Genetic dissection of the grain-filling rate and related traits through linkage analysis and genome-wide association study in bread wheat

Wheat grain yield is generally sink-limited during grain filling.The grain-filling rate(GFR)plays a vital role but is poorly studied due to the difficulty of phenotype surveys.This study explored the grain-filling traits in a recombinant inbred population and wheat collection using two highly saturated genetic maps for linkage analysis and genome-wide association study(GWAS).Seventeen stable additive quantitative trait loci(QTLs)were identified on chromosomes 1B,4B,and 5A.The linkage interval between IWB19555 and IWB56078 showed pleiotropic effects on GFR_(1),GFR_(max),kernel length(KL),kernel width(KW),kernel thickness(KT),and thousand kernel weight(TKW),with the phenotypic variation explained(PVE)ranging from 13.38%(KW)to 33.69%(TKW).198 significant marker-trait associations(MTAs)were distributed across most chromosomes except for 3D and 4D.The major associated sites for GFR included IWB44469(11.27%),IWB8156(12.56%)and IWB24812(14.46%).Linkage analysis suggested that IWB35850,identified through GWAS,was located in approximately the same region as QGFR_(max)2B.3-11,where two high-confidence candidate genes were present.Two important grain weight(GW)-related QTLs colocalized with grain-filling QTLs.The findings contribute to understanding the genetic architecture of the GFR and provide a basic approach to predict candidate genes for grain yield trait QTLs.

Molecular Genetic Diagnostics of Prader-Willi Syndrome:a Validation of Linkage Analysis for the Chinese Population

Prader-Willi Syndrome （PWS） is a genetic disorder that is difficult to detect, particularly at an early age. PWS is caused by disruption of normal, epigenetically controlled gene function in the chromosome 15q11-q13 region. Clinical symptoms are difficult to diagnose in infants and only become clearer at later ages as the patients develop hyperphagia and morbid obesity. Molecular genetic tests are able to definitively diagnose PWS and allow early diagnosis of the syndrome. High resolution cytogenetic testing, methylation-specific PCR （MS-PCR）, and linkage analysis are routinely used to diagnose PWS. To establish a linkage analysis method for Chinese patients, this study identified a useful set of STR markers in the typical PWS deletion and adjacent area, for linkage analysis in two Chinese families with PWS offspring. Using this method, the authors confn＇rned that one patient had a paternal deletion in chromosome 15q 11-q 13 and the other patient had maternal uniparental heterodisomy of chromosome 15. MS -PCR and high resolution chromosome G-banding also confirmed this diagnosis. This linkage analysis method can detect both deletion and uniparental disomy, thus providing valuable information for genetic counseling and the opportunity to analyze the relationship between the genotype and phenotype of PWS.

Mobility Analysis of Altmann Overconstrained Linkages by Modified Grübler-Kutzbach Criterion

Developing a general mobility method/formula is a hot topic lasting for more than 150 years in kinematics. It is necessary to apply any mobility method to puzzling overconstrained mechanisms for verification of its generality. Altmann linkages are such recognized puzzling mechanisms that their mobility analysis is of important significance. A necessary condition for judging a general mobility method is that the method can be fit for Altmann linkages. Firstly, this study classes Altmann linkages into 17 types in terms of the numbers and types of kinematic pairs, and then Altmann overconstrained linkages are further classified into 4 types. Secondly, the mobility of Altmann overconstrained linkages is systematically analyzed by the Modified Grübler-Kutzbach criterion based on screw theory, where passive freedoms are defined as limb passive freedoms and mechanism passive freedoms. In addition, the full-cycle mobility is judged, which overcomes the shortcoming of instantaneous property of screw theory. It is shown that Modified Grübler-Kutzbach criterion not only obtains the correct numerical mobility, but also gives the mobility character by resolving reciprocal screws for the constraint system. This study lays the foundation of verification for the generality of Modified Grübler-Kutzbach criterion. Besides, Altmann overconstrained linkages almost comprise all kinds of modern parallel mechanisms and some classical mechanisms, which provides an important reference for mechanism mobility calculation.

Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study(GWAS) and linkage mapping

Wheat powdery mildew(Blumeria graminis f.sp.tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies.Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development.A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism(SNP)markers.The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15.Linkage disequilibrum(LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel.Association analysis using a mixed linear model(MLM) identified three loci for powdery mildew resistance on chromosome 2 B, designated QPm.stars-2BL1,QPm.stars-2BL2, and QPm.stars-2BL3.To evaluate the efficacy of GWAS in gene discovery,QPm.stars-2BL2 was validated using F2 and F2:3 populations derived from PI420646 × OK1059060-126135-3.Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results.QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.

An approach to incorporate linkage disequilibrium structure into genomic association analysis

In this study, we propose to use the principal component analysis （PCA） and regression model to incorporate linkage disequilibrium （LD） in genomic association data analysis. To accommodate LD in genomic data and reduce multiple testing, we suggest performing PCA and extracting the PCA score to capture the variation of genomic data, after which regression analysis is used to assess the association of the disease with the principal component score. An empirical analysis result shows that both genotype-based correlation matrix and haplotype-based LD matrix can produce similar results for PCA. Principal component score seems to be more powerful in detecting genetic association because the principal component score is quantitatively measured and may be able to capture the effect of multiple loci.

Genome-wide identification and expression analysis of NtbHLH gene family in tobacco(Nicotiana tabacum)and the role of NtbHLH86 in drought adaptation

The bHLH transcription factors play pivotal roles in plant growth and development,production of secondary metabolites and responses to various environmental stresses.Although the bHLH genes have been well studied in model plant species,a comprehensive investigation of the bHLH genes is required for tobacco with newly obtained high-quality genome.In the present study,a total of 309 NtbHLH genes were identified and can be divided into 23 subfamilies.The conserved amino acids which are essential for their function were predicted for the NtbHLH proteins.Moreover,the NtbHLH genes were conserved during evolution through analyzing the gene structures and conserved motifs.A total of 265 NtbHLH genes were localized in the 24 tobacco chromosomes while the remained 44 NtbHLH genes were mapped to the scaffolds due to the complexity of tobacco genome.Moreover,transcripts of NtbHLH genes were obviously tissue-specific expressed from the gene-chip data from 23 tobacco tissues,and expressions of 20 random selected NtbHLH genes were further confirmed by quantitative real-time PCR,indicating their potential functions in the plant growth and development.Importantly,overexpressed NtbHLH86 gene confers improve drought tolerance in tobacco indicating that it might be involved in the regulation of drought stress.Therefore,our findings here provide a valuable information on the characterization of NtbHLH genes and further investigation of their functions in tobacco.

PROBABILISTIC ANALYSIS AND MONTE CARLO SIMULATION OF THE KINEMATIC ERROR IN A SPATIAL LINKAGE

The stochastic models of the usual joints are first established through intro-ducing the concepts of“clearance characteristic element”and“clearance space”.After de-riving the probability density function of the joint clearance and making the probabilisticanalysis of the resulted kinematic errors,the sampling formulas of the independent varia-bles of the joint clearances are further deduced.Through Monte Carlo simulation,the sta-tistical characteristics and frequency histograms of the kinematic errors are then analysedon computer.

Genome-wide Identification and Analysis of MVD Gene Family in Euphorbiaceae Plants

The mevalonate diphosphate deearboxylase （MVD） is an essential enzyme in mevalonate （MVA） pathway that catalyzes the irreversible Mg2＋ -ATP de- pendent decarboxylation of 6-carben compound mevalonate-5-diphosphate （MVAPP） into 5-carbon isopentenyl diphosphate （ IPP）, the building block of sterol and isoprenoid biosynthesis. In this study, based on the published geanme sequences and ESTs, a genome-wide search was carried out for the first time to identify MVD gene family in four genome-sequenced Euphorbiaceae plants, i.e. castor bean （ Ricinus communis）, physic nut （ Jatropha curcas）, cassava （Manihot esculenta） and rubber tree （Hevea brasiliensis）, and to analyze the gene structure and phylogenetic characteristics. According to the experimental results, 1, 1,2 and 2 MVD genes, which all contain 9 introns, were identh＇ied from castor bean, physic nut, cassava and rubber tree, respectively. Homology analysis indicates that MVD genes are widely distributed in eukaryotes, some archaea and eubacteria, which suggests an early origin of this gerte family. Although MVD genes were identified in most green plants, no homologous genes were found in unicellular green algae. In most genome-sequenced plants including castor bean and physic nut, a single copy of MVD gene was found; however, in cassava and rubber tree, two copies were identified just like that in moss, maize, Arabidopsis and poplar. ＂In castor bean, digital expression profiling suggests that in five examined tissues, i.e. leaf, flower, II/III stage endosperm, V/VI stage endosperm and seed, RcPMK was expressed strongly in flower and II/III stage endosperm, moderately in V/VI stage endosperm and leaf, and weakly in seed.

A Study of Dynamic Analysis Method for the Rigid-Flexible Coupled Bar Linkage System

In order to present a dynamic analysis method for the rigid-flexible coupled bar linkage system(RFCBLS),the flexible element motion equation was gotten by Lagrange Equation and the rigid element motion equation was gotten based on rigid constraint conditions.The multi-body system(MBS) is a complex mechanism and its components have quite different rigidities.If it is considered as a rigid MBS(RMBS) to do its dynamic analysis,elastic deformation's ignorance will lead to inaccurate analysis.If it is considered as a flexible MBS(FMBS) to establish,analyze,and solve the model,quite large system equations make it difficult to solve.The better method is as follows:the complex mechanism system is regarded as a rigid-flexible coupled system(RFCS) to make dynamic characteristic of rigid components be equivalent,system equation is established by FMBS' way,and system equation dimensions are reduced by transition matrices' introduction.A dynamic analysis method for rigid element and flexible element coupling was presented based on the FMBS.The analyzed crank slide-block mechanism results show that the dynamic analysis method for RFCBLS is quick and convenient.

Comparison of dimension reduction-based logistic regression models for case-control genome-wide association study:principal components analysis vs.partial least squares

With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression （LR） based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression （PC-LR）, partial least squares-based logistic regression （PLS-LR）, have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism （SNP） set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis. On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.

Pathway-based analysis of genome-wide association study of circadian phenotypes

Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms（SNPs） which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies（GWAS） dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters. Furthermore, genotype-phenotype association analysis was performed with HapMap database. Four SNPs in three different genes were determined to correlate with usual weekday bedtime,totally providing seven hypothetical mechanisms. Eleven SNPs in six genes were identified to correlate with usual weekday sleep duration, which provided six hypothetical pathways. Our results demonstrated that fifteen candidate SNPs in eight genes played vital roles in six hypothetical pathways implicated in usual weekday bedtime and six potential pathways involved in usual weekday sleep duration.

Genome-Wide Analysis of the Cyclin-Dependent Kinases(CDK)and Cyclin Family in Molluscs

Cell cycle regulation that plays a pivotal role during organism growth and development is primarily driven by cyclindependent kinases(CDKs)and Cyclins.Although CDK and Cyclin genes have been characterized in some animals,the studies of CDK and Cyclin families in molluscs,the ancient bilaterian groups with high morphological diversity,is still in its infancy.In this study,we identified and characterized 95 CDK genes and 114 Cyclin genes in seven representative species of molluscs,including Octopus bimaculoides,Pomacea canaliculata,Biomphalaria glabrata,Lottia gigantea,Mizuhopecten yessoensis,Crassostrea gigas and Aplysia californica.Genes in CDK and Cyclin families were grouped into eight and 15 subfamilies by phylogenetic analysis,respectively.It should be noted that duplication of CDK9 gene was detected in P.canaliculate,L.gigantea and M.yessoensis genomes,which has never been recorded in animals.It is speculated that duplication may be the main course of expansion of the CDK9 subfamily in the three molluscs,which also sheds new light on the function of CDK9.In addition,Cyclin B is the largest subfamily among the Cyclin family in the seven molluscs,with the average of three genes.Our findings are helpful in better understanding CDK and Cyclin function and evolution in molluscs.

FURTHER RESEARCH ON THE SPLINE MODEL METHOD OF KED ANALYSIS IN A PLANAR FLEXIBLE LINKAGE

This paper relates to the deep research on the Splinc Model Method of KED analysis. With the use of cubic B-splinc function as a link’s transverse deflection interpolation function, the principle of virtual displacement is presented as a basic theory for the general formulation of the equations of motion, and thus abandoned the kinematic assumption and the instantaneous structure assumption which arc used in the Spline Model Method. In thc same time, the nonlinear terms sue as coupling terms between thc rigid body motion and elastic deformation arc included. New member’s spline models are established. Mass matrix, Coriolis mass matrix, normal and tangential mass matrix, linear stiffness matrix, nonlinear stiffness matrix and rotation matrix arc derived. The kinematic differential equations of a member and system are deduced in the end. The Newmark direct integration method is used as the solution scheme of the kinematic differential equations to get the periodic response.

Genetic Linkage Analysis of the Natural Colored Fiber and Fuzzless Traits in Cotton

Genetic linkage relationship of the natural colored fiber and six fuzzless seed germplasms in obsolete backgrounds of Gossypium hirsutum(AD genome) and G.barbadense were analyzed in the

A genome-wide analysis of the chloroplast NADH dehydrogenase - like genes in Zostera marina

The chloroplast NADH dehydrogenase-like(NDH)complex,homologous to respiratory complex I,participates in photosystem I cyclic electron flow(PSI-CEF)and chlororespiration in photosynthesis.Phylogenetic analyses indicated that Zostera marina,a widely distributed seagrass,has a complete NDH complex,which is rarely observed in marine macrophytes.We identified all 31 ndh genes necessary for the functional NDH complex,of which ndhB and pnsb3 occurred as duplication events.Secondary structural analyses of antiporter-like subunits showed that the long amphipathic helix of NdhF was lost in Z.marina,which could exhibit an alternative mode in the generation of trans-thylakoid proton gradient.The splicing pattern of ndh exhibited tissue-specific patterns and responded to light stress.RNA editing in Z.marina presented the ancestral pattern with many of the primitive editing sites and types.The partial editing in ndhF reflected the link between light stress and RNA editing.Moreover,the predominant expression in leaves of most ndh genes suggested that their major function is in photosynthesis.The quantitative real time-PCR results show that the expression of ndh was signifi cantly upregulated in response to light stress.Nevertheless,there were two diverse responsive mechanisms of the NDH complex in PSI-CEF and chlororespiration.Overall,the presence of a complete structure,upregulated gene expression level,and multiple post-transcriptional regulations could provide a molecular basis for the powerful NDH complex and enable Z.marina to maintain eff ective photosynthetic performance.

Genome-wide identification of NAC gene family and expression analysis under abiotic stresses in Salvia miltiorrhiza

NAC(NAM,ATAF,CUC)is a class of transcription factors involved in plant growth regulation,abiotic stress responses,morphogenesis and metabolism.Salvia miltiorrhiza is an important Chinese medicinal herb,but the characterization of NAC genes in this species is limited.In this study,based on the Salvia miltiorrhiza genomic databases,82 NAC transcription factors were identified,which were divided into 14 groups.Meanwhile,phylogenetic analysis,gene structure,chromosomal localization and potential role of SmNACs in abiotic stress conditions were also studied.The results revealed that some SmNACs had different structures than others,which advised that these genes may have multiple/distinct functions.Real-time quantitative polymerase chain reaction(RT-qPCR)analysis showed that SmNACs exhibited differential expression patterns under salt and drought stress.The NaCl induced salinity treatments modulated the expression of several SmNAC genes more in roots compared with leaves.Conversely,under drought stress conditions,more genes were upregulated in leaves compared with roots.These results will be useful for the further study involved in the functional characteristics of SmNAC genes,especially in response to salt and drought stresses,thereby may facilitate genetic breeding in Salvia miltiorrhiza.

Genome-wide Association Analysis of Maize Flowering Traits

Flowering regulation is important for maize to adapt to a variety of environments as well as associated with high yield.In this study,the genetic mechanism of three flowering traits of 310 maize inbred lines with rich genetic background was investigated in three years at three different environments such as days to tasseling(DTT),days to silking(DTS)and days to pollen shedding(DTP).Based on mean performance,the longest flowering time was observed in Zhanyi(2018),whereas the shortest in Shizong(2019).The coefficient of variance depicted the range from 3.62%to 9.06%for three flowering traits under all environments.Therefore,we have integrated these flowering traits corresponding to SNP molecular markers for genome-wide association study(GWAS).Results showed that 22 SNPs markers were significantly associated with DTT according to physical position and average linkage disequilibrium(LD)decay distance,and a total of 234 candidate genes were identified near these significantly associated SNP markers.Moreover,KEGG and GO analysis showed that these genes were enriched in the regulation of the physiological pathways for flowering.In more details,16 genes involved in development of floral organs are more worthy of our attention in future studies.

Genetic Linkage Map and Comparative Genome Analysis for the Atlantic Killifish (Fundulus heteroclitus)

Genetic linkage maps are valuable tools in evolutionary biology;however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.

Dynamic Analysis of aSelected Spatial One-DOF Linkage Mechanism with Friction in Joints

The dynamic analysis of a one-DOF RSRRR spatial linkage mechanism, including four rotational joints R and one spherical joint S, is presented in the paper. It is assumed that friction occurs in the rotational joints, whereas a spherical joint can be treated as an ideal one. The mechanism in the form of a closed-loop kinematic chain was divided by cut joint technique into two open-loop kinematic chains in place of the spherical joint. Joint coordinates and homogeneous transformation matrices were used to describe the geometry of the system. Equations of the chains＇ motion were derived using formalism of Lagrange equations. Cut joint constraints and reaction forces, acting in the cutting place---i.e, in the spherical joint, have been introduced to complete the equations of motion. As a consequence, a set of differential-algebraic equations has been obtained. In order to solve these equations, a procedure based on differentiation twice of the formulated constraint equations with respect to time has been applied. In order to determine values of friction torques in the rotational joints in each integrating step of the equations of motion, joint forces and torques were calculated using the recursive Newton-Euler algorithm taken from robotics. For the requirements of the method, a model of a rotational joint has been developed. Some examples of results of the numerical calculations made have been presented in the conclusions of the paper.

An Analysis-of-Variance (ANOVA) Approach for Sib-pair Linkage Analysis of Complex Ordinal Human Diseases

Sib-pair linkage analysis of complex human diseases has become a method of choice in modern human genetic studies, especially for the diseases with a late age at onset. The traditional parametric methods for sib pair data need to take the categorical nature of a disease phenotype into account and to explicitly model the non-linear relationship between the discrete phenotype and genetic determinants, or to force their relationship to be linear. The first approach is desirable theoretically, but explicitly modeling the sophisticated genetic architecture of a complex disease can be prohibitively complex and computational demand is high. The second approach, typically a linear regression, relies on a large sample theory and is not appropriate. In this paper, we propose to apply Analysis of Variance (ANOVA) to sib pair linkage analysis of complex human diseases. This approach has avoided building the complicated relationship between the phenotype (the affection group or status of a sib pair) and the underlying genetic determinant (identical-by-decent (IBD) values etc). We have explored its statistical efficiency and properties in sibpair linkage analysis of ordinal complex human diseases via simulation. The simulation suggests that it is a powerful approach for locating genes that presumably control phenotypic expression of complex human diseases.