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The novel wheat powdery mildew and stripe rust resistance genes Pm5V/Yr5V are introgressed from Dasypyrum villosum and fine mapped to a narrowed region in 5VS, and their effects on yield-related traits were characterized. The powdery mildew and stripe rust seriously threaten wheat production worldwide. Dasypyrum villosum (2n = 2x = 14, VV), a relative of wheat, is a valuable resource of resistance genes for wheat improvement. Here, we describe a platform for rapid introgression of the resistance genes from D. villosum into the wheat D genome. A complete set of new wheat-D. villosum V (D) disomic substitution lines and 11 D/V Robertsonian translocation lines are developed and characterized by molecular cytogenetic method. A new T5DL·5V#5S line NAU1908 shows resistance to both powdery mildew and stripe rust, and the resistances associated with 5VS are confirmed to be conferred by seedling resistance gene Pm5V and adult-plant resistance gene Yr5V, respectively. We flow-sort chromosome arm 5VS and sequence it using the Illumina NovaSeq 6000 system that allows us to generate 5VS-specific markers for genetic mapping of Pm5V/Yr5V. Fine mapping shows that Pm5V and Yr5V are closely linked and the location is narrowed to an approximately 0.9 Mb region referencing the sequence of Chinese Spring 5DS. In this region, a NLR gene in scaffold 24,874 of 5VS orthologous to TraesCS5D02G044300 is the most likely candidate gene for Pm5V. Soft- and hard-grained T5DL·5V#5S introgressions confer resistance to both powdery mildew and stripe rust in diverse wheat genetic backgrounds without yield penalty. Meanwhile, significant decrease in plant height and increase in yield were observed in NIL-5DL·5V#5S compared with that in NIL-5DL·5DS. These results indicate that Pm5V/Yr5V lines might have the potential value to facilitate wheat breeding for disease resistance.

To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata2. We established that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Aegilopstriuncialis3, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.

Chromatids of mitotic chromosomes were suggested to coil into a helix in early cytological studies and this assumption was recently supported by chromosome conformation capture (3C) sequencing. Still, direct differential visualization of a condensed chromatin fibre confirming the helical model was lacking. Here, we combined Hi-C analysis of purified metaphase chromosomes, biopolymer modelling and spatial structured illumination microscopy of large fluorescently labeled chromosome segments to reveal the chromonema - a helically-wound, 400 nm thick chromatin thread forming barley mitotic chromatids. Chromatin from adjacent turns of the helix intermingles due to the stochastic positioning of chromatin loops inside the chromonema. Helical turn size varies along chromosome length, correlating with chromatin density. Constraints on the observable dimensions of sister chromatid exchanges further supports the helical chromonema model.

Leaf rust, caused byPuccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley (Hordeumspp.). The barley leaf rust resistance locusRph7, located on the short arm of chromosome 3H, confers defence at all growth stages and was previously shown to have unusually high sequence and haplotype divergence. Earlier, four candidate genes forRph7were reported and, despite an in-depth comparative sequence analysis and haplotypic characterisation, the causal gene could not be resolved. Here, we successfully clonedRph7utilising a fine mapping approach in combination with an RNA-Seq based expression analysis. We identified three up-regulated and pathogen-induced genes with presence/absence variation (PAV) at this locus. Sequence analysis of chemically inducedRph7knockout mutant lines identified multiple independent non-synonymous variants, including a premature stop codon in a single non-canonical resistance gene that encodes a 302-amino acid protein. Progeny from four independent transgenic lines segregated for the expected avirulentRph7infection type in response to several avirulentP. hordeipathotypes, however, all plants were susceptible to a single virulent pathotype confirming the specificity. Structural analysis using an AlphaFold2 protein model suggests thatRph7encodes a putative NAC transcription factor, as it shares structural similarity to ANAC019 fromArabidopsis, with a C-terminal BED domain. A global gene expression analysis suggestsRph7is involved in the activation of basal defence.

In sweet cherry (Prunus avium L.), quantitative trait loci have been identified for fruit maturity, colour, firmness, and size to develop markers for marker-assisted selection. However, resolution is usually too low in those analyses to directly target candidate genes, and some associations are missed. In contrast, genome-wide association studies are performed on broad collections of accessions, and assemblies of reference sequences from Tieton and Satonishiki cultivars enable identification of single nucleotide polymorphisms after whole-genome sequencing, providing high marker density. Two hundred and thirty-five sweet cherry accessions were sequenced and phenotyped for harvest time and fruit colour, firmness, and size. Genome-wide association studies were used to identify single nucleotide polymorphisms associated with each trait, which were verified in breeding material consisting of 64 additional accessions. A total of 1 767 106 single nucleotide polymorphisms were identified. At that density, significant single nucleotide polymorphisms could be linked to co-inherited haplotype blocks (median size ~10 kb). Thus, markers were tightly associated with respective phenotypes, and individual allelic combinations of particular single nucleotide polymorphisms provided links to distinct phenotypes. In addition, yellow-fruit accessions were sequenced, and a ~ 90-kb-deletion on chromosome 3 that included five MYB10 transcription factors was associated with the phenotype. Overall, the study confirmed numerous quantitative trait loci from bi-parental populations using high-diversity accession populations, identified novel associations, and genome-wide association studies reduced the size of trait-associated loci from megabases to kilobases and to a few candidate genes per locus. Thus, a framework is provided to develop molecular markers and evaluate and characterize genes underlying important agronomic traits.

The extensive annual loss of honey bees (Apis mellifera L.) represents a global problem affecting agriculture and biodiversity. The parasitic mite Varroa destructor, associated with viral co-infections, plays a key role in this loss. Despite years of intensive research, the complex mechanisms of Varroa - honey bee interaction are still not fully defined. Therefore, this study employed a unique combination of transcriptomic, proteomic, metabolomic, and functional analyses to reveal new details about the effect of Varroa mites and naturally associated factors, including viruses, on honey bees. We focused on the differences between Varroa parasitised and unparasitised ten-day-old worker bees collected before overwintering from the same set of colonies reared without anti-mite treatment. Supplementary comparison to honey bees collected from colonies with standard anti-Varroa treatment can provide further insights into the effect of a pyrethroid flumethrin. Analysis of the honey bees exposed to mite parasitisation revealed alterations in the transcriptome and proteome related to immunity, oxidative stress, olfactory recognition, metabolism of sphingolipids, and RNA regulatory mechanisms. The immune response and sphingolipid metabolism were strongly activated, whereas olfactory recognition and oxidative stress pathways were inhibited in Varroa parasitised honey bees compared to unparasitised ones. Moreover, metabolomic analysis confirmed the depletion of nutrients and energy stores, resulting in a generally disrupted metabolism in the parasitised workers. The combined omics-based analysis conducted on strictly parasitised bees revealed the key molecular components and mechanisms underlying the detrimental effects of Varroa sp. and its associated pathogens. This study provides the theoretical basis and interlinked datasets for further research on honey bee response to biological threats and the development of efficient control strategies against Varroa mites.

To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum. Sr43 encodes a protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.

Summary Pm1a, the first powdery mildew resistance gene described in wheat, is part of a complex resistance (R) gene cluster located in a distal region of chromosome 7AL that has suppressed genetic recombination.A nucleotide‐binding, leucine‐rich repeat (NLR) immune receptor gene was isolated using mutagenesis and R gene enrichment sequencing (MutRenSeq). Stable transformation confirmed Pm1a identity which induced a strong resistance phenotype in transgenic plants upon challenge with avirulent Blumeria graminis (wheat powdery mildew) pathogens.A high‐density genetic map of a B. graminis family segregating for Pm1a avirulence combined with pathogen genome resequencing and RNA sequencing (RNAseq) identified AvrPm1a effector gene candidates. In planta expression identified an effector, with an N terminal Y/FxC motif, that induced a strong hypersensitive response when co‐expressed with Pm1a in Nicotiana benthamiana.Single chromosome enrichment sequencing (ChromSeq) and assembly of chromosome 7A suggested that suppressed recombination around the Pm1a region was due to a rearrangement involving chromosomes 7A, 7B and 7D. The cloning of Pm1a and its identification in a highly rearranged region of chromosome 7A provides insight into the role of chromosomal rearrangements in the evolution of this complex resistance cluster.

More than a century has passed since the B chromosomes were first discovered. Today we know much of their variability, morphology, and transmission to plant progeny. With the advent of modern technologies, B chromosome research has accelerated, and some of their persistent mysteries have since been uncovered. Building on this momentum, here we extend current knowledge of B chromosomes in Sorghum purpureosericeum to the sequence level. To do this, we estimated the B chromosome size at 421 Mb, sequenced DNA from flow-sorted haploid pollen nuclei of both B-positive (B+) and B-negative (B0) plants, and performed a repeat analysis on the Illumina raw sequence data. This analysis revealed nine putative B-specific clusters, which were then used to develop B chromosome-specific markers. Additionally, cluster SpuCL4 was identified and verified to be a centromeric repeat. We also uncovered two repetitive clusters (SpuCL168 and SpuCL115), which hybridized exclusively on the B chromosome under fluorescence in situ hybridization and can be considered as robust cytogenetic markers. Given that B chromosomes in Sorghum are rather unstable across all tissues, our findings could facilitate expedient identification of B+ plants and enable a wide range of studies to track this chromosome type in situ., We sequenced plants of the tropical grass Sorghum purpureosericeum carrying B chromosomes. Based on repeat clustering, we assigned nine clusters to B chromosome and developed B-specific PCR and cytogenetic markers.

The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of VRN1 homoeologs (VRN-A1, VRN-B1 and VRN-D1). We performed an in-depth sequence analysis of VRN1 homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele Vrn-B1f with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the Vrn-A1b allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of VRN1 homoeologs showed that VRN-B1 and VRN-D1 are present in only one copy. The copy number of recessive vrn-A1 ranged from one to four, while that of dominant Vrn-A1 was one or two. Different numbers of Vrn-A1a copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more vrn-A1 copies.

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Background Cultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species (Lolium) and diploid and hexaploid fescue species (Festuca). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species as well as one fescue and two ryegrass cultivars. Results Partial genome sequences produced by Illumina sequencing technology were used for genome-wide comparative analyses with the RepeatExplorer pipeline. Retrotransposons were the most abundant repeat type in all seven grass species. The Athila element of the Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of the long terminal repeat (LTR) element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of fluorescence in situ hybridization (FISH) with a probe specific to the Fesreba element and immunostaining with centromeric histone H3 (CENH3) antibody showed their co-localization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative repeatome analyses in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of the LTR element Fesreba. A new LTR element Fesreba was identified and found in abundance in centromeric regions of the fescues and ryegrasses. It may play a role in the function of their centromeres.

Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up the development of new cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species ( Festuca spp.). In this work we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species, as well as one fescue and two ryegrass cultivars. Results Partial genome sequences produced by Illumina technology were used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative repeatome analysis in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. A new LTR element Fesreba was identified and found abundant in centromeric regions of the fescues and ryegrasses. It may have a role in the function of their centromeres.

Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up development of cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass ( Lolium ) species and diploid and hexaploid fescues ( Festuca ) species. In this work we characterized repetitive DNA sequences and their contribution to genome size in seven fescue and ryegrass species. Results Partial genome sequences were produced by Illumina technology and used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed most striking difference in copy numbers in nuclear genomes between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative analysis of repeatome in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. The element was abundant in centromeric regions of the fescues and ryegrasses and may have a role in function of their centromeres.

Background: Short arm of chromosome 6V (6VS) of Haynaldia villosa has been used in wheat breeding programs to introduce Pm21 resistance gene against powdery mildew and some other genes. Results: In this work, 6VS was isolated from a wheat ( Triticum aestivum ) - 6VS telosome addition line by flow cytometric sorting and sequenced by illumina technology. The assembly length was 230.39 Mb with contig N50 of 9,788 bp. The sequence annotation identified 3,276 high confidence genes supported by RNA sequencing data, representing about 2.3% of the chromosome arm sequence; repetitive elements accounted for 74.91% of the arm sequence. Sequences homologous to 6VS genes were identified on short arms of chromosomes 6A of T. urartu , 6D of Aegilops tauschii , 6A and 6B of T. dicoccoides , 6A, 6B and 6D of T. aestivum and 6H of Hordeum vulgare , revealing synteny relationships among these chromosome arms. Based on differences in intron size between the homologous genes on 6VS and 6AS/6BS/6DS of T. aestivum , 222 primer pairs were designed. Out of them, 120 amplified 6VS-specific products and are suitable as intron-target (IT) markers to trace the 6VS chromatin introduced into wheat. Conclusions: The results obtained and markers developed in this work will facilitate introduction of important genes to common wheat from its wild relative, while reducing the presence of unfavorable genes due to linkage drag.

Additional file 7: Fig. S4. Original images of Southern hybridization depicted in Fig. 5 and Additional file 2: Fig. S1, respectively. Original images of Southern hybridization with sequences derived from cluster CL1 (A), cluster CL38 (B), and cluster CL20 (C) and with sequences for the reverse transcriptase domain (D) and non-coding LTR region (E) of the Fesreba element. Lanes contained genomic DNA digested by HaeIII restriction endonuclease. Lane 1: diploid F. pratensis cv. Fure; lane 2: tetraploid F. pratensis cv. Westa; lane 3: hexaploid F. arundinacea subsp. arundinacea; lane 4: hexaploid F. gigantea; lane 5: tetraploid F. glaucescens; lane 6: tetraploid F. mairei; lane 7: tetraploid L. multiflorum cv. Mitos; lane 8: diploid L. multiflorum cv. Kuri1; lane 9: tetraploid L. perenne cv. Neptun; lane 10: diploid L. perenne.

Additional file 6: Table S3. Primers used for PCR amplification of DNA repeats.

Additional file 3: Table S2. Representation of the RT domain and non-coding part of the LTR region of the Fesreba element estimated by ddPCR. Copy numbers of the reverse transcriptase (RT) domain and non-coding part of the LTR region of the Fesreba element were estimated with droplet digital PCR. Values are averages of three independent experiments with standard deviations.

Additional file 1: Table S1. List of clusters containing putative tandem repeats identified in Festuca and Lolium.

Cyanobacteria represent an ancient, monophyletic lineage of bacteria with the ability to undertake oxygenic photosynthesis. Although they possess a relatively high degree of morphological variability compared with other prokaryotes and there is a wealth of molecular data, there are still significant gaps in our knowledge of cyanobacterial diversity, especially in tropical areas. Here, we present a novel, filamentous, tropical cyanobacterium, which could be classified as Pseudophormidium based on morphological criteria. A total evidence investigation employing ecological, morphological and genomic data, indicated that our strains form a new and ancient evolutionary lineage among cyanobacteria unrelated to Pseudophormidium. Based on this polyphasic assessment, our strains represent a novel, monospecific genus: Elainella. This new genus represents an example of phenotypic convergence, which seems to be a prevalent macroevolutionary pattern in cyanobacteria, a likely cause of the frequently cited poly...

Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D. Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47 Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.

This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-ncnd/4.0/)PublicationType:FULL_TEXT;; Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is a serious invasive pest of small-grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat (Triticum aestivum L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene Dn2401 into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long-read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long-read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the Dn2401 region facilitated the identification of new markers and precise annotation of the interval, revealing six high-confidence genes. Identification of Epoxide hydrolase 2 as the most likely Dn2401 candidate opens an avenue for its validation through functional genomics approaches.

In many plant species, somatic cell differentiation is accompanied by endoreduplication, a process during which cells undergo one or more rounds of DNA replication cycles in the absence of mitosis, resulting in nuclei with multiples of 2C DNA amounts (4C, 8C, 16C, etc.). In some orchids, a disproportionate increase in nuclear DNA contents has been observed, where successive endoreduplication cycles result in DNA amounts 2C + P, 2C + 3P, 2C + 7P, etc., where P is the DNA content of the replicated part of the 2C nuclear genome. This unique phenomenon was termed "progressively partial endoreplication" (PPE). We investigated processes behind the PPE in Ludisia discolor using flow cytometry (FCM) and Illumina sequencing. In particular, we wanted to determine whether chromatin elimination or incomplete genome duplication was involved, and to identify types of DNA sequences that were affected. Cell cycle analysis of root tip cell nuclei pulse-labeled with EdU revealed two cell cycles, one ending above the population of nuclei with 2C + P content, and the other with a typical "horseshoe" pattern of S-phase nuclei ranging from 2C to 4C DNA contents. The process leading to nuclei with 2C + P amounts therefore involves incomplete genome replication. Subsequent Illumina sequencing of flow-sorted 2C and 2C + P nuclei showed that all types of repetitive DNA sequences were affected during PPE; a complete elimination of any specific type of repetitive DNA was not observed. We hypothesize that PPE is part of a highly controlled transition mechanism from proliferation phase to differentiation phase of plant tissue development.

Sequence comparison between spelt and common wheat reveals that the former has huge potential in enriching the genetic variation of the latter. Genetic variation is the foundation of crop improvement. By comparing genome sequences of a Triticum spelta accession and one of its derived hexaploid lines with the sequences of the international reference genotype Chinese Spring, we detected variants more than tenfold higher than those present among common wheat (T. aestivum L) genotypes. Furthermore, different from the typical ‘V-shaped’ pattern of variant distribution often observed along wheat chromosomes, the sequence variation detected in this study was more evenly distributed along the 3B chromosome. This was also the case between T. spelta and the wild emmer genome. Genetic analysis showed that T. spelta and common wheat formed discrete groups. These results showed that, although it is believed that the spelt and common wheat are evolutionarily closely related and belong to the same species, a significant sequence divergence exists between them. Thus, the values of T. spelta in enriching the genetic variation of common wheat can be huge.

Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning. It comprises 869 contigs with a cumulative length of 274.5 Mbp and represents 85.5% of the estimated chromosome arm size. Eighty-six Mbp of survey sequences from chromosome arm 3DS were assigned in silico to physical map contigs via next-generation sequencing of bacterial artificial chromosome pools, thus providing a high-density framework for physical map ordering along the chromosome arm. About 60% of the physical map was anchored in this single experiment. Finally, 1393 high-confidence genes were anchored to the physical map. Comparisons of gene space of the chromosome arm 3DS with genomes of closely related species [Brachypodium distachyon (L.) P. Beauv., rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] and homeologous wheat chromosomes provided information about gene movement on the chromosome arm.

The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence indicating that they could be associated with adaptation in wheat.

Research related to the allometric relationships of tree height and projected tree crown area to diameter at breast height was conducted to look at the biological suitability and timber production potential of Douglas fir under the conditions present in central Europe. The dependence of allometric relationships on soil nutrient conditions were described in forest stands of Douglas fir and Norway spruce. The studied sites were climatically similar but differed in soil nutrient availability. A significant difference was found in the allometric relationships of Norway spruce trees from the nutrient poor and nutrient rich site. In contrast to the Norway spruce, there was no significant effect of site fertility on allometric relationships for Douglas fir suggesting that its allocation patterns were less sensitive to site nutrient conditions. Stem growth increment, which was measured weekly during two consecutive seasons for both species, was related to the weather conditions and available soil moisture. Stem growth of Douglas fir began about 2 weeks earlier than in the Norway spruce at both sites. At the nutrient rich site, most of the stem growth of both species occurred at the beginning of the season, while growth at the other site was more evenly distributed throughout the season. Data obtained in this study will be useful for modeling stem growth and analysis of water use efficiency of these two tree species.