Next-generation phenotyping: Requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement

Theoretical and Applied Genetics

Volumn 126, Issue 4, 2013, Pages 867-887

  Cobb, Joshua N ^a,b   DeClerck, Genevieve ^a   Greenberg, Anthony ^a,c   Clark, Randy ^b,d   McCouch, Susan ^a  

^a Department of Obstetrics Gynecology   (United States)

^b ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

^c Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^d Department of Biological and Environmental Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONSERVATION; CROPS; DATA INTEGRATION; DIGITAL STORAGE; ENVIRONMENTAL MICROBIOLOGY; REMOTE SENSING; SIGNAL PROCESSING; STATISTICAL MECHANICS; STATISTICS;

BIOLOGICAL ORGANIZATION; COMPUTER SCIENTISTS; DEVELOPMENTAL STAGE; GENOME-WIDE ASSOCIATION STUDIES; GENOMIC PREDICTIONS; OPERATIONAL BOTTLENECKS; PHENOTYPIC VARIATIONS; POPULATION STRUCTURES;

INFORMATION MANAGEMENT;

EID: 84875426911     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-013-2066-0     Document Type: Review

References (198)

1. Ali M, Sanchez PL, Yu S, Lorieux M, Eizenga GC (2010) Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from wild species of Rice (Oryza spp.). Rice 3: 218-234.
2. Armengaud P, Zambaux K, Hills A, Sulpice R, Pattison RJ, Blatt MR, Amtmann A (2009) EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture. Plant J 57: 945-956.
3. Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JDG, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
4. Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM (2008) The plant ontology database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res 36: D449-D454.
5. Bachlava E, Taylor CA, Tang S, Bowers JE, Mandel JR, Burke JM, Knapp SJ (2012) SNP discovery and development of a high-density genotyping array for sunflower. PLoS ONE. doi: 10. 1371/journal. pone. 0029814.
6. Backhaus A, Kuwabara A, Bauch M, Monk N, Sanguinetti G, Fleming A (2010) LEAFPROCESSOR: a new leaf phenotyping tool using contour bending energy and shape cluster analysis. New Phytol 187: 251-261.
7. Bakker M, Manter D, Sheflin A, Weir T, Vivanco J (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil 360: 1-13.
8. Bartlett MK, Scoffoni C, Ardy R, Zhang Y, Sun S, Cao K, Sack L (2012a) Rapid determination of comparative drought tolerance traits: using an osmometer to predict turgor loss point. Methods Ecol Evol 3: 880-888.
9. Bartlett MK, Scoffoni C, Sack L (2012b) The determinants of leaf turgor loss point and prediction of drought tolerance of species and biomes: a global meta-analysis. Ecol Lett 15: 393-405.
10. Basu P, Pal A, Lynch JP, Brown KM (2007) A novel image-analysis technique for kinematic study of growth and curvature. Plant Physiol 145: 305-316.
11. Baxter I, Ouzzani M, Orcun S, Kennedy B, Jandhyala SS, Salt DE (2007) Purdue ionomics information management system. An integrated functional genomics platform. Plant Physiol 143: 600-611.
12. Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, New York, pp 145-162.
13. Bennett D, Reynolds M, Mullan D, Izanloo A, Kuchel H, Langridge P, Schnurbusch T (2012) Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments. Theor Appl Genet 125: 1473-1485.
14. Berger B, Parent B, Tester M (2010) High-throughput shoot imaging to study drought responses. J Exp Bot 61: 3519-3528.
15. Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin G (2007) A large-effect QTL for grain yield under reproductive-stage drought stress in upland Rice. Crop Sci 47: 507-518.
16. Bhattacharyya MK (2010) Map-based cloning of genes and QTL in soybean. In: Bilyeu K, Ratnaparkhe MB, Kole C (eds) Genetics, genomics, and breeding of soybean. Science Publishers, Enfield, pp 169-186.
17. Blake VC, Kling JG, Hayes PM, Jannink JL, Jillella SR, Lee J, Matthews DE, Chao S, Close TJ, Muehlbauer GJ (2012) The hordeum toolbox: the Barley coordinated agricultural project genotype and phenotype resource. Plant Gen 5: 81-91.
18. 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.
19. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2011) The Sol Genomics Network (http://solgenomics. net): growing tomatoes using perl. Nucleic Acids Res 39: D1149-D1155.
20. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Oropeza Rosas M, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of Maize flowering time. Science 325(5941): 714-718. doi: 10. 1126/science. 1174276.
21. Bylesjö M, Segura V, Soolanayakanahally RY, Rae AM, Trygg J, Gustafsson P, Jansson S, Street NR (2008) LAMINA: a tool for rapid quantification of leaf size and shape parameters. BMC Plant Biol 8: 82.
22. Cabrera-Bosquet L, Crossa J, von Zitzewitz J, Dolors Serret M, Araus JL (2012) High-throughput phenotyping and genomic selection: the frontiers of crop breeding converge. J Intergr Plant Bio 54: 312-320.
23. Cai X, Molden D, Mainuddin M, Sharma B, Ahmad M, Karimi P (2011) Producing more food with less water in a changing world: assessment of water productivity in 10 major river basins. Water Int 36: 42-62.
24. Calus MPL, Meuwissen THE, Roos APW, Veerkamp RF (2008) Accuracy of genomic selection using different methods to define haplotypes. Genetics 178: 553-561.
25. Campos H, Cooper M, Habben J, Edmeades G, Schussler J (2004) Improving drought tolerance in Maize: a view from industry. Field Crops Res 90: 19-34.
26. Canaran P, Buckler ES, Glaubitz JC, Stein L, Sun Q, Zhao W, Ware D (2008) Panzea: an update on new content and features. Nucleic Acids Res 36: D1041-D1043.
27. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11: 215-221.
28. Chen C, DeClerck G, Casstevens T, Youens-Clark K, Zhang J, Ware D, Jaiswal P, McCouch S, Buckler E (2010) The gramene genetic diversity module: a resource for genotype-phenotype association analysis in grass species. Nature Precedings doi: 10101/npre. 2010. 4645. 1.
29. Chen H, He H, Zou Y, Chen W, Yu R, Liu X, Yang Y, Gao YM, Xu JL, Fan LM, Li Y, Li ZK, Deng XW (2011) Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of Rice (Oryza sativa L.). Theor Appl Genet doi. doi: 10. 1007/s00122-011-1633-5.
30. Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV (2011) Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 156: 455-465.
31. Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV (2012) High-throughput two dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environ doi. doi: 10. 1111/j. 1365-3040. 2012. 02587. x.
32. Clarke JM, DePauw RM, Townley-Smith TF (1992) Evaluation of methods for quantification of drought tolerance in wheat. Crop Sci 32: 723-728.
33. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363: 557-572.
34. Crouch J, Payne T, Dreisigacker S, Wu H, Braun H (2009) Improved discovery and utilization of new traits for breeding. In: Dixon JM (ed) Wheat facts and futures 2009. CIMMYT, Mexico, pp 42-51.
35. Czyczyło-Mysza I, Marcińska I, Skrzypek E, Chrupek M, Grzesiak S, Hura T, Stojałowski S, Myśków B, Milczarski P, Quarrie S (2011) Mapping QTLs for yield components and chlorophyll a fluorescence parameters in wheat under three levels of water availability. Plant Gen Res 9: 291-295.
36. De Boever J, De Brabander D, De Smet A, Vanacker J, Boucqué CV (1993) Evaluation of physical structure. 2. Maize silage. J Dairy Sci 76: 1624-1634.
37. Dickerson G (1955) Genetic slippage in response to selection for multiple objectives. Cold Spring Harb Symp Quant Biol 20: 213-224.
38. Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid Rice. Proc Natl Acad Sci 109: 2654-2659.
39. Dodig D, Zoric M, Kobiljski B, Savic J, Kandic V, Quarrie S, Barnes J (2012) Genetic and association mapping study of wheat agronomic traits under contrasting water regimes. Int J Mol Sci 13: 6167-6188.
40. Dornbusch T, Andrieu B (2010) Lamina2Shape-an image processing tool for an explicit description of lamina shape tested on winter wheat (Triticum aestivumL.). Comput Electron Agric 70: 217-224.
41. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.
42. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE (2012) The mouse genome database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 40: D881-D886.
43. Famoso AN, Clark RT, Shaff JE, Craft E, McCouch SR, Kochian LV (2010) Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into Rice aluminum tolerance mechanisms. Plant Physiol 153: 1678-1691.
44. Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in Rice, encodes a putative transmembrane protein. Theor Appl Genet 112: 1164-1171.
45. Ferguson ME, Hearne SJ, Close TJ, Wanamaker S, Moskal WA, Town CD, de Young J, Marri PR, Rabbi IY, de Villiers EP (2011) Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava. Theor Appl Genet. doi: 10. 1007/s00122-011-1739-9.
46. Fernie AR, Schauer N (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends Genet 25: 39-48.
47. Foolad MR, Panthee DR (2012) Marker-assisted selection in Tomato breeding. Crit Rev Plant Sci 31: 93-123.
48. French A, Ubeda-Tomás S, Holman TJ, Bennett MJ, Pridmore T (2009) High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiol 150: 1784-1795.
49. Frison E, Cherfas J, Hodgkin T (2011) Agricultural biodiversity is essential for a sustainable improvement in food and nutrition security. Sustainability 3: 238-253.
50. Fukuoka S, Nonoue Y, Yano M (2010) Germplasm enhancement by developing advanced plant materials from diverse Rice accessions. Breed Sci 60: 509-517. doi: 10. 1270/jsbbs. 60. 509.
51. Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, Topp CN, Iyer-Pascuzzi AS, Zurek PR, Fang S (2012) GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biol 12: 116.
52. Gelman A, Hill J (2007) Data analysis using regression and multilevel/hierarchical models. Cambridge University Press, New York.
53. Gelman A, Carlin JB, Stern HS, Rubin DB (2003) Bayesian data analysis. Chapman & Hall CRC Press, New York.
54. Ghimire KH, Quiatchon LA, Vikram P, Swamy B, Dixit S, Ahmed H, Hernandez JE, Borromeo TH, Kumar A (2012) Identification and mapping of a QTL (qDTY1. 1) with a consistent effect on grain yield under drought. Field Crops Res 131: 88-96.
55. Gilbert ME, Zwieniecki MA, Holbrook NM (2011) Independent variation in photosynthetic capacity and stomatal conductance leads to differences in intrinsic water use efficiency in 11 soybean genotypes before and during mild drought. J Exp Bot 62: 2875-2887.
56. Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK (2010) Accessing genetic diversity for crop improvement. Curr Opin Plant Biol. doi: 10. 1016/j. pbi. 2010. 01. 004.
57. Golabadi M, Arzani A, Mirmohammadi Maibody SAM, Sayed Tabatabaei B, Mohammadi S (2011) Identification of microsatellite markers linked with yield components under drought stress at terminal growth stages in durum wheat. Euphytica 177: 207-221.
58. Goltsev V, Zaharieva I, Chernev P, Kouzmanova M, Kalaji HM, Yordanov I, Krasteva V, Alexandrov V, Stefanov D, Allakhverdiev SI (2012) Drought-induced modifications of photosynthetic electron transport in intact leaves: analysis and use of neural networks as a tool for a rapid non-invasive estimation. Biochim Biophys Acta 1817: 1490-1498.
59. Golzarian MR, Frick RA, Rajendran K, Berger B, Roy S, Tester M, Lun DS (2011) Accurate inference of shoot biomass from high-throughput images of cereal plants. Plant Methods 7: 2.
60. Gordon D, Finch SJ (2005) Factors affecting statistical power in the detection of genetic association. J Clin Invest 115: 1408-1418.
61. Granier C, Aguirrezabal L, Chenu K, Cookson SJ, Dauzat M, Hamard P, Thioux JJ, Rolland G, Bouchier-Combaud S, Lebaudy A (2006) PHENOPSIS, an automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit. New Phytol 169: 623-635.
62. Grant D, Nelson RT, Cannon SB, Shoemaker RC (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res 38: D843-D846.
63. Greenberg AJ, Hackett SR, Harshman LG, Clark AG (2010) A hierarchical Bayesian model for a novel sparse partial Diallel crossing design. Genetics 185: 361-373.
64. Greenberg AJ, Hackett SR, Harshman LG, Clark AG (2011) Environmental and genetic perturbations reveal different networks of metabolic regulation. Mol Syst Biol 7: 563.
65. Guo Z, Tucker DM, Lu J, Kishore V, Gay G (2012) Evaluation of genome-wide selection efficiency in Maize nested association mapping populations. Theor Appl Genet 124: 261-275.
66. Hartmann A, Czauderna T, Hoffmann R, Stein N, Schreiber F (2011) HTPheno: an image analysis pipeline for high-throughput plant phenotyping. BMC Bioinforma 12: 148.
67. Hayes B, Bowman P, Chamberlain A, Goddard M (2009) Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92: 433-443.
68. Heffner EL, Sorrells ME, Jannink J (2009) Genomic selection for crop improvement. Crop Sci 49: 1-12.
69. Heffner EL, Jannink J, Sorrells ME (2010) Genomic selection accuracy using multifamily prediction models in a wheat breeding program. The Plant Genome 4: 65-75.
70. Herridge RP, Day RC, Baldwin S, Macknight RC (2011) Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery. Plant Methods 7: 3.
71. Heslot N, Sorrells ME, Jannink JL, Yang HP (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52: 146-160.
72. Houle D, Govindaraju DR, Omholt S (2010) Phenomics: the next challenge. Nat Rev Genet 11: 855-866.
73. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in Rice landraces. Nat Genet 42: 961-967.
74. Huang X, Paulo MJ, Boer M, Effgen S, Keizer P, Koornneef M, van Eeuwijk FA (2011) Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc Natl Acad Sci 108: 4488-4493.
75. Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J 10: 826-839.
76. Hyten D, Song Q, Fickus E, Quigley C, Lim J, Choi I, Hwang E, Pastor-Corrales M, Cregan P (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics. doi: 10. 1186/1471-2164-11-475.
77. Ibrahim S, Schubert A, Pillen K, Léon J (2012) QTL analysis of drought tolerance for seedling root morphological traits in an advanced backcross population of spring wheat. Int J AgriSci 2: 619-629.
78. International Rice Research Institute (1996) Standard evaluation system for Rice.
79. Iwata H, Ukai Y (2002) SHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. J Hered 93: 384-385.
80. Iwata H, Ebana K, Uga Y, Hayashi T, Jannink JL (2010) Genome-wide association study of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis. Mol Breed 25: 203-215.
81. Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M (2005) Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp Funct Genomics 6: 388-397.
82. Jansen M, Gilmer F, Biskup B, Nagel KA, Rascher U, Fischbach A, Briem S, Dreissen G, Tittmann S, Braun S (2009) Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance in Arabidopsis thaliana and other rosette plants. Funct Plant Biol 36: 902-914.
83. Jia Y, Jannink JL (2012) Multiple-trait genomic selection methods increase genetic value prediction accuracy. Genetics 192: 1513-1522.
84. Jin L, Lu Y, Shao Y, Zhang G, Xiao P, Shen S, Corke H, Bao J (2010) Molecular marker assisted selection for improvement of the eating, cooking and sensory quality of Rice (Oryza sativa L.). J Cereal Sci 51: 159-164.
85. Juliette F, Myriam D, Vincent N, Nathalie W, Emilie G, Pascal N, Sébastien T, Catherine M, Irène H, Christine G (2011) PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. BMC Plant Biol 11: 77.
86. Kahraman A, Avramov A, Nashev LG, Popov D, Ternes R, Pohlenz HD, Weiss B (2005) PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics. Bioinformatics 21: 418-420.
87. Kholová J, Hash CT, Kakkera A, Kočová M, Vadez V (2010) Constitutive water-conserving mechanisms are correlated with the terminal drought tolerance of pearl millet [Pennisetum glaucum (L.) R. Br.]. J Exp Bot 61: 369-377.
88. Kloth KJ, Thoen MPM, Bouwmeester HJ, Jongsma MA, Dicke M (2012) Association mapping of plant resistance to insects. Trends Plant Sci 17: 311-319.
89. Krattinger S, Wicker T, Keller B (2009) Map-based cloning of genes in Triticeae (Wheat and Barley). Genet Genomics Triticeae 7: 337-357.
90. Kuhn C, Smith T (1977) Effectiveness of a disease index system in evaluating corn for resistance to Maize dwarf mosaic virus. Phytopathology 67: 288-291.
91. Kumar S, Bink MCAM, Volz RK, Bus VGM, Chagné D (2012) Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: prospects, challenges and strategies. Tree Genet Genomes 8: 1-14.
92. Lai K, Lorenc MT, Edwards D (2012) Genomic databases for crop improvement. Agronomy 2: 62-73.
93. Landi P, Giuliani S, Salvi S, Ferri M, Tuberosa R, Sanguineti MC (2010) Characterization of root-yield-1. 06, a major constitutive QTL for root and agronomic traits in Maize across water regimes. J Exp Bot 61: 3553-3562.
94. Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C (2008) Oryza tag line, a phenotypic mutant database for the genoplante Rice insertion line library. Nucleic Acids Res 36: D1022-D1027.
95. Le Bot J, Serra V, Fabre J, Draye X, Adamowicz S, Pagès L (2010) DART: a software to analyse root system architecture and development from captured images. Plant Soil 326: 261-273.
96. Lee TB, Hendler J, Lassila O (2001) The semantic web. Sci Am 284: 34-43.
97. Lenarcic AB, Svenson KL, Churchill GA, Valdar W (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190: 413-435.
98. Li Q, Yang X, Bai G, Warburton ML, Mahuku G, Gore M, Dai J, Li J, Yan J (2010) Cloning and characterization of a putative GS3 ortholog involved in Maize kernel development. Theor Appl Genet 120: 753-763.
99. Liu S, Pumphrey MO, Gill BS, Trick HN, Zhang JX, Dolezel J, Chalhoub B, Anderson JA (2008) Toward positional cloning of Fhb1, a major QTL for Fusarium head blight resistance in wheat. Cereal Res Commun 36: 195-201.
100. Liu Y, Subhash C, Yan J, Song C, Zhao J, Li J (2011) Maize leaf temperature responses to drought: thermal imaging and quantitative trait loci (QTL) mapping. Environ Exp Bot 71: 158-165.
101. Lobet G, Pagès L, Draye X (2011) A novel image-analysis toolbox enabling quantitative analysis of root system architecture. Plant Physiol 157: 29-39.
102. Loehlin DW, Oliveira DCSG, Edwards R, Giebel JD, Clark ME, Cattani MV, van de Zande L, Verhulst EC, Beukeboom LW, Muñoz-Torres M (2010) Non-coding changes cause sex-specific wing size differences between closely related species of Nasonia. PLoS Genet 6: e1000821.
103. Lopes MS, Araus JL, van Heerden PDR, Foyer CH (2011) Enhancing drought tolerance in C4 crops. J Exp Bot 62: 3135-3153.
104. Lu MY, Li XH, Shang AL, Wang YM, Xi ZY (2011) Characterization of a set of chromosome single-segment substitution lines derived from two sequenced elite Maize inbred lines. Maydica 56: 399-407.
105. Lunn D, Spiegelhalter D, Thomas A, Best N (2009) The BUGS project: evolution, critique and future directions. Stat Med 28: 3049-3067.
106. Lynch M, Walsh B (1997) Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland.
107. Mabee P, Balhoff J, Dahdul W, Lapp H, Midford P, Vision T, Westerfield M (2012) 500, 000 fish phenotypes: the new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. J Appl Ichthyol 28: 300-305.
108. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L (2007) The NCBI dbGaP database of genotypes and phenotypes. Nat Genet 39: 1181-1186.
109. Manolio TA, Collins FS (2009) The hapmap and genome-wide association studies in diagnosis and therapy. Annu Rev Med 2009(60): 443-456.
110. Masuka B, Araus JL, Das B, Sonder K, Cairns JE (2012) Phenotyping for abiotic stress tolerance in Maize. J Integr Plant Biol 54: 238-249.
111. Maughan P, Smith S, Fairbanks D, Jellen E (2011) Development, characterization, and linkage mapping of single nucleotide polymorphisms in the grain Amaranthus (Amaranthus sp.). The Plant Genome 4: 92-101.
112. McCouch SR, McNally KL, Wang W, Sackville Hamilton R (2012) Genomics of gene banks: a case study in Rice. Am J Bot 99: 407-423.
113. Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) In silico screening of a saturated mutation library of Tomato. Plant J 38: 861-872.
114. Messmer R, Fracheboud Y, Bänziger M, Vargas M, Stamp P, Ribaut JM (2009) Drought stress and tropical Maize: QTL-by-environment interactions and stability of QTLs across environments for yield components and secondary traits. Theor Appl Genet 119: 913-930.
115. Mir RR, Zaman-Allah M, Sreenivasulu N, Trethowan R, Varshney RK (2012) Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theor Appl Genet 125: 625-645.
116. Mitchell SE, Casa AM, Tuinstra MR, Brown PJ, Pressoir G, Rooney WL, Franks CD, Kresovich S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci 48: 30-40.
117. Molina-Cano J (1987) The EEC Barley and Malt Committee index for the evaluation of malting quality in Barley and its use in breeding. Plant Breed 98: 249-256.
118. Montes JM, Melchinger AE, Reif JC (2007) Novel throughput phenotyping platforms in plant genetic studies. Trends Plant Sci 12: 433-436.
119. Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. PNAS 110(2): 453-458. doi: 10. 1073/pnas. 1215985110.
120. Munoz P, Resende M, Peter G, Huber D, Kirst M, Quesada T (2011) Effect of BLUP prediction on genomic selection: practical considerations to achieve greater accuracy in genomic selection. BMC Proc 5: 49.
121. Naeem A, French AP, Wells DM, Pridmore TP (2011) High-throughput feature counting and measurement of roots. Bioinformatics 27: 1337-1338.
122. Nagel KA, Putz A, Gilmer F, Heinz K, Fischbach A, Pfeifer J, Faget M, Blossfeld S, Ernst M, Dimaki C (2012) GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons. Funct Plant Biol 39(11): 891-904.
123. Nakaya A, Isobe SN (2012) Will genomic selection be a practical method for plant breeding? Ann Bot 110: 1303-1316. doi: 10. 1093/aob/mcs229.
124. National Science Foundation (2011) Phenomics: genotype to phenotype, a report of the NIFA-NSF phenomics workshop.
125. Neumann K (2013) Using automated high-throughput phenotyping using the LemnaTec Imaging Platform to visualize and quantify stress influence in Barley. PAG XXI, San Diego.
126. Neumann K, Kobiljski B, Denčić S, Varshney R, Börner A (2011) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed 27: 37-58.
127. Ogburn R, Edwards EJ (2012) Quantifying succulence: a rapid, physiologically meaningful metric of plant water storage. Plant Cell Environ 35: 1533-1542.
128. Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world wide spring Barley collection. BMC Plant Biol 12: 16. doi: 10. 1186/1471-2229-12-16.
129. Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8: 196-210.
130. Pereyra-Irujo GA, Gasco ED, Peirone LS, Aguirrezábal LAN (2012) GlyPh: a low-cost platform for phenotyping plant growth and water use. Funct Plant Biol 39: 905-913.
131. Perlin MW, Lancia G, Ng SK (1995) Toward fully automated genotyping: genotyping microsatellite markers by deconvolution. Am J Hum Genet 57: 1199.
132. Pieruschka R, Poorter H (2012) Phenotyping plants: genes, phenes and machines. Funct Plant Biol 39: 813-820.
133. Plummer M (2003) JAGS: a program for analysis of Bayesian graphical models using Gibbs sampling. In: Proceedings of the 3rd international workshop on distributed statistical computing. http://citeseer. ist. psu. edu/plummer03jags. html.
134. Poland J, Nelson R (2010) In the eye of the beholder: the effect of rater variability and different rating scales on QTL mapping. Phytopathology. doi: 10. 1094/PHYTO-03-10-0087.
135. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genet 38(8): 904-909. doi: 10. 1038/ng1847.
136. Price CA, Symonova O, Mileyko Y, Hilley T, Weitz JS (2011) Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles. Plant Physiol 155: 236-245.
137. Pritchard JK, Cox NJ (2002) The allelic architecture of human disease genes: common disease-common variant... or not? Hum Mol Genet 11(20): 2423-2427.
138. Pypers P, Sanginga JM, Kasareka B, Walangululu M, Vanlauwe B (2011) Increased productivity through integrated soil fertility management in cassava-legume intercropping systems in the highlands Sud-Kivu DR Congo. Field Crops Res 120: 76-85.
139. Rafalski JA (2010) Association genetics in crop improvement. Curr Opin Plant Biol 13: 174-180.
140. Rafalski JA, Tingey SV (1993) Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends Genet 9: 275-280.
141. Rakshit S, Rakshit A, Patil J (2012) Multiparent intercross populations in analysis of quantitative traits. J Genet 91: 111-117.
142. Rehman A, Malhotra R, Bett K, Tar'an B, Bueckert R, Warkentin T (2011) Mapping QTL associated with traits affecting grain yield in Chickpea (L.) under terminal drought stress. Crop Sci 51: 450-463.
143. Reich DE, Lander ES (2001) On the allelic spectrum of human disease. Trends Genet 17: 502-510.
144. Rengasamy P (2010) Osmotic and ionic effects of various electrolytes on the growth of wheat. Soil Res 48: 120-124.
145. Resende M Jr, Muñoz P, Resende MDV, Garrick DJ, Fernando RL, Davis JM, Jokela EJ, Martin TA, Peter GF, Kirst M (2012) Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.). Genetics 190: 1503-1510.
146. Reuzeau C, Frankard V, Hatzfeld Y, Sanz A, van Camp W, Lejeune P, De Wilde C, Lievens K, de Wolf J, Vranken E (2006) Traitmill™: a functional genomics platform for the phenotypic analysis of cereals. Plant Gen Res 4: 20.
147. Robbins MD, Massud Mohammed AT, Panthee DR, Gardner RG, Francis DM, Stevens MR (2010) Marker-assisted selection for coupling phase resistance to Tomato spotted wilt virus and Phytophthora infestans (late blight) in Tomato. Hort Sci 45: 1424-1428.
148. Saisho D, Takeda K (2011) Barley: emergence as a new research material of crop science. Plant Cell Physiol 52: 724-727.
149. Saito K, Hayano-Saito Y, Kuroki M, Sato Y (2010) Map-based cloning of the Rice cold tolerance geneCtb1. Plant Sci 179: 97-102.
150. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, Meeley R, Ananiev EV, Svitashev S, Bruggemann E (2007) Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in Maize. Proc Natl Acad Sci 104: 11376-11381.
151. Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8: 552.
152. Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EKS, Sen TZ, Lawrence CJ (2011) MaizeGDB: curation and outreach go hand-in-hand. Database (Oxford). doi: 10. 1093/database/bar022.
153. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9: 671-675.
154. Schuster I (2011) Marker-assisted selection for quantitative traits. CBAB 11: 50-55.
155. Sheffield VC, Nishimura DY, Stone EM (1995) Novel approaches to linkage mapping. Curr Opin Genet Dev 5: 335-341.
156. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251-1255.
157. Smýkal P, Aubert G, Burstin J, Coyne CJ, Ellis NTH, Flavell AJ, Ford R, Hýbl M, Macas J, Neumann P, McPhee KE, Redden RJ, Rubiales D, Weller JL, Warkentin TD (2012) Pea (Pisum sativum L.) in the genomic era. Agronomy 2: 74-115.
158. Sorensen D, Gianola D (2002) Likelihood, Bayesian and MCMC methods in quantitative genetics. Springer, Berlin. doi: 10. 1007/b98952.
159. Steele K, Virk D, Kumar R, Prasad S, Witcombe J (2007) Field evaluation of upland Rice lines selected for QTLs controlling root traits. Field Crops Res 101: 180-186.
160. Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11: 207.
161. Swamy BPM, Vikram P, Dixit S, Ahmed H, Kumar A (2011) Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genomics 12: 319.
162. Tanabata T, Shibaya T, Hori K, Ebana K, Yano M (2012) SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis. Plant Physiol 160: 1871-1880.
163. Tavakkoli E, Rengasamy P, McDonald GK (2010) The response of Barley to salinity stress differs between hydroponic and soil systems. Funct Plant Biol 37: 621-633.
164. Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung C, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail AM, de Ocampo M, Mojica C, Reveche MY, Dilla-Ermita CJ, Mauleon R, Leung H, Bustamante C, McCouch SR (2011) High-throughput single nucleotide polymorphism genotyping for breeding applications in Rice using the BeadXpress platform. Mol Breed 29: 875-886. doi: 10. 1007/s11032-011-9663-x.
165. Trebbi D, Maccaferri M, de Heer P, Sorensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen EA, Tuberosa R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticumdurum Desf.). Theor Appl Genet doi. doi: 10. 1007/s00122-011-1607-7.
166. Tuberosa R (2012) Phenotyping for drought tolerance of crops in the genomics era. Front Physio 3: 347.
167. Tucker SS, Craine JM, Nippert JB (2011) Physiological drought tolerance and the structuring of tallgrass prairie assemblages. Ecosphere 2: art48.
168. Tung C, Zhao K, Wright MH, Ali ML, Jung J, Kimball J, Tyagi W, Thomson MJ, McNally K, Leung H, Kim H, Ahn S, Reynolds A, Scheffler B, Eizenga G, McClung A, Bustamante C, McCouch SR (2010) Development of a research platform for dissecting phenotype-genotype associations in Rice (Oryza spp.). Rice 3: 205-217. doi: 10. 1007/s12284-010-9056-5.
169. Valdar W, Flint J, Mott R (2006) Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172: 1783-1797.
170. van Ommen B, Bouwman J, Dragsted LO, Drevon CA, Elliott R, de Groot P, Kaput J, Mathers JC, Müller M, Pepping F (2010) Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. Genes Nutrition 5: 189-203.
171. Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR (2009) Orphan legume crops enter the genomics era! Curr Opin Plant Biol 12: 202-210.
172. Varshney RK, Glaszmann JC, Leung H, Ribaut JM (2010) More genomic resources for less-studied crops. Trends Biotechnol. doi: 10. 1016/j. tibtech. 2010. 06. 007.
173. Venuprasad R, Impa S, Gowda R, Atlin G, Serraj R (2011) Rice near-isogenic-lines (NILs) contrasting for grain yield under lowland drought stress. Field Crops Res 123: 38-46.
174. Venuprasad R, Bool M, Quiatchon L, Sta Cruz M, Amante M, Atlin G (2012) A large-effect QTL for Rice grain yield under upland drought stress on chromosome 1. Mol Breed 30: 535-547.
175. Vikram P, Swamy B, Dixit S, Ahmed H, Cruz MT, Singh A, Kumar A (2011) qDTY1. 1, a major QTL for Rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genet 12: 89.
176. Vision T, Blake J, Lapp H, Mabee P, Westerfield M (2011) Similarity between semantic description sets: addressing needs beyond data integration. LISC2011 783.
177. Wang L, Uilecan IV, Assadi AH, Kozmik CA, Spalding EP (2009) HYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis. Plant Physiol 149: 1632-1637.
178. Wang Z, Yu C, Liu X, Liu S, Yin C, Liu L, Lei J, Jiang L, Yang C, Chen L (2012) Identification of Indica Rice chromosome segments for the improvement of Japonica inbreds and hybrids. Theor Appl Genet 124: 1351-1364.
179. Weber JL, Broman KW (2001) 7 genotyping for human whole-genome scans: past, present, and future. Adv Genet 42: 77-96.
180. Weight C, Parnham D, Waites R (2007) TECHNICAL ADVANCE: LeafAnalyser: a computational method for rapid and large-scale analyses of leaf shape variation. Plant J 53: 578-586.
181. White JW, Andrade-Sanchez P, Gore MA, Bronson KF, Coffelt TA, Conley MM, Feldmann KA, French AN, Heun JT, Hunsaker DJ (2012) Field-based phenomics for plant genetics research. Field Crops Res 133: 101-112.
182. Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in Rice (Oryza sativa L.). BMC Genomics 11: 656. doi: 10. 1186/1471-2164-11-656.
183. Yadav RS, Sehgal D, Vadez V (2011) Using genetic mapping and genomics approaches in understanding and improving drought tolerance in pearl millet. J Exp Bot 62: 397-408.
184. Yazdanbakhsh N, Fisahn J (2009) High throughput phenotyping of root growth dynamics, lateral root formation, root architecture and root hair development enabled by PlaRoM. Funct Plant Biol 36: 938-946.
185. Yin X, Struik P (2008) Applying modeling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics. New Phytol 179: 629-642.
186. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
187. Yuan G, Luo Y, Sun X, Tang D (2004) Evaluation of a crop water stress index for detecting water stress in winter wheat in the North China Plain. Agric Water Manage 64: 29-40.
188. Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q, Wang S (2006) RMD: a Rice mutant database for functional analysis of the Rice genome. Nucleic Acids Res 34: D745-D748.
189. Zhang H, Zhao Q, Sun Z, Zhang C, Feng Q, Tang S, Liang G, Gu M, Han B, Liu Q (2011) Development and high-throughput genotyping of substitution lines carrying the chromosome segments of indica 9311 in the background of Japonica Nipponbare. J Genet Genomics 38: 603-611.
190. Zhao K, Tung C, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011a) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Com 2: 467.
191. Zhao Y, Gowda M, Liu W, Wurschum T, Maurer HP, Longin FH, Ranc N, Reif JC (2011b) Accuracy of genomic selection in European Maize elite breeding populations. Theor Appl Genet. doi: 10. 1007/s00122-011-1745-y.
192. Zhong S, Dekkers JCM, Fernando RL, Jannink JL (2009) Factors affecting accuracy from genotypic selection in populations derived from multiple inbred lines: a Barley case study. Genetics 182: 355-364.
193. Zhou H, Liu Q, Li J, Jiang D, Zhou L, Wu P, Lu S, Li F, Zhu L, Liu Z (2012) Photoperiod-and thermo-sensitive genic male sterility in Rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res 22: 649-660.
194. Zhu D, Deng XW (2012) A non-coding RNA locus mediates environment-conditioned male sterility in Rice. Cell Res 22: 791-792.
195. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. The Plant Genome 1: 5-20.
196. Zhu J, Ingram PA, Benfey PN, Elich T (2011a) From lab to field, new approaches to phenotyping root system architecture. Curr Opin Plant Biol 14: 310-317.
197. Zhu J, Wang X, Sun C, Zhu X, Li M, Zhang G, Tian Y, Wang Z (2011b) Mapping of QTL associated with drought tolerance in a semi-automobile rain shelter in Maize (Zea mays L.). Agric Sci China 10: 987-996.
198. Zia S, Romano G, Spreer W, Sanchez C, Cairns J, Araus J, Müller J (2012) Infrared thermal imaging as a rapid tool for identifying water-stress tolerant Maize genotypes of different phenology. J Agron Crop Sci. doi: 10. 1111/j. 1439-037X. 2012. 00537. x.