Resistance in Tomato

2006 ◽  
Vol 131 (2) ◽  
pp. 267-272 ◽  
Author(s):  
H.A. Agrama ◽  
J.W. Scott
Keyword(s):  
Quantitative Trait Loci ◽  
Resistance Genes ◽  
Quantitative Trait ◽  
Rapd Markers ◽  
Tomato Yellow Leaf ◽  
Mottle Virus ◽  
Chromosome 6 ◽  
Yellow Leaf ◽  
Leaf Curl Virus ◽  
Leaf Curl

The genetic basis of resistance to tomato yellow leaf curl virus (TYLCV) and tomato mottle virus (ToMoV) was studied in three different mapping populations of tomato (Lycopersicon esculentum Mill.). Bulked segregant analysis (BSA) was used to identify random amplification of polymorphic DNA (RAPD) markers linked to TYLCV and ToMoV resistance. Segregated RAPD markers associated with resistance were linked to morphological markers self-pruning (sp) and potato leaf (c) on chromosome 6. RAPD genetic linkage maps of chromosome 6 were constructed for each of the three populations. Common mapped markers revealed straightforward homologies between the chromosome 6 linkage group of the three populations. Multiple-QTL mapping (MQM) was used to identify quantitative trait loci (QTL) for resistance linked to chromosome 6. These revealed that the resistance against TYLCV and ToMoV was mainly explained by two QTL in two populations and one QTL in another. For all of the resistance QTL detected, the favorable allele was provided by the resistant parents. The presence of three different sources of TYLCV and ToMoV resistance, and the markers in tight linkage with them, provide a means of systemically combining multiple resistance genes. Successful cloning of the R gene from tomatoes would lead to deeper understanding of the molecular basis of resistance to TYLCV and ToMoV, and might also shed light on the evolution of resistance genes in plants in general.

scholarly journals RFLP-based Analysis of Recombination among Resistance Genes to Fusarium Wilt Races 1, 2, and 3 in Tomato

2004 ◽  
Vol 129 (3) ◽  
pp. 394-400 ◽  
Author(s):  
J.W. Scott ◽  
H.A. Agrama ◽  
J.P. Jones
Keyword(s):  
Fusarium Wilt ◽  
Resistance Genes ◽  
Fragment Length Polymorphism ◽  
Dominant Gene ◽  
Chromosome 7 ◽  
Rflp Markers ◽  
Chromosome 11 ◽  
Race 1 ◽  
Race 2 ◽  
Restriction Fragment Length

Tomato (Lycopersicon esculentum) line E427 has resistance genes to all three races of Fusarium oxysporum f.sp. lycopersici derived from L. pennellii accession LA 716 and L. pimpinellifolium accession PI 126915. To determine genes that confer resistance to specific races of fusarium wilt, line E427 was crossed to susceptible `Bonny Best' and then F2 and backcross (to `Bonny Best') seed were obtained. Self-pollinations resulted in 337 lines and progeny of each line was inoculated separately with fusarium wilt races 1, 2, or 3. Plants from lines whose segregation suggested recombination of resistance were self-pollinated and reinoculated until disease reactions were homozygous. Four lines were obtained with resistance to both races 2 and 3, but susceptible to race 1. These lines had the L. pennellii alleles at restriction fragment length polymorphism (RFLP) markers linked to I-3 on chromosome 7 and lacked L. pimpinellifolium alleles linked to I and I-2 on chromosome 11. Complementation (F2) data indicated race 2 resistance on chromosome 7 was controlled by a single dominant gene. Three lines were resistant to race 2, but susceptible to races 1 and 3. These lines had L. pimpinellifolium alleles at TG105 and flanking markers encompassing a 14.4 cM region indicating the presence of I-2, and no L. pennellii alleles at markers linked to I-3. Three lines were resistant to race 1, but susceptible to races 2 and 3. All three lines had L. pimpinellifolium alleles at TG523 confirming linkage to I on chromosome 11 and no L. pennellii alleles at markers tightly linked to I-3. However, one of the lines, 415, had L. pennellii alleles at CT113 on chromosome 7. This data along with F2 complementation data suggests the possible existence of a second race 1 resistant locus, I1, in this region. The four lines resistant to both races 2 and 3 were backcrossed again to `Bonny Best' and self-pollinated progeny from 174 plants were screened as described above. Two lines derived from different BC1S1 lines that were fusarium wilt race 3 resistant and susceptible to race 1 had intermediate resistance to race 2. These two lines did not have the L. pennellii alleles at TG183, TG174, and CT43 near the I-3 locus indicating crossovers in this region resulted in reduced race 2 resistance. Collectively, this is the first clear break in the fusarium wilt race 2 and race 1 resistance linkage on chromosome 11. It appears that the race 1 resistance derived from PI 126915 is controlled by the I gene. On chromosome 7, there was a break between the I-3 and I1 genes indicating I-3 does not confer race 1 resistance. The crossovers resulting in reduced resistance to race 2 could be within a complex I-3 locus or a tightly linked race 2 locus.

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