Mapping Of Markers Research Articles

Identification and mapping of sex-linked markers in giant abalone (Haliotis gigantea Gmelin)

Giant abalone (Haliotis gigantea Gmelin) is an economically important species within Haliotis genus, yet the genetic basis of sex in this species is still poorly understood. Therefore, we screened and mapped sex-linked SNPs and InDels, and subsequently developed a PCR-based method for genetic sex identification in giant abalone. Based on whole-genome sequencing reads, we obtained a total 6,159,941 high-quality SNPs and 2,623,263 high-quality InDels. Among them, 1,737 SNPs and 179 InDels were detected as sexually dimorphic, assuming a male heterogametic sex determination system. The majority of these variants, 99.1 % for SNPs and 99.4 % for InDels, were clustered on Chr.4 (0.02 Mb to 23.22 Mb). Furthermore, the estimation of genetic divergence between the sexes using FST showed that the genomic windows with the top 1 % FST values were concentrated on Chr.4 (0.5 Mb to 19.0 Mb) and Chr.5 (20.0 Mb to 35.0 Mb). Based on the sexually dimorphic variants on Chr.4, three PCR-based markers were successfully developed to determine the genetic sex of giant abalone. PCR validation using a tested panel of 67 females and 67 males from a cultivated population demonstrated compliance rates for these three markers ranging from 97.7 % to 99.3 %. These results suggest that the sex determination system is male heterogametic in giant abalone. Thus, this study provides valuable insights and tools for further research on the mechanisms of sex determination and differentiation, as well as for monitoring sex ratios in wild and cultivated populations in giant abalone.

A semantic segmentation-based algorithm for fast flotation bubble size distribution measurement

The visual characteristics of froths on flotation cell surfaces are crucial for the optimal control of the flotation process. However, previous research has primarily focused on optimizing markers to prevent the over-segmentation of froth images, often overlooking computational efficiency. This work proposes a deep learning-based froth segmentation algorithm that prioritizes both segmentation speed and quality. We propose a dataset construction strategy based on pseudo-labeling, which utilizes traditional methods to extract marker maps from froth images to build the dataset for deep learning. Subsequently, a semantic segmentation model is trained to derive marker maps from raw froth images. These marker maps are then employed in a marker-based watershed algorithm, enabling end-to-end segmentation of froth images. The proposed method is validated using froth images from a gold and nickel flotation plant, demonstrating the ability to accurately and efficiently identify different bubbles in real froth images without requiring complex pre-processing or post-processing steps. Industrial experiments show a tenfold increase in segmentation efficiency with virtually no loss of accuracy.

What can be said?

Abstract We employ a cluster approach to explore the comparative semantic maps of several markers of modal possibility – the “potential” prefix nga‑ and expressions meaning, roughly, ‘know how to’ and ‘be able to’ – in four South African Nguni languages: isiNdebele, isiZulu, isiXhosa, Siswati. We also compare the Nguni results with results from Xitsonga, a closely related language outside of the Nguni clade. The languages exhibit cross-linguistic differences in the expansion of core meanings, some of which do not appear to follow the cross-linguistically common diachronic pattern in which goal-oriented modality precedes deontic modality. In addition, the distinction between inherent and learned ability is salient in several of these languages. Semantic maps of the markers’ functional distributions further show the diversity of modal systems that can be found even in closely related languages in significant contact with one another.

Characterization and Mapping of a Rolling Leaf Mutant Allele rlT73 on Chromosome 1BL of Wheat.

Leaf rolling is regarded as an important morphological trait in wheat breeding. Moderate leaf rolling is helpful to keep leaves upright and improve the photosynthesis of plants, leading to increased yield. However, studies on the identification of genomic regions/genes associated with rolling leaf have been reported less frequently in wheat. In this study, a rolling leaf mutant, T73, which has paired spikelets, dwarfism, and delayed heading traits, was obtained from a common wheat landrace through ethyl methanesulfonate mutagenesis. The rlT73 mutation caused an increase in the number of epidermal cells on the abaxial side and the shrinkage of bulliform cells on the adaxial side, leading to an adaxially rolling leaf phenotype. Genetic analysis showed that the rolling leaf phenotype was controlled by a single recessive gene. Further Wheat55K single nucleotide polymorphism array-based bulked segregant analysis and molecular marker mapping delimited rlT73 to a physical interval of 300.29-318.33 Mb on the chromosome arm 1BL in the Chinese Spring genome. We show that a point mutation at the miRNA165/166 binding site of the HD zipper class III transcription factor on 1BL altered its transcriptional level, which may be responsible for the rolling leaf phenotype. Our results suggest the important role of rlT73 in regulating wheat leaf development and the potential of miRNA-based gene regulation for crop trait improvement.

Ancient and recent origins of shared polymorphisms in yeast.

Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.

Status, Gaps and Perspectives of Powdery Mildew Resistance Research and Breeding in Cucurbits

Cucurbitaceae, the gourd family of flowering plants, is a very large and diverse family, the order Cucurbitales, contains 95 genera and 950–980 species of food and ornamental plants, and wild and weedy species mostly with high genetic diversity. This review is focused on the most important cucurbit crops (Cucumis sativus, Cucumis melo, Cucurbita spp., Citrullus lanatus, Momordica charantia, Lagenaria siceraria, and Luffa acutangula) and some their wild relatives as hosts of cucurbit powdery mildews (CPM). Powdery mildews (PM) (Ascomycota, Erysiphales) are one of the most frequently encountered and easily visible groups of plant pathogenic fungi with > 900 species. They are obligate biotrophs, they colonize above-ground plant tissues, mostly leaves, though they may also colonize stems, petioles, flowers and fruits, and they are usually debilitators, not killers. These parasitic fungi have been problematic on cucurbits for a long time world-wide, causing serious economic losses in yield and quality. All economically important cucurbit crops host CPM. Seven PM species with different taxonomic positions, host ranges, geographic distributions and ecological requirements are known on cucurbits. CPM species taxonomy and denomination rapidly changed during last few decades through detailed analyses and clarifications. At least three PM species frequently parasitize cucurbits: the endoparasite Leveillula taurica (Lt) with marginal economic importance; and two ectoparasitic species, Golovinomyces orontii (Go), and Podosphaera xanthii (Px), which are economically important world-wide. The two pathogens differ in ecological requirements and distribution, though they may occur together in mixed infections. They are highly variable at the population level for virulence, race identities, and fast adaptation of pathogens. Cucurbit-CPM species interactions are diverse and complicated, and differ between hosts and their respective pathogen genera and species. Here we present a critical overview of obstacles, gaps and recent progress in these matters for six cucurbit genera with respect to resistance resources, genetics of resistance, genetic mapping and development of molecular markers, physiology and mechanisms of resistance, developments in mlo-mediated resistance, patents, and CPM resistance breeding.

Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut.

Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS.

Analysis of actionable gene fusions in a large cohort of Chinese patients with colorectal cancer.

The prevalence of gene fusion is extremely low in unselected patients with colorectal cancer (CRC). Published data on gene fusions are limited by relatively small sample sizes, with a primary focus on Western populations. This study aimed to analyse actionable gene fusions in a large consecutive Chinese CRC population. This study included 5,534 consecutive CRC patients from the Genecast database. Genomic profiling was performed using a panel of 769 cancer-related genes. Data for 34 CRC patients with actionable gene fusions were also collected from cBioPortal and ChimerSeq. Among 5,534 CRC patients, 54 (0.98%) had actionable gene fusions, with NTRK1/2/3 being the most common fusion (0.38%), accounting for 38.9% (21/54) of those with fusions. Actionable gene fusion enrichment was higher in patients with microsatellite instability-high (MSI-H) (6.7% vs. 0.5%, P < 0.001), RAS/BRAF wildtype (2.0% vs. 0.2%, P < 0.001) and RNF43 mutation (7.7% vs. 0.4%, P < 0.001) than in patients with microsatellite stability/MSI-low, RAS/BRAF mutation and RNF43 wildtype, respectively. When these markers were combined, the fusion detection rate increased. Among patients with RAS/BRAF wildtype and MSI-H, fusions were detected in 20.3% of patients. The fusion detection rate further increased to 37.5% when RNF43 mutation was added. The fusion detection rate was also higher in colon cancer than in rectal cancer. No significant differences in clinical or molecular features were found in patients with actionable gene fusions between the Genecast, cBioPortal, and ChimerSeq databases. Approximately 1% of the unselected Chinese CRC population carries actionable gene fusions, mostly involving NTRK. Actionable gene fusions are more prevalent in MSI-H, RAS/BRAF wildtype, or RNF43-mutated CRC, as well as in colon cancer. Mapping of these molecular markers can markedly increase the fusion detection rate, which can help clinicians select candidates for fusion testing and targeted therapy.

Contributions of Remote Sensing and GIS to the Inventory and Mapping of Colonial Geodetic Markers in the Katangese Copper Belt

Contributions of Remote Sensing and GIS to the Inventory and Mapping of Colonial Geodetic Markers in the Katangese Copper Belt

OneGene PGT: comprehensive preimplantation genetic testing method utilizing next-generation sequencing.

Preimplantation genetic testing for monogenic disorders (PGT-M) allows early diagnosis in embryos conceived in vitro. PGT-M helps to prevent known genetic disorders in affected families and ensures that pathogenic variants in the male or female partner are not passed on to offspring. The trend in genetic testing of embryos is to provide a comprehensive platform that enables robust and reliable testing for the causal pathogenic variant(s), as well as chromosomal abnormalities that commonly occur in embryos. In this study, we describe PGT protocol that allows direct mutation testing, haplotyping, and aneuploidy screening. Described PGT protocol called OneGene PGT allows direct mutation testing, haplotyping, and aneuploidy screening using next-generation sequencing (NGS). Whole genome amplification product is combined with multiplex PCR used for SNP enrichment. Dedicated bioinformatic tool enables mapping, genotype calling, and haplotyping of informative SNP markers. A commercial software was used for aneuploidy calling. OneGenePGT has been implemented for seven of the most common monogenic disorders, representing approximately 30% of all PGT-M indications at our IVF centre. The technique has been thoroughly validated, focusing on direct pathogenic variant testing, haplotype identification, and chromosome abnormality detection. Validation results show full concordance with Sanger sequencing and karyomapping, which were used as reference methods. OneGene PGT is a comprehensive, robust, and cost-effective method that can be established for any gene of interest. The technique is particularly suitable for common monogenic diseases, which can be performed based on a universal laboratory protocol without the need for set-up or pre-testing.

Has recombination changed during the recent evolution of the guppy Y chromosome?

Genome sequencing and genetic mapping of molecular markers have demonstrated nearly complete Y-linkage across much of the guppy (Poecilia reticulata) XY chromosome pair. Predominant Y-linkage of factors controlling visible male-specific coloration traits also suggested that these polymorphisms are sexually antagonistic (SA). However, occasional exchanges with the X are detected, and recombination patterns also appear to differ between natural guppy populations, suggesting ongoing evolution of recombination suppression under selection created by partially sex-linked SA polymorphisms. We used molecular markers to directly estimate genetic maps in sires from 4 guppy populations. The maps are very similar, suggesting that their crossover patterns have not recently changed. Our maps are consistent with population genomic results showing that variants within the terminal 5 Mb of the 26.5 Mb sex chromosome, chromosome 12, are most clearly associated with the maleness factor, albeit incompletely. We also confirmed occasional crossovers proximal to the male-determining region, defining a second, rarely recombining, pseudo-autosomal region, PAR2. This fish species may therefore have no completely male-specific region (MSY) more extensive than the male-determining factor. The positions of the few crossover events suggest a location for the male-determining factor within a physically small repetitive region. A sex-reversed XX male had few crossovers in PAR2, suggesting that this region's low crossover rate depends on the phenotypic, not the genetic, sex. Thus, rare individuals whose phenotypic and genetic sexes differ, and/or occasional PAR2 crossovers in males can explain the failure to detect fully Y-linked variants.

Transseptal puncture using electroanatomical mapping: a safe and cost-effective technique

Abstract Background The usual technique of transseptal puncture (TSP) uses fluoroscopy or intracardiac echocardiography. New techniques for oval fossa (OF) identification by electroanatomical mapping (EAM) have been described. However, the technique of direct visualization of the TSP needle added to the OF location by impedance mapping has not been investigated yet. Purpose To evaluate feasibility and safety of the TSP technique guided by the interatrial septum (IAS) impedance mapping and the TSP needle visualization using EAM system. Methods Consecutive patients who underwent ablation using TSP in July and August 2022 in our institute were included. The standard material for the procedure was used in addition to a temporary pacemaker (PM) connection cable. In all cases, the EAM system was CARTO 3 version 7 (Biosense Webster and a bipolar voltage map of right atrium and a impedance map of the IAS were constructed. The OF location was estimated based on the septal region with the lowest impedance and on traditional anatomical landmarks. Using a temporary PM cable connected to the proximal part of the TSP needle stylet, it was possible to visualize its distal portion on the 3D map used to guide the TSP. The entire process was simultaneously monitored under fluoroscopic visualization by an experienced professional. Results A total of 25 patients were included; mean age of 56 +/- 15 years, 16 (64%) were male. The most frequent procedure was atrial fibrillation ablation (86%); left atrium mean size of 40,26 +/- 5,2 mm. 9 patients (36%) were already submetted to a previous procedure using TSP. None of the patients had congenital heart disease. In all cases, the TSP was successfully performed and a correlation between the anatomical references and the lowest impedance region on the map was observed. There were no complications. Conclusion The technique of visualization of the TSP needle using EAM system added to IAS impedance mapping and use of anatomical markers seems to be a safe and cost-effective alternative for performing TSP. This technique could reduce ionizing radiation without need for additional materials.Impedance map and bipolar voltage mapLA (bipolar voltage map) and TSP orifice

Annotation of cell types (ACT): a convenient web server for cell type annotation

BackgroundThe advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge.MethodsTo address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods.ResultsBy integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT (http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified.ConclusionsWe developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification.

Construction of a high-density genetic map and mapping of a spike length locus for rye.

Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.

Breeding evaluation and precise mapping of Fhb8 for Fusarium head blight resistance in wheat (Triticum aestivum)

AbstractThe percentage of Fusarium‐damaged kernels (FDK) was proposed as a type of Fusarium head blight (FHB) resistance displayed in matured wheat kernels. In this study, Qfdk.nau‐7D, a QTL identified in the Wangshuibai genome for its association with FDK, was introduced into FHB‐susceptible common wheat line PH691 through marker‐assisted selection and backcrossing. Evaluation of two resulted near‐isogenic lines (NILs) showed that the contribution of Qfdk.nau‐7D interval to lower FDK resulted from its effects on resistance to pathogen infection and to disease spread within the spike. Of a few major agronomic traits evaluated, head length was the only one that made difference between PH691 and the NILs. To reduce the QTL interval, a high‐density marker map was constructed using a BC3F2 population of 97 plants. Through resistance evaluation of the homozygous recombinant lines in repeated field trials, Qfdk.nau‐7D, designated as Fhb8, was placed in a 1.0‐cM Xwgrb1500‐Xwgrb1559 interval (from 93.9–96.5 Mb in CS) and showed co‐segregation with Xwgrb1587. Moreover, it was found that the association of Fhb8 with head length was due to close linkage with spike length QTL HL2.

Mapping and identification ofmolecular markers forthePc96 gene conferring resistance tocrown rust inoat.

Oat crown rust caused by Puccinia coronata f. sp. avenae P. Syd. & Syd (Pca) is a major constraint to oat (Avena sativa L.) production in many parts of the globe. The objectives of this study were to locate Pc96 on the oat consensus map and to develop SNP markers linked to Pc96 for use in marker-assisted selection. SNP loci linked to the crown rust resistance gene Pc96 were identified by linkage analysis and PACE assays were developed for marker-assisted selection in breeding programs. Pc96 is a race-specific crown rust resistance gene originating from cultivated oat that has been deployed in North American oat breeding programs. Pc96 was mapped in a recombinant inbred line population (n = 122) developed from a cross between the oat crown rust differential known to carry Pc96 and the differential line carrying Pc54. A single resistance locus was identified on chromosome 7D between 48.3 and 91.2 cM. The resistance locus and linked SNPs were validated in two additional biparental populations, Ajay × Pc96 (F2:3, n = 139) and Pc96 × Kasztan (F2:3, n = 168). Based on all populations, the most probable location of the oat crown rust resistance gene Pc96 on the oat consensus map was on chromosome 7D approximately at 87.3 cM. In the Ajay × Pc96 population, a second unlinked resistance gene was contributed by the Pc96 differential line, which mapped to chromosome 6C at 75.5 cM. A haplotype of nine linked SNPs predicted the absence of Pc96 in a diverse group of 144 oat germplasm. SNPs that are closely linked to the Pc96 gene may be beneficial as PCR-based molecular markers in marker-assisted selection.

Ontogeny and Trophic Factor Sensitivity of Gastrointestinal Projecting Vagal Sensory Cell Types.

Vagal sensory neurons (VSNs) located in the nodose ganglion provide information, such as stomach stretch or the presence of ingested nutrients, to the caudal medulla via specialized cell types expressing unique marker genes. Here, we leverage VSN marker genes identified in adult mice to determine when specialized vagal subtypes arise developmentally and the trophic factors that shape their growth. Experiments to screen for trophic factor sensitivity revealed that brain-derived neurotrophic factor (BDNF) and glial cell-derived neurotrophic factor (GDNF) robustly stimulate neurite outgrowth from VSNs in vitro Perinatally, BDNF was expressed by neurons of the nodose ganglion itself, while GDNF was expressed by intestinal smooth muscle cells. Thus, BDNF may support VSNs locally, whereas GDNF may act as a target-derived trophic factor supporting the growth of processes at distal innervation sites in the gut. Consistent with this, expression of the GDNF receptor was enriched in VSN cell types that project to the gastrointestinal tract. Last, the mapping of genetic markers in the nodose ganglion demonstrates that defined vagal cell types begin to emerge as early as embryonic day 13, even as VSNs continue to grow to reach gastrointestinal targets. Despite the early onset of expression for some marker genes, the expression patterns of many cell type markers appear immature in prenatal life and mature considerably by the end of the first postnatal week. Together, the data support location-specific roles for BDNF and GDNF in stimulating VSN growth, and a prolonged perinatal timeline for VSN maturation in male and female mice.

Genome-wide Development and Physical Mapping of SSR Markers in Sugar Beet (Beta vulgaris L.)

Sugar beet (Beta vulgaris L.) is one of the important sugar crops. Thus, development of molecular tools to understand molecular mechanism of agronomic traits such as root yield and sucrose content by using comprehensive genome analysis is important for sugar beet molecular breeding. A prime to such a comprehensive genome analysis is high throughout marker development. In the present study, mining of sugar beet genome for simple sequence repeats (SSRs) revealed 37704 motifs. Dinucleotide repeats were the most abundant accounting for 69.3 %. A total of 22500 SSR primers were developed and these markers were physically mapped in sugar beet genome. The markers distributed over nine chromosomes and the map had a higher resolution (16.73 kb SSR-1). Also 102 SSR markers were found to be putatively associated with carbohydrate synthesis. The present study is the first report of genome-wide development of SSR markers and construction of SSR based physical map in sugar beet. SSR markers increased the number of available sugar beet specific SSR markers by 55-fold. SSR markers developed in the present study are valuable molecular genetic tools for comprehensive genome analysis to facilitate sugar beet molecular breeding

Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.

Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH, an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. With a starting error rate of 10%, SD reduced it to ∼5% in diploids, ∼7% in tetraploids and ∼8.5% in hexaploids. Conversely, the correlation between true and estimated genetic maps increased by 0.03 in tetraploids and by 0.2 in hexaploids, while worsening slightly in diploids (∼0.0011). We also show that the combination of genotype curation and map re-estimation allowed us to obtain better genetic maps while correcting wrong genotypes. We have implemented this algorithm in the R package Smooth Descent.

Neurocircuitry underlying the antidepressant effect of retrograde facial botulinum toxin in mice

BackgroundsBotulinum toxin type A (BoNT/A) is extensively applied in spasticity and dystonia as it cleaves synaptosome-associated protein 25 (SNAP25) in the presynaptic terminals, thereby inhibiting neurotransmission. An increasing number of randomized clinical trials have suggested that glabellar BoNT/A injection improves depressive symptoms in patients with major depressive disorder (MDD). However, the underlying neuronal circuitry of BoNT/A-regulated depression remains largely uncharacterized.ResultsHere, we modeled MDD using mice subjected to chronic restraint stress (CRS). By pre-injecting BoNT/A into the unilateral whisker intrinsic musculature (WIM), and performing behavioral testing, we showed that pre-injection of BoNT/A attenuated despair- and anhedonia-like phenotypes in CRS mice. By applying immunostaining of BoNT/A-cleaved SNAP25 (cl.SNAP25197), subcellular spatial localization of SNAP25 with markers of cholinergic neurons (ChAT) and post-synaptic membrane (PSD95), and injection of monosynaptic retrograde tracer CTB-488-mixed BoNT/A to label the primary nucleus of the WIM, we demonstrated that BoNT/A axonal retrograde transported to the soma of whisker-innervating facial motoneurons (wFMNs) and subsequent transcytosis to synaptic terminals of second-order neurons induced central effects. Furthermore, using transsynaptic retrograde and monosynaptic antegrade viral neural circuit tracing with c-Fos brain mapping and co-staining of neural markers, we observed that the CRS-induced expression of c-Fos and CaMKII double-positive neurons in the ventrolateral periaqueductal grey (vlPAG), which sent afferents to wFMNs, was down-regulated 3 weeks after BoNT/A facial pre-administration. Strikingly, the repeated and targeted silencing of the wFMNs-projecting CaMKII-positive neurons in vlPAG with a chemogenetic approach via stereotactic injection of recombinant adeno-associated virus into specific brain regions of CRS mice mimicked the antidepressant-like action of BoNT/A pre-treatment. Conversely, repeated chemogenetic activation of this potential subpopulation counteracted the BoNT/A-improved significant antidepressant behavior.ConclusionWe reported for the first time that BoNT/A inhibited the wFMNs-projecting vlPAG excitatory neurons through axonal retrograde transport and cell-to-cell transcytosis from the injected location of the WIM to regulate depressive-like phenotypes of CRS mice. For the limited and the reversibility of side effects, BoNT/A has substantial advantages and potential application in MDD.