High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae

The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested

The Rosa genome provides new insights into the domestication of modern roses

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals

Impact of TQM on company's performance

Purpose - The purpose of this paper is to investigate the impact of total quality management (TQM) implementation on different dimensions of company performance. Design/methodology/approach - The study investigates Canadian finalists (winners and certificates of merit) in the Total Quality category of the Canada Awards for Business Excellence. The data were collected either through in-depth personal interviews or by mail/telephone using the questionnaire and then analyzed. Findings - The data analysis confirmed the hypothesized positive impact of TQM on all investigated dimensions of company performance, i.e. employee relations (improved employee participation and morale), operating procedures (improved products and services quality, process and productivity, and reduced errors/defects), customer satisfaction (reduced number of customer complaints), and financial results (increased profitability). Research limitations/implications - Small sample size limited the scope of statistical analysis. Also, the results of this study are only valid for TQM adopters and give an indication of what performance can be achieved by companies that undertake a successful TQM program. Practical implications - The study provides useful insights into the performance improvement that can be achieved through TQM. Originality/value - The study provides evidence on how different dimensions of performance are affected by TQM and gives insights into how long does it take to obtain these benefits. Business performance Canada Performance management Quality awards Total quality managemen

Performance measurement by TQM adopters

Purpose - Organizations wishing to implement TQM face unavoidable profound changes in performance measurement and are in need of guidance and better understanding of the role of different performance measurement methods and systems. The objective of this paper is therefore to provide guidance for future TQM adopters through investigation of existing practices implemented by a group of finalists in the total quality category of Canada Awards for Business Excellence. Especially the usage and perceived appropriateness of different methods are of interest. Design/methodology/approach - A sample of finalists in the total quality category of Canada Awards for Business Excellence was surveyed. The data were collected either through in-depth personal interviews or by mail/phone using a questionnaire. Next, descriptive statistical techniques were used to analyze the data. T-statistic tests were performed in order to determine the significance of the results. Findings - Regarding the extent of use and appropriateness of the traditional and TQM-related performance measures (PMs) and systems/methods (PMS) found in TQM environment, the findings reported that PMs and PMS, used and considered appropriate by TQM adopters, are predominantly process-oriented (process sequence flow charts, Pareto chart, cause and effect diagram), long-term-oriented (market research/customer survey, percentage of sales from new products and absolute market share), and customer-oriented (number of complaints, percentage on-time delivery, overall customer satisfaction). Research limitations/implications - The small sample limited exclusively to finalists in the total quality category of Canada Awards for Business Excellence may be a limitation. Practical implications - This research provides guidance for companies considering implementation of TQM or in the process of adopting TQM with regard to the design of a performance measurement system that would support their TQM efforts successfully. Originality/value - This research is looking at extent of use of performance measures and methods and at their perceived appropriateness by TQM adopters at the same time. Thanks to this approach it provides valuable insights into performance measurement in TQM both for academics and for practitioners

An Unsupervised Data-Driven Model to Classify Gait Patterns in Children with Cerebral Palsy

Ankle and foot orthoses are commonly prescribed to children with cerebral palsy (CP). It is unclear whether 3D gait analysis (3DGA) provides sufficient and reliable information for clinicians to be consistent when prescribing orthoses. Data-driven modeling can probe such questions by revealing non-intuitive relationships between variables such as 3DGA parameters and gait outcomes of orthoses use. The purpose of this study was to (1) develop a data-driven model to classify children with CP according to their gait biomechanics and (2) identify relationships between orthotics types and gait patterns. 3DGA data were acquired from walking trials of 25 typically developed children and 98 children with CP with additional prescribed orthoses. An unsupervised self-organizing map followed by k-means clustering was developed to group different gait patterns based on children’s 3DGA. Model inputs were gait variable scores (GVSs) extracted from the gait profile score, measuring root mean square differences from TD children’s gait cycle. The model identified five pathological gait patterns with statistical differences in GVSs. Only 43% of children improved their gait pattern when wearing an orthosis. Orthotics prescriptions were variable even in children with similar gait patterns. This study suggests that quantitative data-driven approaches may provide more clarity and specificity to support orthotics prescription

The Apple Genome and Methylome : New Gene Regulatory Roles for DNA Methylation?

Accurate sequence information and genome assemblies are critical for studies on genomic and epigenomic variations. Although partial genome information was already available for apple (Velasco et al. 2010), the assembled sequence is fragmented and lacks repeated regions. First, using second- (Illumina) and third-generation sequencing and optical mapping technologies (PacBio and BioNano), we have generated a high quality genome assembly of a 'Golden Delicious' doubled haploid tree (Daccord, Celton et al. 2017). Our de novo assembly resulted in a genome of 649.7 Mb, with a N50 of 5.6 Mb. Seventeen pseudo-chromosomes were constructed and validated using a high density integrated genetic linkage map (Di Pierro, E. A. et al. 2016) and linkage disequilibrium analysis. Using similarities, transcript resources and the EuGene predictor/combiner (Foissac et al. 2008), 45,115 protein coding genes were predicted and tagged, when possible, by putative function. In a second time, to understand the potential role of epigenetic marks on fruit development, we constructed genome-wide DNA methylation maps that compared different tissues and two isogenic apple lines that produce large or small fruits. We established general correlations between methylation patterns in promoters and gene expression. Moreover, this led to the identification of differentially methylated regions that may be associated with genes involved in fruit development

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development