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| 1 | QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations显示文摘QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials. | Lei Meng Huihui Li Luyan Zhang Jiankang Wang | 2015 | The Crop Journal2015，3，3： | 174 |
| 2 | Stable classi?cation with limited sample: transferring a 30-m resolution sample set collected in 2015 to mapping 10-m resolution global land cover in 2017显示文摘As the world strives to reduce the impact of population growth, urbanization, agricultural expansion, and climate change on food security, energy and water shortage, resource over-exploration, biodiversity loss, environmental pollution, and ultimately human health, timely and higher resolution land cover information is urgently needed to achieve the sustainable development goals of the United Nations. | Peng Gong Han Liu Meinan Zhang Congcong Li Jie Wang Huabing Huang Nicholas Clinton Luyan Ji Wenyu Li Yuqi Bai Bin Chen Bing Xu Zhiliang Zhu Cui Yuan Hoi Ping Suen Jing Guo Nan Xu Weijia Li Yuanyuan Zhao Jun Yang Chaoqing Yu Xi Wang Haohuan Fu Le Yu Iryna Dronova Fengming Hui Xiao Cheng Xueli Shi Fengjin Xiao Qiufeng Liu Lianchun Song | 2019 | Science Bulletin2019，64，6： | 166 |
| 3 | Dissecting and Enhancing the Contributions of High-Molecular-Weight Glutenin Subunits to Dough Functionality and Bread Quality显示文摘Dear Editor, Seed storage proteins (SSPs) are frequently important determinants of crop quality traits (Shewry and Casey,1999).Dissecting and enhancing the genetic contributions of individual SSPs to their target traits are essential for effectively improving crop quality attributes.However,such a task is often difficult to accomplish,because SSPs are frequently expressed from multigene families and exhibit strong allelic variation.Consequently,detailed knowledge of the function of individual SSPs in crop quality trait is still limited.This scenario is well illustrated by high-molecular-weight glutenin subunits (HMWGSs),a complex family of SSPs that are involved in wheat enduse quality through affecting dough functionality (Békés,2012;Rasheed et al.,2014). | Yiwen Li Xuefi An Ran Yang Xiaomin Guo Guidong Yue Renchun Fan Bin Li Zhensheng Li Kunpu Zhang Zhenying Dong Luyan Zhang Jiankang Wang Xu Jia Hong-Qing Ling Aimin Zhang Xiangqi Zhang Daowen Wang | 2015 | Molecular Plant2015，8，2： | 9 |
| 4 | The Statistical Power of Inclusive Composite Interval Mapping in Detecting Digenic Epistasis Showing Common F_2 Segregation Ratios显示文摘Epistasis is a commonly observed genetic phenomenon and an important source of variation of complex traits,which could maintain additive variance and therefore assure the long-term genetic gain in breeding.Inclusive composite interval mapping(ICIM) is able to identify epistatic quantitative trait loci(QTLs) no matter whether the two interacting QTLs have any additive effects.In this article,we conducted a simulation study to evaluate detection power and false discovery rate(FDR) of ICIM epistatic mapping,by considering F_2 and doubled haploid(DH) populations,different F_2 segregation ratios and population sizes.Results indicated that estimations of QTL locations and effects were unbiased,and the detection power of epistatic mapping was largely affected by population size,heritability of epistasis,and the amount and distribution of genetic effects.When the same likelihood of odd(LOD) threshold was used,detection power of QTL was higher in F_2 population than power in DH population;meanwhile FDR in F_2 was also higher than that in DH.The increase of marker density from 10 cM to 5 cM led to similar detection power but higher FDR.In simulated populations,ICIM achieved better mapping results than multiple interval mapping(MIM) in estimation of QTL positions and effect.At the end,we gave epistatic mapping results of ICIM in one actual population in rice(Oryza sativa L.). | Luyan Zhang Huihui Li Jiankang Wang | 2012 | Journal of Integrative Plant Biology2012，54，4： | 6 |
| 5 | Ordering of high-density markers by the k-Optimal algorithm for the traveling-salesman problem显示文摘Construction of accurate and high-density linkage maps is a key research area of genetics.We investigated the efficiency of genetic map construction(MAP)using modifications of the k-Optimal(k-Opt)algorithm for solving the traveling-salesman problem(TSP).For TSP,different initial routes resulted in different optimal solutions.The most optimal solution could be found only by use of as many initial routes as possible.But for MAP,a large number of initial routes resulted in one optimal order.k-Opt using open route length gave a slightly higher proportion of correct orders than the method of adding one virtual marker and using closed route length.Recombination frequency(REC)and logarithm of odds(LOD)score gave similar proportions of correct order,higher than that given by genetic distance.Both missing markers and genotyping error reduced ordering accuracy,but the best order was still achieved with high probability by comparison of the optimal orders from multiple initial routes.Computation time increased rapidly with marker number,and 2-Opt took much less time than 3-Opt.The 2-Opt algorithm was compared with ordering methods used in two other software packages.The best method was 2-Opt using open route length as the criterion to identify the optimal order and using REC or LOD as the measure of distance between markers.We describe a unified software interface for using k-Opt in high-density linkage map construction for a wide range of genetic populations. | Luyan Zhang Huihui Li Lei Meng Jiankang Wang | 2020 | The Crop Journal2020，8，5： | 6 |
| 6 | Linkage analysis and integrated software GAPL for pure-line populations derived from four-way and eight-way crosses显示文摘Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses.First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents.Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate(MLE) of recombination frequency is calculated.An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete.A linkage map can thus be constructed using estimated recombination frequencies.We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations.Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages.The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations. | Luyan Zhang Lei Meng Jiankang Wang | 2019 | The Crop Journal2019，7，3： | 5 |
| 7 | A Study of Estimation Model for the Chlorophyll Content of Wheat Leaf Based on Hyperspectral Imaging显示文摘In order to explore the spectral features and sensitive wave band of wheat leaf,we establish a quantitative relationship model between wheat chlorophyll content and spectral features to promote the application of hyperspectral technology in precise wheat fertilization and fast,non-destructive growth monitoring.Using the relational analysis,we analyze the relationship between chlorophyll content and spectral reflectance or the first derivative,and establish the chlorophyll content monitoring model.By selection and verification,the best estimation models for wheat chlorophyll content are as follows:SPAD = 36.75 + 188.168R387,SPAD =2094.242R'7153+ 112646.744 R'7152-1.561E7 R'715+42.991.The two models can well estimate the SPAD value of wheat leaf,and comparatively speaking,the SPAD estimation model based on wave band R387 has greater accuracy. | Luyan NIU Xiaoyan ZHANG | 2016 | Asian Agricultural Research2016，8，8： | 4 |
| 8 | Modeling and simulation of recurrent phenotypic and genomic selections in plant breeding under the presence of epistasis显示文摘Recurrent selection is an important breeding method for population improvement and selecting elite inbreds or fixed lines from the improved germplasm.Recently,a computer simulation tool called QuMARS has been developed,which allows the simulation and optimization of various recurrent selection strategies.Our major objective in this study was to use the QuMARS tool to compare phenotypic recurrent,marker-assisted recurrent,and genomic selections(abbreviated respectively as PS,MARS and GS)for both short-and long-termbreeding procedures.ForMARS,twomarker selection models were considered,i.e.,stepwise(Rstep)and forward regressions(Forward).For GS,three prediction models were considered,i.e.,genomic best linear unbiased predictors(GBLUP),ridge regression(Ridge),and regression by Moore-Penrose general inverse(InverseMP).To generate genotypes and phenotypes for a given individual during simulation,one additive and two epistasis genetic models were considered with three levels of heritability.Results demonstrated that selection responses from GBLUP-based GS and MARS(Forward)were consistently greater than those from PS under the additive model,particularly in early selection cycles.In contrast,selection response from PS was consistently superior over MARS and GS under epistatic models.For the two epistasis models,total genetic variance and the additive variance component were increased in some cases after selection.Through simulation,we concluded that GS and PS were effective recurrent selection methods for improved breeding of targeted traits controlled by additive and epistatic quantitative trait loci(QTL).QuMARS provides an opportunity for breeders to compare,optimize and integrate new technology into their conventional breeding programs. | Mohsin Ali Luyan Zhang Ian DeLacy Vivi Arief Mark Dieters Wolfgang H.Pfeiffer Jiankang Wang Huihui Li | 2020 | The Crop Journal2020，8，5： | 4 |
| 9 | Quantitative trait locus mapping with background control in genetic populations of clonal F_1 and double cross显示文摘In this study, we considered five categories of molecular markers in clonal F_1 and double cross populations,based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F_1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping(ICIM) of quantitative trait locus(QTL). The ef ficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple-QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize. | Luyan Zhang Huihui Li Junqiang Ding Jianyu Wu Jiankang Wang | 2015 | Journal of Integrative Plant Biology2015，57，12： | 4 |
| 10 | Rapid room-temperature synthesis of a porphyrinic MOF for encapsulating metal nanoparticles显示文摘While metal nanoparticles(NPs)have shown great promising applications as heterogeneous catalysts,their agglomeration caused by thermodynamic instability is detrimental to the catalytic performance.To tackle this hurdle,we successfully prepared a functional and stable porphyrinic metal-organic framework(MOF),PCN-224-RT,as a host for encapsulating metal nanoparticles by direct stirring at room temperature.As a result,Pt@PCN-224-RT composites with well-dispersed Pt NPs can be constructed by introducing pre-synthesized Pt NPs into the precursor solution of PCN-224-RT.Of note,the rapid and simple stirring method in this work is more in line with the requirements of environmental friendly and industrialization compared with traditional solvothermal methods. | Huihui He Luyan Li Yang Liu Meruyert Kassymova Dandan Li Liangliang Zhang Hai-Long Jiang | 2021 | Nano Research2021，14，2： | 3 |
| 11 | Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation显示文摘Many QTL mapping methods have been developed in the past two decades.Statistically,the best method should have a high detection power but a low false discovery rate (FDR).Power and FDR cannot be derived theoretically for most QTL mapping methods,but they can be properly evaluated using computer simulations.In this paper,we used four genetic models (two for independent loci and two for linked loci) to illustrate power and FDR estimation for interval mapping (IM) and inclusive composite interval mapping (ICIM).For each model,we simulated 1000 populations each of 200 doubled haploids.A support interval (SI) was first defined to indicate to which predefined QTL the significant QTL belonged.Power was calculated by counting the number of simulation runs with significant peaks higher than the logarithm of odds (LOD) threshold in the SI.Quantitative trait loci not identified in any SIs were viewed as false positives.The FDR is the rate at which QTLs are identified as significant when they are actually non-significant.Simulation results allowed us to estimate power and FDR of IM and ICIM for two independent and two linkage genetic models.Our estimates allowed us to readily compare the efficiencies of different statistical methods for QTL mapping,including the ability to separate linkage,under a wide range of genetic models.We used IM and ICIM as examples of how to estimate power and FDR,but the principles shown in this paper can be used for power analysis and comparison of any other QTL mapping methods,especially those based on interval tests. | LI HuiHui ZHANG LuYan WANG JianKang | 2012 | Chinese Science Bulletin2012，57，21： | 3 |
| 12 | Effects of missing marker and segregation distortion on QTL mapping in F2 populations显示文摘 | Luyan Zhang Shiquan Wang Huihui Li Qiming Deng Aiping Zheng Shuangcheng Li Ping Li Zhonglai Li Jiankang Wang | 2010 | Theoretical and Applied Genetics2010，，6： | 2 |
| 13 | Effects of missing marker and segregation distortion on QTL mapping in F2 populations显示文摘 | Luyan Zhang Shiquan Wang Huihui Li Qiming Deng Aiping Zheng Shuangcheng Li Ping Li Zhonglai Li Jiankang Wang | 2010 | Theoretical and Applied Genetics2010，，6： | 1 |
| 14 | Interactions Between Markers Can Be Caused by the Dominance Effect of Quantitative Trait Loci显示文摘 | Zhang Luyan Li Huihui Li Zhonglai Wang Jiankang | 2008 | Genetics2008，，2： | 1 |
| 15 | Separation of six purine bases by capillary electrophoresis with elecrochemical detection显示文摘 | Gang Chen Qingcui Chu Luyan Zhang | 2002 | Analytica Chimica Acta2002，457，： | 1 |
| 16 | Effects of Cracks on the Mass Transfer of Polymer Electrolyte Membrane Fuel Cell with High Performance Membrane Electrode Assembly显示文摘A two-dimensional geometric model is developed for a polymer electrolyte based on the liquid water penetration mechanism in the membrane electrode assemblies under the action of capillary pressure.The effects of the diameter,number,and distribution of cracks in the micro-pore layers(MPLs)of the modeled MEA on the performance of the PEMFC are simulated to investigate the influence of mass transfer across the membrane.The results indicate that liquid water in the catalyst layer(CL)of the MEA can be discharged to gas channels through the cracks in MEA under the action of capillary pressure,thereby alleviating the flooding in the CL and enhancing the diffusion of oxygen to the CL.When the proportion of the total area of cracks in the active area of the MEA was 8%-12%,crack diameter was 20-30μm,and cracks were distributed uniformly.MEAs with and without cracks were prepared,fuel cells were assembled,and their performance was measured.The effects of cracks on mass transfer were then verified.This study helps prepare MEAs with controllable cracks. | 施金蓉 詹志刚 ZHANG Di YU Yuan YANG Xiaoxiang HE Luyan PAN Mu | 2021 | Journal of Wuhan University of Technology(Materials Science)2021，36，3： | 1 |
| 17 | Determination of three bioactive constituents in moutan cortex by capillary elec- trophoresis with electrochemical detection显示文摘 | Chen Gang Zhang Luyan Yang Pengyuan | 2005 | Analytical Sciences2005，21，： | 1 |
| 18 | Rapid Determination of Paeoniflorin and Three Sugars in Radix Paeoniae Alba by Capillary Electrophoresis显示文摘 | Gang CHEN Luyan ZHANG Pengyuan YANG | 2005 | Analytical Sciences2005，21，3： | 1 |
| 19 | Determination of hesperidin and synephrine in Pericarpium Cirri Reticulatae by capillary electrophoresis with electrochemical detection 显示文摘 | Gang Chen Luyan Zhang Jiequan Zhao Jiannong Ye | | Analytical and Bioanalytical Chemistry0，373，3： | 1 |
| 20 | Preparation of a carbon nanotube-copper nanoparticle hybrid by chemical reduction for use in the electrochemical sensing of carbohydrates显示文摘 | Fu Yuejiao Zhang Luyan | 2012 | Carbon2012，50，： | 1 |
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