Barley is an economically important model for the Triticeae tribe. We recently developed a new resource: the 'Nure' x '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 HvCBF gene cluster was then constructed, and after fine mapping, six recombinations between the HvCBFs were observed. It was therefore possible to genetically divide seven HvCBF 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 HvCBF subclusters are being marker-selected and taken to homozygosity, to phenotypically separate the effects of the single HvCBF genes.
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.
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 r ² 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.
Tomato (
Solanum lycopersicum
Mill.) is sensitive to chilling stress during all stages of plant development. Genetic variation for chilling tolerance exists between cultivated tomato and its related ...wild species, but intra-specific variation has not been thoroughly investigated so far. Seedlings of 63 tomato accessions were evaluated under low temperature and two contrasting cultivars were identified for the trait: Albenga and San Marzano, the former being more chillingtolerant. To clarify the molecular mechanisms of chilling tolerance in tomato, changes in candidate gene expressions in the two tomato genotypes were analysed, using quantitative RT-PCR. Candidate genes were chosen among those known to be induced by chilling and/or with putative roles in CBF/DREB and ROS-mediated pathways. Results show that besides a CBF regulon, whose function is conserved, ROS and C2H2-type zinc finger protein-mediated cold signalling pathways were also involved in chilling tolerance. Under the chilling stress, the up-regulation of respective transcripts was consistently higher in the chilling-tolerant genotype than in the chilling-sensitive ones.
Iodine is an essential microelement for human health, and the recommended daily allowance (RDA) of such element should range from 40 to 200 μg day−1. Because of the low iodine contents in vegetables, ...cereals, and many other foods, iodine deficiency disorder (IDD) is one of the most widespread nutrient-deficiency diseases in the world. Therefore, investigations of I uptake in plants with the aim of fortifying them can help reach the important health and social objective of IDD elimination. This study was conducted to determine the effects of the absorption of iodine from two different chemical forms—potassium iodide (I−) and potassium iodate (IO− 3)—in a wide range of wild and cultivated plant species. Pot plants were irrigated with different concentrations of I− or IO− 3, namely 0.05% and 0.1% (w/v) I− and 0.05%, 0.1%, 0.2%, and 0.5% (w/v) IO− 3. Inhibiting effects on plant growth were observed after adding these amounts of iodine to the irrigation water. Plants were able to tolerate high levels of iodine as IO− 3 better than I− in the root environment. Among cultivated species, barley (Hordeum vulgare L.) showed the lowest biomass reductions due to iodine toxicity and maize (Zea mays L.) together with tobacco (Nicotiana tabacum L.) showed the greatest. After the screening, cultivated tomato and potato were shown to be good targets for a fortification-rate study among the species screened. When fed with 0.05% iodine salts, potato (Solanum tuberosum L.) tubers and tomato (Solanum lycopersicum L.) fruits absorbed iodine up to 272 and 527 μg/100 g fresh weight (FW) from IO− 3 and 1,875 and 3,900 μg/100 g FW from I−. These uptake levels were well more than the RDA of 150 μg day−1 for adults. Moreover, the agronomic efficiency of iodine accumulation of potato tubers and tomato fruits was calculated. Both plant organs showed greater accumulation efficiency for given units of iodine from iodide than from iodate. This accumulation efficiency decreased in both potato tubers and tomato fruits at iodine concentrations greater than 0.05% for iodide and at respectively 0.2% and 0.1% for iodate. On the basis of the uptake curve, it was finally possible to calculate the doses of supply in the irrigation water of iodine as iodate (0.028% for potato and 0.014% for tomato) as well as of iodide (0.004% for potato and 0.002% for tomato) to reach the 150 μg day−1 RDA for adults in 100 g of such vegetables, to efficiently control IDD, although these results still need to be validated.
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' x 'Tremois', 'Proctor' x 'Nudinka', and 'Steptoe' x '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 HvCBF 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.
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.
An 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 m², 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.
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.
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' x '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.
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