Effects of exercise training on obesity‐related parameters in people with intellectual disabilities: systematic review and meta‐analysis

.Background: Efforts to synthesise existing knowledge concerning the effects of exercise interventions on obesity (i.e. changes in body weight and composition) have been made, but scientific evidence in this matter is still limited. This systematic review and meta-analysis aims to identify and critically analyse the best available evidence regarding the use of physical exercise as a strategy to attenuate obesity through its effects on adiposity-related anthropometric parameters in people with intellectual disability (ID). Methods: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a literature search was performed using PubMed, Scopus, SPORTDiscus, CINAHL and the Cochrane Library through specific keywords up to July 2020. The search adhered to the population, intervention, comparison and outcome strategy. Randomised controlled trials addressing the effects of the exercise intervention on adiposity-related anthropometric parameters (body mass index, waist circumference, waist–hip ratio, fat percentage or body weight) in children, adolescents and adults with ID were included. The methodological quality of the studies found was evaluated through the PEDro scale. Results: A total of nine investigations with children and/or adolescents (10–19 years) and 10 investigations with adults (18–70 years) were selected, mostly experiencing mild and moderate ID. Methodological quality was fair in 13 of these publications, good in five and excellent in one. Seventeen trials reported comparable baseline and post-intervention data for the intervention and control groups and were included in the meta-analysis. In nine studies, the intervention group performed a cardiovascular training programme. Five papers described a combined training programme. Two trials executed whole-body vibration training programmes, and one publication proposed balance training as the primary intervention. According to the meta-analysis results, the reviewed studies proposed exercise modalities that, in comparison with the activities performed by the participants' in the respective control groups, did not have a greater impact on the variables assessed. Conclusions: While physical exercise can contribute to adiposity-related anthropometric parameters in people with mild and moderate ID, these findings show that exercise alone is not sufficient to manage obesity in this population. Multicomponent interventions appear to be the best choice when they incorporate dietary deficit, physical activity increase and behaviour change strategies. Finding the most effective modality of physical exercise can only aid weight loss interventions. Future research would benefit from comparing the effects of different exercise modalities within the framework of a multicomponent weight management intervention.S

Structure and expression analysis of rice paleo duplications

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution

Development of new SSR markers for homoeologous WFZP loci based on the study of structure and location of microsatellites in gene-rich regions of chromosomes 2AS , 2BS, 2DS

Microsatellites, or simple sequence repeats (SSRs), are ubiquitous in genomes of eukaryotes, including plant genomes. The structure and location of SSR loci determine their potential as molecular genetic markers and may have impact on the potential function of microsatellites in important biological processes. Identification and study of the distribution of SSR loci in gene-rich regions of the bread wheat genome and development of novel SSR markers based on these data are of practical interest, being important for the study of bread wheat genome organization. Bread wheat BACclone sequences containing homoeologous WFZP genes that control spikelet development served as the base for the identification and localization of SSR loci in generich regions of chromosomes 2AS, 2BS, and 2DS. It was found that di- and trinucleotide motifs were predominant. The most common dinucleotide motifs were AG and GA/TC. They were distributed in noncoding regions of genes, transposable elements (TEs) and unannotated sequences. Most identified trinucleotide motifs were associated with transposable elements. Homoeologous SSR loci were found in either genes or unannotated sequences. Comparison of these loci showed that the divergence in their structure was caused both by changes in repeat number and nucleotide substitutions. New SSR markers were developed and mapped. On the genetic maps of chromosomes 2A, 2B и 2D, they collocated with the WFZP-A-B-D genes. Thus, they can be used for gene tagging in molecular research and in marker-assisted selection

Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains

Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of expression data are higher than 0.7. In rice, such local coexpression domains range from predominantly two genes, up to 4, and make up ∼5% of the genomic neighboring genes, when examining different expression platforms from the public domain. The genes in local coexpression domains do not fall in the same ontology category significantly more than neighboring genes that are not coexpressed. Duplication, orientation or the distance between the genes does not solely explain coexpression. The regulation of coexpression is therefore thought to be regulated at the level of chromatin structure. The characteristics of the local coexpression domains in rice are strikingly similar to such domains in the Arabidopsis genome. Yet, no microsynteny between local coexpression domains in Arabidopsis and rice could be identified. Although the rice genome is not yet as extensively annotated as the Arabidopsis genome, the lack of conservation of local coexpression domains may indicate that such domains have not played a major role in the evolution of genome structure or in genome conservation

Evidence of intense chromosomal shuffling during conifer evolution

Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkagemapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma Pinaceae and Cupressaceae.We propose for the first time amodel based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n=12) and Cupressaceae (with n=11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes. ©The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

<p>Abstract</p> <p>Background</p> <p>Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL).</p> <p>Results</p> <p>Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the <it>Hordeum </it>genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (<it>ZEO) </it>and the <it>VRS1 </it>gene, which determines the two-row and six-row germplasm groups of barley.</p> <p>Conclusions</p> <p>We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in <it>de novo </it>genome assembly, development of ultra-high density genetic maps and association mapping.</p

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes-and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement. (Résumé d'auteur