Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content

English version

Autoři: Marco Giovannetti ^aff001; Christian Göschl ^aff001; Christof Dietzen ^aff002; Stig U. Andersen ^aff003; Stanislav Kopriva ^aff002; Wolfgang Busch ^aff001
Působiště autorů: Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria ^aff001; University of Cologne, Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany ^aff002; Department of Molecular Biology and Genetics, Aarhus University, Denmark ^aff003; Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, La Jolla, California, United States of America ^aff004
Vyšlo v časopise: Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content. PLoS Genet 15(12): e32767. doi:10.1371/journal.pgen.1008126
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008126

Souhrn

Phosphate represents a major limiting factor for plant productivity. Plants have evolved different solutions to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions. Here we elucidated plant responses and their genetic basis to different phosphate levels in a plant species that is widely used as a model for AM symbiosis: Lotus japonicus. Rather than focussing on a single model strain, we measured root growth and anion content in response to different levels of phosphate in 130 Lotus natural accessions. This allowed us not only to uncover common as well as divergent responses within this species, but also enabled Genome Wide Association Studies by which we identified new genes regulating phosphate homeostasis in Lotus. Among them, we showed that insertional mutants of a cytochrome B5 reductase and a Leucine-Rich-Repeat receptor showed different phosphate concentration in plants grown under phosphate sufficient condition. Under low phosphate conditions, we found a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, representing a dilution effect. Altogether our data of the genetic and phenotypic variation within a species capable of AM complements studies that have been conducted in Arabidopsis, and advances our understanding of the continuum of genotype by phosphate level interaction existing throughout dicot plants.

Klíčová slova:

Anions – Arabidopsis thaliana – Genetic loci – Genome-wide association studies – Molecular genetics – Phosphates – Plant genetics – Root growth

Zdroje

1. López-Bucio J, Hernández-Abreu E, Sánchez-Calderón L, Nieto-Jacobo MF, Simpson J, Herrera-Estrella L. Phosphate Availability Alters Architecture and Causes Changes in Hormone Sensitivity in the Arabidopsis Root System. Plant Physiol. 2002;129: 244–256. doi: 10.1104/pp.010934 12011355

2. Svistoonoff S, Creff A, Reymond M, Sigoillot-Claude C, Ricaud L, Blanchet A, et al. Root tip contact with low-phosphate media reprograms plant root architecture. Nat Genet. 2007;39: 792–796. doi: 10.1038/ng2041 17496893

3. Wang X, Wang Z, Zheng Z, Dong J, Song L, Sui L, et al. Genetic dissection of Fe-dependent signaling in root developmental responses to phosphate deficiency. Plant Physiol. 2019; pp.00907.2018. doi: 10.1104/pp.18.00907 30420567

4. Müller J, Toev T, Heisters M, Teller J, Moore KL, Hause G, et al. Iron-Dependent Callose Deposition Adjusts Root Meristem Maintenance to Phosphate Availability. Dev Cell. 2015;33: 216–230. doi: 10.1016/j.devcel.2015.02.007 25898169

5. Rubio V, Linhares F, Solano R, Martín AC, Iglesias J, Leyva A, et al. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 2001;15: 2122–2133. doi: 10.1101/gad.204401 11511543

6. Bustos R, Castrillo G, Linhares F, Puga MI, Rubio V, Pérez-Pérez J, et al. A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis. PLOS Genet. 2010;6: e1001102. doi: 10.1371/journal.pgen.1001102 20838596

7. Puga MI, Mateos I, Charukesi R, Wang Z, Franco-Zorrilla JM, Lorenzo L de, et al. SPX1 is a phosphate-dependent inhibitor of PHOSPHATE STARVATION RESPONSE 1 in Arabidopsis. Proc Natl Acad Sci. 2014;111: 14947–14952. doi: 10.1073/pnas.1404654111 25271326

8. Wang Z, Ruan W, Shi J, Zhang L, Xiang D, Yang C, et al. Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner. Proc Natl Acad Sci U S A. 2014;111: 14953–14958. doi: 10.1073/pnas.1404680111 25271318

9. Lv Q, Zhong Y, Wang Y, Wang Z, Zhang L, Shi J, et al. SPX4 Negatively Regulates Phosphate Signaling and Homeostasis through Its Interaction with PHR2 in Rice. Plant Cell. 2014;26: 1586–1597. doi: 10.1105/tpc.114.123208 24692424

10. Essigmann B, Güler S, Narang RA, Linke D, Benning C. Phosphate availability affects the thylakoid lipid composition and the expression of SQD1, a gene required for sulfolipid biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1998;95: 1950–1955. doi: 10.1073/pnas.95.4.1950 9465123

11. Sakuraba Y, Kanno S, Mabuchi A, Monda K, Iba K, Yanagisawa S. A phytochrome-B-mediated regulatory mechanism of phosphorus acquisition. Nat Plants. 2018;4: 1089. doi: 10.1038/s41477-018-0294-7 30518831

12. Briat J-F, Rouached H, Tissot N, Gaymard F, Dubos C. Integration of P, S, Fe, and Zn nutrition signals in Arabidopsis thaliana: potential involvement of PHOSPHATE STARVATION RESPONSE 1 (PHR1). Front Plant Sci. 2015;6. doi: 10.3389/fpls.2015.00290 25972885

13. Kisko M, Bouain N, Safi A, Medici A, Akkers RC, Secco D, et al. LPCAT1 controls phosphate homeostasis in a zinc-dependent manner. Harrison MJ, editor. eLife. 2018;7: e32077. doi: 10.7554/eLife.32077 29453864

14. Almario J, Jeena G, Wunder J, Langen G, Zuccaro A, Coupland G, et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. Proc Natl Acad Sci. 2017;114: E9403–E9412. doi: 10.1073/pnas.1710455114 28973917

15. Hiruma K, Gerlach N, Sacristán S, Nakano RT, Hacquard S, Kracher B, et al. Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent. Cell. 2016;165: 464–474. doi: 10.1016/j.cell.2016.02.028 26997485

16. Castrillo G, Teixeira PJPL, Paredes SH, Law TF, de Lorenzo L, Feltcher ME, et al. Root microbiota drive direct integration of phosphate stress and immunity. Nature. 2017;543: 513–518. doi: 10.1038/nature21417 28297714

17. Paredes SH, Gao T, Law TF, Finkel OM, Mucyn T, Teixeira PJPL, et al. Design of synthetic bacterial communities for predictable plant phenotypes. PLOS Biol. 2018;16: e2003962. doi: 10.1371/journal.pbio.2003962 29462153

18. Choi J, Summers W, Paszkowski U. Mechanisms Underlying Establishment of Arbuscular Mycorrhizal Symbioses. Annu Rev Phytopathol. 2018;56: 135–160. doi: 10.1146/annurev-phyto-080516-035521 29856935

19. Giovannetti M, Volpe V, Salvioli A, Bonfante P. Chapter 7—Fungal and Plant Tools for the Uptake of Nutrients in Arbuscular Mycorrhizas: A Molecular View. In: Johnson NC, Gehring C, Jansa J, editors. Mycorrhizal Mediation of Soil. Elsevier; 2017. pp. 107–128. doi: 10.1016/B978-0-12-804312-7.00007–3

20. Lanfranco L, Fiorilli V, Gutjahr C. Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis. New Phytol. 2018;220: 1031–1046. doi: 10.1111/nph.15230 29806959

21. MacLean AM, Bravo A, Harrison MJ. Plant Signaling and Metabolic Pathways Enabling Arbuscular Mycorrhizal Symbiosis. Plant Cell. 2017;29: 2319–2335. doi: 10.1105/tpc.17.00555 28855333

22. Carbonnel S, Gutjahr C. Control of arbuscular mycorrhiza development by nutrient signals. Front Plant Sci. 2014;5. doi: 10.3389/fpls.2014.00462 25309561

23. Shah N, Wakabayashi T, Kawamura Y, Skovbjerg CK, Wang M-Z, Mustamin Y, et al. Extreme genetic signatures of local adaptation during plant colonization. bioRxiv. 2018; 485789. doi: 10.1101/485789

24. Kellermeier F, Armengaud P, Seditas TJ, Danku J, Salt DE, Amtmann A. Analysis of the Root System Architecture of Arabidopsis Provides a Quantitative Readout of Crosstalk between Nutritional Signals. Plant Cell. 2014;26: 1480–1496. doi: 10.1105/tpc.113.122101 24692421

25. Giovannetti M, Małolepszy A, Göschl C, Busch W. Large-Scale Phenotyping of Root Traits in the Model Legume Lotus japonicus. In: Busch W, editor. Plant Genomics: Methods and Protocols. New York, NY: Springer New York; 2017. pp. 155–167. doi: 10.1007/978-1-4939-7003-2_11

26. Slovak R, Göschl C, Su X, Shimotani K, Shiina T, Busch W. A Scalable Open-Source Pipeline for Large-Scale Root Phenotyping of Arabidopsis. Plant Cell. 2014;26: 2390–2403. doi: 10.1105/tpc.114.124032 24920330

27. Chevalier F, Pata M, Nacry P, Doumas P, Rossignol M. Effects of phosphate availability on the root system architecture: large-scale analysis of the natural variation between Arabidopsis accessions. Plant Cell Environ. 2003;26: 1839–1850. doi: 10.1046/j.1365-3040.2003.01100.x

28. Ristova D, Giovannetti M, Metesch K, Busch W. Natural genetic variation shapes root system responses to phytohormones in Arabidopsis. Plant J. 2018;96: 468–481. doi: 10.1111/tpj.14034 30030851

29. Jarrell WM, Beverly RB. The Dilution Effect in Plant Nutrition Studies. In: Brady NC, editor. Advances in Agronomy. Academic Press; 1981. pp. 197–224. doi: 10.1016/S0065-2113(08)60887-1

30. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006;38: 203–208. doi: 10.1038/ng1702 16380716

31. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, et al. Efficient Control of Population Structure in Model Organism Association Mapping. Genetics. 2008;178: 1709–1723. doi: 10.1534/genetics.107.080101 18385116

32. Seren Ü, Vilhjálmsson BJ, Horton MW, Meng D, Forai P, Huang YS, et al. GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis. Plant Cell. 2012;24: 4793–4805. doi: 10.1105/tpc.112.108068 23277364

33. Di Laurenzio L, Wysocka-Diller J, Malamy JE, Pysh L, Helariutta Y, Freshour G, et al. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell. 1996;86: 423–433. doi: 10.1016/s0092-8674(00)80115-4 8756724

34. Cattaneo P, Hardtke CS. BIG BROTHER Uncouples Cell Proliferation from Elongation in the Arabidopsis Primary Root. Plant Cell Physiol. 2017;58: 1519–1527. doi: 10.1093/pcp/pcx091 28922745

35. Mora-Macías J, Ojeda-Rivera JO, Gutiérrez-Alanís D, Yong-Villalobos L, Oropeza-Aburto A, Raya-González J, et al. Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate. Proc Natl Acad Sci. 2017;114: E3563–E3572. doi: 10.1073/pnas.1701952114 28400510

36. Balzergue C, Dartevelle T, Godon C, Laugier E, Meisrimler C, Teulon J-M, et al. Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation. Nat Commun. 2017;8: 15300. doi: 10.1038/ncomms15300 28504266

37. Domergue F, Vishwanath SJ, Joubès J, Ono J, Lee JA, Bourdon M, et al. Three Arabidopsis Fatty Acyl-Coenzyme A Reductases, FAR1, FAR4, and FAR5, Generate Primary Fatty Alcohols Associated with Suberin Deposition. Plant Physiol. 2010;153: 1539–1554. doi: 10.1104/pp.110.158238 20571114

38. Mun T, Bachmann A, Gupta V, Stougaard J, Andersen SU. Lotus Base: An integrated information portal for the model legume Lotus japonicus. Sci Rep. 2016;6: 39447. doi: 10.1038/srep39447 28008948

39. Małolepszy A, Mun T, Sandal N, Gupta V, Dubin M, Urbański D, et al. The LORE1 insertion mutant resource. Plant J. 2016;88: 306–317. doi: 10.1111/tpj.13243 27322352

40. Benjamini Y, Yekutieli D. The Control of the False Discovery Rate in Multiple Testing under Dependency. Ann Stat. 2001;29: 1165–1188.

41. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29: 24–26. doi: 10.1038/nbt.1754 21221095

42. Ames BN. [10] Assay of inorganic phosphate, total phosphate and phosphatases. Methods in Enzymology. Academic Press; 1966. pp. 115–118. doi: 10.1016/0076-6879(66)08014-5

43. Ward JT, Lahner B, Yakubova E, Salt DE, Raghothama KG. The Effect of Iron on the Primary Root Elongation of Arabidopsis during Phosphate Deficiency. Plant Physiol. 2008;147: 1181–1191. doi: 10.1104/pp.108.118562 18467463

44. Volpe V, Giovannetti M, Sun X-G, Fiorilli V, Bonfante P. The phosphate transporters LjPT4 and MtPT4 mediate early root responses to phosphate status in non mycorrhizal roots. Plant Cell Environ. 2016;39: 660–671. doi: 10.1111/pce.12659 26476189

45. Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, et al. Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines. Nature. 2010;465: 627–631. doi: 10.1038/nature08800 20336072

46. Kerdaffrec E, Filiault DL, Korte A, Sasaki E, Nizhynska V, Seren Ü, et al. Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis. Hardtke CS, editor. eLife. 2016;5: e22502. doi: 10.7554/eLife.22502 27966430

47. Chao D-Y, Silva A, Baxter I, Huang YS, Nordborg M, Danku J, et al. Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana. PLOS Genet. 2012;8: e1002923. doi: 10.1371/journal.pgen.1002923 22969436

48. Koprivova A, Giovannetti M, Baraniecka P, Lee B-R, Grondin C, Loudet O, et al. Natural Variation in the ATPS1 Isoform of ATP Sulfurylase Contributes to the Control of Sulfate Levels in Arabidopsis. Plant Physiol. 2013;163: 1133–1141. doi: 10.1104/pp.113.225748 24027241

49. Huang X-Y, Chao D-Y, Koprivova A, Danku J, Wirtz M, Müller S, et al. Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana. PLOS Genet. 2016;12: e1006298. doi: 10.1371/journal.pgen.1006298 27622452

50. Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, et al. A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1. PLOS Genet. 2010;6: e1001193. doi: 10.1371/journal.pgen.1001193 21085628

51. Satbhai SB, Setzer C, Freynschlag F, Slovak R, Kerdaffrec E, Busch W. Natural allelic variation of FRO2 modulates Arabidopsis root growth under iron deficiency. Nat Commun. 2017;8: 15603. doi: 10.1038/ncomms15603 28537266

52. Li B, Sun L, Huang J, Göschl C, Shi W, Chory J, et al. GSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity. Nat Commun. 2019;10: 1–13. doi: 10.1038/s41467-018-07882-8

53. Julkowska MM, Koevoets IT, Mol S, Hoefsloot H, Feron R, Tester MA, et al. Genetic Components of Root Architecture Remodeling in Response to Salt Stress. Plant Cell. 2017;29: 3198–3213. doi: 10.1105/tpc.16.00680 29114015

54. Bouain N, Satbhai SB, Korte A, Saenchai C, Desbrosses G, Berthomieu P, et al. Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition. PLOS Genet. 2018;14: e1007304. doi: 10.1371/journal.pgen.1007304 29608565

55. Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, et al. Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments. PLOS Genet. 2013;9: e1003760. doi: 10.1371/journal.pgen.1003760 24039603

56. Stetter MG, Schmid K, Ludewig U. Uncovering Genes and Ploidy Involved in the High Diversity in Root Hair Density, Length and Response to Local Scarce Phosphate in Arabidopsis thaliana. PLOS ONE. 2015;10: e0120604. doi: 10.1371/journal.pone.0120604 25781967

57. Orgiazzi A, Ballabio C, Panagos P, Jones A, Fernández‐Ugalde O. LUCAS Soil, the largest expandable soil dataset for Europe: a review. Eur J Soil Sci. 2018;69: 140–153. doi: 10.1111/ejss.12499

58. Yang M, Lu K, Zhao F-J, Xie W, Ramakrishna P, Wang G, et al. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. Plant Cell. 2018;30: 2720–2740. doi: 10.1105/tpc.18.00375 30373760

59. Oh YJ, Kim H, Seo SH, Hwang BG, Chang YS, Lee J, et al. Cytochrome b5 Reductase 1 Triggers Serial Reactions that Lead to Iron Uptake in Plants. Mol Plant. 2016;9: 501–513. doi: 10.1016/j.molp.2015.12.010 26712506

60. Yang H, Zhang X, Gaxiola RA, Xu G, Peer WA, Murphy AS. Over-expression of the Arabidopsis proton-pyrophosphatase AVP1 enhances transplant survival, root mass, and fruit development under limiting phosphorus conditions. J Exp Bot. 2014;65: 3045–3053. doi: 10.1093/jxb/eru149 24723407

61. Tabata R, Sumida K, Yoshii T, Ohyama K, Shinohara H, Matsubayashi Y. Perception of root-derived peptides by shoot LRR-RKs mediates systemic N-demand signaling. Science. 2014;346: 343–346. doi: 10.1126/science.1257800 25324386

62. Okamoto S, Shinohara H, Mori T, Matsubayashi Y, Kawaguchi M. Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase. Nat Commun. 2013;4: 2191. doi: 10.1038/ncomms3191 23934307