Summary Inter simple sequence repeat (ISSR)-PCR is a technique, which involves the use of microsatellite sequences as primers in a polymerase chain reaction to generate multilocus markers. It is a simple and quick method that combines most of the advantages of microsatellites (SSRs) and amplified fragment length polymorphism (AFLP) to the universality of random amplified polymorphic DNA (RAPD). ISSR markers are highly polymorphic and are useful in studies on genetic diversity, phylogeny, gene tagging, genome mapping and evolutionary biology. This review provides an overview of the details of the technique and its application in genetics and plant breeding in a wide range of crop plants.

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Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding

We have compiled from literature and other sources a list of 1261 proteins believed to be differentially expressed in human cancer. These proteins, only some of which have been detected in plasma to date, represent a population of candidate plasma biomarkers that could be useful in early cancer detection and monitoring given sufficiently sensitive specific assays. We have begun to prioritize these markers for future validation by frequency of literature citations, both total and as a function of time. The candidates include proteins involved in oncogenesis, angiogenesis, development, differentiation, proliferation, apoptosis, hematopoiesis, immune and hormonal responses, cell signaling, nucleotide function, hydrolysis, cellular homing, cell cycle and structure, the acute phase response and hormonal control. Many have been detected in studies of tissue or nuclear components; nevertheless we hypothesize that most if not all should be present in plasma at some level. Of the 1261 candidates only 9 have been approved as "tumor associated antigens" by the FDA. We propose that systematic collection and large-scale validation of candidate biomarkers would fill the gap currently existing between basic research and clinical use of advanced diagnostics.

/pdf/a-list-of-candidate-cancer-biomarkers-for-targeted-lu8garq70x.pdf

A list of candidate cancer biomarkers for targeted proteomics.

An integrated molecular marker map of the chickpea genome was established using 130 recombinant inbred lines from a wide cross between a cultivar resistant to fusarium wilt caused by Fusarium oxysporum Schlecht. emend. Snyd. &. Hans f. sp. ciceri (Padwick) Snyd & Hans, and an accession of Cicer reticulatum (PI 489777), the wild progenitor of chickpea. A total of 354 markers were mapped on the RILs including 118 STMSs, 96 DAFs, 70 AFLPs, 37 ISSRs, 17 RAPDs, eight isozymes, three cDNAs, two SCARs and three loci that confer resistance against different races of fusarium wilt. At a LOD-score of 4.0, 303 markers cover 2077.9 cM in eight large and eight small linkage groups at an average distance of 6.8 cM between markers. Fifty one markers (14.4%) were unlinked. A clustering of markers in central regions of linkage groups was observed. Markers of the same class, except for ISSR and RAPD markers, tended to generate subclusters. Also, genes for resistance to races 4 and 5 of fusarium wilt map to the same linkage group that includes an STMS and a SCAR marker previously shown to be linked to fusarium wilt race 1, indicating a clustering of several fusarium-wilt resistance genes around this locus. Significant deviation from the expected 1 : 1 segregation ratio was observed for 136 markers (38.4%, P<0.05). Segregation was biased towards the wild progenitor in 68% of the cases. Segregation distortion was similar for all marker types except for ISSRs that showed only 28.5% aberrant segregation. The map is the most extended genetic map of chickpea currently available. It may serve as a basis for marker-assisted selection and map-based cloning of fusarium wilt resistance genes and other agronomically important genes in future.

A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum×C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5

Ascochyta blight (AB), caused by Ascochyta rabiei is a major disease of chickpea (Cicer arietinum L.), especially in areas where cool, cloudy, and humid weather persists during the crop season. Several epidemics of AB causing complete yield loss have been reported. The fungus mainly survives between seasons through infected seed and in infected crop debris. Despite extensive pathological and molecular studies, the nature and extent of pathogenic variability in A. rabiei have not been clearly established. Accumulation of phenols, phytoalexins (medicarpin and maackiain), and hydrolytic enzymes has been associated with host-plant resistance (HPR). Seed treatment and foliar application of fungicides are commonly recommended for AB management, but further information on biology and survival of A. rabiei is needed to devise more effective management strategies. Recent studies on inheritance of AB resistance indicate that several quantitative trait loci (QTLs) control resistance. In this paper we review the biology of A. rabiei, HPR, and management options, with an emphasis on future research priorities.

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Ascochyta blight of chickpea (Cicer arietinum L.): a review of biology, pathogenicity, and disease management

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

/pdf/integration-of-novel-ssr-and-gene-based-snp-marker-loci-in-1brg0d142m.pdf

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome.

Fifty sequence-tagged microsatellite site (STMS) markers and a resistant gene-analog (RGA) locus were integrated into a chickpea (Cicer arietinum L., 2n = 2x = 16 chromosomes) genetic map that was previously constructed using 142 F6-derived recombinant inbred lines (RILs) from a cross of C. arietinum × Cicer reticulatum Lad. The map covers 1,174.5 cM with an average distance of 7.0 cM between markers in nine linkage groups (LGs). Nine markers including the RGA showed distorted segregation (P < 0.05). The majority of the newly integrated markers were mapped to marker-dense regions of the LGs. Six co-dominant STMS markers were integrated into two previously reported major quantitative trait loci (QTLs) conferring resistance to Ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. Using common STMS markers as anchors, three maps developed from different mapping populations were joined, and genes for resistance to Ascochyta blight, Fusarium wilt (caused by Fusarium oxysporum Schlechtend.: Fr. f. sp. ciceris), and for agronomically important traits were located on the combined linkage map. The integration of co-dominant STMS markers improves the map of chickpea and makes it possible to consider additional fine mapping of the genome and also map-based cloning of important disease resistance genes.

Integration of sequence tagged microsatellite sites to the chickpea genetic map.

Fusarium oxysporum Schlechtend.: Fr. f. sp. ciceris (Padwick) causes a vascular wilt of chickpea (Cicerarietinum L.) and significantly limits production worldwide. The objectives of this study were (i) to determine the inheritance of resistance to races 0 and 5 of fusarium wilt and the genetic map positions of the resistance genes and (ii) to assess the linkage relationships between these two genes and other known wilt resistance genes in chickpea. Seedlings of 131 F 6 -derived recombinant inbred lines (RILs) were tested for reaction to races 0 and 5. A 1 resistant:1 susceptible segregation ratio was observed for both races, indicating that resistance to each race is controlled by a single gene. Linkage analysis indicated that the genes for resistance to races 4 and 5 were in the same linkage group and were separated by 11.2 centiMorgans (cM). The gene for resistance to race 0 was not linked to the race 4 and 5 resistance genes. In addition, an allele-specific associated primer (ASAP) product (CS-27R/CS-27F), developed from the CS-27 primer, was located between the two resistance genes and was 7.2 and 4 cM from the genes for resistance to races 4 and 5, respectively. Map positions of these two race-specific resistance genes and the marker reported to be linked to the genes for resistance to races I and 4 support the hypothesis that wilt resistance genes are clustered on the same chromosome, Since the gene conferring resistance to race 0 is found in a different region of the genome, other genomic regions may be responsible for resistance to wilt pathogens. The gene symbols foc-0, foc-4, and foc-5 are proposed for the genes for resistance to races 0,4, and 5 of the pathogen, respectively. Identification and further evaluation of disease resistance gene clusters would improve our understanding of wilt resistance in chickpea and facilitate the transfer of resistance genes to new cultivars.

Inheritance and Linkage of Two Genes that Confer Resistance to Fusarium Wilt in Chickpea

Resistance gene analog polymorphism (RGAP)is a targeted homology based method, which has been used in different crops to identify tightly linked markers for disease resistance genes and also to enrich the map with a different class of markers. In chickpea, using the RGA primers, which are designed based on the conserved motifs present in characterized R-genes, Bulk Segregant Analysis (BSA) was performed on a resistant bulk and a susceptible bulk along with parents for ascochyta blight resistance. Of all available RGAs and their48 different combinations, only one RGA showed polymorphism during BSA. This marker was evaluated in an F7:8 population of142 RILs from an interspecific cross ofC. arietinum (FLIP 84-92C) × C. reticulatum (PI 599072) and was mapped toCicer linkage map. The genomic location of chickpea RGA was compared with the locations of mapped chickpea R-genes. This is the first RGA marker mapped to chickpea linkage map.

Molecular mapping and characterization of an RGA locus RGAPtokin1-2171 in chickpea

The most effective control of Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) is achieved by using the seeds of resistant cultivars. During conventional breeding, resistance against BCMV and BCMNV in common bean can be developed by pyramiding the strain-nonspecific dominant I gene with strain-specific recessive (bc-) resistance genes for long-term virus control. In this study, a total of 58 bean genotypes involving registered green and dry bean cultivars, local genotypes, and breeding lines were tested for the presence of known resistance genes. First of all, each genotype was inoculated with the NL-3 strain of BCMNV and the NL-4 strain of BCMV separately, and the plants were evaluated for the symptom appearance and tested by DAS-ELISA to confirm the presence or absence of the virus after three weeks of sap-inoculation. In the last part of the study, the resistance genes in bean genotypes were investigated by SCAR markers of SW-13 linked with the I gene and SBD-5 linked to bc-12. According to the phenotypic and molecular tests, out of 58 common bean genotypes tested, 37 involved the I gene, and seven and three genotypes contained bc-22 and bc-12 genes, respectively.

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Screening of dry and snap bean (Phaseolus vulgaris L.) genotypes for resistance to Bean common mosaic virus and Bean common mosaic necrosis virus

We describe a simple and new approach, based on inter-simple sequence repeats (ISSRs), for finding markers linked to clusters of disease resistance genes. In this approach, simple sequence repeats (SSR) are used directly in PCR reactions, and markers found to be linked to disease resistance genes provide important information for the selection of other sequences which can be used with PCR to find other linked markers. Based on an ISSR marker linked to a gene of interest, many new markers can be identified in the same region. We previously demonstrated that ISSR markers are useful in gene tagging and identified a marker, UBC-855500, linked to the gene for resistance to fusarium wilt race 4 in chickpea. This ISSR marker provided the information used in the present study for selecting other primers which amplified a region linked to the gene for resistance to fusarium wilt race 4. The primers were based on homology with the (AC)n sequence and were used for PCR amplifications. Changes in the sequence were at the anchor region of the primers. The repeat (AC)8T amplified a marker, UBC-8251200, which was located 5.0 cM from the gene for resistance to fusarium wilt race 4 and was closer than other markers. These results indicated that ISSR markers can provide important information for the design of other primers and that by making changes at the 3′ and 5′ anchors close linkage to the desired gene can be found. The approach allows rapid scanning of the targeted region and may provide important information for genome analysis of plant species.

Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters

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