Characterizing variation of branch angle and genome-wide association mapping in rapeseed (Brassica napus L.)

Frontiers in Plant Science

Volumn 7, Issue FEB2016, 2016, Pages

  Liu, Jia ^a   Wang, Wenxiang ^a   Mei, Desheng ^a   Wang, Hui ^a   Fu, Li ^a   Liu, Daoming ^b   Li, Yunchang ^a   Hu, Qiong ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b Agricultural Sciences Institute of Lu'an Municipal   (China)

Author keywords

Association mapping; Branch angle; Brassica napus L.; Candidate genes; Genetic variation; Multiple environments

Indexed keywords

EID: 84958552840     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2016.00021     Document Type: Article

References (56)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/s0022-2836(05)80360-2.
2. Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., et al. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627-631. doi: 10.1038/nature08800.
3. Bai, F., Reinheimer, R., Durantini, D., Kellogg, E. A., and Schmidt, R. J. (2012). TCP transcription factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), is required for normal tassel branch angle formation in maize. Proc. Natl. Acad. Sci. U.S.A. 109, 12225-12230. doi: 10.1073/pnas.1202439109.
4. Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., and Buckler, E. S. (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635. doi: 10.1093/bioinformatics/btm308.
5. Breseghello, F., and Sorrells, M. E. (2006). Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172, 1165-1177. doi: 10.1534/genetics.105.044586.
6. Cai, D., Xiao, Y., Yang, W., Ye, W., Wang, B., Younas, M., et al. (2014). Association mapping of six yield-related traits in rapeseed (Brassica napus L.). Theor. Appl. Genet. 127, 85-96. doi: 10.1007/s00122-013-2203-9.
7. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., et al. (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.Science 345, 950-953. doi: 10.1126/science.1253435.
8. Dabney, A., and Storey, J. D. (2004). Q-value estimation for false discovery rate control. Medicine 344, 539-548.
9. Diepenbrock, W. (2000). Yield analysis of winter oilseed rape (Brassica napus L.): a review. Field Crop. Res. 67, 35-49. doi: 10.1016/s0378-4290(00)00082-4.
10. Donald, C. M. (1968). The breeding of crop ideotypes. Euphytica 17, 385-403. doi: 10.1007/BF00056241.
11. Dong, Z., Jiang, C., Chen, X., Zhang, T., Ding, L., Song, W., et al. (2013). Maize LAZY1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response. Plant Physiol. 163, 1306-1322. doi: 10.1104/pp.113.227314.
12. Edwards, D., Batley, J., and Snowdon, R. J. (2013). Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 126, 1-11. doi: 10.1007/s00122-012-1964-x.
13. Evanno, G., Regnaut, S., and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611-2620. doi: 10.1111/j.1365-294x.2005.02553.x.
14. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., et al. (2002). The structure of haplotype blocks in the human genome. Science 296, 2225-2229. doi: 10.1126/science.1069424.
15. Hardy, O. J., and Vekemans, X. (2002). SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2, 618-620. doi: 10.1046/j.1471-8286.2002.00305.x.
16. Harper, A. L., Trick, M., Higgins, J., Fraser, F., Clissold, L., Wells, R., et al. (2012). Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat. Biotechnol. 30, 798-802. doi: 10.1038/nbt.2302.
17. Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y., et al. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967. doi: 10.1038/ng.695.
18. Ihaka, R., and Gentleman, R. R. (1996). A language for data analysis and graphics. J. Comput. Graph. Statist. 5, 299-314.
19. Jakobsson, M., and Rosenberg, N. A. (2007). CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801-1806. doi: 10.1093/bioinformatics/btm233.
20. Jin, J., Huang, W., Gao, J. P., Yang, J., Shi, M., Zhu, M. Z., et al. (2008). Genetic control of rice plant architecture under domestication. Nat. Genet. 40, 1365-1369. doi: 10.1038/ng.247.
21. Ku, L., Wei, X., Zhang, S., Zhang, J., Guo, S., and Chen, Y. (2011). Cloning and characterization of a putative TAC1 ortholog associated with leaf angle in maize (Zea mays L.). PLoS ONE 6:e20621. doi: 10.1371/journal.pone.0020621.
22. Li, F., Chen, B., Xu, K., Wu, J., Song, W., Bancroft, I., et al. (2014). Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). DNA Res. 21, 355-367. doi: 10.1093/dnares/dsu002.
23. Li, P., Wang, Y., Qian, Q., Fu, Z., Wang, M., Zeng, D., et al. (2007). LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res. 17, 402-410. doi: 10.1038/cr.2007.38.
24. Liu, K., and Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128-2129. doi: 10.1093/bioinformatics/bti282.
25. Liu, S., Liu, Y., Yang, X., Tong, C., Edwards, D., Parkin, I. A., et al. (2014). TheBrassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.Nat. Commun. 5:3930. doi: 10.1038/ncomms4930.
26. Lomax, T. L. (1997). Molecular genetic analysis of plant gravitropism. Gravit. Space Biol. Bull. 10, 75-82.
27. Lu, G., Harper, A. L., Trick, M., Morgan, C., Fraser, F., O'Neill, C., et al. (2014). Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus. DNA Res. 21, 613-625. doi: 10.1093/dnares/dsu024.
28. Mansfield, B. D., and Mumm, R. H. (2014). Survey of plant density tolerance in US maize germplasm. Crop Sci. 54, 157-173. doi: 10.2135/cropsci2013.04.0252.
29. Mei, D., Wang, H., Hu, Q., Li, Y., Xu, Y., and Li, Y. (2009). QTL analysis on plant height and flowering time in Brassica napus. Plant Breed. 128, 458-465. doi: 10.1111/j.1439-0523.2008.01528.x.
30. Nordborg, M., and Tavaré, S. (2002). Linkage disequilibrium: what history has to tell us. Trends Genet. 18, 83-90. doi: 10.1016/S0168-9525(02)02557-X.
31. Parkin, I. A., Gulden, S. M., Sharpe, A. G., Lukens, L., Trick, M., Osborn, T. C., et al. (2005). Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171, 765-781. doi: 10.1534/genetics.105.042093.
32. Pritchard, J. K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
33. Raman, H., Raman, R., Kilian, A., Detering, F., Carling, J., Coombes, N., et al. (2014). Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS ONE 9:e101673. doi: 10.1371/journal.pone.0101673.
34. Robert, H. S., and Friml, J. (2009). Auxin and other signals on the move in plants. Nat. Chem. Biol. 5, 325-332. doi: 10.1038/nchembio.170.
35. Rosenberg, N. A. (2004). DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4, 137-138. doi: 10.1046/j.1471-8286.2003.00566.x.
36. Sang, D., Chen, D., Liu, G., Liang, Y., Huang, L., Meng, X., et al. (2014). Strigolactones regulate rice tiller angle by attenuating shoot gravitropism through inhibiting auxin biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 111, 11199-11204. doi: 10.1073/pnas.1411859111.
37. Shi, J., Li, R., Qiu, D., Jiang, C., Long, Y., Morgan, C., et al. (2009). Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napus. Genetics 182, 851-861. doi: 10.1534/genetics.109.101642.
38. Snowdon, R. J., and Iniguez Luy, F. L. (2012). Potential to improve oilseed rape and canola breeding in the genomics era. Plant Breed. 131, 351-360. doi: 10.1111/j.1439-0523.2012.01976.x.
39. Song, X., and Zhang, T. (2009). Quantitative trait loci controlling plant architectural traits in cotton. Plant Sci. 177, 317-323. doi: 10.1016/j.plantsci.2009.05.015.
40. Stich, B., and Melchinger, A. E. (2009). Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis. BMC Genomics 10:94. doi: 10.1186/1471-2164-10-94.
41. Teichmann, T., and Muhr, M. (2015). Shaping plant architecture. Front. Plant Sci. 6:233. doi: 10.3389/fpls.2015.00233.
42. Tian, F., Bradbury, P. J., Brown, P. J., Hung, H., Sun, Q., Flint-Garcia, S., et al. (2011). Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43, 159-162. doi: 10.1038/ng.746.
43. Turner, S. D. (2014). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv. doi: 10.1101/005165.
44. Wang, N., Li, F., Chen, B., Xu, K., Yan, G., Qiao, J., et al. (2014). Genome-wide investigation of genetic changes during modern breeding of Brassica napus. Theor. Appl. Genet. 127, 1817-1829. doi: 10.1007/s00122-014-2343-6.
45. Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., et al. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43, 1035-1039. doi: 10.1038/ng.919.
46. Wang, Y., and Li, J. (2005). The plant architecture of rice (Oryza sativa). Plant Mol. Biol. 59, 75-84. doi: 10.1007/s11103-004-4038-x.
47. Wang, Y., and Li, J. (2008). Rice, rising. Nat. Genet. 40, 1273-1275. doi: 10.1038/ng1108-1273.
48. Xu, J., Song, X., Cheng, Y., Zou, X., Zeng, L., Qiao, X., et al. (2014). Identification of QTL for branch number in oilseed rape (Brassica napus L.). J. Genet. Genomics 41, 557-559. doi: 10.1016/j.jgg.2014.06.006.
49. Yoshihara, T., Spalding, E. P., and Iino, M. (2013). AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence. Plant J. 74, 267-279. doi: 10.1111/tpj.12118.
50. Yu, B., Lin, Z., Li, H., Li, X., Li, J., Wang, Y., et al. (2007). TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J. 52, 891-898. doi: 10.1111/j.1365-313X.2007.03284.x.
51. Yu, J., Pressoir, G., Briggs, W. H., Bi, I. V., Yamasaki, M., Doebley, J. F., et al. (2005). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203-208. doi: 10.1038/ng1702.
52. Ziolkowski, P. A., Kaczmarek, M., Babula, D., and Sadowski, J. (2006). Genome evolution in Arabidopsis/Brassica: conservation and divergence of ancient rearranged segments and their breakpoints. Plant J. 47, 63-74. doi: 10.1111/j.1365-313X.2006.02762.x.
53. Zhang, Z., Ersoz, E., Lai, C. Q., Todhunter, R. J., Tiwari, H. K., Gore, M. A., et al. (2010). Mixed linear model approach adapted for genome-wide association studies.Nat. Genet. 42, 355-360. doi: 10.1038/ng.546.
54. Zhao, K., Aranzana, M. J., Kim, S., Lister, C., Shindo, C., Tang, C., et al. (2007). An Arabidopsis example of association mapping in structured samples. PLoS Genet. 3:e4. doi: 10.1371/journal.pgen.0030004.
55. Zhao, K., Tung, C. W., Eizenga, G. C., Wright, M. H., Ali, M. L., Price, A. H., et al. (2011). Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2:467. doi: 10.1038/ncomms1467.
56. Zhao, S. Q., Xiang, J. J., and Xue, H. W. (2012). Studies on the rice leaf INCLINATION1 (LC1), an IAA-amido synthetase, reveal the effects of auxin in leaf inclination control. Mol. Plant 6, 174-187. doi: 10.1093/mp/sss064.