Genetic variation revealed in the chloroplast-encoded RNA polymerase beta' subunit of downy mildew-resistant genotype of opium poppy

Two accessions of opium poppy, Pps-1 (dark green leaves, highly resistant to downy mildew [DM]) and H-9 (yellowish green leaves, susceptible to DM), which originated from common progenitor SPS49 were selected, and their F(1) and F(2) progenies showed that leaf color trait was governed by single recessive nuclear gene, whereas DM resistance appeared to be the interaction between cytoplasmic and nuclear genes. Chloroplast DNA (cpDNA) analysis of these 2 accessions through arbitrarily-primed polymerase chain reaction generated a unique fragment in Pps-1. Subsequent sequence analysis upon cloning of this cpDNA fragment revealed its similarity with the plastid-encoded RNA polymerase beta' subunit (rpoCI). Full-length rpoCI DNA was therefore isolated from both the genotypes that was 2707 bp long with a 658-bp intron (436-1093) and a 2049-bp open reading frame encoding 682 amino acid long polypeptide. Comparative sequence analysis of the rpoC1 gene from both the genotypes, revealed 4 single-nucleotide substitutions at 4 positions that caused 3 amino acid changes in the protein sequence--1) A to C transversion at position 825 (Glu275Asp), 2) A to G transition at position 1203 (Ile401Met), and 3) T to C transition at position 1422 and G to A transition at position 1423 both in same codon of the reading frame (Ala475Thr). This investigation is the first report indicating base substitution changes in the plastid-encoded rpoCI gene in DM-resistant genotypes of opium poppy. This finding may lead to implication of possible role of RNA polymerase beta' subunit in resistance to DM caused by Peronospora arborescens.     

Detection of a true breeding homeotic gene mutant Pps-1 with partially petaloid sepals in opium poppy (Papaver somniferum L.) and its genetic behavior

A spontaneous true breeding homeotic gene mutant Pps-1 with distinct partial petaloid sepals was detected in the population of downy mildew (DM)-resistant elite accession I-14 during our studies for the identification of disease resistance sources in opium poppy. The trait was found to be stable and inherited truly in the subsequent generations. Genetic studies were carried out through systematic reciprocal crosses with the parental wild-type genotype I-14, and segregation pattern of phenotypic characteristics in F(1) and F(2) populations clearly indicated single recessive nuclear gene control of the mutant character. The studies have demonstrated that the mutant phenotype is due to mutations at the Pps-1 locus that possibly corresponds to B-class function (according to ABC model) with negative control function. The mutant Pps-1 being single-whorl homeotic mutant might greatly help in providing insight into mechanisms of flower development in opium poppy.     

Molecular genetic diversity and association mapping of morphine content and agronomic traits in Turkish opium poppy (<Emphasis Type="Italic">Papaver somniferum</Emphasis>) germplasm

As the sole plant source of many potent alkaloids, opium poppy (Papaver somniferum L.) is an important medicinal crop. Nevertheless, few studies have characterized opium poppy germplasm with crop-specific molecular markers. Because Turkey is a diversity center for opium poppy, Turkish germplasm is a valuable genetic resource for association mapping studies aimed at identifying QTLs controlling morphine content and agronomic traits. In this study, the morphological diversity and molecular diversity of 103 Turkish opium poppy landraces and 15 cultivars were analyzed. Potentially useful morphological variation was observed for morphine content, plant height, and capsule index. However, the landraces exhibited limited breeding potential for stigma number, and seed and straw yields. Both morphological and molecular analyses showed distinct clustering of cultivars and landraces. In addition, a total of 164 SSR and 367 AFLP polymorphic loci were applied to an opium poppy association mapping panel composed of 95 opium poppy landraces which were grown for two seasons. One SSR and three AFLP loci were found to be significantly associated with morphine content (P < 0.01 and LD value (r ²) = 0.10–0.32), and six SSR and 14 AFLP loci were significantly associated with five agronomic traits (plant height, stigma number, capsule index, and seed and straw yields) (P < 0.01 and LD value (r ²) = 0.08–0.35). This is the first report of association mapping in this crop. The identified markers provide initial information for marker-assisted selection of important traits in opium poppy breeding.     

Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing

Opium poppy (Papaver somniferum L.) is an important pharmaceutical crop with very few genetic marker resources. To expand these resources, we sequenced genomic DNA using pyrosequencing technology and examined the DNA sequences for simple sequence repeats (SSRs). A total of 1,244,412 sequence reads were obtained covering 474 Mb. Approximately half of the reads (52 %) were assembled into 166,724 contigs representing 105 Mb of the opium poppy genome. A total of 23,283 non-redundant SSRs were identified in 18,944 contigs (11.3 % of total contigs). Trinucleotide and tetranucleotide repeats were the most abundant SSR repeats, accounting for 49.0 and 27.9 % of all SSRs, respectively. The AAG/TTC repeat was the most abundant trinucleotide repeat, representing 19.7 % of trinucleotide repeats. Other SSR repeat types were AT-rich. A total of 23,126 primer pairs (98.7 % of total SSRs) were designed to amplify SSRs. Fifty-three genomic SSR markers were tested in 37 opium poppy accessions and seven Papaver species for determination of polymorphism and transferability. Intraspecific polymorphism information content (PIC) values of the genomic SSR markers were intermediate, with an average 0.17, while the interspecific average PIC value was slightly higher, 0.19. All markers showed at least 88 % transferability among related species. This study increases sequence coverage of the opium poppy genome by sevenfold and the number of opium poppy-specific SSR markers by sixfold. This is the first report of the development of genomic SSR markers in opium poppy, and the genomic SSR markers developed in this study will be useful in diversity, identification, mapping and breeding studies in opium poppy.     

Detection of DNA polymorphism in Papaver somniferum genotypes differing in straw morphinan alkaloid content

Abstract

Thirty‐two distinct accessions of Papaver somniferum were screened for morphinan alkaloid content in the straw. The combined content of major morphinan alkaloids (morphine+codeine+thebaine) was found to vary in the range 0.2260–0.0683%. Two genotypes each, were selected as prototypes for low [I‐48 (0.0683%) and I‐344 (0.0878%)] and high [Pps‐1 (0.2260%) and N‐3 (0.2074%)] morphinan alkaloid content for studying DNA polymorphism. RAPD analysis of these four genotypes using 80 primers could not detect the polymorphism. However, AFLP analysis of these genotypes with 12 EcoRI/MseI primer pairs could distinctly group the high‐ and low‐morphinan alkaloid genotypes separately. Furthermore, 50 AFLP fragments, specific to high‐straw morphinan alkaloid genotypes (Pps‐1 and N‐3) and 28 DNA fragments specific to low‐straw morphinan alkaloid genotypes (I‐48 and I‐344) could be identified. This investigation is the first report on the polymorphism identified in the genotypes differing in their straw morphinan alkaloid content. This DNA polymorphism could be exploited for defining chemotypes at an early seedling stage in poppy breeding programmes.     

Establishment of a local map of AFLP markers around the powdery mildew resistance gene Run1 in grapevine and assessment of their usefulness for marker assisted selection

The monogenic dominant genetic determinism of total resistance to powdery mildew, introduced from Muscadinia rotundifolia into Vitis vinifera, was further assessed in BC₄ and BC₅ full-sib families. A BC₅ population of 157 individuals was used to select AFLP markers linked to the resistance gene, Run1. Thirteen AFLP markers were selected and a local map was constructed around the Run1 gene. Ten markers among the 13 were found to co-segregate with the resistance gene. The usefulness of these 13 AFLP markers for the selection of Run1-carrying genotypes was further assessed through their analysis in a set of 22 Run1-carrying resistant genotypes and 16 susceptible genotypes. Three markers out of the 13 analysed were found to be absent in all susceptible genotypes and present in all resistant individuals, and may thus represent good tools for the marker-assisted selection of grapevine varieties resistant to powdery mildew. A recombination event among the markers that were originally found to co-segregate was observed in one of the resistant individuals, showing that recombination is possible in this region and may therefore be observed in larger populations. Received: 18 October 2000 / Accepted: 4 April 2001     

Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines

 Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints. The AFLP diversity of sunflower has not been described, and much of the public germ plasm of sunflower has not yet been fingerprinted. Our objectives were to: (1) estimate genetic similarities, polymorphism rates, and polymorphic information contents (PICs) for AFLP markers among elite public oilseed inbred lines, and (2) assess the genetic diversity of inbred lines using genetic similarities estimated from AFLP fingerprints. We produced fingerprints for 24 public inbred lines of sunflower (Helianthus annuus L.) using six AFLP primer combinations. These primers produced a total of 359 AFLP markers or about 60 markers per primer combination. Genetic similarities ranged from 0.70 to 0.91, polymorphism rates ranged from 7 to 24%, and PICs ranged from 0.0 to 0.5. Genetic similarities were lower overall for maintainer (B)×restorer (R) crosses than for B×B or R×R crosses. Principal-coordinate and cluster analyses separated lines into two groups, one for B-lines and another for R-lines. These groupings illustrate the breeding history and basic heterotic pattern (B×R) of sunflower and the widespread practice of using B×B and R×R crosses to develop new lines. There were, nevertheless, distinct subgroups within these groups. These subgroups may represent unique heterotic groups and create a basis for formally describing heterotic patterns in sunflower. Received: 10 June 1996 / Accepted: 4 April 1997     

Lipid Peroxidation and Antioxidant Activities Involved in Resistance Response against Downy Mildew in Opium Poppy

The aim of this study was to observe the lipid peroxidation (LP) of cell membranes and antioxidant systems in response to inoculation of Peronospora arborescens causing downy mildew (DM) in opium poppy. Contents of the LP product, malondialdehyde (MDA) and antioxidant glutathione (GSH) were determined in leaves of two opium poppy genotypes, Pps‐1 (highly resistant to DM) and Jawahar‐16 (highly susceptible to DM) at different time intervals after inoculation (12 h, 24 h, 48 h and 72 h). The provided GSH content corresponded to that of total non‐protein sulfhydryl groups. In leaves of Jawahar‐16, a significant decrease in concentration of GSH and a persistent increase in concentration of MDA were recorded after inoculation in comparison to leaves of control plants. The continuous decrease in GSH content contributed to damage of cell membranes leading to disease development in Jawahar‐16. On the other hand in a resistant genotype (Pps‐1), initially at 12 h after inoculation (hai) the level of GSH was found to be high, but a transient and highly significant decrease in content of GSH and increase in content of MDA was observed at 24 hai in comparison to control plants of same genotype and also in comparison to inoculated plants of susceptible genotype (Jawahar‐16). These results indicate that generation of GSH and MDA is negatively correlated during the infection process as found in the case of DM‐resistant genotype Pps‐1 at 24hai, which also suggests an increased need by the host plant for oxidative stress, required for hypersensitive response mediated defense mechanism.     

Cloning of AFLP markers linked to resistance to Peronosclerospora sorghi in maize

Genetic mapping of resistance genes for sorghum downy mildew (SDM) in maize revealed multiple-locus inheritance. A combination of AFLP (amplified fragment length polymorphism) technique with bulked segregant analysis (BSA) was applied to map the genes involved in the resistance to SDM (Peronosclerospora sorghi) in a recombinant inbred population. Three AFLP markers were identified and mapped to chromosomes 1 and 9, in regions previously associated with SDM resistance. One other AFLP marker was found to be associated with disease susceptibility but could not be linked to any chromosome. These four AFLP fragments were isolated, cloned and sequenced. A BLAST search of the GenBank database showed that none of these four sequences was closely related to resistance genes that have been reported previously. Sequence-characterized amplified regions (SCARs) were produced and used to assess the presence of SDM resistance genes and characterize specific genotypes. These markers may be useful in marker-assisted breeding programs.     

Association of AFLP markers with downy mildew resistance in autotetraploid alfalfa

The amplified fragment length polymorphism (AFLP) assay is an efficient method for the identification of molecular markers useful in the improvement of numerous crop species. The identification of AFLP markers linked to disease resistance genes has been shown in segregating populations from crosses of inbred lines. The development of inbred lines in alfalfa is not possible, but existing breeding programs have produced populations selected for resistance to a single pest. Two such populations, UC-123 and UC-143, differing only in selection for resistance to downy mildew (Peronospora trifoliorum de Bary) isolate I-8, were used in this study. Thirty-six resistant plants from UC-143, and 36 susceptible plants from UC-123 were screened for DNA polymorphisms using fourteen AFLP primer combinations. Four AFLP fragment markers, ACACTC₂₀₈, ACACTC₁₅₀, ACACAT₂₁₆ and ACACTC₄₈₆, were found to be significantly associated with disease susceptibility or resistance. Resistant and susceptible plants were crossed in a diallel scheme and the progeny were screened for resistance to P. trifoliorum isolate I8. Two of the AFLP markers, ACACTC₂₀₈ and ACACTC₄₈₆ were significantly associated with resistance in the F₁ and S₁ progeny. The utilization of two populations, comprised of 36 resistant and 36 susceptible plants, for the identification of DNA fragments associated with disease resistance proved successful. Seventy-two plants is a very manageable number and provides a starting point for further refinement of marker-trait associations.     

Susceptibility of opium poppy and pyrethrum to root infection by Spongospora subterranea

Spongospora subterranea, which causes powdery scab of potato, infects a diverse range of plant species. Crop rotation as a powdery scab management tool will be compromised if pathogen hosts exist between potato crops. Opium poppy (Papaver somniferum) and pyrethrum (Tanacetum cinerariifolium) are important crops within intensive vegetable production rotations in NW Tasmania. Measurements of S. subterranea soil inoculum within a commercial field showed pathogen amounts were substantially elevated following an opium poppy crop, which suggested host status. In glasshouse testing, opium poppy and pyrethrum were confirmed as hosts of S. subterranea, with opium poppy the more susceptible of the two. Both species were less susceptible than tomato, a known host. Observations of early growth suggested inoculation impacts on all three plant species, although at 16 (tomato and opium poppy) or 26 (pyrethrum) weeks postinoculation, only tomato had significantly reduced shoot and root development. The role of rotation crops in inoculum persistence and the possible role of S. subterranea as a minor pathogen of nonpotato crops are discussed.     

Assessing wheat (Triticum aestivum L.) genetic diversity using quality traits, amplified fragment length polymorphisms, simple sequence repeats and proteome analysis

The genetic diversity among 10 Iranian bread wheat (Triticum aestivum) genotypes was analysed using 12 quality traits, 320 amplified fragment length polymorphisms (AFLP) polymorphic fragments, 491 simple sequence repeats (SSR) alleles and 294 proteome markers. The results revealed that the genotypes differed for quality traits, AFLP, SSR and proteome markers. The average genetic diversity based on quality traits (0.684 with a range of 0.266–0.997) was higher than AFLP (0.502 with a range of 0.328–0.717), SSR (0.503 with a range of 0.409–0.595) and proteome (0.464 with a range of 0.264–0.870) markers. Although there were apparent similarities between the groupings of particular genotypes, the overall correspondence between the distance matrices appeared to be rather low. In this study, the cluster analysis based on AFLP data showed the closest agreement with genotypes’ regions of origin or pedigree information. In addition to the genetic diversity assessment, specific proteins with known function were detected uniquely for the studied genotypes. Our results suggest that the classification based on quality traits and genotypic markers of these wheat genotypes will be useful for wheat breeders to plan crosses for positive traits.     

Cleaved AFLP (cAFLP), a modified amplified fragment length polymorphism analysis for cotton

In certain plant species including cotton (Gossypium hirsutum L. or Gossypium barbadense L.), the level of amplified fragment length polymorphism (AFLP) is relatively low, limiting its utilization in the development of genome-wide linkage maps. We propose the use of frequent restriction enzymes in combination with AFLP to cleave the AFLP fragments, called cleaved AFLP analysis (cAFLP). Using four Upland cotton genotypes (G. hirsutum) and three Pima cotton (G. barbadense), we demonstrated that cAFLP generated 67% and 132% more polymorphic markers than AFLP in Upland and Pima cotton, respectively. This resulted in 15.5 and 25.5 polymorphic cAFLP markers per AFLP primer combination, as compared to 9.1 and 11.0 polymorphic AFLP. The cAFLP-based genetic similarity (GS) is generally lower than the AFLP-based GS, even though both marker systems are overall congruent. In some cases, cAFLP can better resolve genetic relationships between genotypes, rendering a higher discriminatory power. Given the high-resolution power of capillary-based DNA sequencing system, we further propose that AFLP and cAFLP amplicons from the same primer combination can be pooled as one sample before electrophoresis. The combination produced an average of 18.5 and 31.0 polymorphic markers per primer pair in Upland and Pima cotton, respectively. Using several restriction enzyme combinations before pre-selective amplification in combination with various frequent 4 bp-cutters or 6 bp-cutters after selective amplification, the pooled AFLP and cAFLP will provide unlimited number of polymorphic markers for genome-wide mapping and fingerprinting.     

Inheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2, and backcross hybrids

Eight primer combinations were used to investigate the application of amplified fragment length polymorphism (AFLP) markers in catfish for genetic analysis. Intraspecific polymorphism was low among channel catfish or blue catfish strains. Interspecific AFLP polymorphism was high between the channel catfish and blue catfish. Each primer combination generated from 70 to more than 200 bands, of which 38.6–75.7% were polymorphic between channel catfish and blue catfish. On average, more than 20 polymorphic bands per primer combination were produced as quality markers suitable for genetic analysis. All AFLP markers were transmitted into channel catfish?×?blue catfish F1 hybrids, except rare markers that were heterozygous in the parents and therefore were segregating in F1 hybrids. The two reciprocal channel catfish?×?blue catfish F1 hybrids (channel catfish female?×?blue catfish male; blue catfish female?×?channel catfish male) produced identical AFLP profiles. The AFLP markers were inherited and segregated in expected Mendelian ratios. At two loci, E8-b9 and E8-b2, markers were found at significantly lower frequencies than expected with F2 and backcross hybrids which had been selected for increased growth rates. The reproducibility of AFLP was excellent. These characteristics of the catfish AFLP markers make them highly useful for genetic analysis of catfish, especially for construction of genetic linkage and quantitative trait loci maps, and for marker-assisted selection.     

Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon

Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes of Cucumis melo L. Each line represented a different melon genotype: Piel de Sapo, Ogen, PI161375, PI414723, Agrestis and C105. A number of polymorphic RAPD, AFLP and RFLP bands were scored on all materials and the genetic similarity measured. Clustering analysis performed with the three types of markers separated the genotypes into two main groups: (1) the sweet type, cultivated melons and (2) the exotic type, not cultivated melons. While the data obtained suggest that all three types of markers are equally informative, AFLPs showed the highest efficiency in detecting polymorphism. Received: 30 December 1999 / Accepted: 24 January 2000     

Molecular mapping of powdery mildew resistance gene <Emphasis Type="Italic">Eg-3</Emphasis> in cultivated oat (<Emphasis Type="Italic">Avena sativa</Emphasis> L. cv. Rollo)

Powdery mildew is a prevalent fungal disease affecting oat (Avena sativa L.) production in Europe. Common oat cultivar Rollo was previously shown to carry the powdery mildew resistance gene Eg-3 in common with cultivar Mostyn. The resistance gene was mapped with restriction fragment length polymorphism (RFLP) markers from Triticeae group-1 chromosomes using a population of F₃ lines from a cross between A. byzantina cv. Kanota and A. sativa cv. Rollo. This comparative mapping approach positioned Eg-3 between cDNA-RFLP marker loci cmwg706 and cmwg733. Since both marker loci were derived from the long arm of barley chromosome 1H, the subchromosomal location of Eg-3 was assumed to be on the long arm of oat chromosome 17. Amplified fragment length polymorphism (AFLP) marker technology featured as an efficient means for obtaining markers closely linked to Eg-3.     

Towards map-based cloning: fine mapping of a recessive genic male-sterile gene (BnMs2) in Brassica napus L. and syntenic region identification based on the Arabidopsis thaliana genome sequences

S45AB, a recessive genic male sterile (RGMS) line, originated as a spontaneous mutant in Brassica napus cv. Oro. The genotypes of sterile (S45A) and fertile plants (S45B) are Bnms1ms1ms2ms2 and BnMs1ms1ms2ms2, respectively. In our previous studies, Yi et al. (Theor Appl Genet 113:643–650, 2006) mapped the BnMs1 locus to a region of 0.4 cM, candidates of which have been identified and genetic transformation is in progress. We describe the fine mapping of BnMs2 exploiting amplified fragment length polymorphism (AFLP) and amplified consensus genetic marker (ACGM) methodologies, and the identification of a collinear region probably containing BnMs2 orthologue in Arabidopsis thaliana. A near isogenic line (NIL) population S4516AB which segregated for BnMs2 locus was generated by crossing, allelism testing and repeated full-sib mating. From the survey of 1,024 AFLP primer combinations, 12 tightly linked AFLP markers were obtained and five of them were successfully converted into co-dominant or dominant sequence characterized amplified region (SCAR) markers. A population of 2,650 sterile plants was screened using these markers and a high-resolution map surrounding BnMs2 was constructed. The closest AFLP markers flanking BnMs2 were 0.038 and 0.075 cM away, respectively. Subsequently, an ACGM marker was developed to delimit the BnMs2 locus at an interval of 0.075 cM. We extended marker sequences to perform BlastN searches against the Arabidopsis genome and identified a collinear region containing 68 Arabidopsis genes, in which the orthologue of BnMs2 might be included. We further integrated BnMs2 linked AFLP or SCAR markers to two doubled-haploid (DH) populations derived from the crosses Tapidor × Ningyou7 (Qiu et al., Theor Appl Genet 114:67–80, 2006) and Quantum × No.2127-17 (available in our laboratory), and BnMs2 was mapped on N16. Molecular markers developed from these investigations will facilitate the marker-assisted selection (MAS) of RGMS lines, and the fine map and syntenic region identified will greatly hasten the process of positional cloning of BnMs2 gene.     

<Emphasis Type="Italic">Rpp1</Emphasis>, a dominant gene providing race-specific resistance to rose powdery mildew (<Emphasis Type="Italic">Podosphaera pannosa</Emphasis>): molecular mapping,SCAR development and confirmation of disease resistance data

We have previously demonstrated that in the diploid rose population 97/9 resistance to the powdery mildew race 9 is controlled by a major dominant resistance gene, Rpp1. In the study reported here, we isolated several molecular markers closely linked to Rpp1 via bulked segregant analysis, with the gene being tagged in an interval of 5 cM between the two most adjacent markers. It was possible to convert the most closely linked amplified fragment length polymorphic (AFLP) marker into a sequence-characterised amplified region (SCAR) segregating in the same manner. Indirect mapping of Rpp1 in relation to the black spot resistance gene Rdr1 revealed no linkage between the two R genes. Furthermore, the genetic model based on a single dominant resistance gene was supported by the marker data.     

Retrotransposon-based molecular markers for grapevine species and cultivars identification

Insertional polymorphisms of two copia-like (Vine-1, Tvv1) and one gypsy-like (Gret1) retrotransposon found in the grapevine genome were studied in 29 Vitis genotypes (Vitis arizonica, Vitis cinerea, Vitis labrusca, Vitis rupestis, Vitis rotundifolia, Vitis vinifera subsp. sylvestris and 23 V. vinifera subsp. sativa) using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and sequence-specific amplified polymorphism (SSAP) techniques. IRAP, REMAP and SSAP polymorphisms were compared with amplified fragment length polymorphism (AFLP), Inter-single sequence repeats (ISSR) and SSR polymorphisms by evaluating the information content, the number of loci simultaneously analysed per experiment, the effectiveness of the analyses in assessing the relationship between accessions and the number of loci needed to obtain a coefficient of variation of 10%. The UPGMA dendrograms of each molecular marker system were compared and the Mantel matrix correspondence test was applied. Furthermore, the corresponding insertion ages of the transposable elements were estimated for each retrotransposon subfamily analysed. The presence of Gret1, Tvv1 and Vine-1 retrotransposons in all analysed genotypes suggests that copia-like and gypsy-like retrotransposons are widespread in Vitis genus. The results indicate that these retrotransposons were active before Vitis speciation and contributed to Vitis genus evolution. IRAP, REMAP and SSAP markers allow the discrimination of Vitis species and V. vinifera subsp. sativa cultivars with certainty as has been shown with AFLP, ISSR and SSR analyses, but phylogenetic trees obtained by retrotransposon-based molecular markers polymorphisms show some significant differences in the allocation of the analysed accessions compare to those obtained by ISSR, AFLP and SSR molecular markers. The phylogenetic tree resulting from REMAP polymorphism appeared the most representative of the effective relationship between all analysed accessions.     

Genetic linkage maps of two interspecific grape crosses (Vitis spp.) used to localize quantitative trait loci for downy mildew resistance

Two populations (Pop) segregating quantitatively for resistance to downy mildew (DM), caused by Plasmopara viticola, were used to construct genetic maps and to carry out quantitative trait locus (QTL) analysis. Pop1 comprised of 174 F₁ individuals from a cross of ‘Moscato Bianco’, a susceptible Vitis vinifera cultivar, and a resistant individual of Vitis riparia. Pop2 consisted of 94 progeny from a cross of two interspecific hybrids, ‘VRH3082 1-42’ and ‘SK77 5/3’, with resistance traits inherited from Vitis rotundifolia and Vitis amurensis, respectively. Resistance of progeny was measured in field and greenhouse conditions by visual evaluation of disease symptoms on leaves. Linkage maps of 1037.2 and 651 cM were built essentially with simple sequence repeat markers and were enriched with gene-derived single-strand conformational polymorphism and single-nucleotide polymorphism markers. Simple interval mapping and Kruskall–Wallis analysis detected a stable QTL involved in field resistance to DM on linkage group (LG) 7 of the Pop1 integrated map co-localized with a putative Caffeoyl-CoA O-methyltransferase-derived marker. Additional QTLs were detected on LGs 8, 12 and 17. We were able to identify genetic factors correlated with resistance to P. viticola with lower statistical significance on LGs 1, 6 and 7 of the Pop2 map. Finally, no common QTLs were found between the two crosses analyzed. A search of the grapevine genome sequence revealed either homologues to non-host-, host- or defense-signalling genes within the QTL intervals. These positional candidate genes may provide new information about chromosomal regions hosting phenotypic loci.