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Molecular Breeding

, 37:138 | Cite as

The vegetative nitrogen response of sorghum lines containing different alleles for nitrate reductase and glutamate synthase

  • Eugene Diatloff
  • Emma S. Mace
  • David R. Jordan
  • Sophie Filleur
  • Shuaishuai Tai
  • Susanne Schmidt
  • Ian D. Godwin
Article

Abstract

Improving the nitrogen (N) responsiveness of crops is crucial for food security and environmental sustainability, and breeding N use efficient (NUE) crops has to exploit genetic variation for this complex trait. We used reverse genetics to examine allelic variation in two N metabolism genes. In silico analysis of the genomes of 44 genetically diverse sorghum genotypes identified a nitrate reductase and a glutamate synthase gene that were under balancing selection in improved sorghum cultivars. We hypothesised that these genes are a potential source of differences in NUE, and selected parents and progeny of nested association mapping populations with different allelic combinations for these genes. Allelic variation was sourced from African (Macia) and Indian (ICSV754) genotypes that had been incorporated into the Australian elite parent R931945-2-2. Nine genotypes were grown for 30 days in a glasshouse and supplied with continuous limiting or replete N, or replete N for 27 days followed by 3 days of N starvation. Biomass, total N and nitrate contents were quantified together with gene expressions in leaves, stems and roots. Limiting N supply universally resulted in less shoot and root growth, increased root weight ratio and reduced tissue nitrate and total N concentrations. None of the tested genotypes exceeded growth or NUE of the elite parent R931945-2-2 indicating that the allelic combinations did not confer an advantage during early vegetative growth. Thus, the next steps for ascertaining potential effects on NUE include growing plants to maturity. We conclude that reverse genetics that take advantage of rapidly expanding genomic databases enable a systematic approach for developing N-efficient crops.

Keywords

Allelic variation Sorghum Nested association mapping population Nitrogen use efficiency (NUE) Vegetative Nitrate reductase Glutamate synthase 

Abbreviations

DW

Dry weight

LA

Leaf area

SLN

Specific leaf nitrogen

FW

Fresh weight

N nitrogen

NAM nested association mapping

Notes

Acknowledgements

This project was conducted under the University of Queensland Master of Philosophy post-graduate program. The authors thank Melissa Alves for assistance during harvest, David Appleton for LECO analyses and Belinda Worland and Nicole Robinson for helpful discussions.

Supplementary material

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Table 5S (DOC 38 kb)

References

  1. Ayongwa GC, Stomph TJ, Emechebe AM, Kuyper TW (2006) Root nitrogen concentration of sorghum above 2% produces least Striga hermonthica seed stimulation. Ann Appl Biol 149(3):255–262.  https://doi.org/10.1111/j.1744-7348.2006.00094.x CrossRefGoogle Scholar
  2. Chapin F (1987) Adaptations and physiological responses of wild plants to nutrient stress. In: Gabelman HL, BC (ed) Genetic aspects of plant mineral nutrition. Martinus Nijhof Publishers, pp 15–25Google Scholar
  3. Clarkson DT, Hawkesford MJ (1993) Molecular biological approaches to plant nutrition. Plant Soil 155:21–31.  https://doi.org/10.1007/bf00024981 CrossRefGoogle Scholar
  4. De Angeli A, Monachello D, Ephritikhine G, Frachisse JM, Thomine S, Gambale F, Barbier-Brygoo H (2006) The nitrate/proton antiporter AtCLCa mediates nitrate accumulation in plant vacuoles. Nature 442(7105):939–942.  https://doi.org/10.1038/nature05013 CrossRefPubMedGoogle Scholar
  5. Delph LF, Kelly JK (2014) On the importance of balancing selection in plants. New Phytol 201(1):45–56.  https://doi.org/10.1111/nph.12441 CrossRefPubMedGoogle Scholar
  6. Dillon SL, Shapter FM, Henry RJ, Cordeiro G, Izquierdo L, Lee LS (2007) Domestication to crop improvement: genetic resources for Sorghum and saccharum (Andropogoneae). Ann Bot 100(5):975–989.  https://doi.org/10.1093/aob/mcm192 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Dodd IC, Munns R, Passioura JB (2002) Does shoot water status limit leaf expansion of nitrogen-deprived barley? J Exp Bot 53(375):1765–1770.  https://doi.org/10.1093/jxb/erf030 CrossRefPubMedGoogle Scholar
  8. Esposito S, Guerriero G, Vona V, Rigano VD, Carfagna S, Rigano C (2005) Glutamate synthase activities and protein changes in relation to nitrogen nutrition in barley: the dependence on different plastidic glucose-6P dehydrogenase isoforms. J Exp Bot 56(409):55–64PubMedGoogle Scholar
  9. Gelli M, Dou Y, Konda AR, Zhang C, Holding D, Dweikat I (2014) Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. BMC Genomics 15:1–16.  https://doi.org/10.1186/1471-2164-15-179 CrossRefGoogle Scholar
  10. Good AG, Shrawat AK, Muench DG (2004) Can less yield more? Is reducing nutrient input into the environment compatible with maintaining crop production? Trends Plant Sci 9(12):597–605.  https://doi.org/10.1016/j.tplants.2004.10.008 CrossRefPubMedGoogle Scholar
  11. Grundon NE, DG Edwards;Takkar, PN; Asher, CJ;Clark, RB (1987) Nutritional disorders of grain sorghum. ACIAR monograph no. 2, p 99. ISBN 0 949511 33 1Google Scholar
  12. Hirel B, Le Gouis J, Ney B, Gallais A (2007) The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches. J Exp Bot 58(9):2369–2387.  https://doi.org/10.1093/jxb/erm097 CrossRefPubMedGoogle Scholar
  13. Jordan DR, Mace ES, Cruickshank AW, Hunt CH, Henzell RG (2011) Exploring and exploiting genetic variation from unadapted sorghum germplasm in a breeding program. Crop Sci 51(4):1444–1457.  https://doi.org/10.2135/cropsci2010.06.0326 CrossRefGoogle Scholar
  14. Jordan DR, Hunt CH, Cruickshank AW, Borrell AK, Henzell RG (2012) The relationship between the stay-green trait and grain yield in elite sorghum hybrids grown in a range of environments. Crop Sci 52(3):1153–1161.  https://doi.org/10.2135/cropsci2011.06.0326 CrossRefGoogle Scholar
  15. Mace ES, Tai SS, Gilding EK, Li YH, Prentis PJ, Bian LL, Campbell BC, WS H, Innes DJ, Han XL, Cruickshank A, Dai CM, Frere C, Zhang HK, Hunt CH, Wang XY, Shatte T, Wang M, Su Z, Li J, Lin XZ, Godwin ID, Jordan DR, Wang J (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun 4:9.  https://doi.org/10.1038/ncomms3320 Google Scholar
  16. Makita Y, Shimada S, Kawashima M, Kondou-Kuriyama T, Toyoda T, Matsui M (2015) MOROKOSHI: Transcriptome database in Sorghum bicolor. Plant Cell Physiol 56(1):8.  https://doi.org/10.1093/pcp/pcu187 CrossRefGoogle Scholar
  17. Maranville JW, Madhavan S (2002) Physiological adaptations for nitrogen use efficiency in sorghum. Plant Soil 245(1):25–34.  https://doi.org/10.1023/a:1020660504596 CrossRefGoogle Scholar
  18. Maranville JW, Pandey RK, Sirifi S (2002) Comparison of nitrogen use efficiency of a newly developed sorghum hybrid and two improved cultivars in the Sahel of West Africa. Commun Soil Sci Plant Anal 33(9–10):1519–1536.  https://doi.org/10.1081/css-120004298 CrossRefGoogle Scholar
  19. Marschner H (1995) Mineral nutrition of higher plants, 2nd edn. Academic PressGoogle Scholar
  20. Massel K, Campbell BC, Mace ES, Tai S, Tao Y, Worland BG, Jordan DR, Botella JR, Godwin ID (2016) Whole genome sequencing reveals potential new targets for improving nitrogen uptake and utilization in sorghum bicolor. Front Plant Sci 7(1544).  https://doi.org/10.3389/fpls.2016.01544
  21. Miranda KM, Espey MG, Wink DA (2001) A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide Biol Chem 5(1):62–71.  https://doi.org/10.1006/niox.2000.0319 CrossRefGoogle Scholar
  22. Myers RJK (1980) The root-system of a grain-sorghum crop. Field Crop Res 3(1):53–64.  https://doi.org/10.1016/0378-4290(80)90007-6 CrossRefGoogle Scholar
  23. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York, NYGoogle Scholar
  24. Nigro D, YQ G, Huo NX, Marcotuli I, Blanco A, Gadaleta A, Anderson OD (2013) Structural analysis of the wheat genes encoding NADH-dependent glutamine-2-oxoglutarate amidotransferases and correlation with grain protein content. PLoS One 8(9):11.  https://doi.org/10.1371/journal.pone.0073751 CrossRefGoogle Scholar
  25. Palmer SJ, Berridge DM, McDonald AJS, Davies WJ (1996) Control of leaf expansion in sunflower (Helianthus annuus L) by nitrogen nutrition. J Exp Bot 47(296):359–368.  https://doi.org/10.1093/jxb/47.3.359 CrossRefGoogle Scholar
  26. Pang JY, Palta JA, Rebetzke GJ, Milroy SP (2014) Wheat genotypes with high early vigour accumulate more nitrogen and have higher photosynthetic nitrogen use efficiency during early growth. Funct Plant Biol 41(2):215–222.  https://doi.org/10.1071/fp13143 CrossRefGoogle Scholar
  27. Parker C (2009) Observations on the current status of Orobanche and Striga problems worldwide. Pest Manag Sci 65(5):453–459.  https://doi.org/10.1002/ps.1713 CrossRefPubMedGoogle Scholar
  28. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang HB, Wang XY, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang LF, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556.  https://doi.org/10.1038/nature07723 CrossRefPubMedGoogle Scholar
  29. Quraishi UM, Abrouk M, Murat F, Pont C, Foucrier S, Desmaizieres G, Confolent C, Riviere N, Charmet G, Paux E, Murigneux A, Guerreiro L, Lafarge S, Gouis J, Feuillet C, Salse J (2011) Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant J 65(5):745–756.  https://doi.org/10.1111/j.1365-313X.2010.04461.x CrossRefPubMedGoogle Scholar
  30. Reuter DR, Robinson JB (1997) Plant analysis: an interpretation manual, vol 2. CSIRO PublishingGoogle Scholar
  31. Reynolds HL, Dantonio C (1996) The ecological significance of plasticity in root weight ratio in response to nitrogen: opinion. Plant Soil 185(1):75–97.  https://doi.org/10.1007/bf02257566 CrossRefGoogle Scholar
  32. Robinson N, Brackin R, Vinall K, Soper F, Holst J, Gamage H, Paungfoo-Lonhienne C, Rennenberg H, Lakshmanan P, Schmidt S (2011) Nitrate paradigm does not hold up for sugarcane. PLoS One 6(4):9.  https://doi.org/10.1371/journal.pone.0019045 Google Scholar
  33. Robinson N, Schmidt S, Lakshmanan P (2015) Genetic improvement of nitrogen use efficiency in sugarcane. In: Bell M (ed) A review of nitrogen use efficiency in sugarcane. Sugar Research Australia, pp 125–156Google Scholar
  34. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, Moorman AFM (2009) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37(6):12.  https://doi.org/10.1093/nar/gkp045 CrossRefGoogle Scholar
  35. Salse J, Quraishi UM, Pont C, Murat F, Gouis JL, Lafarge S (2013) Grain filling of a plant through the modulation of NADH-glutamate synthase. US patent 20130047300 A1. https://www.google.ch/patents/US20130047300
  36. Siddiqi MY, Glass ADM (1981) Utilization index—a modified approach to the estimation and comparison of nutrient utilization efficiency in plants. J Plant Nutr 4(3):289–302.  https://doi.org/10.1080/01904168109362919 CrossRefGoogle Scholar
  37. Silberbush M, Gbur EE (1994) Using the Williams equation to evaluate nutrient-uptake rate by intact plants. Agron J 86(1):107–110CrossRefGoogle Scholar
  38. Singh V, van Oosterom EJ, Jordan DR, Hunt CH, Hammer GL (2011) Genetic variability and control of nodal root angle in sorghum. Crop Sci 51(5):2011–2020.  https://doi.org/10.2135/cropsci2011.01.0038 CrossRefGoogle Scholar
  39. Stuart NS (2012) Toxicology and associated agronomy of forage sorghum. University of Queensland, PhD thesisGoogle Scholar
  40. Suzuki A, Knaff DB (2005) Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism. Photosynth Res 83(2):191–217.  https://doi.org/10.1007/s11120-004-3478-0 CrossRefPubMedGoogle Scholar
  41. Tajima F (1989) Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585–595PubMedPubMedCentralGoogle Scholar
  42. Tamura W, Kojima S, Toyokawa A, Watanabe H, Tabuchi-Kobayashi M, Hayakawa T, Yamaya T (2011) Disruption of a novel NADH-glutamate synthase2 gene caused marked reduction in spikelet number of rice. Front Plant Sci 2:9.  https://doi.org/10.3389/fpls.2011.00057 CrossRefGoogle Scholar
  43. Tian DC, Araki H, Stahl E, Bergelson J, Kreitman M (2002) Signature of balancing selection in Arabidopsis. Proc Natl Acad Sci U S A 99(17):11525–11530.  https://doi.org/10.1073/pnas.172203599 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Vanderlip RL, Reeves HE (1972) Growth stages of Sorghum sorghum bicolor, (L) Moench. Agron J 64(1):13CrossRefGoogle Scholar
  45. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3(7):12.  https://doi.org/10.1186/gb-2002-3-7-research0034 CrossRefGoogle Scholar
  46. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7(2):256–276.  https://doi.org/10.1016/0040-5809(75)90020-9 CrossRefPubMedGoogle Scholar
  47. Williams RF (1948) The effects of phosphorus supply on the rates of intake of phosphorus and nitrogen and upon certain aspects of phosphorus metabolism in gramineous plants. Aust J Sci Res Series B Biol Sci 1(3):333–361Google Scholar
  48. Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22(3):506–519.  https://doi.org/10.1093/molbev/msi035 CrossRefPubMedGoogle Scholar
  49. Xu GH, Fan XR, Miller AJ (2012) Plant nitrogen assimilation and use efficiency. Annu Rev Plant Biol 63(63):153–182CrossRefPubMedGoogle Scholar
  50. Yamaya T, Obara M, Nakajima H, Sasaki S, Hayakawa T, Sato T (2002) Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice. J Exp Bot 53(370):917–925.  https://doi.org/10.1093/jexbot/53.370.917 CrossRefPubMedGoogle Scholar
  51. Yang Z, Hammer, G., van Oosterom, E., Rochais, D., Deifel, K. (2010) Effects of pot size on growth of maize and sorghum plants. Edited paper presented at the Proceedings of the 1st Australian summer grains conference, Gold Coast, Australia, 21st-24th June 2010Google Scholar
  52. Youngquist JB, Bramelcox P, Maranville JW (1992) Evaluation of alternative screening criteria for selecting nitrogen-use efficient genotypes in sorghum. Crop Sci 32(6):1310–1313CrossRefGoogle Scholar
  53. Zhao X-Q, Nie X-L, Xiao X-G (2013) Over-expression of a tobacco nitrate Reductase gene in wheat (Triticum aestivum L.) increases seed protein content and weight without augmenting nitrogen supplying. PLoS One 8(9):e74678.  https://doi.org/10.1371/journal.pone.0074678 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Eugene Diatloff
    • 1
  • Emma S. Mace
    • 2
  • David R. Jordan
    • 3
  • Sophie Filleur
    • 4
    • 5
  • Shuaishuai Tai
    • 6
  • Susanne Schmidt
    • 1
  • Ian D. Godwin
    • 1
  1. 1.The University of QueenslandSchool of Agriculture and Food SciencesBrisbaneAustralia
  2. 2.Department of Agriculture, Fisheries and ForestryHermitage Research FacilityWarwickAustralia
  3. 3.Queensland Alliance for Agriculture and Food Innovation, Hermitage Research FacilityUniversity of QueenslandWarwickAustralia
  4. 4.Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS Université Paris-SudGif-sur-YvetteFrance
  5. 5.Université Paris 7 Denis DiderotU.F.R. Sciences du VivantParis Cedex 13France
  6. 6.BGI GenomicsBGI-ShenzhenShenzhenChina

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