Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper

2005 ◽  
Vol 110 (4) ◽  
pp. 605-612 ◽  
Author(s):  
E. A. Quirin ◽  
E. A. Ogundiwin ◽  
J. P. Prince ◽  
M. Mazourek ◽  
M. O. Briggs ◽  
...  
Keyword(s):  
Phytophthora Capsici ◽  
Sequence Characterized Amplified Region ◽  
Scar Primers ◽  
Major Qtl

scholarly journals Development of Clustered Resistance Gene Analogs-Based Markers of Resistance toPhytophthora capsiciin Chili Pepper

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Nayoung Kim ◽  
Won-Hee Kang ◽  
Jundae Lee ◽  
Seon-In Yeom
Keyword(s):  
Molecular Markers ◽  
Resistance Gene ◽  
Phytophthora Capsici ◽  
Resistance Gene Analogs ◽  
Chromosome 5 ◽  
Germplasm Screening ◽  
Melting Analysis ◽  
Leucine Rich Repeats ◽  
Protein Sequence Comparison ◽  
Major Qtl

The soil-borne pathogenPhytophthora capsicicauses severe destruction ofCapsicumspp. Resistance inCapsicumagainstP. capsiciis controlled by numerous minor quantitative trait loci (QTLs) and a consistent major QTL on chromosome 5. Molecular markers onCapsicumchromosome 5 have been developed to identify the predominant genetic contributor to resistance but have achieved little success. In this study, previously reported molecular markers were used to reanalyze the major QTL region on chromosome 5 (6.2 Mbp to 139.2 Mbp). Candidate resistance gene analogs (RGAs) were identified in the extended major QTL region including 14 nucleotide binding site leucine-rich repeats, 3 receptor-like kinases, and 1 receptor-like protein. Sequence comparison of the candidate RGAs was performed between twoCapsicumgermplasms that are resistant and susceptible, respectively, toP. capsici.11 novel RGA-based markers were developed through high-resolution melting analysis which were closely linked to the major QTL forP. capsiciresistance. Among the markers, CaNB-5480 showed the highest cosegregation rate at 86.9% and can be applied to genotyping of the germplasms that were not amenable by previous markers. With combination of three markers such as CaNB-5480, CaRP-5130 and CaNB-5330 increased genotyping accuracy for 61Capsicumaccessions. These could be useful to facilitate high-throughput germplasm screening and further characterize resistance genes againstP. capsiciin pepper.

SCAR molecular markers of the B biotype and two non-B populations of the whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae)

2006 ◽  
Vol 3 (3) ◽  
pp. 189-194 ◽  
Author(s):  
Zang Lian-Sheng ◽  
Jiang Tong ◽  
Xu Jing ◽  
Liu Shu-Sheng ◽  
Zhang You-Jun
Keyword(s):  
Bemisia Tabaci ◽  
Random Amplified Polymorphic Dna ◽  
Trialeurodes Vaporariorum ◽  
Chain Reaction ◽  
Specific Sequence ◽  
Sequence Characterized Amplified Region ◽  
Scar Primer ◽  
Polymerase Chain ◽  
Scar Primers ◽  
B Biotype

AbstractRandom amplified polymorphic DNA (RAPD) analyses were performed with random primer H16 for the B biotype and two non-B populations of Bemisia tabaci collected from Zhejiang (China). The specific sequence fragments containing 446, 390 and 1317 nucleotides were amplified for the B biotype, ZHJ-1, ZHJ-2 populations, respectively. The three specific fragments were cloned and sequenced, and three pairs of SCAR primers were designed according to the sequences determined. With improvement of the conditions of the polymerase chain reaction (PCR), the specific fragments of B biotype, ZHJ-1 and ZHJ-2 populations, namely 439, 366 and 1238 nucleotides, respectively, were amplified with the sequence characterized amplified region (SCAR) primer of the corresponding population, while specific fragments of the other populations of B. tabaci or Trialeurodes vaporariorum could not be amplified.

scholarly journals Resistance of Capsicum annuum genotypes against various isolates of Phytophthora capsici from Java, Indonesia

2019 ◽  
Vol 20 (12) ◽  
Author(s):  
Wartono Tono ◽  
SURYO WIYONO ◽  
MUHAMAD SYUKUR ◽  
GIYANTO ◽  
PUJI LESTARI
Keyword(s):  
Salicylic Acid ◽  
Capsicum Annuum ◽  
Partial Resistance ◽  
Plant Disease ◽  
Scar Marker ◽  
Phytophthora Capsici ◽  
Chilli Pepper ◽  
Growing Medium ◽  
Different Levels ◽  
Scar Primers

Abstract. Wartono, Wiyono S, Syukur M, Giyanto, Lestari P. 2019. Resistance of Capsicum annuum genotypes against various isolates of Phytophthora capsici from Java, Indonesia. Biodiversitas 20: 3723-3730. Phytophthora capsici Leonian is one of the pathogenic oomycetes that can reduce chilli production worldwide. In this study, Indonesian local chilli genotypes were evaluated for their resistance to P.capsici on chilli in Java, under controlled conditions. P. capsici used in this study consisted of four isolates derived from chilli plants in Java Island. The chilli genotypes tested were 38 local chilli (Capsicum annuum L.) originated from Indonesia and 3 introduced C. annuum. Inoculation was carried out by drenching 5 ml suspension of zoospore (1 x 104) on the growing medium suitable for the oomycetes around the plant. Disease symptom was measured at 21 days after inoculation. Salicylic acid and b-1.3-glucanase analyses were conducted to 7-week old plant with specific interval. Molecular characterization to complement disease assay was carried out using SCAR primers (OpD04,717-F/D04,717-R). Significant differences were found in genotypes, isolates, and interactions between chilli genotypes x P. capsici isolates. Four tested isolates had different levels of virulence ranging from moderate (CpnsCK1, KdrRM3, WnsbCk) to high (WnsbCK2). The chilli genotypes revealed high partial resistance to P. capsici, as demonstrated by six genotypes resistant to CpnsCK1, two genotypes to KdrRM3, and one genotype resistant to WnsbCK1. Resistance of one of chilli pepper, Ungara was positively associated with an increase of salicylic acid and b-1.3-glucanase. There is no association between the SCAR marker with resistance of chilli to P. capsici suggested these pathogens from Java are probably controlled by another locus which is not detected by this SCAR marker.

Combined use of bulked segregant analysis and microarrays reveals SNP markers pinpointing a major QTL for resistance to Phytophthora capsici in pepper

2014 ◽  
Vol 127 (11) ◽  
pp. 2503-2513 ◽  
Author(s):  
Wing-Yee Liu ◽  
Jin-Ho Kang ◽  
Hyeon-Seok Jeong ◽  
Hye-Jeong Choi ◽  
Hee-Bum Yang ◽  
...  
Keyword(s):  
Bulked Segregant Analysis ◽  
Phytophthora Capsici ◽  
Snp Markers ◽  
Combined Use ◽  
Major Qtl

Development of SCAR markers for sex determination in the dioecious shrub Aucuba japonica (Cornaceae)

Genome ◽  
2009 ◽  
Vol 52 (3) ◽  
pp. 231-237 ◽  
Author(s):  
Masayuki Maki
Keyword(s):  
Sex Identification ◽  
The Other ◽  
Scar Markers ◽  
Specific Sequence ◽  
Sequence Characterized Amplified Region ◽  
Annealing Temperatures ◽  
Aucuba Japonica ◽  
Males And Females ◽  
Male Specific ◽  
Scar Primers

Two sex-linked fragments were identified by RAPD analyses in the dioecious diploid shrub Aucuba japonica var. ovoidea and were converted into markers of male-specific sequence characterized amplified region (SCAR) markers. PCRs using the primers designed in this study correctly discriminated 24 flowering males and 24 flowering females at higher annealing temperatures (SCAR markers OPA10-424 at 55 °C and OPN11-1095 at 65 °C), although at relatively low annealing temperatures, the fragments were amplified in both males and females. These SCAR primers were also tested to see whether they were applicable to sex identification in the conspecific tetraploid Aucuba japonica var. japonica. One set pf SCAR primers could be used for sex identification even in this tetraploid variety, although the other failed. The SCAR markers developed in this study will provide a powerful tool in identifying the sex of immature plants of dioecious A. japonica, which is a commercially valuable shrub due to its conspicuous fruits.

Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 568-577 ◽  
Author(s):  
Muhammad A. Khan ◽  
Charles-Eric Durel ◽  
Brion Duffy ◽  
Damien Drouet ◽  
Markus Kellerhals ◽  
...  
Keyword(s):  
Linkage Group ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Fire Blight ◽  
Ssr Marker ◽  
Pedigree Analysis ◽  
Blight Resistance ◽  
Sequence Characterized Amplified Region ◽  
Moderately Resistant ◽  
Major Qtl

A fire blight resistance QTL explaining 34.3%–46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar ‘Fiesta’ (F7). However, markers flanking this QTL were AFLP and RAPD markers unsuitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for the region was developed. Pedigree analysis of ‘Fiesta’ with these markers enabled tracking of the F7 QTL allele back to ‘Cox’s Orange Pippin’. Stability of the effect of this QTL allele in different backgrounds was analyzed by inoculating progeny plants of a cross between ‘Milwa’, a susceptible cultivar, and ‘1217’, a moderately resistant cultivar, and a set of cultivars that carry or lack the allele conferring increased fire blight resistance. Progenies and cultivars that carried both markers were significantly more resistant than those that did not carry both markers, indicating high stability of the F7 QTL allele in different backgrounds. This stability and the availability of reproducible markers bracketing the QTL make this locus promising for use in MAS.

Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 862-870 ◽  
Author(s):  
Onivaldo Randig ◽  
Michel Bongiovanni ◽  
Regina M.D.G Carneiro ◽  
Philippe Castagnone-Sereno
Keyword(s):  
Genetic Diversity ◽  
Multiplex Pcr ◽  
Rapd Markers ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Scar Markers ◽  
Meloidogyne Hapla ◽  
Root Knot Nematodes ◽  
Sequence Characterized Amplified Region ◽  
Scar Primers

RAPD markers were used to characterize the genetic diversity and relationships of root-knot nematodes (RKN) (Meloidogyne spp.) in Brazil. A high level of infraspecific polymorphism was detected in Meloidogyne arenaria, Meloidogyne exigua, and Meloidogyne hapla compared with the other species tested. Phylogenetic analyses showed that M. hapla and M. exigua are more closely related to one another than they are to the other species, and illustrated the early divergence of these meiotically reproducing species from the mitotic ones. To develop a PCR-based assay to specifically identify RKN associated with coffee, three RAPD markers were further transformed into sequence-characterized amplified region (SCAR) markers specific for M. exigua, Meloigogyne incognita and Meloidogyne paranaensis, respectively. After PCR using the SCAR primers, the initial polymorphism was retained as the presence or absence of amplification. Moreover, multiplex PCR using the three pairs of SCAR primers in a single reaction enabled the unambiguous identification of each species, even in mixtures. Therefore, it is concluded that the method developed here has potential for application in routine diagnostic procedures.Key words: diagnostic, multiplex PCR, phylogeny, RAPD, root-knot nematodes.

scholarly journals Eastern Filbert Blight-resistant Hazelnuts from Russia, Ukraine, and Poland

HortScience ◽  
2013 ◽  
Vol 48 (4) ◽  
pp. 466-473 ◽  
Author(s):  
John M. Capik ◽  
Megan Muehlbauer ◽  
Ari Novy ◽  
Josh A. Honig ◽  
Thomas J. Molnar
Keyword(s):  
Genetic Resistance ◽  
Corylus Avellana ◽  
Eastern North America ◽  
Sources Of Resistance ◽  
Sequence Characterized Amplified Region ◽  
Disease Phenotypes ◽  
Anisogramma Anomala ◽  
The Russian Federation ◽  
Eastern Filbert Blight ◽  
Scar Primers

Stable genetic resistance to the fungal disease eastern filbert blight (EFB), caused by Anisogramma anomala, is vital for sustainable production of European hazelnut (Corylus avellana) in eastern North America. In this study, new hazelnut germplasm from the Russian Federation, Ukraine, and Poland (a total of 1844 trees from 66 seed lots) was subjected to A. anomala under field conditions over at least five years in New Jersey. Plants were then rated for the presence of EFB using an index of 0 (no disease) through 5 (all stems containing cankers). Nuts of the resistant trees were evaluated to identify plants with improved kernel characteristics. Genomic DNA of these trees was also screened with sequence-characterized amplified region (SCAR) markers generated by the primers BE-03, BE-33, and BE-68, which are closely linked to the single dominant R-gene of ‘Gasaway’, to assess the resistant seedlings for the presence of this well-known source of resistance. At final evaluation, 76 trees remained free of disease with nine expressing only minor symptoms (rating 1 or 2). The resistant trees spanned 24 different seed lots representing all three countries. The remaining trees ranged from moderately to severely infected with 81% of the total collection rating 5. Several of the resistant trees were found to produce commercial-sized (≈12 mm diameter), round kernels that blanched well. Although the results of the ‘Gasaway’ SCAR primers were inconclusive, the diverse collection origins and disease phenotypes provide evidence that novel sources of resistance were likely identified in this study. These new plants should broaden the genetic base of EFB-resistant C. avellana hazelnut germplasm available for breeding.

Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

2009 ◽  
Vol 8 (8) ◽  
pp. 910-919 ◽  
Author(s):  
Hong-liang SHI ◽  
Xin-hai LI ◽  
De-gui ZHANG ◽  
Chuan-xiao XIE ◽  
Zhuan-fang HAO ◽  
...  
Keyword(s):  
Sequence Characterized Amplified Region ◽  
Sporisorium Reiliana ◽  
Scar Primers

scholarly journals Sequence-characterized amplified region (SCAR) technique used for variety discrimination in vinca (Catharanthus roseus (L.) G.Don)

2002 ◽  
Vol 24 (1) ◽  
pp. 299-305 ◽  
Author(s):  
Carlos C.E Menezes ◽  
Tara Vantoai ◽  
Miller B McDonald ◽  
Tocio Sediyama
Keyword(s):  
Catharanthus Roseus ◽  
Seed Quality ◽  
Sequence Information ◽  
Genetic Purity ◽  
Banding Patterns ◽  
Sequence Characterized Amplified Region ◽  
Purity Testing ◽  
Polymorphic Bands ◽  
Scar Primers

Sequence-Characterized Amplified Region (SCAR) appears as a useful technique for genetic purity testing and variety discrimination, applicable to species in which some other techniques have failed. In particular, this technique is very attractive with species in which RAPD results were not consistent. The RAPD polymorphic bands were cloned, sequenced and from the sequence information, primers pairs for normal PCR were developed. Since the probability of obtaining successful SCAR primers from RAPD polymorphic bands was about 50%, a larger number of RAPD polymorphic bands are needed to develop sufficient SCAR primers for varietal discrimination in vinca. In addition, the efficiency of the SCAR technique is strongly affected by the quality of DNA extracted from seeds. The SCAR banding patterns obtained from vinca seed were consistent and repeatable making the results reliable for genetic purity testing and variety discrimination. The SCAR technique is simple, fast, relatively inexpensive and allows the use of DNA extracted from dry seeds, which is very important in a seed-quality evaluating program

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