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BioMed Research International
Volume 2017 (2017), Article ID 7641362, 6 pages
https://doi.org/10.1155/2017/7641362
Research Article

Association Analysis of Arsenic-Induced Straighthead in Rice (Oryza sativa L.) Based on the Selected Population with a Modified Model

1State Key Lab of Rice Biology, IAEA Collaborating Center, Zhejiang University, Hangzhou, Zhejiang, China
2Zhejiang Academy of Agricultural Sciences, Hangzhou, China
3Rice Research Institute, Jiangxi Academy of Agricultural Sciences and Nanchang National Sub-Center for Rice Improvement, Nanchang, Jiangxi, China
4Institute of Tobacco Research of Chinese Academy of Agricultural Sciences, Qingzhou, Shandong, China

Correspondence should be addressed to Ning Zhang; moc.621@ujzgningnahz

Received 19 January 2017; Accepted 4 June 2017; Published 25 July 2017

Academic Editor: Momiao Xiong

Copyright © 2017 Xiaobai Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. W. Yan, R. H. Dilday, T. H. Tai, J. W. Gibbons, R. W. McNew, and J. N. Rutger, “Differential response of rice germplasm to straighthead induced by arsenic,” Crop Science, vol. 45, no. 4, pp. 1223–1228, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. J. S. Collier, Rice Blight, Illinois Agricultural Experimental Station Circular 156, University of Illinois, Urbana, Ill, USA, 1912.
  3. J. M. A. Cunha and J. E. Baptista, Estudo da branca do arroz. I. Combated a doenca Agronomia lusit, vol. 20, 17-64, 1958.
  4. P. Weerapat, “Straighthead disease of rice suspected in southern Thailand,” IRRN, vol. 4:67, 1979. View at Google Scholar
  5. Y. Takeoka, Y. Tsutsui, and K. Matsuo, “Morphogenetic alterations of spikelets on a straighthead panicle in rice,” Japanese Journal of Crop Science, vol. 59, no. 4, pp. 785–791, 1990. View at Publisher · View at Google Scholar · View at Scopus
  6. B. W. Dunn, G. D. Batten, T. S. Dunn, R. Subasinghe, and R. L. Williams, “Nitrogen fertiliser alleviates the disorder straighthead in Australian rice,” Australian Journal of Experimental Agriculture, vol. 46, no. 8, pp. 1077–1083, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. W. G. Yan, F. Correa, A. Marin, J. Marassi, X. Li, and J. Re, “Comparative study on induced straighthead in the U.S. with natural straighthead in the U.S. with natural straighthead in Argentina,” in Proceedings of the 33rd Rice Technical Working Group conference, Biloxi, Mississippi, Miss, USA, 2010.
  8. B. Stich, J. Möhring, H.-P. Piepho, M. Heckenberger, E. S. Buckler, and A. E. Melchinger, “Comparison of mixed-model approaches for association mapping,” Genetics, vol. 178, no. 3, pp. 1745–1754, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. H. A. Agrama, G. C. Eizenga, and W. Yan, “Association mapping of yield and its components in rice cultivars,” Molecular Breeding, vol. 19, no. 4, pp. 341–356, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. H. A. Agrama and W. G. Yan, “Association mapping of straighthead disorder induced by arsenic in Oryza sativa,” Plant Breeding, vol. 128, no. 6, pp. 551–558, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. K. J. F. Verhoeven, G. Casella, and L. M. McIntyre, “Epistasis: Obstacle or advantage for mapping complex traits?” PLoS ONE, vol. 5, no. 8, Article ID e12264, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. W. G. Yan, J. N. Rutger, H. E. Bockelman, and T. H. Tai, “Germplasm accessions resistant to straighthead in the USDA rice core collection,” in Arkansas Agricultural Experiment Station, University of Arkansas, Arkansas, Ark, USA.
  13. W. Yan, J. N. Rutger, R. J. Bryant et al., “Development and evaluation of a core subset of the USDA rice germplasm collection,” Crop Science, vol. 47, no. 2, pp. 869–878, 2007. View at Publisher · View at Google Scholar · View at Scopus
  14. X. Li, W. Yan, H. Agrama et al., “Genetic analysis of genetic basis of a physiological disorder “straighthead” in rice (Oryza sativa L.),” Genes and Genomics, vol. 38, no. 5, pp. 453–457, 2016. View at Publisher · View at Google Scholar · View at Scopus
  15. X. Li, W. Yan, H. Agrama et al., “Mapping QTLs for improving grain yield using the USDA rice mini-core collection,” Planta, vol. 234, no. 2, pp. 347–361, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. H. Gao, S. Williamson, and C. D. Bustamante, “A markov chain monte carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data,” Genetics, vol. 176, no. 3, pp. 1635–1651, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. N. A. Rosenberg, “DISTRUCT: a program for the graphical display of population structure,” Molecular Ecology Notes, vol. 4, no. 1, pp. 137-138, 2004. View at Publisher · View at Google Scholar · View at Scopus
  18. F. Rohlf, “FNTSYS-PC numerical taxonomy and multivariate analysis system ver 2.11L,” Applied Biostatistics, 2000. View at Google Scholar
  19. M. Nei, “The theory and estimation of genetic distance,” N. E. Morton, Ed., University Press of Hawaii, Honolulu, Hawaii, USA, 1973. View at Google Scholar
  20. X. Li, W. Yan, H. Agrama et al., “Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.),” PLoS ONE, vol. 7, no. 1, Article ID e29350, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Benjamini and D. Yekutieli, “The control of the false discovery rate in multiple testing under dependency,” The Annals of Statistics, vol. 29, no. 4, pp. 1165–1188, 2001. View at Publisher · View at Google Scholar · View at MathSciNet · View at Scopus
  22. Y. Shao, L. Jin, G. Zhang, Y. Lu, Y. Shen, and J. Bao, “Association mapping of grain color, phenolic content, flavonoid content and antioxidant capacity in dehulled rice,” Theoretical and Applied Genetics, vol. 122, no. 5, pp. 1005–1016, 2011. View at Publisher · View at Google Scholar · View at Scopus
  23. J. Yu, G. Pressoir, W. H. Briggs et al., “A unified mixed-model method for association mapping that accounts for multiple levels of relatedness,” Nature Genetics, vol. 38, no. 2, pp. 203–208, 2006. View at Publisher · View at Google Scholar · View at Scopus
  24. C. Zhu and J. Yu, “Nonmetric multidimensional scaling corrects for population structure in whole genome association studies,” Genetics, vol. 182, no. 3, pp. 875–888, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. X. Li, W. Yan, H. Agrama et al., “Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection,” Genetica, vol. 138, no. 11, pp. 1221–1230, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. W. Yan, H. Agrama, M. Jia, R. Fjellstrom, and A. McClung, “Geographic description of genetic diversity and relationships in the USDA rice world collection,” Crop Science, vol. 50, no. 6, pp. 2406–2417, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. N. Patterson, A. L. Price, and D. Reich, “Population structure and eigenanalysis,” PLoS Genetics, vol. 2, p. e190, 2006. View at Publisher · View at Google Scholar
  28. A. L. Price, N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick, and D. Reich, “Principal components analysis corrects for stratification in genome-wide association studies,” Nature Genetics, vol. 38, no. 8, pp. 904–909, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. T. W. T. C. C. Consortium, “Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls,” Nature, vol. 447, Article ID 661678, pp. 661–678, 2007. View at Google Scholar
  30. D. J. Hunter, P. Kraft, K. B. Jacobs et al., “A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer,” Nature Genetics, vol. 39, no. 7, pp. 870–874, 2007. View at Publisher · View at Google Scholar · View at Scopus
  31. L. A. Kiemeney, “Re: Genome-wide Association Study of Prostate Cancer Identifies a Second Risk Locus at 8q24,” European Urology, vol. 52, no. 3, pp. 920-921, 2007. View at Publisher · View at Google Scholar
  32. L. R. Cardon and J. I. Bell, “Association study designs for complex diseases,” Nature Reviews Genetics, vol. 2, no. 2, pp. 91–99, 2001. View at Publisher · View at Google Scholar · View at Scopus
  33. K. A. B. Goddard, P. J. Hopkins, J. M. Hall, and J. S. Witte, “Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms five populations,” American Journal of Human Genetics, vol. 66, no. 1, pp. 216–234, 2000. View at Publisher · View at Google Scholar · View at Scopus
  34. X. Pan, Q. Zhang, W. Yan et al., “Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.),” PLoS ONE, vol. 7, no. 12, p. e52540, 2012. View at Publisher · View at Google Scholar
  35. S. A. Flint-Garcia, A.-C. Thuillet, J. Yu et al., “Maize association population: a high-resolution platform for quantitative trait locus dissection,” Plant Journal, vol. 44, no. 6, pp. 1054–1064, 2005. View at Publisher · View at Google Scholar · View at Scopus
  36. A. Rasamivelona, K. A. Gravois, and R. H. Dilday, “Heritability and genotype x environment interactions for straighthead in rice,” Crop Science, vol. 35, no. 5, pp. 1365–1368, 1995. View at Publisher · View at Google Scholar · View at Scopus
  37. L. Jin, Y. Lu, P. Xiao, M. Sun, H. Corke, and J. Bao, “Genetic diversity and population structure of a diverse set of rice germplasm for association mapping,” Theoretical and Applied Genetics, vol. 121, no. 3, pp. 475–487, 2010. View at Publisher · View at Google Scholar · View at Scopus