Harnessing genetic variation in leaf angle to increase productivity of sorghum bicolor

Genetics

Volumn 201, Issue 3, 2015, Pages 1229-1238

  Truong, Sandra K ^a   McCormick, Ryan F ^a   Rooney, William L ^a   Mullet, John E ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Auxin transport; Bioenergy sorghum; Crop modeling; Dwarf 3; Leaf angle; P glycoprotein; Sorghum canopy

Indexed keywords

MULTIDRUG RESISTANCE PROTEIN; VEGETABLE PROTEIN;

ALLELE; ARTICLE; CANOPY; CONTROLLED STUDY; CROP PRODUCTION; GENE LOCUS; GENETIC VARIABILITY; LEAF INCLINATION ANGLE; LIGHT INTERCEPTION; NONHUMAN; PLANT GENETICS; PLANT LEAF; PRIORITY JOURNAL; RECOMBINANT INBRED STRAIN; SOLAR RADIATION; SORGHUM; AGRICULTURE; GENETIC VARIATION; GENETICS; GROWTH, DEVELOPMENT AND AGING;

AGRICULTURE; GENETIC VARIATION; P-GLYCOPROTEINS; PLANT LEAVES; SORGHUM;

EID: 84946935437     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.178608     Document Type: Article

References (78)

1. Bartek, M. S., S. C. Murray, P. E. Klein, J. E. Mullet, and W. L. Rooney, 2012 QTL for biomass yield and composition in energy sorghum (Sorghum bicolor L. Moench). Proceedings of the Sun Grant National Conference: Science for Biomass Feedstock Production and Utilization, New Orleans. Available at: http:// sungrant.tennessee.edu/NatConference/.
2. Beavis, W., 1994 The power and deceit of QTL experiments: Lessons from comparative QTL studies, pp. 250-266 in Proceedings of the Forty-Ninth Annual Corn and Sorghum Industry Research Conference. American Seed Trade Association, Washington, DC.
3. Beavis, W., 1998 QTL Analyses power, precision, and accuracy, pp. 145-162 in Molecular Dissection of Complex Traits, edited by A. Patterson. CRC Press, Boca Raton, FL.
4. Birch,C. J., J. Vos, J. Kiniry,H. J. Bos, and A. Elings, 1998 Phyllochron responds to acclimation to temperature and irradiance in maize. Field Crops Res. 59: 187-200.
5. Blakeslee, J. J., A. Bandyopadhyay, O. R. Lee, J. Mravec, B. Titapiwatanakun et al., 2007 Interactions among PINFORMED and P-glycoprotein auxin transporters in Arabidopsis. Plant Cell 19: 131-147.
6. Boudon, F., C. Pradal, T. Cokelaer, P. Prusinkiewicz, and C. Godin, 2012 L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language. Front. Plant Sci. 3: 76.
7. Broman, K. W., H. Wu, S. Sen, and G. A. Churchill, 2003 R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889- 890.
8. Burow, G. B., R. R. Klein, C. D. Franks, P. E. Klein, K. F. Schertz et al., 2011 Registration of the BTx623/IS3620C recombinant inbred mapping population of sorghum. J. Plant Reg. 5: 141- 145.
9. Chelle, M., and B. Andrieu, 1998 The nested radiosity model for the distribution of light within plant canopies. Ecol. Modell. 111: 75-91.
10. Chelle, M., J. Hanan, and H. Autret, 2004 Lighting virtual crops: the CARIBU solution for open L-systems, p. 194 in Proceedings of the 4th International Workshop on Functional-Structural Plant Models, Montpellier France, edited by C. Godin et al. UMR AMAP, Montpellier, France.
11. Clerget, B., M. Dingkuhn, E. Goze, H. F. W. Rattunde, and B. Ney, 2008 Variability of phyllochron, plastochron and rate of increase in height in photoperiod-sensitive sorghum varieties. Ann. Bot. 101: 579-594.
12. DePristo, M. A., E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire et al., 2011 A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491-498.
13. Dong, Z., C. Jiang, X. Chen, T. Zhang, L. Ding 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.
14. Drewry, D. T., P. Kumar, and S. P. Long, 2014 Simultaneous improvement in productivity, water use, and albedo through crop structural modification. Glob. Change Biol. 20: 1955-1967.
15. Drouet, J. L., and R. Bonhomme, 1999 Do variations in local leaf irradiance explain changes to leaf nitrogen within row maize canopies? Ann. Bot. 84: 61-69.
16. Duvick, D. N., 2005 Genetic progress in yield of United States maize (Zea mays L.). Maydica 50: 193-202.
17. Farfan, I. D. B., B. R. Bergsma, G. Johal, and M. R. Tuinstra, 2012 A stable dw3 allele in sorghum and a molecular marker to facilitate selection. Crop Sci. 52: 2063-2069.
18. Foley, J. A., N. Ramankutty, K. A. Brauman, E. S. Cassidy, J. S. Gerber et al., 2011 Solutions for a cultivated planet. Nature 478: 337-342.
19. George-Jaeggli, B., D. R. Jordan, E. J. van Oosterom, I. J. Broad, and G. L. Hammer, 2013 Sorghum dwarfing genes can affect radiation capture and radiation use efficiency. Field Crops Res. 149: 283-290.
20. George-Jaeggli, B., D. R. Jordan, E. J. van Oosterom, and G. L. Hammer, 2011 Decrease in sorghum grain yield due to the dw3 dwarfing gene is caused by reduction in shoot biomass. Field Crops Res. 124: 231-239.
21. Gill, J. R., P. S. Burks, S. A. Staggenborg, G. N. Odvody, R. W. Heiniger et al., 2014 Yield results and stability analysis from the sorghum regional biomass feedstock trial. BioEnergy Res. 7: 1026-1034.
22. Hammer, G. L., Z. S. Dong, G. McLean, A. Doherty, C. Messina et al., 2009 Can changes in canopy and/or root system architecture explain historical maize yield trends in the US corn belt? Crop Sci. 49: 299-312.
23. Hart, G. E., K. F. Schertz, Y. Peng, and N. H. Syed, 2001 Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theor. Appl. Genet. 103: 1232-1242.
24. Hurng, W. P., L. Y. Su, and C. H. Kao, 1986 Senescence of rice leaves: regulation by light. Bot. Bull. Academia Sinica 27: 163- 174.
25. Jones, E., Oliphant, T., Peterson, P. et al., 2001 SciPy: open source scientific tools for Python. Available at: http://www.scipy.org/. Accessed: July 10, 2014.
26. Knoller, A. S., J. J. Blakeslee, E. L. Richards, W. A. Peer, and A. S. Murphy, 2010 Brachytic2/ZmABCB1 functions in IAA export from intercalary meristems. J. Exp. Bot. 61: 3689-3696.
27. Lambert, R. J., and R. R. Johnson, 1978 Leaf angle, tassel morphology, and performance of maize hybrids. Crop Sci. 18: 499-502.
28. Lee, E. A., and M. Tollenaar, 2007 Physiological basis of successful breeding strategies for maize grain yield. Crop Sci. 47: S202- S215.
29. Li, C. H., Y. X. Li, Y. S. Shi, Y. C. Song, D. F. Zhang et al., 2015 Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations. PLoS One 10: e0121624.
30. Li, H., and R. Durbin, 2010 Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
31. Li, P., Y. Wang, Q. Qian, Z. Fu, M. Wang et al., 2007 LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res. 17: 402-410.
32. Long, S. P., X. G. Zhu, S. L. Naidu, and D. R. Ort, 2006 Can improvement in photosynthesis increase crop yields? Plant Cell Environ. 29: 315-330.
33. Manichaikul, A., J. Y. Moon, S. Sen, B. S. Yandell, and K.W. Broman, 2009 A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics 181: 1077-1086.
34. Mansfield, B. D., and R. H. Mumm, 2014 Survey of plant density tolerance in US maize germplasm. Crop Sci. 54: 157-173.
35. McCormick, R. F., S. K. Truong, and J. E. Mullet, 2015 RIG: recalibration and interrelation of genomic sequence data with the GATK. G3 5: 655-665.
36. McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., 2010 The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297-1303.
37. McMullen, M. D., S. Kresovich, H. S. Villeda, P. Bradbury, H. H. Li et al., 2009 Genetic properties of the maize nested association mapping population. Science 325: 737-740.
38. Monsi, M., and T. Saeki, 2005 On the factor light in plant communities and its importance for matter production. Ann. Bot. 95: 549-567.
39. Monteith, J. L., and C. J. Moss, 1977 Climate and the efficiency of crop production in Britain. Philos. Trans. R. Soc. Lond. Series B 281: 277-294.
40. Moon, J., H. Candela, and S. Hake, 2013 The Liguleless narrow mutation affects proximal-distal signaling and leaf growth. Development 140: 405-412.
41. Moreno, M. A., L. C. Harper, R. W. Krueger, S. L. Dellaporta, and M. Freeling, 1997 liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis. Genes Dev. 11: 616-628.
42. Morishige, D. T., P. E. Klein, J. L. Hilley, S. M. E. Sahraeian, A. Sharma et al., 2013 Digital genotyping of sorghum: a diverse plant species with a large repeat-rich genome. BMC Genomics 14: 448.
43. Mravec, J., M. Kubes, A. Bielach, V. Gaykova, J. Petrasek et al., 2008 Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development. Development 135: 3345-3354.
44. Mullet, J., D. Morishige, R. McCormick, S. Truong, J. Hilley et al., 2014 Energy sorghum: a genetic model for the design of C4 grass bioenergy crops. J. Exp. Bot. 65: 3479-3489.
45. Multani, D. S., S. P. Briggs, M. A. Chamberlin, J. J. Blakeslee, A. S. Murphy et al., 2003 Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants. Science 302: 81-84.
46. Murchie, E., and M. Reynolds, 2012 Crop radiation capture and use efficiency, pp. 2615-2638 in Encyclopedia of Sustainability Science and Technology, edited by R. A. Meyers. Springer, New York.
47. Murchie, E. H., M. Pinto, and P. Horton, 2009 Agriculture and the new challenges for photosynthesis research. New Phytol. 181: 532-552.
48. Nobel, P. S., 2005 Physicochemical and Environmental Plant Physiology. Academic Press, New York.
49. Olson, S. N., K. Ritter, W. Rooney, A. Kemanian, B. A. McCarl et al., 2012 High biomass yield energy sorghum: developing a genetic model for C4 grass bioenergy crops. Biofuels Bioprod. Bioref. 6: 640-655.
50. Paterson, A. H., J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood et al., 2009 The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
51. Pendleton, J. W., G. E. Smith, S. R. Winter, and T. J. Johnston, 1968 Field investigations of the relationships of leaf angle in corn (Zea mays L.) to grain yield and apparent photosynthesis. Agron. J. 60: 422-424.
52. Peng, B., R. K. Yu, K. L. Dehoff, and C. I. Amos, 2007 Normalizing a large number of quantitative traits using empirical normal quantile transformation. BMC Proc. 1(Suppl. 1): S156.
53. Perez, M. B. M., J. Zhao, Y. H. Yin, J. Y. Hu, and M. G. S. Fernandez, 2014 Association mapping of brassinosteroid candidate genes and plant architecture in a diverse panel of Sorghum bicolor. Theor. Appl. Genet. 127: 2645-2662.
54. Pradal, C., S. Dufour-Kowalski, F. Boudon, C. Fournier, and C. Godin, 2008 OpenAlea: a visual programming and component- based software platform for plant modelling. Funct. Plant Biol. 35: 751-760.
55. Prusinkiewicz, P., M. Shirmohammadi, and F. Samavati, 2012 L-Systems in geometric modeling. Int. J. Found. Comput. Sci. 23: 133-146.
56. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira et al., 2007 PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81: 559-575.
57. Rooney, W. L., J. Blumenthal, B. Bean, and J. E. Mullet, 2007 Designing sorghum as a dedicated bioenergy feedstock. Biofuels Bioprod. Bioref. 1: 147-157.
58. Sakamoto, T., Y. Morinaka, T. Ohnishi, H. Sunohara, S. Fujioka et al., 2006 Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nat. Biotechnol. 24: 105-109.
59. Schmitt, J., J. R. Stinchcombe, M. S. Heschel, and H. Huber, 2003 The adaptive evolution of plasticity: phytochromemediated shade avoidance responses. Integr. Comp. Biol. 43: 459-469.
60. Sinclair, T. R., and J. E. Sheehy, 1999 Erect leaves and photosynthesis in rice. Science 283: 1456-1457.
61. Song, Q. F., G. L. Zhang, and X. G. Zhu, 2013 Optimal crop canopy architecture to maximise canopy photosynthetic CO2 uptake under elevated CO2: a theoretical study using a mechanistic model of canopy photosynthesis. Funct. Plant Biol. 40: 109-124.
62. Tian, F., P. J. Bradbury, P. J. Brown, H. Hung, Q. Sun et al., 2011 Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43: 159-162.
63. Tollenaar, M., and J. Wu, 1999 Yield improvement in temperate maize is attributable to greater stress tolerance. Crop Sci. 39: 1597-1604.
64. Truong, S. K., R. F. McCormick, D. T. Morishige, and J. E. Mullet, 2014 Resolution of genetic map expansion caused by excess heterozygosity in plant recombinant inbred populations. G3 4: 1963-1969.
65. Van der Auwera, G. A., M. O. Carneiro, C. Hartl, R. Poplin, G. Del Angel et al., 2013 From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics 11: 11.10.11-11.10.33.
66. van Oosterom, E. J., A. K. Borrell, K. S. Deifel, and G. L. Hammer, 2011 Does increased leaf appearance rate enhance adaptation to postanthesis drought stress in sorghum? Crop Sci. 51: 2728- 2740.
67. van Zanten, M., T. L. Pons, J. A. M. Janssen, L. A. C. J. Voesenek, and A. J. M. Peeters, 2010 On the relevance and control of leaf angle. Crit. Rev. Plant Sci. 29: 300-316.
68. Walsh, J., C. A. Waters, and M. Freeling, 1998 The maize gene liguleless2 encodes a basic leucine zipper protein involved in the establishment of the leaf blade-sheath boundary. Genes Dev. 12: 208
69. Warnasooriya, S. N., and T. P. Brutnell, 2014 Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks. J. Exp. Bot. 65: 2825-2834.
70. Xin, Z., D. Gitz, G. Burow, C. Hayes, and J. J. Burke, 2015 Registration of two allelic erect leaf mutants of sorghum. J. Plant Reg. 9: 254-257.
71. Xu, S. Z., 2003 Theoretical basis of the Beavis effect. Genetics 165: 2259-2268.
72. Yang, J. A., S. H. Lee, M. E. Goddard, and P. M. Visscher, 2011 GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88: 76-82.
73. Yang, J. A., S. H. Lee, M. E. Goddard, and P. M. Visscher, 2013 Genome-wide complex trait analysis (GCTA): methods, data analyses, and interpretations, pp. 215-236 in Genome- Wide Association Studies and Genomic Prediction (Methods in Molecular Biology Series, Vol. 1019), edited by C. Gondo, J. van der Werf, and B. Hayes. Humana Press, New York.
74. Yoshida, S., 1972 Physiological aspects of grain yield. Annu. Rev. Plant Physiol. 23: 437-445.
75. Zhang, J., L. X. Ku, Z. P. Han, S. L. Guo, H. J. Liu et al., 2014 The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.). J. Exp. Bot. 65: 5063-5076.
76. Zhao, S. Q., J. A. Hu, L. B. Guo, Q. A. Qian, and H. W. Xue, 2010 Rice leaf inclination2, a VIN3-like protein, regulates leaf angle through modulating cell division of the collar. Cell Res. 20: 935-947.
77. Zhu, X. G., S. P. Long, and D. R. Ort, 2008 What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? Curr. Opin. Biotechnol. 19: 153-159.
78. Zhu, X. G., S. P. Long, and D. R. Ort, 2010 Improving photosynthetic efficiency for greater yield. Annu. Rev. Plant Biol. 61: 235-261.