The FIGS (Focused Identification of Germplasm Strategy) Approach Identifies Traits Related to Drought Adaptation in Vicia faba Genetic Resources

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Khazaei, Hamid ^a   Street, Kenneth ^b   Bari, Abdallah ^b   Mackay, Michael ^c   Stoddard, Frederick L ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b INTERNATIONAL CENTER FOR AGRICULTURAL RESEARCH IN THE DRY AREAS ICARDA   (Syrian Arab Republic)

^c UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANOPY; CANOPY TEMPERATURE; CONTROLLED STUDY; DIFFERENTIATION; DROUGHT TOLERANCE; FOCUSED IDENTIFICATION OF GERMPLASM STRATEGY; GENE POOL; GENETIC RESOURCE; GERMPLASM; LEAF MORPHOLOGY; LEAFLET TEMPERATURE; MACHINE LEARNING; MOISTURE; MORPHOLOGICAL TRAIT; NONHUMAN; PHENOLOGY; PLANT LEAFLET; PLANT WATER CONTENT; PLANT WATER USE; TEMPERATURE; VICIA FABA;

ADAPTATION, BIOLOGICAL; BIODIVERSITY; CLIMATE CHANGE; DROUGHTS; GENE POOL; GENETIC VARIATION; PLANT LEAVES; TEMPERATURE; VICIA FABA; WATER;

EID: 84877270751     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063107     Document Type: Article

References (82)

1. Barnabás B, Jäger K, Fehér A, (2008) The effect of drought and heat stress on reproductive processes in cereals. Plant Cell Environ 31: 11-38.
2. IPCC (2012) Managing the risks of extreme events and disasters to advance climate change adaptation. A special report of working groups I and II of the intergovernmental panel on climate change [Field CB, Barros V, Stocker TF, Qin D, Dokken DG,et al. editors]. Cambridge University Press, Cambridge, UK, and New York, NY, USA, 582 pp.
3. Duc G, (1997) Faba bean (Vicia faba L.). Field Crops Res 53: 99-109.
4. Crépon K, Marget P, Peyronnet C, Carrouée B, Arese P, et al. (2010) Nutritional value of faba bean (Vicia faba L.) seeds for feed and food. Field Crops Res 115: 329-339.
5. Khan HR, Link W, Hocking TJH, Stoddard FL, (2007) Evaluation of physiological traits for improving drought tolerance in faba bean (Vicia faba L.). Plant Soil 292: 205-217.
6. Khan HR, Paull JG, Siddique KHM, Stoddard FL, (2010) Faba bean breeding for drought-affected environments: A physiological and agronomic perspective. Field Crops Res 115: 279-286.
7. Duc G, Link W, Marget P, Redden RJ, Stoddard FL, et al. (2011) Genetic adjustment to changing climates: faba bean. In: Yadav SS, Redden RJ, Hatfield JL, Lotze-Campen H, Hall AE, editors. Crop adaption to climate change, 1rd edn. John Wiley & Sons, 269-286.
8. Gollin D, Smale M, Skovmand B, (2000) Searching an ex situ collection of wheat genetic resources. Am J Agric Econ 82: 812-827.
9. Frankel OH (1984) Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P, editors. Genetic manipulation: Impact on man and society, Cambridge University Press, Cambridge, 161-170.
10. Hodgkin T, Brown ADH, van Hintum Th JL, Morales EAV (1995) Core collections of plant genetic resources, John Wiley & Sons, Chichester UK, 265 p.
11. Brown AHD, (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818-824.
12. Brown AHD (1989) The case for core collections. In: Brown AHD, Frankel OH, Marshall DR, Williams JT, editors. The use of plant genetic resources. Cambridge, Cambridge University Press, 136-156.
13. Holbrook CC, Anderson WF, Pittman RN, (1993) Selection of a core collection from the United-States germplasm collection of peanut. Crop Sci 33: 859-861.
14. Ortiz R, Ruiz-Tapia EN, Mujica-Sanchez A, (1998) Sampling strategy for a core collection of Peruvian quinoa germplasm. Theor Appl Genet 96: 475-483.
15. Hu J, Zhu J, Xu HM, (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101: 264-268.
16. Malosetti M, Abadie T, (2001) Sampling strategy to develop a core collection of Uruguayan maize landraces based on morphological traits. Genet Resour Crop Evol 48: 381-390.
17. Casler MD, (1995) Patterns of variation in a collection of perennial ryegrass accessions. Crop Sci 35: 1169-1177.
18. Tohme J, Gonzalez DO, Beebe S, Duque MC, (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36: 1375-1384.
19. Bartish GI, Jeppsson N, Bartish IV, Nybom H, (2000) Assessment of genetic diversity using RAPD analysis in a germplasm collection of sea buckthorn. Agric Food Sci 9: 279-289.
20. Fu YB, Peterson GW, Williams D, Richards KW, Fetch JM, (2005) Patterns of AFLP variation in a core subset of cultivated hexaploid oat germplasm. Theor Appl Genet 111: 530-539.
21. Brown AHD, Spillane C (1999) Implementing core collections- principles, procedures, progress, problems and promise. Johnson RC, Hodgkin T, editors. Core collections for today and tomorrow. Rome, International Plant Genetic Resources Institute, 1-9.
22. Upadhyaya HD, Ortiz R, (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102: 1292-1298.
23. McKhann HI, Camilleri C, Bérard A, Bataillon T, David JL, et al. (2004) Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J 38: 193-202.
24. Furman BJ, (2006) Methodology to establish a composite collection: case study in lentil. Plant Genet Resour 4: 2-12.
25. Polignano GB, Uggenti P, Scippa G, (2001) Diversity analysis and core collection formation in Bari faba bean germplasm. Plant Genet Resour Newslett 125: 33-38.
26. Gepts P, (2006) Plant genetic resources conservation and utilization: the accomplishments and future of a societal insurance policy. Crop Sci 46: 2278-2292.
27. Dwivedi SL, Upadhyaya HD, Stalker HT, Blair MW, Bertioli DJ, et al. (2008) Enhancing crop gene pools with beneficial traits using wild relatives. Plant Breed Rev 30: 180-230.
28. Pessoa-Filho M, Rangel PHN, Ferreira ME, (2010) Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach. BMC Plant Biol 10: 127 doi:10.1186/1471-2229-10-127.
29. Xu Y (2010) Plant genetic resources: Management, evaluation and enhancement. In: Molecular plant breeding. Wallingford, UK, CAB International, 15-194.
30. Mackay M (1990) Strategic planning for effective evaluation of plant germplasm. In: Srivastava JP, Damania AB, editors. Wheat genetic resources: meeting diverse needs. John Wiley & Sons, Chichester, 21-25.
31. Mackay M (1995) One core collection or many? In: Hodgkin T, Brown AHD, Van Hintum TJL, Morales EAV, editors. Core collections of plant genetic resources. John Wiley & Sons Ltd., Chichester, 199-210.
32. Mackay M, Street K (2004) Focused identification of germplasm strategy - FIGS. In: Proceedings of the 54th Australian Cereal Chemistry Conference and the 11th Wheat Breeders' Assembly, editors. Cereal Chemestry Division, Royal Australian Chemical Institute (RACI), Melbourne, Victoria, Australia. 138-141.
33. Mackay M, von Bothmer R, Skovmand B, (2005) Conservation and utilization of plant genetic resources - future directions. Czech J Genet Plant Breed 41: 335-344.
34. Endresen DTF, Street K, Mackay M, Bari A, De Pauw E, (2011) Predictive association between biotic stress traits and ecogeographic data for wheat and barley landraces. Crop Sci 51: 2036-2055.
35. Bari A, Street K, Mackay M, Endresen DTF, De Pauw E, et al. (2012) Focused identification of germplasm strategy (FIGS) detects wheat stem rust resistance linked to environmental variables. Genet Resour Crop Evol 59: 1465-1481.
36. Kaur N, Street K, Mackay M, Yahiaoui N, Keller B, (2008) Molecular approaches for characterization and use of natural disease resistance in wheat. Eur J Plant Pathol 121: 387-397.
37. Bhullar NK, Street K, Mackay M, Yahiaoui N, Keller B, (2009) Unlocking wheat genetic resources for the molecular identification of previously undescribed functional alleles at the Pm3 resistance locus. Proc Natl Acad Sci USA 106: 9519-9524.
38. El Bouhssini M, Street K, Joubi A, Ibrahim Z, Rihawi F, (2009) Sources of wheat resistance to sunn pest, Eurygaster integriceps Puton, in Syria. Genet Resour Crop Evol 56: 1065-1069.
39. El Bouhssini M, Street K, Amri A, Mackay M, Ogbonnaya FC, et al. (2011) Sources of resistance in bread wheat to Russian wheat aphid (Diuraphis noxia) in Syria identified using the Focused Identification of Germplasm Strategy (FIGS). Plant Breed 130: 96-97.
40. Endresen DTF, (2010) Predictive association between trait data and ecogeographic data for Nordic barley landraces. Crop Sci 50: 2418-2430.
41. FAO (2010) The second report on the state of the world's plant genetic resources for food and agriculture. Rome, Italy, 398 p.
42. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A, (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25: 1965-1978.
43. Wang H, Clarke JM, (1993) Genotypic, intraplant, and environmental variation in stomatal frequency and size in wheat. Can J Plant Sci 73: 671-678.
44. Muratova V, (1931) Common Beans (Vicia faba). Bull Appl Bot Genet Plant Breed 50: 1-298.
45. Cubero J, (1974) On the evolution of Vicia faba L. Theor Appl Genet. 45: 47-51.
46. Fischer RA, Rees D, Sayre KD, Lu Z-M, Condon AG, et al. (1998) Wheat yield progress associated with higher stomatal conductance and photosynthetic rate, and cooler canopies. Crop Sci 38: 1467-1475.
47. Barrs HD, Weatherley PE, (1962) A re-examination of the relative turgidity technique for estimating water deficit in leaves. Aust J Biol Sci 15: 413-428.
48. R Development Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. Available: http://www.R-project.org.
49. Kuhn M (2008) Building predictive models in R using the caret package. J Stat Softw 28 (5).
50. Steinberg D (2009) CART: Classification and Regression Trees. Taylor & Francis Group, LLC.
51. Breiman L, (2001) Random forests. Mach Learn 45: 5-32.
52. Cutler DR, Edwards Jr TC, Beard KH, Cutler A, Hess KT, et al. (2007) Random forests for classification in ecology. Ecology 88: 2783-2792.
53. Prasad AM, Iverson LR, Liaw A, (2006) Newer classification and regression tree techniques: bagging and random forests for ecological prediction. Ecosystems 9: 181-199.
54. Dimitriadou E, Hornik K, Leisch F, Meyer D, Weingessel A (2010) R library (e1071). The R foundation for statistical computing. ISBN: 3-900051-07-0.
55. Karatzoglou A, Meyer D, Hornik K (2006) Support vector machines in R. J Stat Softw 15 (9).
56. Tirelli T, Pozzi L, Pessani D, (2009) Use of different approaches to model presence/absence of Salmo marmoratus in Piedmont (Northwestern Italy). Ecol Inform 4: 234-242.
57. Drake JM, Randin C, Guisan A, (2006) Modelling ecological niches with support vector machines. J Appl Ecol 43: 424-432.
58. Swets JA, Dawes RM, Monahan J, (2000) Better decisions through science. Sci Am 283: 82-87.
59. Fawcett T, (2006) An introduction to ROC analysis. Pattern Recognit Lett 27: 861-874.
60. Freeman EA, Moisen GG, (2008) A comparison of the performance of threshold criteria for binary classification in terms of predicted prevalence and kappa. Ecol Modell 217: 48-58.
61. Landis JR, Koch GG, (1977) The measurement of observer agreement for categorical data. Biometrics 33: 159-174.
62. Lin W, Bradshaw AD, Thurman DA, (1975) The potential for evolution of heavy metal tolerance in plants. III. The rapid evolution of copper tolerance in Agrostis stolonifera. Heredity 34: 165-187.
63. Spieth PT, (1979) Environmental heterogeneity: a problem of contradictory selection pressures, gene flow, and local polymorphism. Am Nat 113: 247-260.
64. Epperson BK, (1990) Spatial autocorrelation of genotypes under directional selection. Genetics 124: 757-771.
65. Peleg Z, Fahima T, Abbo S, Krugman T, Nevo E, et al. (2005) Genetic diversity for drought resistance in wild emmer wheat and its ecogeographical associations. Plant Cell Environ 28: 176-191.
66. Bouchabke O, Chang F, Simon M, Voisin R, Pelletire G, et al. (2008) Natural variation in Arabidopsis thaliana as a tool for highlighting differential drought response. PLoS ONE 3: e1705 doi:10.1371/journal.pone.0001705.
67. Vavilov NI, (1926) Tzentry proiskhozhdeniya kulturnykh rastenii. (Studies on the origin of cultivated plants). Trudy Byuro prikl Bot [in Russian] 16: 139-248.
68. Mba C, Guimaraes EP, Ghosh K, (2012) Re-orienting crop improvement for the changing climate conditions for the 21st century. Agric Food Secur 1: 7 doi:10.1186/2048-7010-1-7.
69. Guerin GR, Wen H, Lowe AJ, (2012) Leaf morphology shift linked to climate change. Biol Lett 8: 882-886.
70. Xu F, Guo W, Xu W, Wei Y, Wang R, (2009) Leaf morphology correlates with water and light availability: what consequences for simple and compound leaves? Prog Nat Sci 19: 1789-1798.
71. Fan JW, Du YL, Turner NC, Li FM, He J, (2012) Germination characteristics and seedling emergence of switchgrass with different agricultural practices under arid conditions in China. Crop Sci 52: 2341-2350.
72. Mut Z, Akay H, (2010) Effect of seed size and drought stress on germination and seedling growth of naked oat (Avena sativa L.). Bulg J Agric Sci 16: 459-467.
73. Avola G, Cavallaro V, Patanè C, Riggi E, (2008) Gas exchange and photosynthetic water use efficiency in response to light, CO2 concentration and temperature in Vicia faba. J Plant Physiol 165: 796-804.
74. Parra-Quijano M, Iriondo JM, Torres E, (2012) Ecogeographical land characterization maps as a tool for assessing plant adaptation and their implications in agrobiodiversity studies. Genet Resour Crop Evol 59: 205-217.
75. Blum A (2011) Plant breeding for water limited environments. Springer-Verlag, New York, 255 p.
76. Blum A, (2009) Effective use of water (EUW) and not water-use efficiency (WUE) is the target of crop yield improvement under drought stress. Field Crops Res 112: 119-123.
77. Blum A, (2011) Drought resistance - is it really a complex trait? Funct Plant Biol 38: 753-757.
78. Masi CEA, Maranville JW, (1998) Evaluation of sorghum root branching using fractals. J Agric Sci 131: 259-265.
79. Therneau TM, Atkinson EJ (1997) An introduction to recursive partitioning using the rpart routine. Technical Report 61, Section of Biostatistics, Mayo Clinic, Rochester. Available: http://www.mayo.edu/hsr/techrpt/61.pdf.
80. Strobl C, Malley J, Tutz G, (2009) An introduction to recursive partitioning: rationale, application, and characteristics of classification and regression trees, bagging, and random forests. Psychol Methods 14: 323-348.
81. Liknes GC, Woodall CW, Perry CH (2009) Predicting forest attributes from climate data using a recursive partitioning and regression tree algorithm. In: McWilliams W, Moisen G, Czaplewski R, editors. Forest Inventory and Analysis (FIA) Symposium 2008; Park City, UT. Proc. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station, 7 p.
82. Hothorn T, Hornik K, Zeileis A, (2006) Unbiased recursive partitioning: A conditional inference framework. J Comput Graph Stat 15: 651-674.