The relationship between population structure and aluminum tolerance in cultivated sorghum

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Caniato, Fernanda F ^a   Guimarães, Claudia T ^a   Hamblin, Martha ^b   Billot, Claire ^c   Rami, Jean François ^c   Hufnagel, Barbara ^a,d   Kochian, Leon V ^b   Liu, Jiping ^b   Garcia, Antonio Augusto F ^e   Hash, C Tom ^f   Ramu, Punna ^f   Mitchell, Sharon ^b   Kresovich, Stephen ^b   Oliveira, Antônio Carlos ^a   de Avellar, Gisela ^a   Borém, Aluízio ^g   Glaszmann, Jean Christophe ^c   Schaffert, Robert E ^a   Magalhaes, Jurandir V ^a  

^a EMBRAPA MILHO E SORGO   (Brazil)

^b Department of Molecular Biology and Genetics   (United States)

^c UMR AGAP   (France)

^d FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

^f INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^g FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALUMINUM; CARRIER PROTEIN; PROTEIN SBMATE; UNCLASSIFIED DRUG; MICROSATELLITE DNA;

ALUMINUM OVERLOAD; ALUMINUM TOLERANCE; ARTICLE; CHROMOSOME 3; CONTROLLED STUDY; CROP; CULTIVATED SPECIES; DOMINANT INHERITANCE; GENE ACTIVITY; GENE EXPRESSION; GENE FREQUENCY; GENE LOCUS; GENETIC ANALYSIS; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; GEOGRAPHIC ORIGIN; GEOGRAPHICAL VARIATION (SPECIES); NONHUMAN; PLANT CHROMOSOME; PLANT GENE; PLANT TAXONOMY; POPULATION STRUCTURE; REAL TIME POLYMERASE CHAIN REACTION; RECESSIVE INHERITANCE; ROOT GROWTH; SBMATE GENE; SORGHUM; BIODIVERSITY; BREEDING; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR EVOLUTION; MUTATION; PHYSIOLOGY; PLANT ROOT; SOIL;

ALUMINUM; BIODIVERSITY; BREEDING; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; MICROSATELLITE REPEATS; MUTATION; PLANT ROOTS; SOIL; SORGHUM;

EID: 79958774138     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020830     Document Type: Article

References (60)

1. Garvin DF, Carver BF, (2003) Role of the genotype in tolerance to acidity and aluminum toxicity. In: Rengel Z, editors. Handbook of soil acidity New York Marcel Dekker Inc pp. 387-406.
2. Doggett H, (1988) Sorghum New York John Wiley & Sons.
3. Kochian LV, Hoekenga OA, Piñeros MA, (2004) How do crop plants tolerate acid soils? Mechanisms of aluminum tolerance and phosphorous efficiency. Annual Review of Plant Biology 55: 459-493.
4. Magalhaes JV, Garvin DF, Wang Y, Sorrells ME, Klein PE, et al. (2004) Comparative mapping of a major aluminum tolerance gene in sorghum and other species in the Poaceae. Genetics 167: 1905-1914.
5. Ma JF, Ryan PR, Delhaize E, (2001) Aluminum tolerance in plants and the complexing role of organic acids. Trends in Plant Science 6: 273-278.
6. Sasaki T, Yamamoto Y, Ezaki B, Katsuhara M, Ahn S, et al. (2004) A wheat gene encoding an aluminum-activated malate transporter. The Plant Journal 37: 645-653.
7. Magalhaes JV, Liu J, Guimaraes CT, Lana UGP, Alves VMC, et al. (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nature Genetics 39: 1156-1161.
8. Furukawa J, Yamaji N, Wang H, Mitani N, Murata Y, et al. (2007) An aluminum-activated citrate transporter in barley. Plant Cell Physiology 48: 1081-1091.
9. Maron LG, Piñeros MA, Guimarães CT, Magalhaes JV, Pleiman JK, et al. (2009) Two functionally distinct members of the MATE (multidrug and toxic compound extrusion) family of transporters potentially underlie two major aluminum tolerance QTLs in maize. The Plant Journal 61: 728-740.
10. Hoekenga OA, Maron LG, Piñeros MA, Cançado GMA, Shaff J, et al. (2006) AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis. Proc Natl Sci U S A 103: 9738-9743.
11. Liu J, Magalhaes JV, Shaff J, Kochian LV, (2009) Aluminum-activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance. The Plant Journal 57: 389-399.
12. Ryan PR, Raman H, Gupta S, Horst WJ, Delhaize E, (2009) A second mechanism for aluminum resistance in wheat relies on the constitutive efflux of citrate from roots. Plant Physiology 149: 340-351.
13. Ligaba A, Katsuhara M, Ryan PR, Shibasaka M, Matsumoto H, (2006) The BnALMT1 and BnALMT2 genes from rape encode aluminum-activated malate transporters that enhance the aluminum resistance of plant cells. Plant Physiology 142: 1294-1303.
14. Collins NC, Shirley NJ, Saeed M, Pallotta M, Gustafson JP, (2008) An ALMT1 gene cluster controlling aluminum tolerance at the Alt4 locus of rye (Secale cereale L). Genetics 179: 669-82.
15. Yokosho K, Yamaji N, Ma JF, (2010) Isolation and characterization of two MATE genes in rye. Functional Plant Biology 37: 296-303.
16. Iuchi S, Koyama H, Iuchi A, Kobayashi Y, Kitabayashi S, et al. (2007) Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance. Proc Natl Sci U S A 104: 9900-9905.
17. Yamaji N, Huang CF, Nagao S, Yano M, Sato Y, et al. (2009) A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice. The Plant Cell 21: 3339-3349.
18. Sawaki Y, Iuchi S, Kobayashi Y, Kobayashi Y, Ikka T, et al. (2009) STOP1 regulates multiple genes that protect Arabidopsis from proton and aluminum toxicities. Plant Physiology 150: 281-294.
19. Larsen PB, Geisler MJ, Jones CA, Williams KM, Cancel JD, (2005) ALS3 encodes a phloem-localized ABC transporter-like protein that is required for aluminum tolerance. Plant Journal 41: 353-363.
20. Larsen PB, Cancel J, Rounds M, Ochoa V, (2007) Arabidopsis ALS1 encodes a root tip and stele localized half type ABC transporter required for root growth in an aluminum toxic environment. Planta 225: 1447-1458.
21. Huang C-F, Yamaji N, Ma JF, (2010) Knockout of a bacterial-type ATP-binding cassette transporter gene, AtSTAR1, results in increased aluminum sensitivity in Arabidopsis. Plant Physiology 153: 1669-1677.
22. Huang C-F, Yamaji N, Mitani N, Yano M, Nagamura Y, et al. (2009) A bacterial-type ABC transporter is involved in aluminum tolerance in rice. The Plant Cell 21: 655-667.
23. Xia J, Yamaji N, Kasai T, Ma JF, (2010) Plasma membrane-localized transporter for aluminum in rice. Proc Natl Sci U S A 107: 18381-18385.
24. de Wet JMJ, (1978) Systematics and evolution of sorghum sect. Sorghum (Gramineae). American Journal of Botany 65: 477-484.
25. Dahlberg JA, (2000) Classification and characterization of sorghum. In: Smith CW, Frederiksen RA, editors. Sorghum: origin, history, technology and production New York John Wiley & Sons pp. 99-130.
26. Harlan JR, de Wet JMJ, (1972) A simplified classification of cultivated sorghum. Crop Science 12: 172-176.
27. de Wet JMJ, Harlan JR, (1971) The origin and domestication of Sorghum bicolor. Economic Botany 25: 128-135.
28. de Wet JMJ, Harlan JR, Kurmarohita B, (1972) Origin and evolution of guinea sorghums. East Afr Agric For J 38: 114-119.
29. Folkertsma RT, Rattunde HFW, Chandra S, Raju GS, Hash CT, (2005) The pattern of genetic diversity of guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theoretical and Applied Genetics 111: 399-409.
30. Prada D, (2009) Molecular population genetics and agronomic alleles in seed banks: searching for a needle in a haystack? Journal of Experimental Botany 60: 2541-2552.
31. Platt A, Horton M, Huang YS, Li Y, Anastasio AE, et al. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genetics 6: e1000843.
32. Hartl DL, Clark AG, (1997) Principles of population genetics Massachusetts Sinauer Associates.
33. Hedrick PW, (2005) Genetics of populations Massachusetts Jones and Bartlett Publishers.
34. Deu M, Rattunde F, Chantereau J, (2006) A global view of genetic diversity in cultivated sorghums using a core collection. Genome 49: 168-180.
35. Caniato FF, Guimaraes CT, Schaffert RE, Alves VMC, Kochian LV, et al. (2007) Genetic diversity for aluminum tolerance in sorghum. Theoretical and Applied Genetics 114: 863-876.
36. Lin J, Quinn TP, Hilborn R, Hauser L, (2008) Fine-scale differentiation between sockeye salmon ecotypes and the effect of phenotype on straying. Heredity 101: 341-350.
37. Reddy BVS, Ramesh S, Reddy PS, (2006) Sorghum genetic resources, cytogenetics and improvement. In: Singh RJ, Jauhar PP, editors. Genetic resources, chromosome, engineering and crop improvement Florida CRC press pp. 309-363.
38. Semon M, Nielsen R, Jones MP, McCouch SR, (2005) The population structure of African cultivated rice Oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation. Genetics 169: 1639-1647.
39. Camus-Kulandaivelu L, Veyrieras J-P, Madur D, Combes V, Fourmann M, et al. (2006) Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172: 2449-2463.
40. Weltzien E, Rattunde HFW, Clerget B, Siart S, Toure A, et al. (2006) Sorghum diversity and adaptation to drought in West Africa. In: Jarvis D, Mar I, Sears L, editors. Enhancing the use of crop genetic diversity to manage abiotic stress in agricultural production systems Rome International Plant Genetic Resources Institute pp. 31-38.
41. Doumbia MD, Hossner LR, Onken AB, (1993) Variable sorghum growth in acid soils of subhumid West Africa. Arid Land Research and Management 7: 335-346.
42. Doumbia MD, Hossner LR, Onken AB, (1998) Sorghum growth in acid soils of West Africa: variations in soil chemical properties. Arid Land Research and Management 12: 179-190.
43. de Alencar Figueiredo LF, Calatayud C, Dupuits C, Billot C, Rami J-F, et al. (2008) Phylogeographic evidence of crop neodiversity in sorghum. Genetics 179: 997-1008.
44. Bourguet D, Prout M, Raymond M, (1996) Dominance of insecticide resistance presents a plastic response. Genetics 143: 407-416.
45. Bourguet D, (1999) The evolution of dominance. Heredity 83: 1-4.
46. Fisher RA, (1928) The possible modification of the response of the wild type to recurrent mutations. The American Naturalist 62: 115-126.
47. Doebley J, Stec A, Gustus C, (1995) teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141: 333-346.
48. Bourguet D, Lenormand T, Guillemaud T, Marcel V, Fournier D, et al. (1997) Variation of dominance of newly arisen adaptive genes. Genetics 147: 1225-1234.
49. Parker DR, Norvell WA, Chaney RL, (1995) GEOCHEM-PC: a chemical speciation program for IBM and compatible computers. In: Loeppert RH, Schwab AP, Goldberg S, editors. Chemical equilibrium and reaction models Madison Soil Science Society of America pp. 253-269.
50. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW, (1984) Ribosomal DNA spacer length polymorphism in barley: mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81: 8014-8018.
51. Scott AJ, Knott M, (1974) A cluster analysis method for grouping means in the analysis of variance. Biometrics 30: 507-512.
52. Hotelling H, (1936) Relations between two sets of variates. Biometrika 28: 321-377.
53. Liu K, Muse SV, (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
54. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
55. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
56. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620.
57. Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38: 203-208.
58. Jin L, Chakraborty R, (1994) Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data. Molecular Biology and Evolution 11: 120-127.
59. Schwarz B, (1978) Estimating the dimension of a model. Annals of Statistics 6: 461-464.
60. Sanchez PA, Palm CA, Buol SW, (2003) Fertility capability soil classification: a tool to help assess soil quality in the tropics. Geoderma 114: 157-185.