Search

European hazelnut (Corylus avellanaL.) is of global agricultural and economic significance, with genetic diversity existing in hundreds of accessions. Breeding efforts have focused on maximizing nut yield and quality and reducing susceptibility to diseases such as Eastern filbert blight (EFB). Here we present the first sequenced genome among the order Fagales, the EFB-resistant diploid hazelnut accession ‘Jefferson’ (OSU 703.007). We assembled the highly heterozygous hazelnut genome using an Illumina only approach and the final assembly has a scaffold N50 of 21.5kb. We captured approximately 91 percent (345 Mb) of the flow-cytometry-determined genome size and identified 34,910 putative gene loci. In addition, we identified over 2 million polymorphisms across seven diverse hazelnut accessions and characterized t heir effect on coding sequences. We produced t wo high-density genetic maps with 3,209 markers from an F1 hazelnut population, representing a five-fold increase in marker density over previous maps. These genomic resources will aide in the discovery of molecular markers linked to genes of interest for hazelnut breeding efforts, and are available to the community athttps://www.cavellanagenomeportal.com/.

Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein-coding genes, we identified 290 very recent small-scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.

The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle 'pseudo-linkage' between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.

The US Pacific Northwest is the primary production region of black raspberry, and this high-value specialty crop has been underutilized for several decades. Black raspberries contain high levels of anthocyanins and other bioactive compounds, which has sparked a renewed interest in breeding programs and cultivation. Despite this potential, black raspberry stands have seen a marked decline that many attribute to disease pressures and only three new cultivars have been released over the last 20 years. Here we discuss the available genomic resources for black raspberry, including the recently released draft genome. These resources will expedite marker-assisted improvement of raspberry with applications across the Rosaceae family. The 243 Mb black raspberry genome was sequenced using an Illumina-based whole genome shotgun sequencing approach, and a chromosome-scale assembly was generated using a high-density genetic map. Black raspberry is the sixth genome to be sequenced in the Rosaceae facilitating in-depth comparative genomics across the family. Black raspberry and the diploid wild strawberry (Fragaria vesca) are largely collinear with some lineage-specific structural rearrangements. The genome has 28,005 genes which is comparable to other Rosaceae species and includes a number of recently duplicated genes which may be related to domestication. Gene expression atlases during fruit ripening and Verticillium inoculation provide insights into ripening and disease resistance, respectively. Together the resources discussed here will provide tools for the improved understanding and breeding of Rosaceae crops.

European hazelnut (Corylus avellana L.) is of worldwide agricultural significance, with breeding efforts focused on combining high nut yield and nut quality with resistance to diseases such as eastern filbert blight (EFB), a cause of severe crop loss in much of the United States. Oregon State University recently released a resistant cultivar, 'Jefferson' (OSU 703.007), that was chosen for transcriptome sequencing to establish further genomic resources for C. avellana L. We used Illumina ribonucleic acid sequencing (RNA-seq) to characterize complementary DNA (cDNA) libraries from four hazelnut tissues, including leaves, catkins, bark, and whole seedlings. The 6.8 Gb of hazelnut transcriptome data was assembled de novo into 28,255 contigs with an average length of 532 bp and an N50 (the minimum contig length necessary such that all contigs of equal or greater length will equal half of the bases of the assembly) of 961 bp. Sequence comparisons using BLASTX and gene ontology (GO) classifications were used to generate automated descriptive function annotations. High similarity of the predicted proteins to sequences in related plants demonstrates the validity of the transcript contigs, with 80.8% having similarity to grape (Vitis vinifera L.), poplar (Populus trichocarpa Torr. & A. Gray), and castor bean (Ricinus communis L.) sequences in the public domain. A survey of GO terms enriched among tissue-specific transcripts further validates the assembly. A basic local alignment search tool (BLAST) portal and web resources (http:// hazelnut.cgrb.oregonstate.edu [accessed 8 Jan. 2010]) are available and will be of importance to breeders for marker-assisted breeding efforts.

Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry. Several methods for gene synthesis have been introduced in the growing area of genomics. In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer) oligo fragments from a library were assembled through successive annealing and ligation processes, followed by PCR. First, two oligo fragments annealed to form a dsDNA molecule. The double-stranded oligo was immobilized onto magnetic beads (solid support) via streptavidin-biotin binding. Next, single-stranded oligo fragments were added successively through ligation to form the complete DNA molecule. The synthesized DNA was amplified through PCR and gel electrophoresis was used to characterize the product. Sanger sequencing showed that more than 97% of the nucleotides matched the expected sequence. Extending the length of the DNA molecule by adding single-stranded oligonucleotides from a basis set (library) via ligation enables a more convenient and rapid mechanism for the design and synthesis of oligonucleotides on the go. Coupled with an automated dispensing system and libraries of short oligo fragments, this novel DNA synthesis method would offer an efficient and cost-effective method for producing dsDNA.

Polymorphisms associated with gene coding regions are useful tools for use as molecular markers, for example in marker-assisted breeding efforts. In particular, single nucleotide polymorphisms (SNPs) have emerged as a preferred marker for high-throughput genotyping studies. The objective of this study was to develop a set of SNPs for European hazelnut (Corylus avellana) by exploiting the exceptional depth and breadth of transcriptome sequencing made possible by high-throughput RNA sequencing (RNA-seq) using the Illumina Genome Analyzer platform. Bioinformatics tools were used to mine SNPs from a database of EST sequences derived from de novo assembly of Illumina RNA-seq reads representing hazelnut transcripts from multiple accessions. This resulted in the identification of 5,398 SNPs. This set of SNP markers for hazelnut provides a new resource for genetic mapping of important agronomic traits and will be useful markers for aligning future physical and genetic maps.

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Agricultural crop plants make up a large proportion of the world's economy and in many countries constitute the main sustenance for humans. Therefore maximizing crop yield is of extreme importance and interest. There are many factors that can limit the yield of a crop; however the main causes of crop failure are abiotic stresses such as salinity, drought, extremes in temperature, intense light, and oxidative stress caused by reactive oxygen species. Plants have evolved mechanisms and pathways allowing them to cope with the environment by modifying their physiological and cellular states. For example, plants living in colder regions undergo a phenomenon known as cold acclimation, resulting in cell membrane composition and protein concentration changes to reduce intracellular ice crystal formation and dehydration due to freezing (Thomashow, 1998). Abiotic stresses alter gene networks and signaling cascades in an effort to restore cellular homeostasis. It has been demonstrated (Reddy, 2007, Palusa et al., 2007) that abiotic stress conditions alter the alternative splicing of a number of genes. Alternative pre-mRNA splicing in higher eukaryotes is a highly regulated mechanism, often allowing for many proteins (isoforms) to be derived from a single gene, thereby increasing overall proteome diversity. These alternative transcripts often result in functionally and structurally distinct proteins (Biamonti, 2009) with their own functions in development, cellular localization, and responses to the environment (Tanabe et al., 2006). Recently genome and transcriptome-wide surveys (Rensink et al., 2005, Kreps et al., 2002, Egawa et al., 2006, Filichkin et al., 2010) have offered glimpses into transcript abundance profiles under abiotic stresses, demonstrating dramatic shifts in alternative splicing patterns, as well as upregulation of key transcription factors controlling stress-induced signaling cascades. This research offers the potential for discovery of candidate genes that, through genetic engineering, may confer increased tolerance to abiotic stresses, several examples of which will be discussed in this chapter. Recent research has demonstrated the possibility of pre-disposing plants to stress tolerance by overexpressing a gene known to be upregulated in response to a certain stress (for example: Haake et al., 2002, Forment et al., 2002, Kim et al., 2010) often acting upstream or in conjunction with a longer signaling cascade, such as the mitogen-activated protein (MAP) kinase cascade (Xiong et al. 2003), salt overly sensitive (SOS) pathway (Liu and Zhu, 1998; Ishitani et al., 2000, Qiu et al., 2004), or C-repeat-binding factor/dehydration-responsive element (CBF/DREB) pathway (Thomashow, 2010).