Refine your search
Collections
Co-Authors
Journals
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z All
Li, Wei
- Genomic Variation Mapping and Detection of Novel Genes Based on Genome-Wide Survey of an Elite Upland Cotton Hybrid (Gossypium hirsutum L.)
Abstract Views :206 |
PDF Views:76
Authors
Zhenyu Wang
1,
Wei Li
1,
Guanghui Xiao
2,
Xiaojian Zhou
1,
Xiaoyu Pei
1,
Yangai Liu
1,
Kehai Zhou
1,
Kunlun He
1,
Junfang Liu
1,
Ying Li
1,
Wensheng Zhang
1,
Zhongying Ren
1,
Qingqin Meng
1,
Haifeng Wang
1,
Xiongfeng Ma
1,
Daigang Yang
1
Affiliations
1 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, CN
2 College of Life Sciences, Shaanxi Normal University, Xi’an 710119, CN
1 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, CN
2 College of Life Sciences, Shaanxi Normal University, Xi’an 710119, CN
Source
Current Science, Vol 115, No 4 (2018), Pagination: 701-709Abstract
CCRI63, with the largest cultivated area among hybrids in China, is a successful promotion of elite up-land cotton (Gossypium hirsutum L.) hybrid cultivar. We have constructed a detailed genomic variation map of CCRI63 by aligning whole-genome shotgun sequencing reads from CCRI63 to the TM-1 reference genome. Genomic single nucleotide poly-morphism (SNP) and insertion-deletion (Indel) muta-tional hotspots were identified, most of which were located on chromosome D02, and associated with dis-ease resistance and lipid glycosylation and modification. The density of heterozygous SNP sites showed 73 quantitative trait loci overlapped with peak intervals of high-density heterozygous SNPs, suggesting that the heterozygous sites in the peak are important for improvement of CCRI63 yield and fibre quality. To avoid loss of genetic components, unmapped reads were used for de novo assembly of the missing regions in the reference genome, and 153 novel functional genes were obtained. The large-scale genetic variation and novel functional genes identified in the CCRI63 genome can facilitate future gene-phenotype studies and provide an additional resource for the improvement of cotton.Keywords
Cotton Hybrid, Genomic Variation Map, Mutational Hotspots, Novel Genes.Full Text
References
- Fryxell, P., A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea, 1992, 2, 108–165.
- Brubaker, C. L., Bourland, F. and Wendel, J. F., The origin and domestication of cotton. In Cotton: Origin, History, Technology and Production, John Wiley, New York, 1999, pp. 3–31.
- Kim, H. J. and Triplett, B. A., Cotton fibre growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol., 2001, 127, 1361–1366.
- Shangguan, X. X., Yang, C. Q., Zhang, X. F. and Wang, L. J., Functional characterization of a basic helix–loop–helix (bHLH) transcription factor GhDEL65 from cotton (Gossypium hirsutum). Physiol. Plant., 2016, 158(2), 200–212.
- Tiwari, N., Sharma, P. K. and Malathi, V. G., Functional charac-terization of C1 gene of cotton leaf curl multan betasatellite. Vi-rus Genes, 2013, 46, 111–119.
- Fang, L., Tian, R., Li, X., Chen, J., Wang, S., Wang, P. and Zhang, T., Cotton fibre elongation network revealed by expression profiling of longer fibre lines introgressed with different Gossypi-um barbadense chromosome segments. BMC Genomics, 2014, 15, 838.
- Zhang, T. et al., Sequencing of allotetraploid cotton (Gossypium hirsutum L. Acc. Tm-1) provides a resource for fibre improve-ment. Nature Biotechnol., 2015, 33, 531–537.
- Wang, K., Huang, G. and Zhu, Y., Transposable elements play an important role during cotton genome evolution and fibre cell de-velopment. Sci. China Life Sci., 2016, 59, 112–121.
- Tang, M. et al., Rapid evolutionary divergence of Gossypium bar-badense and G. hirsutum mitochondrial genomes. BMC Genomics, 2015, 16, 770.
- Liu, Y. et al., A Gossypium BAC clone contains key repeat com-ponents distinguishing sub-genome of allotetraploidy cottons. Mol. Cytogenet., 2016, 9, 27.
- Campbell, B. T. et al., Status of the global cotton germplasm re-sources. Crop Sci., 2010, 50, 1161.
- Shang, L. et al., Genetic analysis of upland cotton dynamic heter-osis for boll number per plant at multiple developmental stages. Sci. Rep., 2016, 6, 35515.
- Li, B. et al., Genetic effects and heterosis of yield and yield com-ponent traits based on Gossypium barbadense chromosome seg-ment substitution lines in two Gossypium hirsutum backgrounds. PLoS One, 2016, 11, e0157978.
- Liu, R. et al., Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Mol. Breed., 2012, 29, 297–311.
- Guo, X. et al., Mapping heterotic loci for yield and agronomic traits using chromosome segment introgression lines in cotton. J. Integr. Plant Biol., 2013, 55, 759–774.
- Liang, Q., Shang, L., Wang, Y. and Hua, J., Partial dominance, overdominance and epistasis as the genetic basis of heterosis in upland cotton (Gossypium hirsutum L.). PLOS ONE, 2015, 10, e0143548.
- Shang, L., Wang, Y., Cai, S., Wang, X., Li, Y., Abduweli, A. and Hua, J., Partial dominance, overdominance, epistasis and QTL by environment interactions contribute to heterosis in two upland cot-ton hybrids. G3: Genes|Genomes|Genetics (Bethesda, Md), 2015, 6, 499–507.
- Mace, E. S. et al., Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Na-ture Commun., 2013, 4, 2320.
- Lin, J. et al., Genome re-sequencing and bioinformatics analysis of a nutraceutical rice. Mol. Genet. Genomics: MGG, 2015, 290, 955–967.
- Kim, M. Y. et al., Whole-genome sequencing and intensive analy-sis of the undomesticated soybean (Glycine soja sieb. and zucc.) ge-nome. Proc. Natl. Acad. Sci. USA, 2010, 107, 22032–22037.
- Chung, W. H. et al., Population structure and domestication re-vealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res., 2014, 21, 153–167.
- Srivastava, S. K., Wolinski, P. and Pereira, A., A strategy for ge-nome-wide identification of gene based polymorphisms in rice re-veals non-synonymous variation and functional genotypic markers. PLoS One, 2014, 9, e105335.
- Li, F. et al., Genome sequence of cultivated upland cotton (Gossy-pium hirsutum TM-1) provides insights into genome evolution. Nature Biotechnol., 2015, 33, 524–530.
- Paterson, A. H., Brubaker, C. L. and Wendel, J. F., A rapid meth-od for extraction of cotton (Gossypium spp.) genomic DNA suita-ble for RFLP or PCR analysis. Plant Mol. Biol. Rep., 1993, 11,122–127.
- Li, H. and Durbin, R., Fast and accurate short read alignment withBurrows–Wheeler transform. Bioinformatics, 2009, 25, 1754–1760.
- Li, H. et al., The sequence alignment/map format and SAMtools.Bioinformatics, 2009, 25, 2078–2079.
- Chen, K. et al., Break dancer: an algorithm for high-resolutionmapping of genomic structural variation. Nature Meth., 2009, 6,677–681.
- Abyzov, A., Urban, A. E., Snyder, M. and Gerstein, M., CNVna-tor: An approach to discover, genotype, and characterize typicaland atypical CNVs from family and population genome sequenc-ing. Genome Res., 2011, 21, 974–984.
- Wang, K., Li, M. and Hakonarson, H., ANNOVAR: functionalannotation of genetic variants from high-throughput sequencing data. Nucl. Acids Res., 2010, 38, e164–e164.
- Li, R. et al., De novo assembly of human genomes with massivelyparallel short read sequencing. Genome Res., 2010, 20, 265– 272.
- Lam, H. M. et al., Resequencing of 31 wild and cultivated soy-bean genomes identifies patterns of genetic diversity and selec-tion. Nature Genet., 2010, 42, 1053–1059.
- McNally, K. L. et al., Genomewide SNP variation reveals rela-tionships among landraces and modern varieties of rice. Proc.Natl. Acad. Sci. USA, 2009, 106, 12273–12278.
- Shull, G. H., What is ‘heterosis’? Genetics, 1948, 33, 439– 446.
- Fu, D. et al., What is crop heterosis: new insights into an old top-ic. J. Appl. Genet., 2015, 56, 1–13.
- Schuster, S. C., Next-generation sequencing transforms today’sbiology. Nat. Meth., 2008, 5, 16–18.
- Zhou, D. et al., Pedigree-based analysis of derivation of genomesegments of an elite rice reveals key regions during its breeding.Plant Biotechnol. J., 2016, 14, 638–648.
- Ouyang, S. et al., The TIGR Rice Genome Annotation Resource:improvements and new features. Nucleic Acids Res., 2007, 35,D883–D887.
- Lai, J. et al., Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genet., 2010, 42, 1027–1030.
- Wang, M. et al., Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nature Genet.,2017, 49, 579–587.
- Fang, L. et al., Genomic insights into divergence and dual domes-tication of cultivated allotetraploid cottons. Genome Biol., 2017,18, 33.
- Yang, Z. and Bielawski, J. P., Statistical methods for detecting molecular adaptation. Trends Ecol. Evol., 2000, 15, 496–503.
- Crow, J. F., 90 years ago: the beginning of hybrid maize. Genet-ics, 1998, 148, 923–928.
- East, E. M., Inbreeding in corn. Rep. Conn. Agric. Exp. Stn, 1908,1907, 419–428.
- Fang, L. et al., Genomic analyses in cotton identify signatures of selection and loci associated with fibre quality and yield traits.Nature Genet., 2017, 49, 1089–1098.
- Fault Detection for Scraper Chain Using an Observer-Based Tension Distribution Estimation Algorithm
Abstract Views :181 |
PDF Views:92
Authors
Affiliations
1 School of Mechatronic Engineering, China University of Mining and Technology, Xuzhou 221116, CN
1 School of Mechatronic Engineering, China University of Mining and Technology, Xuzhou 221116, CN
Source
Current Science, Vol 118, No 11 (2020), Pagination: 1792-1802Abstract
Here we describe a fault detection scheme for a scraper chain based on a new tension distribution estimation algorithm (TDEA). A multi-body dynamic model of the ring chain transmission system (RCTS) has been developed to simulate the actual production environment of the scraper conveyer, and the fixedpoint strain measurement experiment was conducted to validate the system performance of the dynamic model. Because of the difficulties with direct measurement and restrictions of high-cost tension sensors, TDEA was achieved using a mathematical modelbased linear state observer for practical applications to monitor tension variation of the scraper chain. Moreover, the desired observer makes it feasible to obtain all the contact forces between ring chains based on the measurable state variables. For research purpose, the proposed fault detection scheme is applicable in detecting chain faults by monitoring the working state of the scraper chain. Theoretical analysis and simulation results show that the developed method is efficient to detect the occurrence of chain failure.Keywords
Dimension-Minimized Algorithm, Multibody Dynamics, Tension Monitoring, Tension Distribution Estimation.Full Text
References
- Wösle, M. and Pfeiffer, F., Dynamics of multibody systems containing dependent unilateral constraints with friction. J. Vib. Control, 1996, 2, 161–192.
- Pfeiffer, F. and Glocker, C., Multibody Dynamics with Unilateral Contacts, John Wiley, 1996, p. 262.
- Zhu, L. et al., Combined finite element and multi-body dynamics analysis of effects of hydraulic cylinder movement on ploughshare of horizontally reversible plough. Soil Tillage Res., 2016, 163, 168–175.
- Wauge, D. H., Modelling of an armoured face conveyor. Department of Mechanical Engineering, The University of Queensland, 2003.
- Nie, R. et al., Modelling of the transmission system in conveying equipment based on Euler method with application. Proc. Inst. Mech. Eng. Part K J. Multi-body Dyn., 2014, 228, 294–306.
- He, B. et al., Dynamic behaviour modelling and simulation of the chain transmission system for an armoured face conveyor. In Proceeding of the 2009 IEEE 10th International Conference on Computer-Aided Industrial Design and Conceptual Design, Wenzhou, People’s Republic of China, 2009, pp. 1000–1004.
- Jiang, S. B. et al., Multi-body dynamics and vibration analysis of chain assembly in armoured face conveyor. Int. J. Simul. Model., 2017, 16, 458–470.
- Myszkowski, M. and Loehning, D., Chain force measurements on armoured face conveyors and coal plows in heavy-duty longwalls. CIM Bull., 2001, 94, 72–75.
- Wang, H., Zhang, Q. and Xie, F., Dynamic tension test and intelligent coordinated control system of a heavy scraper conveyor. IET Sci. Meas. Technol., 2017, 11, 871–877.
- Krebs, S. et al., Reduced-order hybrid interval observer for verified state estimation of an induction machine. Control Eng. Pract., 2016, 57, 157–168.
- Rajshekhar, G. and Rastogi, P., Phase estimation using a statespace approach based method. Opt. Lasers Eng., 2013, 51, 1004– 1007.
- Mata-Machuca, J. L., Martínez-Guerra, R. and Aguilar-Sierra, H., Fault estimation using a polynomial observer: a real-time application. IFAC Proc. Vol., 2012, 45, 552–557.
- Sun, S., Ma, X. M. and Yang, Z. S., Diagnosis of coal scraper conveyor based on fuzzy fault tree. In Seventh International Conference on Measuring Technology and Mechatronics Automation, Nanchang, People’s Republic of China, 2015, pp. 392–395.
- Zhang, Y. et al., Fuzzy neural network fault diagnosis and online vibration monitoring system for the coal scraper conveyor based on rough set theory. In Proceedings of the 32nd Chinese Control Conference, Xi’an, People’s Republic of China, 2013, pp. 6134– 6138.
- Gong, X., Ma, X., Zhang, Y. and Yang, J., Application of fuzzy neural network in fault diagnosis for scraper conveyor vibration. In International Conference on Information and Automation, Yinchuan, People’s Republic of China, 2013, pp. 1135–1140.
- Xue, S., Li, X. and Xu, X., Fault tree and bayesian network based scraper conveyer fault diagnosis. In Proceedings of the 22nd International Conference on Industrial Engineering and Engineering Management 2015, Singapore, 2016, pp. 783–795.
- Sedighi, T., Foote, P. D. and Sydor, P., Feed-forward observerbased intermittent fault detection. CIRP J. Manuf. Sci. Technol., 2017, 17, 10–17.
- Emami, K., Fernando, T., Nener, B., Trinh, H. and Zhang, Y., A functional observer based fault detection technique for dynamical systems. J. Franklin Inst., 2015, 352, 2113–2128.
- Hippmann, G., An algorithm for compliant contact between complexly shaped surfaces in multibody dynamics. Multibody Dyn., 2003, 12, 345–362.
- Beyhan, S., Runge-Kutta model-based nonlinear observer for synchronization and control of chaotic systems. ISA Trans., 2013, 52, 501–509.
- Zhang, X. et al., Tension monitoring for the ring chain transmission system using an observer-based tension distribution estimation method. Adv. Mech. Eng., 2017, 9, 1687814017727251.
- Xu, S. and Zeng, B., Network traffic prediction model based on auto-regressive moving average. J. Networks, 2014, 9, 653–659.