Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed

Rapeseed(Brassica napus)is an oil crop grown worldwide,making it a key plant species in molecular breeding research.However,the complexity of its polyploid genome increases sequencing costs and reduces sequencing accuracy.Target capture coupled with high-throughput sequencing is an efficient approach for detecting genetic variation at genomic regions or loci of interest.In this study,588 resequenced accessions of rapeseed were used to develop a target capture sequencing SNP genotyping platform named BnaPan50T.The platform comprised 54,765,with 54,058 resequenced markers from the pan-genome,and 855 variant trait-associated markers for 12 agronomic traits.The capture quality of BnaPan50T was demonstrated well in 12 typical accessions.Compared with a conventional genotyping array,BnaPan50T has a high SNP density and a high proportion of SNPs in unique physical positions and in annotated functional genes,promising wide application.Target capture sequencing and wholegenome resequencing in 90 doubled-haploid lines yielded 60%specificity,78%uniformity within tenfold coverage range,and 93%genotyping accuracy for the platform.BnaPan50T was used to construct a genetic map for quantitative trait loci(QTL)mapping,identify 21 unique QTL,and predict several candidate genes for yield-related traits in multiple environments.A set of 132 core SNP loci was selected from BnaPan50T to construct DNA fingerprints and germplasm identification resources.This study provides genomics resources to support target capture sequencing,genetic analysis and genomic breeding of rapeseed.

The collision-free trajectory planning for the space robot to capture a target based on the wavelet interpolation algorithm

In the research of path planning for manipulators with many DOF, generally there is a problem in most traditional methods, which is that their computational cost (time and memory space) increases exponentially as DOF or resolution of the discrete configuration space increases. So this paper presents the collision-free trajectory planning for the space robot to capture a target based on the wavelet interpolation algorithm. We made wavelet sample on the desired trajectory of the manipulator’s end-effector to do trajectory planning by use of the proposed wavelet interpolation formula, and then derived joint vectors from the trajectory information of the end-effector based on the fixed-attitude-restrained generalized Jacobian matrix of multi-arm coordinated motion, so as to control the manipulator to capture a static body along the desired collision-free trajectory. The method overcomes the shortcomings of the typical methods, and the desired trajectory of the end-effector can be any kind of complex nonlinear curve. The algorithm is simple and highly effective and the real trajectory is close to the desired trajectory. In simulation, the planar dual-arm three DOF space robot is used to demonstrate the proposed method, and it shows that the algorithm is feasible.

A grasp planning algorithm under uneven contact point distribution scenario for space non-cooperative target capture

The contact point configuration should be carefully chosen to ensure a stable capture,especially for the non-cooperative target capture mission using multi-armed spacecraft.In this work scenario,the contact points on the base and on the arms are distributed on the opposite side of the target.Otherwise,large forces will be needed.To cope with this problem,an uneven-oriented distribution union criterion is proposed.The union criterion contains a virtual symmetrical criterion and a geometry criterion.The virtual symmetrical contact point criterion is derived from the proof of the force closure principle using computational geometry to ensure a stable grasp,and the geometry criterion is calculated by the volume of the minimum polyhedron formed by the contact points to get a wide-range distribution.To further accelerate the optimization rate and enhance the global search ability,a line array modeling method and a continuous-discrete global search algorithm are proposed.The line array modeling method reduces the workload of calculating the descent direction and the gradient available,while the continuous-discrete global search algorithm reducing the optimization dimension.Then a highly efficient grasping is achieved and the corresponding contact point is calculated.Finally,an exhaustive verification is conducted to numerically analyze the disturbance resistance ability,and simulation results demonstrate the effectiveness of the proposed algorithms.

Plant phylogenomics based on genome-partitioning strategies:Progress and prospects

The rapid expansion of next-generation sequencing （NGS） has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome- partitioning approaches in plant phylogenomics： genome skimming, transcriptome sequencing （RNA- seq）, restriction site associated DNA sequencing （RAD-Seq）, and targeted capture （Hyb-seq）. Of these four genome-partitioning approaches, targeted capture （especially Hyb-seq） shows the greatest promise for plant phy^ogenetics over the next fex~ years. This reviex~ wi~ aid ~esea^chers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion ofwhole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

Grasping Strategy in Space Robot Capturing Floating Target

When the space robot captures a floating target, contact impact occurs inevitably and frequently between the manipulator hand and the target, which seriously impacts the position and attitude of the robot and grasping security. ＂Dynamic grasping area＂ is introduced to describe the collision process of manipulator grasping target, and grasping area control equation is established. By analyzing the impact of grasping control parameters, base and target mass on the grasping process and combining the life experience, it is found that if the product of speed control parameter and dB adjustment parameter is close to but smaller than the minimum grasping speed, collision impact in the grasping process could be reduced greatly, and then an ideal grasping strategy is proposed. Simulation results indicate that during the same period, the strategy grasping is superior to the accelerating grasping, in that the amplitude of impact force is reduced to 20%, and the attitude control torque is reduced to 15%, and the impact on the robot is eliminated significantly. The results would have important academic value and engineering significance.

Detumbling strategy based on friction control of dual-arm space robot for capturing tumbling target

The rotational motion of a tumbling target brings great challenges to space robot on successfully capturing the tumbling target.Therefore,it is necessary to reduce the target's rotation to a rate at which capture can be accomplished by the space robot.In this paper,a detumbling strategy based on friction control of dual-arm space robot for capturing tumbling target is proposed.This strategy can reduce the target's rotational velocity while maintaining base attitude stability through the establishment of the rotation attenuation controller and base attitude adjustment controller.The rotation attenuation controller adopts the multi-space hybrid impedance control method to control the friction precisely.The base attitude adjustment controller applies the dual-arm extended Jacobian matrix to stabilize the base attitude.The main contributions of this paper are as follows:(1)The compliant control method is adopted to achieve a precise friction control,which can reduce the target angular velocity steadily;(2)The dual-arm extended Jacobian matrix is applied to stabilize the base attitude without affecting the target capture task;(3)The detumbling strategy of dualarm space robot is designed considering base attitude stabilization,realizing coordinated planning of the base attitude and the arms.The strategy is verified by a dual-arm space robot with two 7-DOF(degrees of freedom)arms.Simulation results show that,target with a rotation velocity of 20(°)/s can be effectively controlled to stop within 30 s,and the final deflection of the base attitude is less than 0.15°without affecting the target capture task,verifying the correctness and effectiveness of the strategy.Except to the tumbling target capture task,the control strategy can also be applied to other typical on-orbit operation tasks such as space debris removal and spacecraft maintenance.

Targeted Genes Sequencing Identified a Novel 15 bp Deletion on GJA8 in a Chinese Family with Autosomal Dominant Congenital Cataracts

Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease remains a challenge. Methods： In this study, we tested a three-generation Chinese family with autosomal dominant CCs by targeted sequencing of 45 CC genes on next generation sequencing and evaluated the pathogenicity of the detected mutation by protein structure, pedigree validation, and molecular dynamics （MD） simulation. Results： A novel 15 bp deletion on GJA8 （c.426_440delGCTGGAGGGGACCCT or p. 143147delLEGTL） was detected in the family. The deletion, concerned with an in-frame deletion of 5 amino acid residues in a highly evolutionarily conserved region within the cytoplasmic loop domain of the gap junction channel protein connexin 50 （CxS0）, was in full cosegregation with the cataract phenotypes in the family but not found in 1100 control exomes. MD simulation revealed that the introduction of the deletion destabilized the Cx50 gap junction channel, indicating the deletion as a dominant-negative mutation, Conclusions： The above results support the pathogenic role of the 15 bp deletion on GJA8 in the Chinese family and demonstrate targeted genes sequencing as a resolution to molecular diagnosis of CCs.

Taming the beast:a revised classification of Cortinariaceae based on genomic data

Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with many vascular plant gen-era from tropicals to arctic regions.Genus Cortinarius contains a lot of morphological variation,and its complexity has led many taxonomists to specialize in particular on infrageneric groups.The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level.Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups.We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species.In addition,a wider 5-locus analysis of 245 species,from the Northern and Southern Hemispheres,was also done.Based on our results,a classification of the family Cortinariaceae into ten genera-Cortinarius,Phlegmacium,Thaxterogaster,Calonarius,Aureonarius,Cystinarius,Volvanarius,Hygronarius,Mystinarius,and Austrocortinarius-is proposed.Seven genera,10 subgenera,and four sec-tions are described as new to science and five subgenera are introduced as new combinations in a new rank.In addition,41 section names and 514 species names are combined in new genera and four lecto-and epitypes designated.The position of Stephanopus in suborder Agaricineae remains to be studied.Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes.It provides a cost-efficient way to produce-omics data in species-rich groups.The-omics data was produced from fungarium specimens up to 21 years old,demonstrating the value of museum specimens in the study of the fungal tree of life.This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.

IVS8 ＋ 1 DelG, a Novel Splice Site Mutation Causing DFNA5 Deafness in a Chinese Family

Background： Nonsyndrornic hearing loss （NSHL） is highly heterogeneous, in which more than 90 causative genes have currently been identified. DFNA5 is one of the deathess genes that known to cause autosomal dominant NSHL. Until date, only five DFN.45 mutations have been described in eight families worldwide. In this study, we reported the identification of a novel pathogenic mutation causing DFNA5 deafness in a five-generation Chinese family. Methods： Alter detailed clinical evaluations of this family, the genomic DNA of three affected individuals was selected for targeted exome sequencing of 101 known deafness genes, as well as mitochondrial DNA and microRNA regions. Co-segregation analysis between the hearing loss and the candidate variant was confirmed in available family members by direct polymerase chain reaction （PCR）-Sanger sequencing. Real-time PCR （RT-PCR） was pertormed to investigate the potential effect of the pathogenic mutation on messenger RNA splicing. Results： Clinical evaluations revealed a similar deafness phenotype in this family to that of previously reported DFNA5 families with autosomal dominant, late-onset bearing loss. Molecular analysis identified a novel splice site mutation in DFNA5 intron 8 （IVSS＋ 1 delG）. The mutation segregated with the hearing loss of the family and was absent in 120 unrelated control DNA samples of Chinese origin. RT-PCR showed skipping of exon 8 in the mutant transcript. Conclusions： We identified a novel DFNA5 mutation IVS8＋1 delG in a Chinese family which led to skipping ofexon 8. This is the sixth DFNA5 mutation relates to hearing loss and the second one in DFNA5 intron 8. Our findings provide further support to the hypothesis that the DFNA5-associated hearing loss represents a mechanism of gain-of-function.