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Statistical method for mapping QTLs for complex traits based on two backcross populations

Chinese Science Bulletin 2012年第21期57卷 2645-2654页

作者： ZHU ZhiHong HAYART Yousaf YANG Jian CAO LiYong LOU XiangYang XU HaiMing Agronomy department College of Agriculture and BioteehnologyZhejiang UniversityHangzhou 310058China department of Mathematics Statistics and Computer ScienceNWFP Agricultural University PeshawarPeshawar 25130Pakistan China National rice Research Institute National Center for Rice ImprovementState Key Laboratory of Rice BiologyHangzhou 310006China department of Biostatistics School of Public HealthUniversity of Alabama at BirminghamBirminghamAlabama 35294USA

Most important agronomic and quality traits of crops are quantitative in *** genetic variations in such traits are usually controlled by sets of genes called quantitative trait loci (QTLs),and the interactions between QTLs and the *** is crucial to understand the genetic architecture of complex traits to design efficient strategies for plant *** the present study,a new experimental design and the corresponding statistical method are presented for QTL *** proposed mapping population is composed of double backcross populations derived from backcrossing both homozygous parents to DH (double haploid) or RI (recombinant inbreeding) lines *** an immortal mapping population allows for across-environment replications,and can be used to estimate dominance effects,epistatic effects,and QTL-environment interactions,remedying the drawbacks of a single backcross *** this method,the mixed linear model approach is used to estimate the positions of QTLs and their various effects including the QTL additive,dominance,and epistatic effects,and QTL-environment interaction effects (QE).Monte Carlo simulations were conducted to investigate the performance of the proposed method and to assess the accuracy and efficiency of its *** results showed that the proposed method could estimate the positions and the genetic effects of QTLs with high efficiency.

关键词：回交群体品质性状基因定位统计方法数量性状位点上位性效应基础相互作用

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Ecological fitness of brown planthopper, Nilaparvata lugens (Stål), to rice nutrient management

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Ecological Processes 2017年第1期6卷 149-158页

作者： Md.Mamunur Rashid Mahbuba Jahan Khandakar S.Islam Md.Abdul Latif Plant Physiology Division Bangladesh Rice Research Institute(BRRI)Gazipur 1701Bangladesh department of Entomology Bangladesh Agricultural UniversityMymensingh 2202Bangladesh Plant Pathology Division Bangladesh Rice Research Institute(BRRI)Gazipur 1701Bangladesh

Introduction:The brown planthopper(BPH),Nilaparvata lugens(Stål)(Hemiptera:Delphacidae),is a notorious insect pest of *** supplementation can alter plant biochemical compositions which may indirectly affect on ecological fitness parameters of its insect ***,few findings are available on nutrient-induced ecological fitness of BPH and relationship of BPH fitness parameters with its host rice plant biochemical ***:We studied the main and interaction effects of nitrogen(N),phosphorus(P),and potassium(K)inputs on BPH fitness,as measured by the following variables:nymph survival,nymphal duration,adult body weight,and its *** planthopper fitness parameters were regressed as function of rice plant(Oryza sativa)biochemical composition.A completely randomized design with four replications in a factorial scheme was used considering N,P,and K levels as ***:Nitrogen application to the host rice plants provided greater survival and enhanced body weight of *** nymphal duration was found to decrease with N subsidy that caused shorter generation time of *** compounds N and soluble protein(SP),total free sugar(TFS),and silicon(Si)content in rice plant tissue correlated strongly with all fitness traits of ***,SP,and TFS associated positively with BPH survival and body weight,while negatively with nymphal *** contrast,Si had negative correlation with BPH survival and body weight,but positive with nymphal *** supplementation to host plant contributed to increase BPH body *** of P with all parameters of BPH were weak except body weight which was highly significant and *** between N and P inputs demonstrated significant effect on BPH body *** of K had no significant effect on BPH survival and *** analysis did not detect significant relationship of BPH fitness parameters with plant tissue content of ***:The res

关键词： Nilaparvata lugens Nutrient management Survival Nymphal duration Body weight

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Identification of flexible buildings with bending deformation and the unmeasured earthquake ground motion

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Science China(Technological Sciences) 2015年第3期58卷 454-461页

作者： LEI Ying HE MingYu LAI ZhiLu LIN ShuZhi department of Civil Engineering Xiamen University State Key Laboratory for Disaster Reduction in Civil Engineering Tongji University department of Civil and Environmental Engineering Rice University Xiamen Construction and Management Bureau

It is important to explore efficient algorithms for the identification of both structural parameters and unmeasured earthquake ground ***,the authors proposed an algorithm for the identification of shear-type buildings and unknown earthquake *** this paper,it is extended to the investigation of the identification of flexible buildings with bending deformation and the unmeasured earthquake ground *** the absolute co-ordinate system,the unmeasured ground motion can be treated as an unknown translational force and a bending moment at the 1st floor level of a flexible *** unknown parameters above the 1st story of the building can be identified by the extended Kalman estimator and the 1st story stiffness and the unmeasured ground motion are subsequently estimated based on the least-squares *** proposed algorithm is further extended to the identification of tall bending-type buildings based on substructure ***-connection effect between sub-buildings is treated as‘additional unknown inputs’to sub-buildings,which are estimated by the extended Kalman estimator without the measurements of rotational *** examples demonstrate the identification of a multi-story,tall bending-type building and its unmeasured earthquake ground motions using only partial measurements of structural absolute responses.

关键词： flexible building bending deformation structural identification unknown ground motion extended Kalman estimator substructure approach

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Genetic and Genotype × Environment Interaction Effects for Appearance Quality of rice

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Agricultural Sciences in China 2009年第8期8卷 891-901页

作者： Sharifi Peyman Dehghani Hamid Mumeni Ali Moghaddam Mohammad department of Plant Breeding Faculty of Agriculture Tarbiat Modares University rice Research Institute of Iran (RRII) department of Agronomy and Plant Breeding Faculty of Agriculture Tabriz University

This study was conducted to generate genetic information in rice varieties based on a complete diallel crosses over two years. The results indicated that genotype effect was significant for all traits. Genotype × environment interaction effects were significant only for cooked grain length （CGL） and cooked grain shape （CGSH）. General combining ability （GCA） and specific combining ability （SCA） effects were significant for entire traits, which indicated the important roles of both additive and non-additive gene actions. GCA x environment interaction effects were significant for CGL, CGSH and grain elongation index （GEI）. In the controlling of the inheritance of milled grain shape （GSH）, milled grain width （MGW）, GEI, milled grain length （MGL）, CGSH and cooked grain width （CGW）, the additive gene effects were more important than non-additive one. The average degree of dominance was within the range of partial dominance for all of the traits. The narrow-sense heritability was ranged from 0.65 （GSH） to 0.36 （CGL）. GCA effects were significant for all of the parents in milled grain length and it was significant for some of the parents in other traits. The crosses of Deilmani × IRFAON-215 exhibited significant SCA for GEI. The positive mean of heterosis was observed for CGW. The highest maximum values of heterosis were revealed in GEI, flowed by GSH, MGW and CGW. GCA and MPV were significantly and positively correlated together for all traits.

关键词： appearance quality diallel analysis genetic main effects environment interaction milling quality rice

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Radical Addition of Perfluorinated Alkyl Iodides to Multi- Layered Graphene and Single-Walled Carbon Nanotubes

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Nano Research 2010年第2期3卷 138-145页

作者： Christopher E.Hamilton Jay R.Lomeda Zhengzong Sun James M.Tour Andrew R.Barron Richard E.Smalley Institute for Nanoscale Science and Technology Department of Chemistry and Department of Mechanical Engineering and Materials ScienceRice UniversityHoustonTexas 77005USA

A simple one-pot reaction that serves to functionalize graphite nanosheets(graphene)and single-walled carbon nanotubes(SWNTs)with perfluorinated alkyl groups is *** radical addition of 1-iodo-1H,1H,2H,2H-perfluorododecane to ortho-dichlorobenzene suspensions of the carbon nanomaterial is initiated by thermal decomposition of benzoyl ***,UV photolysis of 1-iodo-perfluorodecane serves to functionalize the carbon ***-SWNTs,perfluorododecyl-graphene,and perfluorodecyl-graphene are characterized by infrared(IR)and Raman spectroscopy,X-ray photoelectron spectroscopy(XPS),thermogravimetric analysis(TGA),and atomic force microscopy(AFM).The products show enhanced dispersability in CHCl3 as compared to unfunctionalized starting *** advantage of this one-pot functionalization procedure lies in the use of pristine graphite as starting material thereby avoiding the use of harsh oxidizing conditions.

关键词： Nanotube single-walled carbon nanotube graphene radical addition

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Joint association analysis method to dissect complex genetic architecture of multiple genetically related traits

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The Crop Journal 2020年第5期8卷 733-744页

作者： Feng Lin Guoan Qi Ting Xu Xiangyang Lou Yongbo Hong Haiming Xu Institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058ZhejiangChina department of Mathematics Zhejiang UniversityHangzhou 310058ZhejiangChina department of Biostatistics Colleges of PHHP and the College of MedicineUniversity of FloridaGainesvilleFL 32610USA State Key Laboratory of rice Biology and Zhejiang Key Laboratory of Super rice Research China National Rice Research InstituteHangzhou 311401ZhejiangChina

Genome-wide association study(GWAS)has been a standard approach to discover the genetic determinants underlying complex *** is a major challenge in GWAS how to improve analysis power,uncover complex genetic correlation,and reveal gene-gene and gene-environment interactions through integrated analysis of multiple genetically related *** combat these challenges,we proposed a mixed linear model-based joint association analysis method for multiple traits,which include epistasis and geneenvironment interaction in the mapping model and utilize within-trait variance and between-trait covariance simultaneously;A F-statistics based on Wilks statistics is used to test the significance of each SNP and paired interacted SNPs,each genetic effects of QTS are estimated and tested by the MCMC method based on a QTS full *** showed that the multi-trait GWAS method could provide increased power in detecting pleiotropic loci affecting more than one trait,and can unbiasedly estimate effects of *** demonstrate the performance of the proposed method,we analyzed four blood lipid traits in Multi-Ethnic Study of Atherosclerosis(MESA)Cohort and two yield-related traits in a rice immortalized F2 dataset.A software package was developed for the proposed method.

关键词： traits analysis complex

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Infection of Ustilaginoidea virens intercepts rice seed formation but activates grain-filling-related genes

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Journal of Integrative Plant Biology 2015年第6期57卷 577-590页

作者： Jing Fan Xiao-Yi Guo Liang Li Fu Huang Wen-Xian Sun Yan Li Yan-Yan Huang Yong-Ju Xu Jun Shi Yang Lei Ai-Ping Zheng Wen-Ming Wang rice Research Institute Sichuan Agricultural University College of Agronomy Sichuan Agricultural University department of Plant Pathology China Agricultural University

rice false smut has become an increasingly serious disease in rice （Oryza sativa L.） production worldwide. The typical feature of this disease is that the fungal pathogen Ustilaginoidea virens （Uv） specifical y infects rice flower and forms false smut bal , the ustiloxin-containing bal-like fungal colony, of which the size is usual y several times larger than that of a mature rice seed. However, the underlying mechanisms of Uv-rice interac-tion are poorly understood. Here, we applied time-course microscopic and transcriptional approaches to investigate rice responses to Uv infection. The results demonstrated that the flower-opening process and expression of associated transcription factors, including ARF6 and ARF8, were inhibited in Uv-infected spikelets. The ovaries in infected spikelets were interrupted in fertilization and thus were unable to set seeds. However, a number of grain-fil ing-related genes, including seed storage protein genes, starch anabolism genes and endosperm-specific transcription factors （RISBZ1 and RPBF）, were highly transcribed as if the ovaries were fertilized. In addition, critical defense-related genes like NPR1 and PR1 were downregulated by;Uv infection. Our data imply that Uv may hijack host nutrient reservoir by activation of the grain-fil ing network because of growth and formation of false smut bal s.

关键词： Flower-infecting grain filling microscopy rice false smut RNA-Seq

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Recombinase Polymerase Amplification Based Rapid Detection of Aroma Gene in rice

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rice science 2023年第2期30卷 96-99,I0010-I0013页

作者： Amrita BANERJEE S.BHARTI J.KUMAR P.SAR PRIYAMEDHA N.P.MANDAL S.SARKAR Somnath ROY Central Rainfed Upland rice Research Station Indian Council of Agricultural Research(ICAR)-National Rice Research InstituteHazaribagJharkhand 825301India department of Biotechnology Vinoba Bhave UniversityHazaribagJharkhand 825301India Crop Improvement Division ICAR-National Rice Research InstituteCuttackOdisha 753006India

Recombinase polymerase amplification(RPA) has been emerged as an alternative to PCR due to its high specificity and sensitivity in diagnostics of animal and plant pathogens. In this study, an RPA protocol was develope... 详细信息

关键词： specificity Rec emerged

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Perspectives on the prevention and treatment of infection for orthopedic tissue engineering applications

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Chinese Science Bulletin 2013年第35期58卷 4342-4348页

作者： SHAH Sarita R KASPER F Kurtis MIKOS Antonios G department of Bioengineering Rice University P.O. Box 1892 MS 142 Houston Texas 77251-1892 USA department of Chemical and Biomolecular Engineering Rice University P.O. Box 1892 MS 142 Houston Texas 77251-1892 USA

The emergence of orthopedic tissue engineering devices as viable clinical solutions demands that the field address significant clinical complications associated with the implantation of foreign materials in the body,especially *** tissue engineering has focused on the development of methods to regenerate and repair,until recently there has been a relative dearth of literature regarding the intersection of tissue engineering and *** particular,local delivery of antimicrobials has long been of clinical interest,but only recently has that been translated into the realm of tissue *** this perspective,we briefly review major modes of local delivery for infection prevention and treatment and discuss possible strategies for preventing implant-associated infections.

关键词：组织工程感染骨科治疗预防应用工程设备工程规划

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Improvement of Upland rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable rice Production

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rice science 2021年第5期28卷 493-500,I0033-I0036页

作者： Vishalakshi Balija Umakanth Bangale Senguttuvel Ponnuvel Kalyani Makarand Barbadikar Srinivas Prasad Madamshetty Sanjeeva Rao Durbha Hari Yadla Sheshu Madhav Maganti Biotechnology Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Hybrid rice Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Plant Pathology Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Plant Physiology Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Regional Agricultural Research Station Professor Jayashankar Telangana State Agricultural UniversityWarangal 506006India department of Biotechnology Acharya Nagajna UniversityGuntur 522510India

Varalu is an early maturing rice variety widely grown in the rainfed ecosystem preferred for its grain type and cooking ***,the yield of Varalu is substantially low since it is being affected by reproductive drought stress along with the blast *** genetic improvement of Varalu was done by introgressing a major yield QTL,qDTY_(12.1),along with two major blast resistance genes ***54 and Pi1 through marker-assisted backcross *** traits were transferred till BC_(2) generation and intercrossing was followed to pyramid the two *** foreground selection was carried out using linked markers as well as peak markers(RM28099,RM28130,RM511 and RM28163)for the targeted QTL(qDTY_(12.1)),RM206 for Pi54 and RM224 for *** background selection was done using genome-wide SSR *** best lines(MSM-36,MSM-49,MSM-53,MSM-57,MSM-60 and MSM-63)having qDTY_(12.1) and two blast resistance genes in homozygous condition with recurrent parent genome of 95.0%-96.5% having minimal linkage drag of about 0.1 to 0.7 Mb were *** lines showed yield advantage under drought stress as well as irrigated ***-36 showed better performance in the national coordinated trials conducted across India,which indicated that improved lines of Varalu expected to replace Varalu and may have an important role in sustaining rice *** present study demonstrated the successful marker-assisted pyramiding strategy for introgression of genes/QTLs conferring biotic stress resistance and yield under abiotic stress in rice.

关键词： blast resistance drought stress marker-assisted gene pyramiding rainfed ecosystem upland rice

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