Segmental duplications are hot spots of copy number variants affecting barley gene content.

Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and for identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16 605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. The present study delivers a comprehensive genome-wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs.

Transcriptomics, chromosome engineering and mapping identify a restorer-of-fertility region in the CMS wheat system msH1.

KEY MESSAGE: An original RNA-seq mapping strategy, validated with chromosome engineering and physical mapping, identifies candidate genes for fertility restoration in the 6HchS chromosome of Hordeum chilense in the wheat msH1 system. Cytoplasmic male sterility (CMS) is a valuable trait for hybrid seed production. The msH1 CMS system in common wheat results from the incompatibility between the nuclear genome of wheat and the cytoplasm of the wild barley Hordeum chilense. This work aims to identify H. chilense candidate genes for fertility restoration in the msH1 system with a multidisciplinary strategy based on chromosome engineering, differential expression analysis and genome mapping. Alloplasmic isogenic wheat lines differing for fertility, associated with the presence of an acrocentric chromosome Hchac resulting from the rearrangement of the short arms of H. chilense chromosomes 1Hch and 6Hch, were used for transcriptome sequencing. Two novel RNA-seq mapping approaches were designed and compared to identify differentially expressed genes of H. chilense associated with male fertility restoration. Minichromosomes (Hchmi), new smaller reorganizations of the Hchac also restoring fertility, were obtained and used to validate the candidate genes. This strategy was successful identifying a putative restorer-of-fertility region on 6HchS, with six candidate genes, including the ortholog of the barley restorer gene Rfm1. Additionally, transcriptomics gave preliminary insights on sterility and restoration networks showing the importance of energy supply, stress, protein metabolism and RNA processing.

Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties.

BACKGROUND: Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susceptibility among grapevine varieties suggest the existence of specific genetic features associated with resistance to the phytoplasma and/or possibly with its vector. In this work, RNA-Seq was used to compare early transcriptional changes occurring during the three-trophic interaction between the phytoplasma, its vector and the grapevine, represented by two different cultivars, one very susceptible to the disease and the other scarcely susceptible. RESULTS: The comparative analysis of the constitutive transcriptomic profiles suggests the existence of passive defense strategies against the insect and/or the phytoplasma in the scarcely-susceptible cultivar. Moreover, the attack by the infective vector on the scarcely-susceptible variety prompted immediate and substantial transcriptomic changes that led to the rapid erection of further active defenses. On the other hand, in the most susceptible variety the response was delayed and mainly consisted of the induction of phytoalexin synthesis. Surprisingly, the jasmonic acid- and ethylene-mediated defense reactions, activated by the susceptible cultivar following FD-free insect feeding, were not detected in the presence of the phytoplasma-infected vector. CONCLUSIONS: The comparison of the transcriptomic response in two grapevine varieties with different levels of susceptibility to Flavescence dorèe highlighted both passive and active defense mechanisms against the vector and/or the pathogen in the scarcely-susceptible variety, as well as the capacity of the phytoplasmas to repress the defense reaction against the insect in the susceptible variety.

Correction to: Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1.

Following publication of the original article [1], we have been notified that some important information was omitted by the authors in the Copyright note. The Copyright note should read as below.

Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1.

BACKGROUND: Fusarium head blight (FHB) is a problem of great concern in small grain cereals, especially wheat. A quantitative trait locus (QTL) for FHB resistance (FHB_SFI) located on the long arm of chromosome 2D in the spring wheat genotype Wuhan 1 is a resistance locus which has potential to improve the FHB resistance of bread wheat since it confers effective resistance to wheat breeding lines. Recently, differentially expressed genes (DEG) have been identified by comparing near isogenic lines (NIL) carrying the susceptible and resistant alleles for the 2DL QTL, using RNA-Seq. In the present study, we aimed to identify candidate genes located within the genetic interval for the 2DL QTL for FHB resistance, as assessed by single floret inoculation (FHB_SFI), and possibly contributing to it. RESULTS: Combining previous and additional bioinformatics analyses, 26 DEG that were located on chromosome arm 2DL were selected for further characterization of their expression profile by RT-qPCR. Seven of those DEG showed a consistent differential expression profile between either three pairs of near isogenic lines or other genotypes carrying the R and S alleles for the 2DL QTL for FHB resistance. UN25696, which was identified in previous expression work using microarray was also confirmed to have a differential expression pattern. Those eight candidate genes were further characterized in 85 lines of a double haploid mapping population derived from the cross Wuhan 1/Nyubai, the population where the 2DL QTL was originally identified. The expression QTL for gene Traes_2DL_179570792 overlapped completely with the mapping interval for the 2DL QTL for FHB_SFI while the expression QTL for UN25696 mapped near the QTL, but did not overlap with it. None of the other genes had a significant eQTL on chromosome 2DL. Higher expression of Traes_2DL_179570792 and UN25696 was associated with the resistant allele at that locus. CONCLUSIONS: Of the 26 DEG from the 2DL chromosome further characterized in this study, only two had an expression QTL located in or near the interval for the 2DL QTL. Traes_2DL_179570792 is the first expression marker identified as associated with the 2DL QTL.

Native soils with their microbiotas elicit a state of alert in tomato plants.

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The 'state of alert' detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi.

BACKGROUND: Fusarium fujikuroi is the causal agent of bakanae, the most significant seed-borne disease of rice. Molecular mechanisms regulating defence responses of rice towards this fungus are not yet fully known. To identify transcriptional mechanisms underpinning rice resistance, a RNA-seq comparative transcriptome profiling was conducted on infected seedlings of selected rice genotypes at one and three weeks post germination (wpg). RESULTS: Twelve rice genotypes were screened against bakanae disease leading to the identification of Selenio and Dorella as the most resistant and susceptible cultivars, respectively. Transcriptional changes were more appreciable at 3 wpg, suggesting that this infection stage is essential to study the resistance mechanisms: 3,119 DEGs were found in Selenio and 5,095 in Dorella. PR1, germin-like proteins, glycoside hydrolases, MAP kinases, and WRKY transcriptional factors were up-regulated in the resistant genotype upon infection with F. fujikuroi. Up-regulation of chitinases and down-regulation of MAP kinases and WRKY transcriptional factors were observed in the susceptible genotype. Gene ontology (GO) enrichment analyses detected in Selenio GO terms specific to response to F. fujikuroi: 'response to chitin', 'jasmonic acid biosynthetic process', and 'plant-type hypersensitive response', while Dorella activated different mechanisms, such as 'response to salicylic acid stimulus' and 'gibberellin metabolic process', which was in agreement with the production of gibberellin A3 in Dorella plants. CONCLUSIONS: RNA-seq profiling was performed for the first time to analyse response of rice to F. fujikuroi infection. Our findings allowed the identification of genes activated in one- and three- week-old rice seedlings of two genotypes infected with F. fujikuroi. Furthermore, we found the pathways involved in bakanae resistance, such as response to chitin, JA-dependent signalling and hypersensitive response. Collectively, this provides important information to elucidate the molecular and cellular processes occurring in rice during F. fujikuroi infection and to develop bakanae resistant rice germplasm.

Genetic analysis of durable resistance to Magnaporthe oryzae in the rice accession Gigante Vercelli identified two blast resistance loci.

Rice cultivars exhibiting durable resistance to blast, the most important rice fungal disease provoking up to 30 % of rice losses, are very rare and searching for sources of such a resistance represents a priority for rice-breeding programs. To this aim we analyzed Gigante Vercelli (GV) and Vialone Nano (VN), two temperate japonica rice cultivars in Italy displaying contrasting response to blast, with GV showing a durable and broad-spectrum resistance, whereas VN being highly susceptible. An SSR-based genetic map developed using a GV × VN population segregating for blast resistance identified two blast resistance loci, localized to the long arm of chromosomes 1 and 4 explaining more than 78 % of the observed phenotypic variation for blast resistance. The pyramiding of two blast resistance QTLs was therefore involved in the observed durable resistance in GV. Mapping data were integrated with information obtained from RNA-seq expression profiling of all classes of resistance protein genes (resistance gene analogs, RGAs) and with the map position of known cloned or mapped blast resistance genes to search candidates for the GV resistant response. A co-localization of RGAs with the LOD peak or the marker interval of the chromosome 1 QTL was highlighted and a valuable tool for selecting the resistance gene during breeding programs was developed. Comparative analysis with known blast resistance genes revealed co-positional relationships between the chromosome 1 QTL with the Pi35/Pish blast resistance alleles and showed that the chromosome 4 QTL represents a newly identified blast resistance gene. The present genetic analysis has therefore allowed the identification of two blast resistance loci in the durable blast-resistant rice cultivar GV and tools for molecular selection of these resistance genes.

Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits.

BACKGROUND: Rice represents one the most important foods all over the world. In Europe, Italy is the first rice producer and Italian production is driven by tradition and quality. All main rice grain quality traits, like cooking properties, texture, gelatinization temperature, chalkiness and yield, are related to the content and composition of starch and seed-storage proteins in the endosperm and to grain shape. In addition, a number of nutraceutical compounds and allergens are known to have a significant effect on grain quality determination. To investigate the genetic bases underlying the qualitative differences that characterize traditional Italian rice cultivars, a comparative RNA-Seq-based transcriptomic analysis of developing caryopsis was conducted at 14 days after flowering on six popular Italian varieties (Carnaroli, Arborio, Balilla, Vialone Nano, Gigante Vercelli and Volano) phenotypically differing for qualitative grain-related traits. RESULTS: Co-regulation analyses of differentially expressed genes showing the same expression patterns in the six genotypes highlighted clusters of loci up or down-regulated in specific varieties, with respect to the others. Among them, we detected loci involved in cell wall biosynthesis, protein metabolism and redox homeostasis, classes of genes affecting in chalkiness determination. Moreover, loci encoding for seed-storage proteins, allergens or involved in the biosynthesis of specific nutraceutical compounds were also present and specifically regulated in the different clusters. A wider investigation of all the DEGs detected in pair-wise comparisons revealed transcriptional variation, among the six genotypes, for quality-related loci involved in starch biosynthesis (e.g. GBSSI, starch synthases and AGPase), genes encoding for transcription factors, additional seed storage proteins, allergens or belonging to additional nutraceutical compounds biosynthetic pathways and loci affecting grain size. Putative functional SNPs associated to amylose content in starch, gelatinization temperature and grain size were also identified. CONCLUSIONS: The present work represents a more extended phenotypic characterization of a set of rice accessions that present a wider genetic variability than described nowadays in literature. The results provide the first transcriptional picture for several of the grain quality differences observed among the Italian rice varieties analyzed and reveal that each variety is characterized by the over-expression of a peculiar set of loci affecting grain appearance and quality. A list of candidates and SNPs affecting specific grain properties has been identified offering a starting point for further works aimed to characterize genes and molecular markers for breeding programs.

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism.

BACKGROUND: Tomato (Solanum lycopersicum) establishes a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The formation of the mycorrhizal association in the roots leads to plant-wide modulation of gene expression. To understand the systemic effect of the fungal symbiosis on the tomato fruit, we used RNA-Seq to perform global transcriptome profiling on Moneymaker tomato fruits at the turning ripening stage. RESULTS: Fruits were collected at 55 days after flowering, from plants colonized with Funneliformis mosseae and from control plants, which were fertilized to avoid responses related to nutrient deficiency. Transcriptome analysis identified 712 genes that are differentially expressed in fruits from mycorrhizal and control plants. Gene Ontology (GO) enrichment analysis of these genes showed 81 overrepresented functional GO classes. Up-regulated GO classes include photosynthesis, stress response, transport, amino acid synthesis and carbohydrate metabolism functions, suggesting a general impact of fungal symbiosis on primary metabolisms and, particularly, on mineral nutrition. Down-regulated GO classes include cell wall, metabolism and ethylene response pathways. Quantitative RT-PCR validated the RNA-Seq results for 12 genes out of 14 when tested at three fruit ripening stages, mature green, breaker and turning. Quantification of fruit nutraceutical and mineral contents produced values consistent with the expression changes observed by RNA-Seq analysis. CONCLUSIONS: This RNA-Seq profiling produced a novel data set that explores the intersection of mycorrhization and fruit development. We found that the fruits of mycorrhizal plants show two transcriptomic "signatures": genes characteristic of a climacteric fleshy fruit, and genes characteristic of mycorrhizal status, like phosphate and sulphate transporters. Moreover, mycorrhizal plants under low nutrient conditions produce fruits with a nutrient content similar to those from non-mycorrhizal plants under high nutrient conditions, indicating that AM fungi can help replace exogenous fertilizer for fruit crops.

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici.

BACKGROUND: Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production. RESULTS: We assembled a 54.9Mb P. lycopersici draft genome sequence based on Illumina short reads, and annotated approximately 17,000 genes. The P. lycopersici genome is closely related to hemibiotrophs and necrotrophs, in agreement with the phenotypic characteristics of the fungus and its lifestyle. Several gene families related to host-pathogen interactions are strongly represented, including those responsible for nutrient absorption, the detoxification of fungicides and plant cell wall degradation, the latter confirming that much of the genome is devoted to the pathogenic activity of the fungus. We did not find a MAT gene, which is consistent with the classification of P. lycopersici as an imperfect fungus, but we observed a significant expansion of the gene families associated with heterokaryon incompatibility (HI). CONCLUSIONS: The P. lycopersici draft genome sequence provided insight into the molecular and genetic basis of the fungal lifestyle, characterizing previously unknown pathogenic behaviors and defining strategies that allow this asexual fungus to increase genetic diversity and to acquire new pathogenic traits.

Identification of biomarker genes from multiple studies for abiotic stress in maize through machine learning.

Abiotic stresses are major limiting factors for maize growth. Therefore, exploration of the mechanisms underlying the response to abiotic stress in maize is of great interest. Toward this end, we performed integration of the feature selection method into the meta-analysis of microarray gene expression. Following extraction of raw data, normalization, and batch effect removal, the data were merged into one expression profile. Differentially expressed genes (DEGs) between control and abiotic conditions were used for the feature selection algorithm to find the minimum features for high-performance classification. Feature selection was performed using a correlation-based feature selection (CFS) algorithm, considering features with a coefficient of 0.7 to 1. Different algorithms of Bayes, Functions, Lazy, Meta, Rules, and Trees were then tested in order to classify the samples and find the best performance classifier in each group. Moreover, the biological pathways and promoter motif analysis of selected genes were identified. The superior and overall performance of classification using all features (DEGs) were 98.86% (Multilayer Perceptron) and 81.25%, respectively. Classification based on feature selection resulted in an average accuracy of 94.69% and 93.56% with 33 and 12 features, respectively. Subsequently, gene ontology and promoter analysis were performed for the 12 selected biomarker genes. Five of them were downregulated and 7 were upregulated. ABRE, unnamed-1, G-box, and G-Box are motifs related to genes involved in several abiotic stress responses and are located upstream of at least nine probes in our study. This study revealed key genes associated with tolerance to abiotic stress in maize.

Solanum torvum responses to the root-knot nematode Meloidogyne incognita.

BACKGROUND: Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nematodes. The little information on Solanum torvum (hereafter Torvum) resistance mechanisms, is mostly attributable to the lack of genomic tools (e.g. dedicated microarray) as well as to the paucity of database information limiting high-throughput expression studies in Torvum. RESULTS: As a first step towards transcriptome profiling of Torvum inoculated with the nematode M. incognita, we built a Torvum 3' transcript catalogue. One-quarter of a 454 full run resulted in 205,591 quality-filtered reads. De novo assembly yielded 24,922 contigs and 11,875 singletons. Similarity searches of the S. torvum transcript tags catalogue produced 12,344 annotations. A 30,0000 features custom combimatrix chip was then designed and microarray hybridizations were conducted for both control and 14 dpi (day post inoculation) with Meloidogyne incognita-infected roots samples resulting in 390 differentially expressed genes (DEG). We also tested the chip with samples from the phylogenetically-related nematode-susceptible eggplant species Solanum melongena. An in-silico validation strategy was developed based on assessment of sequence similarity among Torvum probes and eggplant expressed sequences available in public repositories. GO term enrichment analyses with the 390 Torvum DEG revealed enhancement of several processes as chitin catabolism and sesquiterpenoids biosynthesis, while no GO term enrichment was found with eggplant DEG.The genes identified from S. torvum catalogue, bearing high similarity to known nematode resistance genes, were further investigated in view of their potential role in the nematode resistance mechanism. CONCLUSIONS: By combining 454 pyrosequencing and microarray technology we were able to conduct a cost-effective global transcriptome profiling in a non-model species. In addition, the development of an in silico validation strategy allowed to further extend the use of the custom chip to a related species and to assess by comparison the expression of selected genes without major concerns of artifacts. The expression profiling of S. torvum responses to nematode infection points to sesquiterpenoids and chitinases as major effectors of nematode resistance. The availability of the long sequence tags in S. torvum catalogue will allow precise identification of active nematocide/nematostatic compounds and associated enzymes posing the basis for exploitation of these resistance mechanisms in other species.

Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus.

The barley Rdg2a locus confers resistance to the leaf stripe pathogen Pyrenophora graminea and, in the barley genotype Thibaut, it is composed of a gene family with three highly similar paralogs. Only one member of the gene family (called as Rdg2a) encoding for a CC-NB-LRR protein is able to confer resistance to the leaf stripe isolate Dg2. To study the genome evolution and diversity at the Rdg2a locus, sequences spanning the Rdg2a gene were compared in two barley cultivars, Thibaut and Morex, respectively, resistant and susceptible to leaf stripe. An overall high level of sequence conservation interrupted by several rearrangements that included three main deletions was observed in the Morex contig. The main deletion of 13,692 bp was most likely derived from unequal crossing over between Rdg2a paralogs leading to the generation of a chimeric Morex rdg2a gene which was not associated to detectable level of resistance toward leaf stripe. PCR-based analyses of genic and intergenic regions at the Rdg2a locus in 29 H. vulgare lines and one H. vulgare ssp. spontaneum accession indicated large haplotype variability in the cultivated barley gene pool suggesting rapid and recent divergence at this locus. Barley genotypes showing the same haplotype as Thibaut at the Rdg2a locus were selected for a Rdg2a allele mining through allele re-sequencing and two lines with polymorphic nucleotides leading to amino acid changes in the CC-NB and LRR encoding domains, respectively, were identified. Analysis of nucleotide diversity of the Rdg2a alleles revealed that the polymorphic sites were subjected to positive selection. Moreover, strong positively selected sites were located in the LRR encoding domain suggesting that both positive selection and divergence at homologous loci are possibly representing the molecular mechanism for the generation of high diversity at the Rdg2a locus in the barley gene pool.

A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant.

Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line '305E40' and as a male parent the partially resistant line '67/3'. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the '305E40' parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.

A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.).

BACKGROUND: Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time of this writing). To extend and to update information on miRNAs and their targets in barley and to identify candidate polymorphisms at miRNA target sites, the features of previously known plant miRNAs have been used to systematically search for barley miRNA homologues and targets in the publicly available ESTs database. Matching sequences have then been related to Unigene clusters on which most of this study was based. RESULTS: One hundred-fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. As expected on the basis of phylogenetic relations, miRNAs putatively orthologous to those of Triticum are significantly over-represented inside the set of identified barley microRNA mature sequences. Many previously known and several putatively new miRNA/target pairs have been identified. When the predicted microRNA targets were grouped into functional categories, biological processes previously known to be regulated by miRNAs, such as development and response to biotic and abiotic stress, have been highlighted and most of the target molecular functions were related to transcription regulation. Candidate microRNA coding genes have been reported and genetic variation (SNPs/indels) both in functional regions of putative miRNAs (mature sequence) and at miRNA target sites has been found. CONCLUSIONS: This study has provided an update of the information on barley miRNAs and their targets representing a foundation for future studies. Many of previously known plant microRNAs have homologues in barley with expected important roles during development, nutrient deprivation, biotic and abiotic stress response and other important physiological processes. Putative polymorphisms at miRNA target sites have been identified and they can represent an interesting source for the identification of functional genetic variability.

Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes.

A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds-related FNTDC has gained increased interest in recent years, but little ab-initio attempts aiming to the identification of FNTDCs covering all biological functions, including primary metabolism compounds, have been carried out. We report an extensive FNTDC dataset accompanied by a detailed assessment on parameters used for genome scanning and their impact on FNTDC detection. We propose 70% identity and 70% alignment coverage as intermediate settings to exclude tandem duplicated genes and a dynamic scanning window of 24 genes. These settings were applied to rice, arabidopsis and grapevine genomes to call for FNTDCs. Besides the best-known secondary metabolism clusters, we identified many FNTDCs associated to primary metabolism ranging from macromolecules synthesis/editing, TOR signalling, ubiquitination, proton and electron transfer complexes. Using the intermediate FNTDC setting parameters (at P-value 1e-6), 130, 70 and 140 candidate FNTDCs were called in rice, arabidopsis and grapevine, respectively, and 20 to 30% of GO tags associated to called FNTDC were common among the 3 genomes. The datasets developed along with this work provide a rich framework for pinpointing candidate FNTDCs reflecting all GO-BP tags covering both primary and secondary metabolism with large macromolecular complexes/metabolons as the most represented FNTDCs. Noteworthy, several FNTDCs are tagged with GOs referring to organelle-targeted multi-enzyme complex, a finding that suggest the migration of endosymbiont gene chunks towards nuclei could be at the basis of these class of candidate FNTDCs. Most FNTDC appear to have evolved prior of genome duplication events. More than one-third of genes interspersed/adjacent to called FNTDCs lacked any functional annotation; however, their co-localization may provide hints towards a candidate biological role.

Transcriptomic and metabolomic analysis of ZmYUC1 mutant reveals the role of auxin during early endosperm formation in maize.

Kernel size in cereal is an important agronomic trait controlled by the interaction of genetic and environmental factors. The endosperm occupies most of the kernel area; for this reason, the endosperm cells dimension, number and metabolic content strongly influence kernel properties. This paper presents the transcriptomic and metabolomic analysis of the maize defective endosperm 18 (de18) mutant, where auxin accumulation in the endosperm is impaired. This mutation, involving the ZmYuc1 gene, leads to a reduced kernel size compared to the wild-type line B37. Our results mainly indicate that IAA concentration controls sugar and protein metabolism during kernel differentiation and it is necessary for BETL formation. Furthermore, a fine tuning of different auxin conjugates is reported as the main mechanism to counteract the auxin deficit. Some candidates as master regulators of endosperm transcriptional regulation mediated by auxin are found between MYB and MADS-box gene families. A link between auxin and storage protein accumulation is highlighted, suggesting that IAA directly or indirectly, through CK or ABA, regulates the transcription of zein coding genes. This study represents a move forward with respect to the current knowledge about the role of auxin during maize endosperm differentiation thus revealing the genes that are modulated by auxin and that control agronomic traits as kernel size and metabolic composition.

Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat.

Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.

Durum wheat genome highlights past domestication signatures and future improvement targets.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.