Conversion of the random amplified polymorphic DNA (RAPD) marker UBC#116 linked to Fusarium crown and root rot resistance gene (Frl) into a co-dominant sequence characterized amplified region (SCAR) marker for marker-assisted selection of tomato

We have characterized strains of Fusarium oxysporum from common bean fields in Spain that were nonpathogenic on common bean, as well as F. oxysporum strains (F. oxysporum f. sp. phaseoli) pathogenic to common bean by random amplified polymorphic DNA (RAPD) analysis. We identified a RAPD marker (RAPD 4.12) specific for the highly virulent pathogenic strains of the seven races of F. oxysporum f. sp. phaseoli. Sequence analysis of RAPD 4.12 allowed the design of oligonucleotides that amplify a 609-bp sequence characterized amplified region (SCAR) marker (SCAR-B310A280). Under controlled environmental and greenhouse conditions, detection of the pathogen by polymerase chain reaction was 100% successful in root samples of infected but still symptomless plants and in stem samples of plants with disease severity of ≥4 in the Centro Internacional de Agricultura Tropical (CIAT; Cali, Colombia) scale. The diagnostic procedure can be completed in 5 h and allows the detection of all known races of the pathogen in plant samples at early stages of the disease with no visible symptoms.

Download Full-text

A Molecular Marker Correlated with Selected Virulence Against the Tomato Resistance Gene Mi in Meloidogyne incognita, M. javanica, and M. arenaria

Phytopathology ◽

10.1094/phyto.2001.91.4.377 ◽

2001 ◽

Vol 91 (4) ◽

pp. 377-382 ◽

Cited By ~ 11

Author(s):

Jianhua Xu ◽

Takashi Narabu ◽

Takayuki Mizukubo ◽

Tadaaki Hibi

Keyword(s):

Resistance Gene ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Nucleotide Polymorphisms ◽

Sequence Characterization ◽

Sequence Characterized Amplified Region ◽

Major Species ◽

Wide Range ◽

Meloidogyne Spp

Root-knot nematodes of the genus Meloidogyne are economically important pathogens of a wide range of crops. The tomato resistance gene Mi typically confers resistance to the three major species, M. incognita, M. javanica, and M. arenaria. However, virulent populations completely overcoming the Mi resistance still occur. In an attempt to develop molecular markers for virulence against Mi and gain insights into the genetic relationships among virulent populations of different species and origins, random amplified polymorphic DNA (RAPD) analyses of laboratory-selected virulent, field virulent, and avirulent populations of M. incognita, M. javanica, and M. arenaria were carried out. A RAPD marker, specific for selected virulent populations, was identified, and subsequently, converted to a sequence characterized amplified region (SCAR). Sequence characterization of the SCAR locus showed that alleles from laboratory- and field-selected virulent populations were highly similar to each other and clearly different from alleles from natural virulent and avirulent populations. This result suggests that the genetic mechanism for virulence against Mi may be similar among selected virulent populations of the three Meloidogyne spp., but different between selected and natural virulent populations. Based on the nucleotide polymorphisms at the SCAR locus, codominant and dominant polymerase chain reaction-based markers were developed enabling rapid diagnosis of selected virulent genotypes in M. incognita, M. javanica, and M. arenaria.

Download Full-text

GENETIC MARKER ASSISTED SELECTION FOR COMMON BUNT RESISTANCE (TILLETIA SP.) IN SOME WHEAT LINES

Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Agriculture ◽

10.15835/buasvmcn-agr:1348 ◽

1970 ◽

Vol 63 ◽

Author(s):

Laura Cristina Cota ◽

C. Botez ◽

Dana Bota ◽

Meda Lucaci

Keyword(s):

Marker Assisted Selection ◽

Random Amplified Polymorphic Dna ◽

Common Bunt ◽

Specific Primers ◽

Sequence Characterized Amplified Region ◽

Selection For ◽

Wheat Lines ◽

Dna Primers ◽

Selection Of ◽

Bunt Resistance

In view of the molecular marker assisted selection for common bunt resistance, wheat lines in segregation have been used, as well as stabilized dihaploid wheat lines – resulted from different hybrid combinations in which parental forms resistant to bunt were used. To identify the polymorphisms between the resistant and sensitive forms, a pair of specific primers for the common bunt resistant gene (Bt-10) were used, as well as a number of twenty non-specific RAPD (Random Amplified Polymorphic DNA) primers. The main objective was finding some polymorphic markers for common bunt resistance in view of the selection of these lines on the basis of the markers. Such a marker were obtained (1450 bp) with specific primers, a marker linked to Bt-10 gene, and with non-specific primers more polymorphic fragments were obtained, present in the resistant forms and absent in the sensitive forms, possibly linked to common bunt resistant genes. In perspective, it is stipulated the conversion of these RAPD molecular markers to SCAR (Sequence Characterized Amplified Region) specific markers.

Download Full-text

Generation and Molecular Mapping of a Sequence Characterized Amplified Region Marker Linked with the Bct Gene for Resistance to Beet curly top virus in Common Bean

Phytopathology ◽

10.1094/phyto.2004.94.4.320 ◽

2004 ◽

Vol 94 (4) ◽

pp. 320-325 ◽

Cited By ~ 31

Author(s):

Richard C. Larsen ◽

Phillip N. Miklas

Keyword(s):

Recombinant Inbred ◽

Marker Assisted Selection ◽

Molecular Mapping ◽

Random Amplified Polymorphic Dna ◽

Recombinant Inbred Lines ◽

Rapd Marker ◽

Dry Bean ◽

Sequence Characterized Amplified Region ◽

Beet Curly Top Virus ◽

Recombinant Inbred Population

A random amplified polymorphic DNA (RAPD) marker directly linked (0.0 cM) with a resistance gene was identified in a snap bean recombinant inbred population (Moncayo × Primo) consisting of 94 F5:7 recombinant inbred lines that had uniform segregation for disease reaction to Beet curly top virus (BCTV) across three field locations. Resistance was conditioned by a single dominant allele tentatively designated Bct. Seven hundred and fifty decamer primers were screened to obtain the linked RAPD marker that was then converted to a sequence characterized amplified region (SCAR) marker SAS8.1550. The SCAR mapped within a cluster of resistance genes on linkage group B7 of the core map. A survey of 103 BCTV-resistant and -susceptible snap and dry bean genotypes was conducted using SAS8.1550. Results showed that the SCAR would be highly useful for marker-assisted selection of Bct in snap and dry bean originating from the Andean gene pool. Marker-assisted selection for Bct will expedite the development of BCTV-resistant cultivars and minimize the need for cumbersome pathogen tests.

Download Full-text

Application of Marker-assisted Selection in Persimmon Breeding of PCNA Offspring Using SCAR Markers among the Population from the Cross between Non-PCNA ‘Taigetsu’ and PCNA ‘Kanshu’

HortScience ◽

10.21273/hortsci.49.9.1132 ◽

2014 ◽

Vol 49 (9) ◽

pp. 1132-1135 ◽

Cited By ~ 9

Author(s):

Nobuhito Mitani ◽

Atsushi Kono ◽

Masahiko Yamada ◽

Akihiko Sato ◽

Shozo Kobayashi ◽

...

Keyword(s):

Marker Assisted Selection ◽

Scar Marker ◽

Segregation Ratio ◽

Complete Agreement ◽

Diospyros Kaki ◽

Marker Genotype ◽

Selection System ◽

Sequence Characterized Amplified Region ◽

The Cross ◽

Selection Of

Persimmon (Diospyros kaki Thunb) is hexaploid, and the pollination-constant, non-astringent (PCNA)/non-PCNA trait of Japanese origin is qualitatively controlled by the AST/ast alleles at a single locus and the PCNA trait is recessive to the non-PCNA trait. To avoid inbreeding depression led by repeated crosses among PCNA genotypes, non-PCNA genotypes should be used as cross parents. The marker-assisted selection system has been developed for the selection of PCNA offspring in the progeny derived from the cross of non-PCNA ‘Taigetsu’ (non-PCNA ‘Kurokuma’ × PCNA ‘Taishu’) to PCNA ‘Kanshu’. The primer pairs E8.5/E9r and 7H9F/AST-R were used for detecting the molecular markers A1 and A3, respectively, which link AST alleles. Complete agreement was found between the sequence-characterized amplified region (SCAR) marker genotype and fruit astringency phenotype of the 48 offspring. The result confirmed that the marker-assisted selection using those markers was highly practical. In a larger offspring population (522 offspring) from the same cross, offspring segregated into 100 with both markers, 162 with only A1, 179 with A3, and 81 with neither, and this segregation ratio was significantly different from 2:3:3:2, which is the segregation ratio of random chromosome assortment in autohexaploid. The percentage of offspring expected to be PCNA was 15.5% (81 of 522), which was slightly lower than 20%.

Download Full-text

Development and validation of molecular markers linked to an Aegilops umbellulata–derived leaf-rust-resistance gene, Lr9, for marker-assisted selection in bread wheat

Genome ◽

10.1139/g05-051 ◽

2005 ◽

Vol 48 (5) ◽

pp. 823-830 ◽

Cited By ~ 30

Author(s):

Sudhir Kumar Gupta ◽

Ashwini Charpe ◽

Sunita Koul ◽

Kumble Vinod Prabhu ◽

Qazi Mohd. Rizwanul Haq

Keyword(s):

Leaf Rust ◽

Resistance Gene ◽

Rust Resistance ◽

Scar Marker ◽

Rapd Marker ◽

Gene Pyramiding ◽

Leaf Rust Resistance ◽

Rust Resistance Gene ◽

Leaf Rust Resistance Gene ◽

Aegilops Umbellulata

An Aegilops umbellulata–derived leaf-rust-resistance gene, Lr9, was tagged with 3 random amplified polymorphic DNA (RAPD) markers, which mapped within 1.8 cM of gene Lr9 located on chromosome 6BL of wheat. The markers were identified in an F2 population segregating for leaf-rust resistance, which was generated from a cross between 2 near-isogenic lines that differed in the alien gene Lr9 in a widely adopted agronomic background of cultivar 'HD 2329'. Disease phenotyping was done in controlled environmental conditions by inoculating the population with the most virulent pathotype, 121 R63-1 of Puccinia triticina. One RAPD marker, S5550, located at a distance of 0.8 ± 0.008 cM from the Lr9 locus, was converted to sequence-characterized amplified region (SCAR) marker SCS5550. The SCAR marker was validated for its specificity to gene Lr9 against 44 of the 50 known Lr genes and 10 wheat cultivars possessing the gene Lr9. Marker SCS5550 was used with another SCAR marker, SCS73719, previously identified as being linked to gene Lr24 on a segregating F2 population to select for genes Lr9 and Lr24, respectively, demonstrating the utility of the 2 markers in marker-assisted gene pyramiding for leaf-rust resistance in wheat.Key words: wheat, leaf rust resistance, Lr9, Lr24, RAPD, SCAR.

Download Full-text

Analysis of strawberry genetic collection (Fragaria L.) for Rca2 and Rpfl genes with molecular markers

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj18.423 ◽

2018 ◽

Vol 22 (7) ◽

pp. 795-799 ◽

Cited By ~ 5

Author(s):

I. V. Luk’yanchuk ◽

A. S. Lyzhin ◽

I. I. Kozlova

Keyword(s):

Molecular Markers ◽

Genetic Distance ◽

Resistance Gene ◽

Wild Species ◽

Root Rot ◽

Scar Marker ◽

Fragaria X Ananassa ◽

Anthracnose Resistance ◽

Monogenic Resistance ◽

Red Stele

Strawberry (Fragaria x ananassa Duch.) varieties are susceptible to many fungal diseases. Identification of forms, carrying resistance genes, is an important stage in breeding programs leading to resistant varieties. The use of molecular markers allows to determine with high reliability the presence of the necessary genes in the genome and to identify promising forms. Some of the common strawberry's diseases, causing significant damage to strawberry plantations, are anthracnose (Colletotrichum acutatum Simmonds) and red stele root rot (Phytophthora fragariae var. fragariae Hickman). Dominant Rca2 gene is involved in monogenic resistance to C. acutatum pathogenicity group 2. Rpf1, Rpf2, Rpf3 genes are determined in monogenic resistance to red stele root rot. The purpose of this study was molecular genetic testing genotypes of genus Fragaria L. to identify carriers of Rca2 allele anthracnose resistance and Rpf1 allele red stele root rot resistance. The objects of study were the wild species of the genus Fragaria L. and strawberry varieties (Fragaria x ananassa Duch.) of different ecological and geographic origin. To assess allelic state Rca2 anthracnose resistance gene the dominant SCAR marker STS-Rca2_240 was used, was linked to the resistance gene Rca2 with a genetic distance of 2.8 cM. Rpf1 gene red stele root rot resistance was identified with the dominant SCAR marker R1A, was linked to the resistance gene Rpf1 with a genetic distance of 3.0 cM. The resistant allele of the marker STS-Rca2_240 was identified in the Laetitia variety (Rca2Rca2 or Rca2rca2 genotype), which allows us to recommend it as a promising source in breeding for anthracnose resistance. The other studied forms have homozygous recessive state of the marker STS-Rca2_240 (putative genotype rca2rca2). The resistant allele of the marker SCAR-R1A in the varieties and wild species of strawberry under study is absent, which presumably indicates their homozygous recessive genotype of Rpf1 gene (rpf1rpf1).

Download Full-text

Development of Scar Markers Tightly Linked to the CTV Resistance Gene in Poncirus trifoliata

HortScience ◽

10.21273/hortsci.30.4.783f ◽

1995 ◽

Vol 30 (4) ◽

pp. 783F-783

Author(s):

Zhan'ao Deng ◽

Fred G. Gmitter ◽

Shunyuan Xiao ◽

Shu Huang

Keyword(s):

Resistance Gene ◽

Marker Assisted Selection ◽

Rapd Markers ◽

Bac Library ◽

Poncirus Trifoliata ◽

Rapid Decline ◽

Viral Pathogen ◽

Sequence Characterized Amplified Region ◽

Stem Pitting ◽

Ctv Resistance

Citrus tristiza virus (CTV) is the most-significant viral pathogen of citrus in the world. Rapid decline of trees on sour orange and stem pitting of grapefruit and sweet orange, two diseases induced by CTV, severely jeopardize citrus production worldwide. It is recognized that all future rootstocks should be resistant to this virus, and scion resistance to stem pitting stains is desirable. To facilitate introgression of the CTV resistance gene from Poncirus trifoliata and development of CTV-resistant varieties in citrus, gene mapping projects have been initiated and more than a dozen RAPD markers have been identified with tight linkage to the resistance gene. As part of our efforts to use marker-assisted selection with a large number of crosses, and ultimately to accomplish map-based cloning of the CTV resistance gene, we have been converting the most tightly linked RAPD markers into SCAR (sequence characterized amplified region) markers by cloning, sequencing the marker fragments, and designing locus-specific primers. One codominant and several dominant SCARs have been developed thus far. The updated progress and utilization of these SCARs in marker-assisted selection and possibly in characterization of a BAC library will be presented and discussed.

Download Full-text

Identification of the B, Q, and native Brazilian biotypes of the Bemisia tabaci species complex using Scar markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2016000500016 ◽

2016 ◽

Vol 51 (5) ◽

pp. 555-562 ◽

Cited By ~ 3

Author(s):

Paulo Roberto Queiroz ◽

Erica Soares Martins ◽

Nazaré Klautau ◽

Luzia Lima ◽

Lilian Praça ◽

...

Keyword(s):

Bemisia Tabaci ◽

Species Complex ◽

Scar Marker ◽

Random Amplified Polymorphic Dna ◽

Scar Markers ◽

Sequence Characterized Amplified Region ◽

Field Samples ◽

Scar Primer ◽

Q Biotype ◽

B Biotype

Abstract: The objective of this work was to develop sequence-characterized amplified region (Scar) markers to identify the B, Q, and native Brazilian biotypes of the sweet potato whitefly [Bemisia tabaci (Hemiptera: Aleyrodidae)]. Random amplified polymorphic DNA (RAPD) amplification products, exclusive to the B and Brazilian biotypes, were selected after the analysis of 12,000 samples, in order to design a specific Scar primer set. The BT-B1 and BT-B3 Scar markers, used to detect the B biotype, produced PCR fragments of 850 and 582 bp, respectively. The BT-BR1 Scar marker, used to identify the Brazilian biotype, produced a PCR fragment of 700 bp. The Scar markers were tested against the Q biotype, and a flowchart was proposed to indicate the decision steps to use these primers, in order to correctly discriminate the biotypes. This procedure allowed to identify the biotypes that occur in field samples, such as the B biotype. The used set of primers allowed to discriminate the B, Q, and native Brazilian biotypes of B. tabaci. These primers can be successfully used to identify the B biotype of B. tabaci from field samples, showing only one specific biotype present in all cultures.

Download Full-text