Although various forms of linkage map construction software are widely available, there is a distinct lack of packages for use in the R statistical computing environment (R Core Team 2017). This ...article introduces the ASMap linkage map construction R package which contains functions that use the efficient MSTmap algorithm (Wu, Bhat, Close, and Lonardi 2008) for clustering and optimally ordering large sets of markers. Additional to the construction functions, the package also contains a suite of tools to assist in the rapid diagnosis and repair of a constructed linkage map. The package functions can also be used for post linkage map construction techniques such as fine mapping or combining maps of the same population. To showcase the efficiency and functionality of ASMap, the complete linkage map construction process is demonstrated with a high density barley backcross marker data set.
Genomic selection applied to plant breeding enables earlier estimates of a line's performance and significant reductions in generation interval. Several factors affecting prediction accuracy should ...be well understood if breeders are to harness genomic selection to its full potential. We used a panel of 10,375 bread wheat (
) lines genotyped with 18,101 SNP markers to investigate the effect and interaction of training set size, population structure and marker density on genomic prediction accuracy. Through assessing the effect of training set size we showed the rate at which prediction accuracy increases is slower beyond approximately 2,000 lines. The structure of the panel was assessed via principal component analysis and K-means clustering, and its effect on prediction accuracy was examined through a novel cross-validation analysis according to the K-means clusters and breeding cohorts. Here we showed that accuracy can be improved by increasing the diversity within the training set, particularly when relatedness between training and validation sets is low. The breeding cohort analysis revealed that traits with higher selection pressure (lower allelic diversity) can be more accurately predicted by including several previous cohorts in the training set. The effect of marker density and its interaction with population structure was assessed for marker subsets containing between 100 and 17,181 markers. This analysis showed that response to increased marker density is largest when using a diverse training set to predict between poorly related material. These findings represent a significant resource for plant breeders and contribute to the collective knowledge on the optimal structure of calibration panels for genomic prediction.
Background. Epidural spinal electrical stimulation at the lumbar spinal level evokes rhythmic muscle activation of lower-limb antagonists, attributed to the central pattern generator. However, the ...efficacy of noninvasive spinal stimulation for the activation of lower-limb muscles is not yet clear. This review aimed to analyze the feasibility and efficacy of noninvasive transcutaneous spinal cord stimulation (tSCS) on motor function in individuals with spinal cord injury. Methods. A search for tSCS studies was made of the following databases: PubMed; Cochrane Registry; and Physiotherapy Evidence Database (PEDro). In addition, an inverse manual search of the references cited by the identified articles was carried out. The keywords transcutaneous, non-invasive, electrical stimulation, spinal cord stimulation Mesh term, and spinal cord injury were used. Results. A total of 352 articles were initially screened, of which 13 studies met the inclusion criteria for systematic review. The total participant sample comprised 55 persons with spinal cord injury. All studies with tSCS provided evidence of induced muscle activation in the lower and upper limbs, and applied stimulation at the level of the T11-T12 and C4-C7 interspinous space, respectively. All studies reported an increase in motor response measured by recording surface electromyography, voluntary movement, muscle strength, or function. Conclusions. Although this review highlights tSCS as a feasible therapeutic neuromodulatory strategy to enhance voluntary movement, muscle strength, and function in patients with chronic spinal cord injury, the clinical impact and efficacy of electrode location and current intensity need to be characterized in statistically powered and controlled clinical trials.
The female reproductive tract has an active microbiome, and it is suggested that these microbes could influence the outcome of assisted reproductive technologies (ART). This systematic review aimed ...to assess the vaginal/uterine microbiome, specifically with regard to improving the outcome of ART. English peer‐reviewed journals were searched for studies investigating the vaginal/uterine micriobiome and female reproductive tract, using PRISMA guidelines. Twenty‐six studies were included, 19 studying the vaginal and seven investigating the uterine microbiome. Studies using culture‐based technologies found an abnormal vaginal microbiome AVM was not associated with ART outcome. However, studies using sequence‐based technologies found an abnormal vaginal microbiome had a negative effect on ART. An abnormal uterine microbiome impacted ART outcome in all of the studies which used culture‐based methods and the most extensive of the two studies using metagenomic sequencing. This review has revealed a lack of translational data relating an abnormal vaginal/uterine microbiome to ART outcomes, with inconsistencies between the results of the different studies. Therefore the nature of the relationship between the vaginal/uterine microbiome and fertility remains unknown. As we better characterize this relationship using modern metagenomic techniques, the potential to manipulate the female reproductive tract microbiome to improve ART could be a reality.
Soil salinity and sodicity are major constraints to global cereal production, but breeding for tolerance has been slow. Narrow gene pools, over-emphasis on the sodium (Na
+
) exclusion mechanism, ...little attention to osmotic stress/tissue tolerance mechanism(s) in which accumulation of inorganic ions such as Na
+
is implicated, and lack of a suitable screening method have impaired progress. The aims of this study were to discover novel genes for Na
+
accumulation using genome-wide association studies, compare growth responses to salinity and sodicity in low-Na
+
bread Westonia with
Nax1
and
Nax2
genes and high-Na
+
bread wheat Baart-46, and evaluate growth responses to salinity and sodicity in bread wheats with varying leaf Na
+
concentrations. The novel high-Na
+
bread wheat germplasm, MW#293, had higher grain yield under salinity and sodicity, in absolute and relative terms, than the other bread wheat entries tested. Genes associated with high Na
+
accumulation in bread wheat were identified, which may be involved in tissue tolerance/osmotic adjustment. As most modern bread wheats are efficient at excluding Na
+
, further reduction in plant Na
+
is unlikely to provide agronomic benefit. The salinity and sodicity tolerant germplasm MW#293 provides an opportunity for the development of future salinity/sodicity tolerant bread wheat.
Introduction
Women are postponing childbearing and preventing age‐related fertility decline with oocyte freezing for non‐medical reasons (OFNMR). The objective of this systematic evaluation was to ...gain an understanding of women's attitudes and knowledge of, and intentions to use OFNMR among users of OFNMR and the general public.
Material and methods
A systematic search of MEDLINE, EMBASE, and PyschINFO databases was undertaken, for studies that examined the psychosocial attitudes among women toward OFNMR. The search was limited to English language and no time restriction was set for publications. Extracted data were analyzed using thematic analysis and the study was performed according to PRISMA guidelines with prospective PROSPERO registration (CRD4201912578).
Results
Overall, 35 studies met the inclusion criteria. Studies were broadly categorized into studies investigating users or potential users of OFNMR, and studies examining the views of members of the general public. Users of OFNMR have good knowledge of age‐related fertility decline and awareness of the OFNMR procedure. Lack of partner was identified as the most common motivating factor to undertake OFNMR, with cost as a predominant concern. Knowledge among the general public of OFNMR is highly variable. Underestimation of age‐related fertility decline is common among the general public. Intentions of women to use OFNMR also varied drastically between studies.
Conclusions
Women are predominantly motivated to freeze eggs by the lack of a suitable partner, but cost is a significant barrier. Increasing the number of women pursuing OFNMR at an earlier stage may positively impact upon the risk of future involuntary childlessness. Better information should be made available to both women and men about their fertility and options to inform their reproductive decision‐making.
The separation of toxic effects of sodium (Na⁺) and chloride (Cl⁻) by the current methods of mixed salts and subsequent determination of their relevance to breeding has been problematic. We report a ...novel method (Na⁺ humate) to study the ionic effects of Na⁺ toxicity without interference from Cl⁻, and ionic and osmotic effects when combined with salinity (NaCl). Three cereal species (Hordeum vulgare, Triticum aestivum and Triticum turgidum ssp. durum with and without the Na⁺ exclusion gene Nax2) differing in Na⁺ exclusion were grown in a potting mix under sodicity (Na⁺ humate) and salinity (NaCl), and water use, leaf nutrient profiles and yield were determined. Under sodicity, Na⁺‐excluding bread wheat and durum wheat with the Nax2 gene had higher yield than Na⁺‐accumulating barley and durum wheat without the Nax2 gene. However, under salinity, despite a 100‐fold difference in leaf Na⁺, all species yielded similarly, indicating that osmotic stress negated the benefits of Na⁺ exclusion. In conclusion, Na⁺ exclusion can be an effective mechanism for sodicity tolerance, while osmoregulation and tissue tolerance to Na⁺ and/or Cl⁻ should be the main foci for further improvement of salinity tolerance in cereals. This represents a paradigm shift for breeding cereals with salinity tolerance.
•mQTL approach in wheat identified potential trait enhancement targets for selection.•QTLs for metabolites, agronomic and plant phenology traits were detected.•558 metabolic features were obtained ...from flag leaves of 179 doubled haploid lines.•Five phenology-related loci differed in impact upon metabolic and agronomic traits.•Reinforces previous results demonstrating importance of phenology in trait assessment.
Mapping of quantitative trait loci associated with levels of individual metabolites (mQTL) was combined with the mapping of agronomic traits to investigate the genetic basis of variation and co-variation in metabolites, agronomic traits, and plant phenology in a field-grown bread wheat population. Metabolome analysis was performed using liquid chromatography–mass spectrometry resulting in identification of mainly polar compounds, including secondary metabolites. A total of 558 metabolic features were obtained from the flag leaves of 179 doubled haploid lines, of which 197 features were putatively identified, mostly as alkaloids, flavonoids and phenylpropanoids. Coordinated genetic control was observed for several groups of metabolites, such as organic acids influenced by two loci on chromosome 7A. Five major phenology-related loci, which were introduced as cofactors in the analyses, differed in their impact upon metabolic and agronomic traits with QZad-aww-7A having more impact on the expression of both metabolite and agronomic QTL than Ppd-B1, Vrn-A1, Eps, and QZad-aww-7D. This QTL study validates the utility of combining agronomic and metabolomic traits as an approach to identify potential trait enhancement targets for breeding selection and reinforces previous results that demonstrate the importance of including plant phenology in the assessment of useful traits in this wheat mapping population.
Atmospheric vapor pressure deficit (VPD) is a key component of drought and has a strong influence on yields. Whole-plant transpiration rate (TR) response to increasing VPD has been linked to drought ...tolerance in wheat, but because of its challenging phenotyping, its genetic basis remains unexplored. Further, the genetic control of other key traits linked to daytime TR such as leaf area, stomata densities and – more recently – nocturnal transpiration remains unknown. Considering the presence of wheat phenology genes that can interfere with drought tolerance, the aim of this investigation was to identify at an enhanced resolution the genetic basis of the above traits while investigating the effects of phenology genes Ppd-D1 and Ppd-B1. Virtually all traits were highly heritable (heritabilities from 0.61 to 0.91) and a total of mostly trait-specific 68 QTL were detected. Six QTL were identified for TR response to VPD, with one QTL (QSLP.ucl-5A) individually explaining 25.4% of the genetic variance. This QTL harbored several genes previously reported to be involved in ABA signaling, interaction with DREB2A and root hydraulics. Surprisingly, nocturnal TR and stomata densities on both leaf sides were characterized by highly specific and robust QTL. In addition, negative correlations were found between TR and leaf area suggesting trade-offs between these traits. Further, Ppd-D1 had strong but opposite effects on these traits, suggesting an involvement in this trade-off. Overall, these findings revealed novel genetic resources while suggesting a more direct role of phenology genes in enhancing wheat drought tolerance.
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