Germplasm molecular and phenotypic characterization is instrumental to its utilization and to genetic variability incorporation into rice breeding programmes. The diversity within 192 Japanese rice accessions was analysed for 22 agro-morphological traits and 24 single sequence repeat markers. A total of 181 alleles were detected, 38 of which were exclusive. The number of alleles/marker ranged from 2 to 16, with an average of 7.54 alleles/locus and the He value ranged from 0.01 to 0.82, with an average of 0.46. The accessions showed diversity at molecular and phenotypic level and few showed also good agronomic performance. Tocher's method applied on a total-dissimilarity matrix was used to determine cluster formation of 13 diversity groups. Most of the accessions (81%) were clustered within a group, whereas eight accessions (Kyuushuu, Eika Ine, Ishiwari Mochi, Col/Fukui/1965, Ookuma Nishiki, Suzume Shirazu, Iwate Ryoon and Toga) did not cluster with other accessions.

In South Europe, rice is grown as an irrigated crop in river deltas where it plays an important role in soil desalinization. Specific varieties are needed for these tough conditions. We analyzed the genetic structure of a set of 305 varieties coming from the European Rice Germplasm Collection (ERGC) with 90 single nucleotide polymorphisms and compared it with a reference set representative of the diversity of Oryza sativa (mini-Germplasm Bank (GB)). These accessions had been characterized for their grain type and growth cycle duration. The polymorphism information contents of the ERGC were lower than those of the mini-GB, indicating a narrower genetic basis. Indeed, almost all ERGC accessions belong to the japonica group. Within the japonica group, both a dendrogram and a Bayesian clustering identified two major clusters. The first cluster encompassed tropical japonicas and American varieties from USA and Argentina characterized by long and narrow grains and medium to long duration. On a finer level, tropical japonicas appear separated from the other accessions. The second cluster is composed of European varieties mostly early or medium in duration and Asian temperate accessions, with a subgrouping based on grain format. A set of 200 accessions was composed for association mapping studies on traits such as salt tolerance.

Root lesion nematodes of the genus Pratylenchus are important pests in crop cultivation that cause severe damage to crops throughout the world. P. neglectus is one of the most important members of this genus. The present study aimed to select barley accessions with resistance to P. neglectus in a greenhouse resistance test and to detect resistance quantitative trait loci (QTLs). Infection rates have been found to vary greatly among different barley accessions; however, immunity could not be found. An existing Igri × Franka doubled-haploid mapping population was used to map resistance genes after artificial inoculation with P. neglectus under controlled environment. QTLs were found with a likelihood of odds score between 2.71 and 6.35 and explaining phenotypic variation of 8 to 16%.

A germplasm panel of 52 six-rowed barley landraces from northern Morocco was analysed by a Cleaved Amplified Polymorphic Sequences (CAPS) assay of a fragment of the elongation factor G (EF-G) gene. Forty-nine of these accessions carried allele A, and the other three carried allele D. The latter all originated from a narrow region close to the border with Algeria, whereas the former were represented across the whole collection area. Since six-rowed D allele carriers are present in North Africa, along with both two-rowed cultivated and wild barleys, it is likely that the European six-rowed barley varieties carrying the D allele have Moroccan parentage.

Microsatellite markers (simple sequence repeats, SSRs) are used for a wide range of crop genetic and breeding applications, including genetic diversity assessment, phylogenetic analysis, genotypic profiling and marker-assisted selection. Genomic SSR (gSSR) have attracted more attention because of abundance in plant genome, reproducibility, high level of polymorphism and codominant inheritance. Recently, the availability of data for expressed sequence tags (EST), has given more emphasis to EST-derived SSRs, which belong to the transcribed regions of DNA, and are expected to be more conserved and have a higher transferability rate across species than gSSR markers. In the present study, several gSSR and EST-SSR markers were investigated for their transferability and level of DNA polymorphism in different ancestral tetraploid and diploid Triticum and Aegilops species. The same gSSR and EST-SSR markers were also evaluated for their applicability in the phylogenetic analysis of wheat. Both gSSR and EST-SSR markers showed differences for the average transferability rate and the number of alleles/locus. Phylogenetic trees based on gSSR and EST-SSR markers were in accordance with phylogenetic relations based on cytogenetic and molecular analyses.

A drought-related gene belonging to the Dehydration Responsive Element Binding protein (DREB) family has been reported and characterized in durum wheat. Unlike other DREB-homologous genes, it consists of four exons and three introns and produces three transcripts by an alternative splicing mechanism. The gene sequence was analysed in a number of varieties/lines/accessions of durum wheat, triticale and in wheat genome donors, Aegilops speltoides, A. tauschii and Triticum urartu, in order to evaluate the variability and to detect other interesting molecular features. Herewith, some results are presented. In the exon 1, a single sequence repeat codifying for a stretch of alanine residues variable in length (from 3 to 7), was identified. A novel non-autonomous transposon was identified, encompassing the intron1–intron3 region and this was characterized in detail. Part of the exon 4, containing the APetala2 (AP2) domain, responsible for DNA recognition and binding, was isolated and sequenced in a collection of Aegilops species and A. speltoides accessions from the Fertile Crescent, a region characterized by a high wheat biodiversity. Although the 338 bp-long analysed sequences did not reveal substantial differences in the polymorphic patterns, using a geographic subdivision with three clusters (east, centre and west), they completely separated Aegilops from the A. speltoides genus.

Allele composition at the major growth habit (Ppd-D1, Vrn-1, Rht-1 and Rht8) loci was determined in 52 Bulgarian bread wheat cultivars and landraces, using recently developed diagnostic molecular markers. The study showed that Bulgarian wheat germplasm varies for photoperiod, vernalization and height-reducing genes. The photoperiod-sensitive allele (Ppd-D1b) was the most frequent one in the old cultivars and landraces (90.9%), while the photoperiod-insensitive allele (Ppd-D1a) showed the highest frequency in the modern cultivars (96.71%). The alleles conferring winter growth habit (vrn-A1, vrn-B1 and vrn-D1) were more common in both the old (72.7%) and the modern (93.3%) wheat genotypes. The spring allele Vrn-A1c was not detected in Bulgarian germplasm, while the spring allele Vrn-B1 was found only in the old genotypes (13.6%). The semi-dwarfing allele Rht-B1b was observed in several modern cultivars. Seven allele variants were found in the microsatellite locus Xgwm261, closely located to the Rht8 gene. Among them, alleles of 164, 212 and 216 bp length were specific for the old genotypes studied, while alleles of 192 and 202 bp length were specific for the modern ones. The allele combination Rht-B1b//192 or 202 bp allele (Xgwm261 locus)//Ppd-D1a//vrn-A1/vrn–B1/vrn-D1 was detected in most of the early-heading modern cultivars. Our study emphasizes on the plasticity of the adaptive response of bread wheat cultivars sown in Bulgaria, as well as on the effect of variation for major growth habit on some yield and reproductive characteristics.

The objective of our study was to determine the composition of high-molecular weight-glutenin subunits (HMW-GS) in 120 cultivars of common wheat (Triticum aestivum L.). Fourteen alleles and 34 allelic compositions were detected using sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The most frequent HMW-GS alleles at the Glu-A1, Glu-B1 and Glu-D1 loci were null (57.1%), 7+9 (43.3%) and 5+10 (61.9%), respectively. However, low-frequency HMW-GS alleles were also observed, such as 13+16, 20, 21, 7 and 18, encoded by the Glu-B1 locus, and 4+12, encoded by the Glu-D1 locus. The wheat–rye 1BL.1RS translocation was identified in 25 cultivars, using acid polyacrylamide gel electrophoresis. The Glu-score varied greatly, and some lines reached the maximum value of 10.

Although oilseed rape has become one of the most important oil crops in Europe, little is known regarding the viability of its seed under conditions of long-term storage. We report here an examination of oilseed rape seed longevity performed on a set of 42 accessions housed at the German ex situ genebank at IPK, Gatersleben. A comparison of germination between the accessions stored for 26 years showed that viability was in part genetically determined, since it ranged between 42 and 98%. An attempt was made to define the genetic basis of viability by subjecting a mapping population of doubled haploids to three artificial ageing treatments. Quantitative trait loci (QTL) were detected on six chromosomes: N6, N7, N8, N15, N16 and N18. The chromosomal locations of these QTL were compared with their syntenic regions in Arabidopsis thaliana in order to explore what genes might underlie genetic variation for longevity.

The worldwide spread of barley cultivation required adaptation to agricultural environments far distant from those found in its centre of domestication. An important component of this adaptation is the timing of flowering, achieved predominantly in response to day length and temperature. Here, we use a collection of cultivars, landraces and wild barley accessions to investigate the origins and distribution of allelic diversity at four major flowering time loci, mutations at which have been under selection during the spread of barley cultivation into Europe. Our findings suggest that while mutant alleles at the PPD-H1 and PPD-H2 photoperiod loci occurred pre-domestication, the mutant vernalization non-responsive alleles utilized in landraces and cultivars at the VRN-H1 and VRN-H2 loci occurred post-domestication. The transition from wild to cultivated barley is associated with a doubling in the number of observed multi-locus flowering-time haplotypes, suggesting that the resulting phenotypic variation has aided adaptation to cultivation in the diverse ecogeographic locations encountered. Despite the importance of early-flowering alleles during the domestication of barley in Europe, we show that novel VRN alleles associated with early flowering in wild barley have been lost in domesticates, highlighting the potential of wild germplasm as a source of novel allelic variation for agronomic traits.

An integrated approach based on the use of bioinformatics and gene expression analysis tools was carried out to evaluate the organ-specific transcription modulation of nine genes relevant to sugar metabolism of Beta vulgaris L. plantlets of the autumn cv. Franca and spring cv. Bianca, in response to low-temperature (LT) treatments. Different growth cycles imply different plant capability to adapt to the environment that includes variations in gene expression of key metabolic enzymes. The transcriptional response was evaluated by quantitative PCR analysis before, during and after the LT treatments. The results were correlated with the LT-induced electrolyte leakage measure and the carbohydrate content. Stress-induced transcript level alterations were detected in the two cultivars, suggesting a modulation of sucrose synthesis and carbohydrate partitioning. Cold stress induced deep changes in the autumn cultivar, especially in fructose-1,6-biphosphatase gene expression, irrespective of temperature or exposure time. These differential features of expression profiles constitute first clues on the molecular basis of the differential LT response of sugarbeet autumn and spring cultivars.

Pine wilt disease, caused by the pinewood nematode Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, is originating severe infections in pine trees. The disease is detected when external symptoms appear (e.g. needle chlorosis), but trees could remain asymptomatic for long periods and serve as a long-term host. The primary goal of this study was to assess the effect of inoculation with an avirulent isolate of B. xylophilus (C14-5) on different Pinus spp. seedlings (P. sylvestris, P. nigra, P. pinea and P. pinaster). At the same time, seedlings were also inoculated with a virulent strain, HF, in order to compare the phenotypic and genomic results of the two types of inoculations. The effect of inoculation was determined in terms of expression of various Pinus genes potentially involved in the response to the disease.The results suggest that P. pinea and P. nigra are more resistant to infection by the nematode than P. sylvestris and P. pinaster. The phenotypic and genetic differences were more marked among P. pinea and P. pinaster.

To date, very limited molecular knowledge and molecular tools are available on grass pea (Lathyrus sativus L.). Herein, we present a genetic diversity analysis of 20 grass pea accessions collected from various regions of Ethiopia by means of seven newly developed Lathyrus expressed sequence tag-derived simple sequence repeat (EST-SSR) markers and four cross-transferable EST-SSRs derived from Medicago truncatula L. Forty-five alleles were detected among all the analyzed accessions. The number of alleles/locus ranged from two to seven with an average of four alleles/locus. The observed heterozygosity (Ho) ranged from 0.320 to 0.504, while the expected heterozygosity (He) ranged from 0.354 to 0.470. FST values estimated by analysis of molecular variance were 0.01, 0.15 and 0.84 for among regions, among accessions and within accessions, respectively, indicating that most of the variation (84%) resides within accession. The model-based cluster analysis grouped the accessions into three clusters grouping accessions, irrespective of their collection regions.

Response to selection is fundamental to plant breeding. To gain insight into the genetic basis of response to selection, we propose a new experimental genetic framework allowing for the identification of trait-specific genomic loci underlying population improvement and the characterization of allelic frequency responses at those loci. This is achieved by employing a sampling scheme for recurrently selected populations that allows for the simultaneous application of genetic association mapping and analysis of allelic frequency change across generations of selection. The combined method unites advantages of the two approaches, permitting the estimation of trait-specific allelic effects by association mapping and the detection of rare favourable alleles by their significant enrichment over generations of selection. Our aim is to develop a framework applicable for many crop species in order to gain a broader and deeper understanding of the genetic architecture of response to artificial selection.

Sugarbeet cultivars are almost exclusively hybrids, which are produced using the sole source of cytoplasmic male sterility (CMS), the so-called Owen CMS. Several alternative sources of CMS have been described. One of these, I-12CMS(3), was derived from wild beets collected in Pakistan, and another CMS source, GCMS, has a cytoplasmic origin in wild sea beets from France. During the past decade, male sterility-associated mitochondrial genes have been identified in these three CMS systems. Moreover, the recent development of a variety of DNA markers has permitted the genetic mapping of nuclear restorer-of-fertility genes for both Owen and GCMS. This review focuses on the mechanism of CMS in beets.

Double ‘free-hybrids’ (DH) in alfalfa were obtained by crossing in a diallelic scheme, six multiplied simple hybrids (SH) derived from four partly inbred (S2) lines. Analysis of the specific combining ability demonstrated that the main source of variation was for dry matter yield (DMY) in DHs and supported heterosis values of DHs versus the best parent of an average +45% (ranging from +5 to +76%). Investigation at the molecular level was carried out by analysis of simple sequence repeat markers on the six parental SHs and 15 DH progenies and by comparison of gene expression profiles using microarrays of a single DH line to its parental lines. The variation of heterozygosity estimates of the DHs explained a small part (about 20%) of their variation in DMY, while the number of alleles was significantly related to DM performance (r = 0.61; P < 0.05). The microarray analysis identified genes with both significant additive and non-additive levels of expression in the hybrid compared with the parents. The majority of the variation in gene expression was additive (87%), but among the genes with a non-additive pattern of expression, the greater proportion of probe sets (86%) fell outside the parental range. Gene ontology analysis of these genes revealed the presence of a number of terms related to metabolism and genetic information processing.

Drought is one of the major factors limiting wheat yield in many developing countries worldwide. Parameters of chlorophyll a fluorescence kinetics under drought stress conditions have been used to characterize dehydration tolerance in wheat. In the present study, a set of 94 doubled haploid lines obtained from Chinese Spring × SQ1 (CSDH), mapped with 450 markers, was evaluated for yield (grain dry weight/main stem ear), number of grains/main stem ear (NG) and chlorophyll a fluorescence parameters (FC) under moderate and severe drought stress, and compared with results for well-watered plants. quantitative trait loci (QTLs) were identified using Windows QTLCartographer version 2.5 software and the results were analysed using single-marker analysis (SMA) and composite interval mapping (CIM). Analysis using SMA and CIM showed mostly similar QTLs for all traits, though more QTLs were identified by SMA than by CIM. The genetic control of yield, NG and FC varied considerably between drought-stressed and non-stressed plants. Although no major QTL co-locations were found for yield and FC using CIM, the co-location of QTLs for NG, yield and Fv/Fm in drought-stressed plants was observed on chromosome 5A using SMA.

Snow mould caused by Microdochium nivale (Fr.) Samuels & Hallett is the most widespread seedling disease in winter cereals. Due to the complexity of the resistance mechanisms, a poorly understood genetic background and strong interaction with winter weather conditions, it is difficult to assess the resistance of triticale cultivars via conventional inoculation methods. Genetic resistance is the most economical and environmental friendly way to control M. nivale infection; therefore, the objective of this study was to detect the quantitative trait loci (QTLs) associated with resistance components of winter triticale in a mapping population derived from a cross of the ‘Modus’ (partly resistant) and ‘SaKa 3006’ (sensitive) varieties. High-resolution mapping was conducted by using 1518 molecular markers (diversity arrays technology, simple sequence repeat and amplified fragment length polymorphism). Partial resistance components assessed in this study, i.e. candidate QTLs, were detected on chromosomes 1B, 2A, 3A, 3B, 5A, 5B, 6A, 6B and 7B, whereas QTLs describing overall seedling vitality in non-infected control plants were located on chromosomes 1B, 2B, 3A, 5A, 7B and 7R.

Rice is a salt-sensitive species with enormous genetic variation for salt tolerance hidden in its germplasm pool. The EcoTILLING technique allows us to assign haplotypes, thus reducing the number of accessions to be sequenced, becoming a cost-effective, time-saving and high-throughput method, ideal to be used in laboratories with limited financial resources. Aiming to find alleles associated with salinity tolerance, we are currently using the EcoTILLING technique to detect single nucleotide polymorphisms (SNPs) and small indels across 375 germplasm accessions representing the diversity available in domesticated rice. We are targeting several genes known to be involved in salt stress signal transduction (OsCPK17) or tolerance mechanisms (SalT). So far, we found a total of 15 and 23 representative SNPs or indels in OsCPK17 and SalT, respectively. These natural allelic variants are mostly located in 3′-untranslated region, thus opening a new path for studying their potential contribution to the regulation of gene expression and possible role in salt tolerance.

A coiled coil-nucleotide binding site-leucine-rich repeat gene RB/Rpi-blb1 isolated from Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans and is currently employed in potato breeding for durable late blight (LB) resistance. RB homologues were reported in several Solanum species; some of them retained defence function. Here, we report additional evidence on RB-like sequences in 21 Solanum species of the section Petota. The panel of Solanum species was screened with three RB-related PCR markers. RB-like sequences were found in every tested Solanum accession, suggesting universal distribution of RB structural homologues among Solanum genomes, while locus-specific RB-629 was found only in 15 species. Phylogenetic analysis of RB-629 sequences suggested a highly conservative pattern of polymorphisms that was neither species- nor series-specific. Apparently, duplication and evolution of RB-like loci preceded Solanum speciation. Marker presence and particular haplotypes were not immediately associated with high LB resistance.