A Strategy for Finding the Optimal Scale of Plant Core Collection Based on Monte Carlo Simulation
作者： Jiancheng Wang , Yajing Guan , Yang Wang , Liwei Zhu , Qitian Wang
DOI: 10.1155/2014/503473
关键词:
摘要: Core collection is an ideal resource for genome-wide association studies (GWAS). A subcore a subset of core collection. strategy was proposed finding the optimal sampling percentage on plant based Monte Carlo simulation. cotton germplasm group 168 accessions with 20 quantitative traits used to construct collections. Mixed linear model approach eliminate environment effect and GE (genotype × environment) effect. Least distance stepwise (LDSS) method combining 6 commonly genetic distances unweighted pair-group average (UPGMA) cluster adopted Homogeneous population assessing assess validity 7 evaluating parameters simulation conducted percentage, number traits, parameters. new “distilling free-form natural laws from experimental data” find best formula determine percentages. The results showed that coincidence rate range (CR) most valid parameter suitable serve as threshold percentage. principal component analysis collections constructed by percentages calculated present were well representative.
hindawi.com参考文章(41)
C. Spillane, T. Hodgkin, Th.J.L. van Hintum, A.H.D. Brown, Core collections of plant genetic resources. IPGRI Technical Bulletin No.3. International Plant Genetic Resources Institute, Rome, Italy, 48 pp. ,(2000)
Hari D. Upadhyaya, C. L. L. Gowda, R. P. S. Pundir, V. Gopal Reddy, Sube Singh, Development of Core Subset of Finger Millet Germplasm Using Geographical Origin and Data on 14 Quantitative Traits Genetic Resources and Crop Evolution. ,vol. 53, pp. 679- 685 ,(2006) , 10.1007/S10722-004-3228-3
L. G. Santesteban, C. Miranda, J.B. Royo, Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data Spanish Journal of Agricultural Research. ,vol. 7, pp. 572- 584 ,(2009) , 10.5424/SJAR/2009073-442
Jian-cheng Wang, Jin Hu, Ya-jing Guan, Yan-fang Zhu, Effect of the scale of quantitative trait data on the representativeness of a cotton germplasm sub-core collection Journal of Zhejiang University SCIENCE B. ,vol. 14, pp. 162- 170 ,(2013) , 10.1631/JZUS.B1200075
Xuehui Huang, Xinghua Wei, Tao Sang, Qiang Zhao, Qi Feng, Yan Zhao, Canyang Li, Chuanrang Zhu, Tingting Lu, Zhiwu Zhang, Meng Li, Danlin Fan, Yunli Guo, Ahong Wang, Lu Wang, Liuwei Deng, Wenjun Li, Yiqi Lu, Qijun Weng, Kunyan Liu, Tao Huang, Taoying Zhou, Yufeng Jing, Wei Li, Zhang Lin, Edward S Buckler, Qian Qian, Qi-Fa Zhang, Jiayang Li, Bin Han, Genome-wide association studies of 14 agronomic traits in rice landraces Nature Genetics. ,vol. 42, pp. 961- 967 ,(2010) , 10.1038/NG.695
Michael Schmidt, Hod Lipson, Distilling Free-Form Natural Laws from Experimental Data Science. ,vol. 324, pp. 81- 85 ,(2009) , 10.1126/SCIENCE.1165893
Zhenqi Su, Chenyang Hao, Lanfen Wang, Yuchen Dong, Xueyong Zhang, Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.) Theoretical and Applied Genetics. ,vol. 122, pp. 211- 223 ,(2011) , 10.1007/S00122-010-1437-Z
Dunia Pino Del Carpio, Ram Kumar Basnet, Ric C. H. De Vos, Chris Maliepaard, Richard Visser, Guusje Bonnema, The patterns of population differentiation in a Brassica rapa core collection Theoretical and Applied Genetics. ,vol. 122, pp. 1105- 1118 ,(2011) , 10.1007/S00122-010-1516-1
Giuseppina Logozzo, Rosa Donnoli, Leonardo Macaluso, Roberto Papa, Helmut Knüpffer, Pierluigi Spagnoletti Zeuli, Analysis of the contribution of Mesoamerican and Andean gene pools to European common bean ( Phaseolus vulgaris L.) germplasm and strategies to establish a core collection Genetic Resources and Crop Evolution. ,vol. 54, pp. 1763- 1779 ,(2007) , 10.1007/S10722-006-9185-2
Magnus Nordborg, Detlef Weigel, Next-generation genetics in plants Nature. ,vol. 456, pp. 720- 723 ,(2008) , 10.1038/NATURE07629