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Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by Pyrenochaeta lycopersici. A comparative RNA-Seq-based transcriptomic analysis was conducted at 96 hpi (hours post infection) on two tomato cultivars: resistant Mogeor and its genetic background, and susceptible Moneymaker to investigate the differences in their transcriptomic response and identify the molecular bases of this plant-pathogen interaction. The number of differentially expressed genes (DEGs) identified was much higher in the susceptible than in the resistant genotype; however, the proportion of upregulated genes was higher in Mogeor (70.81%) than in Moneymaker (52.95%). Gene Ontology (GO) analysis enabled identification of 24 terms shared by the two cultivars that were consistent with responses to external stimulus, such as fungal infection. On the other hand, as many as 54 GO were enriched solely in Moneymaker, including terms related to defense response and cell wall metabolism. Our results could support the previous observations in other pathosystems, that susceptibility and resistance have overlapping signaling pathways and responses, suggesting that the P. lycopersici resistance gene pyl might be a recessive allele at a susceptibility locus, for which different candidate genes were identified based on the differences in induction or expression levels, observed between the resistant and susceptible genotype. MapMan analysis highlighted a complex hormone and transcription factors interplay where SA- and JA-induced pathways are modulated in a similar way in both genotypes and thus take part in a common response while the ethylene signaling pathways, induced mainly in susceptible Moneymaker, seem putatively contribute to its susceptibility. [ABSTRACT FROM AUTHOR]

A prime objective for improving perennial grasses for Mediterranean environments is the identification and selection of genotypes well adapted to semi-arid conditions. This study was conducted at an experimental site in Algeria over three consecutive seasons, with the aim of evaluating the agronomic performance and genetic diversity of 13 cultivars of two species of perennial grasses: six cocksfoot ( Dactylis glomerata L.) and seven tall fescue ( Festuca arundinacea Schreb. = syn.Lolium arundinaceum (Schreb.) Darbysh.) cultivars. Variation was found in both species for dry-matter yield, sward recovery, heading date, water-use efficiency (WUE), and summer senescence. Tall fescue cultivars gave greater yield in spring, with earlier heading date and higher WUE than cocksfoot, with no differences for the other traits. Among the genotypes, 'Flecha' was the most promising, together with 'E-542', 'Fraydo' and 'Centurion', all of which are tall fescue cultivars. Principal component analysis indicated that persistence of grass cover is relatively independent from dry-matter yield and water-use efficiency. The level of genetic diversity within each species was assessed using AFLP markers, and the molecular variation was analysed together with agronomic trait variation, with identification of molecular markers potentially associated with the relevant traits. [ABSTRACT FROM AUTHOR]

Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology-based barley map has been developed in the 'Nure' × 'Tremois' biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent 'Nure' in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN- H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD- H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes. [ABSTRACT FROM AUTHOR]

Gelatinization temperature and apparent amylose content are key parameters used to describe the eating and cooking qualities of rice. Sequence variants of SSIIa and Waxy genes are important determinants of gelatinization temperature and apparent amylose content, respectively. A collection of Italian non-glutinous japonica rice accessions was characterized for sequence polymorphisms in SSIIa and Waxy genes, in comparison with non-Italian japonica and indica genotypes. For SSIIa two markers, SNP3 and SNP4, were used. A PCR amplification of multiple specific alleles protocol was developed for the identification of G/T polymorphism in 5′ splice site of first intron and A/C polymorphism in exon 6 of the Waxy gene. Based on simple allele-specific PCR, it can be proposed as a user-friendly, cost-effective tool for marker-assisted selection of amylose content. The collection was characterized also for the (CT)n repeats in exon 1 of the Waxy gene. The results showed that while SSIIa haplotypes were rather similar between Italian and non-Italian japonica rice, the Waxy gene haplotype T/A/(CT)18 was largely predominant in Italian accessions, other haplotypes, well represented in non-Italian japonica [T/A/(CT)19] and indica [e.g. G/C/(CT)20] genotypes, were present at lower frequency. Grain starch quality traits as apparent amylose content and RVA profile were also analysed. The In1/Ex6 SNP haplotypes of Wx gene were found to explain 79 % of variation in apparent amylose content, and 36, 22 and 25 %, of variation in the RVA parameters peak viscosity, breakdown and setback, respectively. The additional use of (CT)n repeats marker further improved the association of haplotypes with RVA parameters. [ABSTRACT FROM AUTHOR]

Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by the fungus Pyrenochaeta lycopersici. However, little is known about the molecular bases of tomato-P. lycopersici interaction. In order to identify genes involved in the basal defence response activated in a susceptible cultivar and in disease symptom development, a set of cDNA-AFLP fragments derived from a profiling experiment was analysed. A total of 247 differentially expressed TDFs (transcript-derived fragments), identified as putative tomato genes, were characterized by similarity searches, and classified into 11 broad functional classes. Timings ranging between the early [48, 72 and 96 h post-infection (hpi)] and the late infection stages (20 and 27 dpi) were used. The changes of tomato root transcriptional profiles showed large differences in quantity and quality between the early and late stages of infection. Mechanisms of basal defence were most likely activated at early stages, when a gene coding for a receptor-like serine-threonine protein kinase and other genes of the signalling class were upregulated. At 20 dpi some of the mechanisms involved in defence were still activated, while at 27 dpi a general repression of gene expression was observed. [ABSTRACT FROM AUTHOR]

n association panel consisting of 185 accessions representative of the barley germplasm cultivated in the Mediterranean basin was used to localise quantitative trait loci (QTL) controlling grain yield and yield related traits. The germplasm set was genotyped with 1,536 SNP markers and tested for associations with phenotypic data gathered over 2 years for a total of 24 year × location combinations under a broad range of environmental conditions. Analysis of multi-environmental trial (MET) data by fitting a mixed model with kinship estimates detected from two to seven QTL for the major components of yield including 1000 kernel weight, grains per spike and spikes per m, as well as heading date, harvest index and plant height. Several of the associations involved SNPs tightly linked to known major genes determining spike morphology in barley ( vrs1 and int- c). Similarly, the largest QTL for heading date co-locates with SNPs linked with eam6, a major locus for heading date in barley for autumn sown conditions. Co-localization of several QTL related to yield components traits suggest that major developmental loci may be linked to most of the associations. This study highlights the potential of association genetics to identify genetic variants controlling complex traits. [ABSTRACT FROM AUTHOR]

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley. [ABSTRACT FROM AUTHOR]

Changes in alleles frequencies of marker loci linked to yield quantitative trait loci (QTL) were studied in 188 barley entries (landraces, old and modern cultivars) grown in six trials representing low and high yielding conditions in Spain (2004) and Syria (2004, 2005). A genome wise association analysis was performed per trial, using 811 DArT® markers of known map position. At the first stage of analysis, spatially adjusted genotypic means were created per trial by fitting mixed models. At the second stage, single QTL models were fitted with correction for population substructure, using regression models. Finally, multiple QTL models were constructed by backward selection from a regression model containing all significant markers from the single QTL analyses. In addition to the association analyses per trial, genotype by environment interaction was investigated across the six trials. Landraces seemed best adapted to low yielding environments, while old and modern entries adapted better to high yielding environments. The number of QTL and the magnitude of their effects were comparable for low and high input conditions. However, none of the QTL were found within a given bin at any chromosome in more than two of the six trials. Changes in allele frequencies of marker loci close to QTL for grain yield in landraces, old and modern barley cultivars could be attributed to selection exercised in breeding, suggesting that modern breeding may have increased frequencies of marker alleles close to QTL that favour production particularly under high yield potential environments. Moreover, these results also indicate that there may be scope for improving yield under low input systems, as breeding so far has hardly changed allele frequencies at marker loci close to QTL for low yielding conditions. [ABSTRACT FROM AUTHOR]

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectively. [ABSTRACT FROM AUTHOR]

In greenhouse studies of three alloplasmic wheat series, plant height, flowering date and yield per plant were least affected when the native cytoplasm was replaced by donor cytoplasm of the Triticum– Aegilops complex than when replaced by Hordeum chilense cytoplasm. On the other hand, significant differences for seed lutein content were found between euplasmic controls and their respective alloplasmic lines in all the alloplasmic lines studied, underscoring the important role of the cytoplasm to determine the seed carotenoid content. Both T. aestivum subesp. macha and Ae. squarrosa cytoplasms increased the lutein content. They may be the most useful sources of cytoplasmic variability for broadening the genetic diversity of wheat for seed carotenoid content since both cytoplasm types do not produce any detrimental effect on agronomic traits, as previously reported by other researchers. These findings demonstrate the role of the nuclear × cytoplasm interaction in the accumulation of carotenoids in wheat. [ABSTRACT FROM AUTHOR]

Barley is an economically important model for the Triticeae tribe. We recently developed a new resource: the ‘Nure’ × ‘Tremois’ mapping population. Two low temperature QTLs were found to segregate on the long arm of chromosome 5H ( Fr-H1, distal; Fr-H2, proximal). With the final aim of positional cloning of the genetic determinants of Fr-H1 and Fr-H2, a large segregating population of 1,849 F2 plants between parents ‘Nure’ and ‘Tremois’ was prepared. These two QT loci were first validated by using a set of F3 families, marker-selected to harbor pairs of reciprocal haplotypes, with one QTL fixed at homozygosity and the alternate one in heterozygous phase. The study was then focused towards the isolation of the determinant of Fr-H2. Subsequent recombinant screens and phenotypic evaluation of F4 segregants allowed us to estimate ( P ≤ 0.01) a refined genomic interval of Fr-H2 (4.6 cM). Several barley genes with the CBF transcription factor signature had been already roughly mapped in cluster at Fr-H2, and they represent likely candidate genes underlying this QTL. Using the large segregating population (3,698 gametes) a high-resolution genetic map of the Hv CBF gene cluster was then constructed, and after fine mapping, six recombinations between the Hv CBFs were observed. It was therefore possible to genetically divide seven Hv CBF subclusters in barley, in a region spanning 0.81 cM, with distances among them varying from 0.03 to 0.32 cM. The few recombinants between the different Hv CBF subclusters are being marker-selected and taken to homozygosity, to phenotypically separate the effects of the single Hv CBF genes. [ABSTRACT FROM AUTHOR]

It is generally assumed that compounds are emitted from flowers in order to attract and guide pollinators. Due to the invisibility and the highly variable nature of floral scent, no efficient and reliable methods to screen for genetic variation have been developed. Moreover, no convenient plant model systems are available for flower scent studies. In the past decade, several floral fragrance-related genes have been cloned; the biosynthesis and metabolic engineering of floral volatiles have been studied with the development of biotechnology. This review summarizes the reported floral fragrance-related genes and the biosynthesis of floral scent compounds, introduces the origin of new modification enzymes for flower scent, compares different methods for floral fragrance-related gene cloning, and discusses the metabolic engineering of floral scent. Finally, the perspectives and prospects of research on floral fragrance are presented. [ABSTRACT FROM AUTHOR]

Cereal crop yield is greatly affected in many growing areas by abiotic stresses, mainly low temperature and drought. In order to find candidates for the tolerance genes for these stresses, 13 genes encoding for transcription factors and upstream regulators were screened by amplification and SSCP on six parental genotypes of three barley mapping populations (‘Nure’ × ‘Tremois’, ‘Proctor’ × ‘Nudinka’, and ‘Steptoe’ × ‘Morex’), and mapped as newly developed STS, SNP, and SSCP markers. A new consensus function map was then drawn using the three maps above, including 16 regulatory candidate genes (CGs). The positions of barley cold and drought tolerance quantitative trait loci (QTLs) presently described in the literature were added to the consensus map to find positional candidates from among the mapped genes. A cluster of six Hv CBF genes co-mapped with the Fr-H2 cold tolerance QTL, while no QTLs for the same trait were positioned on chromosome 7H, where two putative barley regulators of CBF expression, ICE1 and FRY1, found by homology search, were mapped in this work. These observations suggest that CBF gene(s) themselves, rather than their two regulators, are at present the best candidates for cold tolerance. Four out of 12 drought tolerance QTLs of the consensus map are associated with regulatory CGs, on chromosomes 2H, 5H, and 7H, and two QTLs with effector genes, on chromosomes 5H and 6H. The results obtained could be used to guide MAS applications, allowing introduction into an ideal genotype of favourable alleles of tolerance QTLs. [ABSTRACT FROM AUTHOR]

Frost tolerance is an important trait for barley breeding. Field selection for this trait is not always efficient since, especially in Southern Europe, severe winter frost occurs erratically. Recent advances of cloned genes and molecular markers in barley provide molecular breeders with the means to develop new, simple PCR-based molecular markers, which can he used to select frost-tolerant genotypes quickly without stress simulation. This paper reports the development of two STS markers derived from the RFLP probes WG644 and PSR637, chosen as they are located on the long arm of homoeologous group 5 chromosomes of Triticeae, known to harbour the most important loci for frost tolerance. The two STS markers were validated together with one selected RAPT) marker, OPA /7, by separating two sets of winter and spring barley genotypes with different levels of frost tolerance. The ability of the developed markers to select segregant frost-tolerant and frost-susceptible genotypes was then investigated in a population of doubled haploid lines derived from a cross between a highly tolerant ('Nure') and a susceptible ('Tremois') genotype. In this population only two markers, OPA/7 and Psr637 demonstrated their efficiency in dividing the phenotypes according to the parental alleles. These two markers mapped on the long arm of chromosome 5H, tightly linked to two frost tolerance QTLs. Two polymorphic bands of the WG644 STS were mapped: the former on the long arm of chromosome 5H (Wg644c) and the latter (Wg644b) on the long arm of chromosome 2H. [ABSTRACT FROM AUTHOR]

Barley (Hordeum vulgare subsp. vulgare) is an economically important diploid model for the Triticeae; and a better understanding of low-temperature tolerance mechanisms could significantly improve the yield of fall-sown cereals. We developed a new resource for genetic analysis of winter hardiness-related traits, the ‘Nure’ × ‘Tremois’ linkage map, based on a doubled-haploid population that is segregating for low-temperature tolerance and vernalization requirement. Three measures of low-temperature tolerance and one measure of vernalization requirement were used and, for all traits, QTLs were mapped on chromosome 5H. The vernalization response QTL coincides with previous reports at the Vrn-1/Fr1 region of the Triticeae. We also found coincident QTLs at this position for all measures of low-temperature tolerance. Using Composite Interval Mapping, a second proximal set, of coincident QTLs for low-temperature tolerance, and the accumulation of two different COR proteins (COR14b and TMC-Ap3) was identified. The HvCBF4 locus, or another member of the CBF loci clustered in this region, is the candidate gene underlying this QTL. There is a CRT/DRE recognition site in the promoter of cor14b with which a CBF protein could interact. These results support the hypothesis that highly conserved regulatory factors, such as members of the CBF gene family, may regulate the stress responses of a wide range of plant species. [ABSTRACT FROM AUTHOR]

Leaf stripe caused by the fungus Pyrenophora graminea represents a serious threat to grain yield in organically grown barley and in conventional Nordic and Mediterranean districts, for which resistant cultivars are necessary. A medium-density, molecular marker map derived from a 'Steptoe' (partially resistant) × 'Morex' (susceptible) spring barley cross and its derived doubled-haploid mapping population inoculated with the fungus made it possible to identify QTLs of resistance to leaf stripe. In order to investigate isolate-specificity of partial resistance, the 'Steptoe' × 'Morex' segregating population was inoculated with two highly virulent P. graminea isolates, Dg2 and Dg5. The present study demonstrates that partial resistance to leaf stripe of cv 'Steptoe' is governed in part by shared loci and in part by isolate-specific ones. One QTL is common to the resistance for the two isolates, on the long arm of chromosome 2 (2H), two QTLs are linked on chromosome 3 (3H), and the remaining two are isolate-specific, respectively for isolate Dg2 on chromosome 2 (2H) and for isolate Dg5 on chromosome 7 (5H). The QTL in common is that with the major effect on the resistance for each isolate, explaining 18.3% and 30.9% R2 respectively for Dg2 and Dg5. The isolate-specific QTLs mapped in the 'Steptoe' × 'Morex' barley reference map support the assumption of Parlevliet and Zadoks (1977) that partial resistance may be due to minor gene-for-minor-gene interactions. Map comparisons of the QTLs with the known qualitative resistance genes to leaf stripe, Rdg1 (2H) and Rdg2 (7H), as well as with other QTLs of partial resistance in barley, show that the QTL for resistance to both isolates mapped on the long arm of chromosome 2 (2H) does not coincide with the qualitative Rdg1 gene but is linked to it at about 30 cM. One isolate-specific QTL of resistance to P. graminea, mapped on the short arm of chromosome 2 (2H), is coincident with a QTL for resistance to Pyrenophora teres previously mapped in the 'Steptoe' × 'Morex' cross. [ABSTRACT FROM AUTHOR]

Pyrenophora graminea is the seed-borne pathogen causal agent of barley leaf stripe disease. Near-isogenic lines (NILs) carrying resistance of the cv ”Thibaut” against the highly virulent isolate Dg2 were obtained by introgressing the resistance into the genetic background of the susceptible cv ”Mirco”. The segregation of the resistance gene was followed in a F2 population of 128 plants as well as on the F3 lines derived from the F2 plants; the segregation fitted the 1:2:1 ratio for a single gene. By using NILs, a RAPD marker associated with the resistance gene was identified; sequence-specific (STS) primers were designed on the basis of the amplicon sequence and a RILs mapping population with an AFLP-based map were used to position this molecular marker to barley chromosome 1 S (7HS). STS and CAPS markers were developed from RFLPs mapped to the telomeric region of barley chromosome 7HS and three polymorphic PCR-based markers were developed. The segregation of these markers was followed in the F2 population and their map position with respect to the resistance gene was determined. Our results indicate that the Thibaut resistance gene, which we designated as Rdg2a, maps to the telomeric region of barley chromosome 7HS and is flanked by the markers OPQ-9700 and MWG 2018 at distances of 3.1 and 2.5 cM respectively. The suitability of the PCR-based marker MWG2018 in selection- assisted barley breeding programs is discussed. [ABSTRACT FROM AUTHOR]

A major gene underlying quantitative resistance of barley against Pyrenophora graminea, a seedborne pathogen causing leaf stripe, was mapped with molecular markers in a barley doubled haploid (DH) population derived from the cross 'Proctor' x 'Nudinka'. This quantitative trait locus (QTL) accounts for r= 58.5% and was mapped on barley chromosome 1, tightly linked to the 'naked' gene. A second resistance QTL accounting for 29.3% of the variation in the trait was identified on the P arm of barley chromosome 2. Another two minor QTLs were detected by further analysis. None of the QTLs was found in the barley chromosome 2 'Vada' region studied by Giese et al. (1993). [ABSTRACT FROM AUTHOR]

Barley middle-repeat sequences were screened for their ability to discriminate 51 barley commercial varieties. Two hordein clones, a clone encoding a leaf-specific thionin, a desiccation induced cDNA clone, a clone coding for 5S-rRNA and one corresponding to ubiquitin genes were tested. A very sensitive RFLP technique including four cutter restriction enzymes and denaturing 4% polyacrylamide gels were used to evidence the highest level of polymorphism. The RFLP data were analyzed by computer. Some probe/enzyme combinations were able to differentiate a large number of the cultivars tested, whereas three probe/enzyme combinations succeeded in identifying all the varieties. The use of this RFLP method can thus be suggested for cultivar identification in barley. [ABSTRACT FROM AUTHOR]