Genomics and plant breeding

Biotechnology Annual Review

Volumn 7, Issue , 2001, Pages 195-238

  Aljanabi, Salah ^a  

^a Mauritius Sugar Industry Research Institute   (Mauritius)

Author keywords

AFLP; Arabidopsis; Bacterial artificial chromosome (BAC); cDNA; Cloning; Expressed sequence Tags (ESTs); Genetic diversity; Genetic mapping; Genomics; Maize; Marker assisted selection (MAS); Molecular markers; P1 derived artificial chromosome (PAC)

Indexed keywords

COMPLEMENTARY DNA; MOLECULAR MARKER;

AGRICULTURE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANGIOSPERM; ARABIDOPSIS; BACTERIAL ARTIFICIAL CHROMOSOME; BARLEY; BIOINFORMATICS; COMPARATIVE GENE MAPPING; COTTON; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DISTANCE; GENETIC ENGINEERING; GENETIC LINKAGE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; LEGUME; LINKAGE ANALYSIS; MAIZE; MARKER ASSISTED BREEDING; MOLECULAR CLONING; MUTAGENESIS; PHILADELPHIA 1 CHROMOSOME; PLANT BIOTECHNOLOGY; PLANT BREEDING; PLANT GENETICS; POACEAE; RANDOM AMPLIFIED POLYMORPHIC DNA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; RICE; RYE; SERIAL ANALYSIS OF GENE EXPRESSION; SORGHUM; SOYBEAN; SUGARCANE; TANDEM REPEAT; TRANSPOSON; WHEAT; YEAST ARTIFICIAL CHROMOSOME; BIOTECHNOLOGY; BREEDING; CHROMOSOME MAP; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENETIC MARKER; GENETICS; PLANT;

ARABIDOPSIS; ZEA MAYS;

AGRICULTURE; BIOTECHNOLOGY; BREEDING; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, ARTIFICIAL, YEAST; CLONING, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENETIC ENGINEERING; GENETIC MARKERS; GENOMICS; LINKAGE (GENETICS); MUTAGENESIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANTS, EDIBLE;

EID: 0035236928     PISSN: 13872656     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1387-2656(01)07038-7     Document Type: Article

References (232)

1. Murray DR (ed). Advanced Methods in Plant Breeding and Biotechnology. CAB International 1991;1-22.
2. Perera A. Plant genomics is revolutionizing agricultural research. Biotechnology and Development Monitor 1999;40:2-7.
3. Ahn S, Tanksley SD. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA. 1993;90:(17)7980-7984.
4. Melchinger AE, Graner A, Singh M, Messmer MM. Relationship among European barley germplasm: I. Genetic diversity among winter and spring cultivars revealed by RFLPs. Crop Sci 1994;34:1191-1199.
5. Smith S, Beavis W. Molecular Markers assisted breeding in a company environment. In: Sobral BWS (ed) The Impact of Plant Molecular Genetics. Birkhäuser, 1996.
6. Daly JL. The Green House Trap. Sydney, Australia: Bantam Books Transworld Publishers, Pty, Ltd, 1989.
7. Schneider S. Prudent planning for a warmer planet. New Scientist 1990;128:39-41.
8. Worrest RC, Caldwell MM. Stratospher Ozone Reduction, Solar Ultraviolate Radiation and Plant life. Berlin: Springer, 1986.
9. Phillips RL, Freeling M. Plant genomics and our food supply: An introduction. Proc Natl Acad Sci USA 1998;95(5):1969-1970.
10. Wirtz UF, Zhang P, Baker B, Ronning C, Buell RC, Tanksley S, Fry W, Helgeson J, Jiang J, May G. Tools for potato structural and functional genomics. Abstract, Plant and Animal Genome VIII Meeting, San Diego, 2000.
11. Burke DT, Carie G, Olsen MV. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 1987;236:806-812.
12. Anderson C. Genome shortcut leads to problems. Science 1993;259:1684-1687.
13. Burke DT. YAC cloning: options and problems. GATA 1990;7:94-99.
14. Green ED, Riethman HC, Dutchik JE, Olson MV. Detection and characterization of chimeric yeast artificial-chromosome clones. Genomics 1991;11:658-669.
15. Venter JC, Smith HO and Hood L. A new strategy for genome sequencing. Nature 1996;381:364-366.
16. Cai W-W, Reneker J, Chow C-W, Vaishnav M, Bradley A. An anchored framework BAC map of mouse chromosome 11 assembled using multiplex oligonucleotide hybridization. Genomics 1998;54:387-397.
17. O'Connor M., Peifer M, Bender W. Construction of large DNA segments in Escherichia coli. Science 1989;244:1307-1312.
18. Woo S-S, Jiang J, Gill BS, Paterson AH, Wing RA. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 1994;22:4922-4931.
19. Shizuya H, Birren B, Kim, U-J, Mancino V, Slepak, T, Tachiiri Y. Simon M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 1992;89:8794-8797.
20. Morisson M, Pitel F, Fillon V, Pouzadoux A, Berge R, Vit JP, Zoorob R, Auffray C, Gellin J, Vignal A. Integration of chicken cytogenetic and genetic maps: 18 new polymorphic markers isolated from BAC and PAC clones. Anim Genet 1998;29348-355.
21. Choi S, Wing RA. The Construction of bacterial artificial chromosome (BAC) libraries. In: Gelvin S, Schilperoort R (eds) Plant Molecular Biology Manual, 2nd Edition, Suppl. IV. The Netherlands: Kluwer Academic Publishers, 1999;1-32.
22. Yang D, Parco A, Nandi S, Subudhi P, Zhu Y, Wang G, Huang N. Construction of a bacterial artificial chromosome (BAC) library and identification of overlapping BAC clones with chromosome 4-specific RFLP markers in rice. Theor Appl Genet 1997;95:1147-1154.
23. Tomkins JP, Mahalingham R, Miller-Smith H, Goicoechea JL, Knapp HT, Wing RA. A soybean bacterial artificial chromosome library for PI 437654 and the identification of clones associated with cyst nematode resistance. Plant Mol Biol 1999;41:25-32.
24. Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing RA. A bacterial artificial chromosome library for sugarcane. Theor Appl Genet 1999;99:419-424.
25. Kim U-J, Birren BW, Slepak T, Mancino V, Boysen C, Kang H-L, Simon MI, Shizuya H. Construction and characterization of a human bacterial artificial chromosome library. Genomics 1996;34:213-218.
26. Boysen C, Simon MI, Hood L. Fluorescence-based sequencing directly from bacterial and P1-derived artificial chromosomes. BioTechniques, 1997;23:978-982.
27. Willetts N, Skurray R. Structure and function of the F factor and mechanism of conjugation. In: Neidhardt FC (ed) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society for Microbiology, Washington DC, 1987; Vol. 2:1110-1133.
28. Paterson AH (ed). Genome Mapping in Plants. Academic Press Inc., 1996.
29. Marra MA, Kucaba TA, Dietrich NJ, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterso RH. High throughput fingerprint analysis of large-insert clones. Genome Res 1997;7:1072-1084.
30. Kelley JM, Field CE, Craven MB, Bocskai D, Kim U-J, Rounsley SD, Adams MD. High throughput direct end sequencing of BAC clones. Nucleic Acids Res 1999;27:1539-1546.
31. Wang G-L, Warren R, Innes R, Osborne B, Baker B, Ronald PC. Construction of an Arabidopsis BAC library and isolation of clones hybridizing with disease-resistance, gene-like sequences. Plant Mol Biol Reptr 1996;14:107-114.
32. Frijters AC, Zhang Z, van Damme M, Wang G-L, Ronald PC, Michelmore RW. Construction of a bacterial artificial chromosome library containing large EcoRI and HindIII genomic fragments of lettuce. Theor Appl Genet 1997;94:390-399.
33. Marec LF, Shoemaker RC. BAC contig development by fingerprint analysis in soybean. Genome 1997;40:420-427.
34. Nakamura S, Asakawa S, Ohmido N, Fukui K, Shimizu N, Kawasaki S. Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta2 using a highly representative rice BAC library. Mol Gen Genet 1997;254:611-620.
35. Danesh D, Penula S, Mudge J, Denny RL, Nordstrom H, Martinez JP, Young ND. A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theor Appl Genet 1998;96:196-202.
36. Vinatzer BA, Zhang H-B, Sansavini S. Construction and characterization of a bacterial artificial chromosome library of apple. Theor Appl Genet 1998;97:1183-1190.
37. Moullet O, Zhang H-B, Lagudah ES. Construction and characterization of a large DNA insert library from the D genome of wheat. Theor Appl Genet 1999;99:305-313.
38. Nam Y-W, Penmesta RV, Endre G, Uribe P, Kim D, Cook DR. Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene-response genes. Theor Appl Genet 1999;98:638-646.
39. Salimath SS, Bhattacharyya MK. Generation of a soybean BAC library, and identification of DNA sequences tightly linked to the Rsp1-k disease resistance gene. Theor Appl Genet 1999;98:712-720.
40. Rosenblum BB, Lee LG, Spurgeon SL, Khan SH, Menchen SM, Heiner CR, Chen SM. New dye-labeled terminators for improved DNA sequencing patterns. Nucleic Acids Res 1997;25:4500-4504.
41. Venter JC, Adams MD, Sutton GG, Kerlavage AR, Smith HO, Hunkapiller M. Shotgun sequencing of the human genome. Science 1998;280:1540-1542.
42. Bouck J, Miller W, Gorrel JH, Muzny D, Gibbs RA. Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res 1998;8:1074-1084.
43. Soderlund C, Longden I, Mott R. FPC: A system for building contigs from restriction fingerprinted clones. CABIOS 1997;13:523-535.
44. Ding Y, Johnson MD, Colayco R, Chen YL, Melnyk J, Schmitt H, Shizuya H. Contig assembly of bacterial artificial chromosome clones through multiplexed fluorescence-labeled fingerprinting. Genomics 1999;56:237-246.
45. Folkertsma RT, Spassova MI, Prins M, Stevens MR, Hille J, Goldbach RW. Construction of a bacterial artificial library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus. Mol Breed 1999;5:197-207.
46. Patocchi A, Vinatzer, BA, Gianfranceschi L, Tartarini S, Zhang H-B, Sansavini S, Gessler C. Construction of a 550 kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf. Mol Gen Genet 1999;262:884-891.
47. Sanchez AC, Hag LL, Yang D, Brar DS, Ausubel F, Khush GS, Yano M, Sasaki T, Li Z, Huang N. Genetic and physical mapping of xa13, a recessive bacterial blight resistance gene in rice. Theor Appl Genet 1999;98:1022-1028.
48. Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet 1999;22:271-275.
49. Goss SJ, Harris H. New method for mapping genes in human chromosomes. Nature 1975;255:680-684.
50. Deloukas P, Schuler GD, Gyapay G, Beasley EM, Soderlund C, Rodriguez-Tome P, Hu, L, Matise TC, McKusick KB, Beckmann JS, et al. A physical map of 30,000 human genes. Science 1998;282:744-746.
51. Hudson TJ, Stein LD, Gerety SS, Ma J, Castle AB, Silva J, Slonim DK, Baptista R, Kruglyak L, Xu S-H, et al. An STS-based map of the human genome. Science 1995;270:1945-1954.
52. Hanson RE, Zwick MS, Choi, Islam-Faridi MN, McKnight TD, Wing RA, Price HJ, Stelly DM. Fluorescent in situ hybridization of a bacterial chromosome. Genome 1995;38:646-651.
53. Lapitan NLV, Brown SE, Kennard W, Stephens JL, Knudson DL. FISH physical mapping with barley BAC clones. Plant J 1997;11:149-156.
54. Gomez MI, Islam-Faridi MN, Woo S-S, Schertz KF, Czeschin Jr D, Zwick MS, Wing RA, Stelly DM, Price HJ. FISH of a maize sh2-selected sorghum BAC to chromosomes of Sorghum bicolor. Genome 1997;40:475-478.
55. Godard S, Oustry-Vaiman A, Cribiu EP, Guérin G. FISH mapping assignment of two horse BAC clones containing HMS41 and HTG3 microsatellites. Anim Genet 1999;30:233-239.
56. Peterson DG, Lapitan NLV, Stack SM. Localization of single- and low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH). Genetics 1999;152:427-439.
57. Gale MD, Devos KM. Comparative genetics in the grasses. Proc Natl Acad Sci USA 1998;95: 1971-1974.
58. Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D, and others. An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 1993;4:1051-1061.
59. Newman T, de Bruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M, and others. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 1994;106:1241-1255.
60. Cooke R, Raynal M, Laudié M, Grellet F, Delseny M, Morris PC, Guerrier D, Giraudat J, Quigley F, Clabault G, et al. Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J 1996;9:101-124.
61. Yamamot K, Song J, Kanamori H, et al. (24 other authors). Rice Genome Sequencing Progress at RGP Chromosomes 1 and 6. Rice genome forum VIII, 2000, Ibaraki, Japan.
62. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995;270:484-487.
63. Drmanac S, Drmanac R. Processing of cDNA and genomic kilobase-siz clones for massive screening, mapping and sequencing by hybridization. Biotechniques 1994;17:328-336.
64. Drmanac S, Stavropoulos NA, Labat I, Vonau J, Hauser B, Saores MB, Drmanac R. Gene-representing CDNA clusters defined by hybridization of 57,914 clones from infant brain libraries with short oligonucleotide probes. Genomics 1996;37:29-40.
65. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997;278:680-686.
66. Martienssen RA. Functional genomics: Probing plant gene function and expression with transposons. Proc Natl Acad Sci USA 1998;95:2021-2026.
67. Walbot V. Genes, Genomes, Genomics. What Can Plant Biologists Expect from the 1998 National Science Foundation Plant Genome Research Program. Plant Physiol 1999;119: 1151-1156.
68. Tanksley SD, Medina-Filho H, Rick CM. Use of naturally occurring enzyme variation to detect and map genes controlling quantitative traits in an interspecific backcross of tomato. Heredity 1982;49:11-25.
69. Weller JI. Mapping and analysis of quantitative trait loci in Lycopersicon (tomato) with the aid of genetic markers using approximate maximum likelyhood method. Heredity 1987;59:413-421.
70. Edwards M, Stuber CW, Wendel JF. Molecular-markers facilitate investigation of quantitative traits loci in maize: I. Numbers, genomic distribution and types of gene action. Genetics 1987;116:113-125.
71. Ragot M, Hoisington D. Molecular markers for plant breeding: comparison of RFLP and RAPD genotyping cost. Theor Appl Genet 1993;86:975-984.
72. Williams J, Kubelik A, Livak K, Rafalski J, Tingey S. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 1990;18:6531-6535.
73. Zabeau M, Vos P. Selective Restriction Fragment Amplification: a general method for DNA fingerprinting European Patent Application No 0534858 1993.
74. Nunberg A, Li Z, Thomas T. Analysis of gene expression and gene isolation by high-throughput sequencing of plant cDNA. In: Paterson A (ed) Genome Mapping in Plants. Academic Press, 1996;169-178.
75. Paterson AH. Mapping genes responsible for differences in phenotype In Paterson AH, (ed) Genome Mapping In Plants. Academic Press, 1996;41-54.
76. th ed, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993.
77. Schwarzacher T. Mapping Plants: progress and prospects. Current Opinion in Genetics and Development 1994;4:868-874.
78. Kuarata N, Nagamura Y, Yamomoto K, et al. A 300 kilobase interval genetic map of rice including 883 expressed sequence Nature Genetics 1994;8:365-372.
79. Dib C, Faure S, Fizanes C, Samson D, Drouo N, et al. comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 1996;380:152-154.
80. Schmidt R, West J, Love K, Lenehan Z, Lister C, Thompson H, Bouchez D, Dean C. Physical map and organization of Arabidopsis thaliana chromosome 4. Science 1995;270:885-891.
81. Moore G, Gale MD, Kurata N, Flavell RB. Molecular analysis of small grain cereal genomes: Current status and prospects. Bio/Technology 1993;11:584-589.
82. Paterson AH, Lin YR, Li Z, Schertzet KF, Doebley JF, Pinson SMR, Liu SC, Stansel A, Irvine JE. Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 1995;269:1714-1718.
83. Al-Shehbaz IA. The biosystematic of the genus Thelypodium (Cruciferae). Contribe Gray Herb Harv Univ 1973;204:3-148.
84. Hedge JC. A systematic and geographical survey of the old world Cruciferae In: MacLeod AJ, Jones BMJ (eds). The biology and chemistry of the Cruciferae London: Academic Press, 1976;1-46.
85. Song W, Wang B, Wang GL, et al. Construction of rice cosmid library and identification of five cosmid clones candidates bacterial blight resistance genes, Xa-21. Poster 218. Plant Genome III. San Diego, Calif. Jan. 15-19, 1995.
86. Chyi Y-S, Hoenecke ME, Sernyk JL. A genetic Linkage map of restriction fragment length polymorphisms loci for Brassica rapa (syn Compestris). Genome 1992;35:746-757.
87. Teutonico RA, Osborn TC. Mapping of RFLP and quantitative trait loci in Brassica rapa and comparison to the linkage maps of B napus, B oleracea and Arabidopsis thaliana. Theor Appl Genet 1994;89:885-894.
88. Langercrantz U, Lydiate DJ. RFLP mapping in Brassica nigra indicates differing recombination rates in male and female meiosis. Genome 1995;38:255-264.
89. Kianian SF, Quiros CF. Generation of a Brassica oleracea composite RFLP map: Linkage arrangements among various populations and evolutionary implications. Theor Appl Genet 1992;84:544-554.
90. Landry BS, Hubert N, Crete R. A genetic Linkage map of Brassica oleracea based on RFLP markers detected with expressed DNA sequence and mapping resistance genes to race 2 of pasmodiophora brassicae (Woronin). Genome 1992;35:409-419.
91. Landry BS, Hubert N, Etoh T. A genetic linkage map for Brassica napus based on restriction fragment length polymorphisms detected with expressed DNA sequences. Genome 1991;34:543-552.
92. Ferreira ME, Satagopan J, Yandell BS. RFLP mapping of Brassica napus using Double haploid lines. Theor Appl Genet 1994;89:615-21.
93. Uzunova M, Ecke W, Weissleder K. Mapping of the genome of rapeseed (Brassica napus L) I Construction of an RFLP linkage map and localization of QTLs for seed glucosinolate content. Theor Appl Genet 1995;90:194-204.
94. Ajisaka H, Kugnuki Y, Shiratori M, Ishiguro K, Enomoto S, Mirai M. Mapping of loci affecting the cultural efficiency of macrospore culture of Brassica napus L. syn Compestris L using DNA polymorphisms. Breeding Science 1999;49(3):187-192.
95. th Int Rape seed Cong GCIRC, Saskatoon 1991;1102-1107.
96. Kowalski SP, Lan T-H, Feldmann KA. Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics 1994;138:1-12.
97. Wing C, Landry BS. Current status of genome mapping in Cruciferae. In: Paterson AH (ed). Genome Mapping In Plants. Academic Press, 1996;193-227.
98. Lan T-H, DelMonte TA, Reischmann KP, Hyman J, Kowalski SP, McFerson J, Kresovich S, Paterson AH. An EST-enriched Comparative Map of Brassica oleracea and Arabidopsis thaliana. Genome Res 2000;10:(6)776-788.
99. Schaffer R, Landgraf J, Simon V, Accerbi M, Larson M, Green P, Wisman E. Genome wide analysis of Arabidopsis genes using DNA microarrays. Plant and Animal Genome VIII, San Diego, Calif. 2000.
100. Ku H-M, Vision T, Jiping Liu J, Tanksley SD. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny Proc. Natl. Acad. Sci. USA, 2000 97(16):9121-9126.
101. nd ed, Cambridge, UK: Cambridge University, 1991.
102. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Amer Journ Hum Genet 1980;32:314-331.
103. Akkaya MS, Bhagwat AA, Creg PB. Length polymorphisms of simple sequence repeats DNA in soybean. Genetics 1992;132:1131-1139.
104. Vos P, Hogers R, Bleeker M, Reijans M, van der Lee T, Homes M, Fritjters A, Pot J, Peleman J, Kuiper M, Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 1995;23:4407-4414.
105. Polhil RM, Raven PH. Advances in legume systematics. Kew, England: Royal Botanic Garden 1981.
106. Simmonds NW. Sugarcane. In: Simmonds NW (ed) Evolution of Crop Plants. Essex, UK: Longman Press, 1978;104-107.
107. Murray MG, Palmer JD, Cullar RE, Thompson WF. Deoxyribonucleic acid sequence organization in the mung bean genome. Biochemistry 1979;18:5259-5264.
108. Arumugnathan K, Earle E. Nuclear DNA content of some important plant species. Plant Molec Biol Report 1991;9:208-218.
109. Shoemaker R, Olsen TC. Molecular linkage map of soybean (Glycine max L. Merr) (2N = 40) In: O'Brien SJ (ed) Genetic Maps, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993;6 131-6 138.
110. Gepts P. Linkage map of common bean (Phaseolus vulgaris, L.) 2N = 22 In: O'Brien SJ (ed) Genetic Maps. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993.
111. Fatokun CA, Danesh D, Menancio-Hautea D, Young ND. A linkage map of cowpea (Vigna unguiculata L. Walp) based on DNA markers (2N = 22). In: O'Brien SJ (ed). Genetic Maps. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993.
112. Menancio-Hautea D, Kumar L, Danesh D, Young N. A genome map for mung bean (Vigna radiata L. Wilczek) based on DNA genetic markers (2N = 2X = 22) In: O'Brien SJ (ed) Genetic Maps. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993;6 256-6 258.
113. Lark KG, Weisemann JM, Matthews BF, Palmer R, Chase K, Macalma T. A genetic map of soybean (Glycine max L.) using an intraspecific cross of two cultivars: 'Minsoy' and 'Noir 1'. Theor Appl Genet 1993;86:901-906.
114. Shoemaker R, Specht J. Integration of the soybean molecular and classical genetic linkage groups. Crop Sci 1995;35:436-446.
115. Skorupska HT, Shoemaker RC, Warner A et al. Restriction fragment length polymorphism in soybean germplasm of the southern USA. Crop Sci 1993;33:1169-1176.
116. Lorenzen LL, Bout S, Young N, Specht JE, Shoemaker RC. Soybean pedigree analysis using map-based molecular markers. Crop Sci 1995;35:1326-1336.
117. Nodari RO, Tsai SM, Guzman P, Gilbertson RL, Gepts P. Toward an integrated linkage map of common bean 3 Mapping genetic factors controlling host bacteria interactions. Genetics 1993;134:341-350.
118. Vallejos CE, Sakiyama NS, Chase CD. A molecular marker-based linkage map of Phaseolus vulgaris L. Genetics 1992;131:733-740.
119. Kami J, Valasquez V, Debouck DG, Gept P. Identification of presumed ancestral DNA sequence of phasolin in Phaseolus vulgaris. Proc Natl Acad Sci USA 1995;92:1101-1104.
120. Boutin S, Young N, Olsen T, Yu ZH, Shoemaker R, Vallejos C. Genome conservation among three legume genera detected with DNA markers. Genome 1995;38:928-37.
121. Helenjaris T. Implication for conserved genomic structure among plant species. Proc Natl Acad Sci USA 1993;90:353-363.
122. Palmer JD, Osorio B, Aldrich J, Thompson WF. Chloroplast DNA evolution among legumes: loss of a large inverted repeats occurred prior to other sequence rearrangement. Curr Genet 1987;11:275-286.
123. Lavin M, Doyle JJ, Palmer JD. Evolutionary significance of the loss of the chloroplast-DNA inverted repeat in the Leguminosae subfamily Papilionoideae. Evolution 1990;44:390-402.
124. Bennet MD, Smith JB. Nuclear DNA amount in angiosperms. Phil Trans Royal Soc Lond B 1987;274:227-273.
125. Blixt S. The Pea. In: King RS (ed) Handbook of Genetics, Vol 2. New York: Plenum Press, 1975.
126. Weeden NF, Wolko B. Linkage map for the garden pea (Pisum sativum) based on molecular markers. In: O'Brien SJ (ed) Genetic Maps. Cold Spring Harbor Laboratory Press, 1990:6106-6112.
127. Ellis THN, Turner L, Hellens RP, Lee D, Harker CL, Enard C, Domoney C, Davies DR. Linkage map in pea. Genetics 1992;130:649-663.
128. Dirlewagner E, Isaac PG, Ranad S. Restriction fragment length polymorphism analysis of loci associated with disease resistance genes and developmental traits in Pisum sativum L. Theor Appl Genet 1994;88:17-27.
129. Weeden NF, Swiecicki WK, Timmerman GM, Ambrose M. Guidelines for future mapping studies in Pisum Pisum. Genetics 1993;25:13-14.
130. Kozik A, Matvienoko M, Scheres B, Paruvangada VG, Bisseling T, Kammen A, Van Ellis, THN, Laru T, Weeden N. The pea early nodulin gene PsEVDO7 maps in the region of linkage group I containing sym2 and leghaemoglobin. Plant Molecular Biology 1996;31:149-156.
131. Havey MJ, Muehlbauer FJ. Linkage between restriction fragment length, isozyme, and morphological markers in lentils. Theor Appl Genet 1989;77:395-401.
132. Simon CJ, Tahir M, Muehlhauer FJ. Linkage map of lentil (lens culinaris). In: O'Brien SJ (ed) Genetic Maps, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993;6 97-6 100.
133. Weeden NF, Muehlbaur FJ, Ladinzinsky G. Extensive conservation of linkage relationships exists between pea and lentil genetic maps. Journ Hered 1992;83:123-129.
134. Kazan K, Muehlbauer FJ, Weeden NF, Ladizinsky G. Inheritance and linkage relationships of morphological and isozyme loci in chickpea (Cicer arietinum L.). Theor Appl Genet 1993;86:417-426.
135. Young ND, Weeden NF, Kochert G. Genome mapping in legumes (Fam. Fabaceae). In: Paterson AH (ed). Genome Mapping In Plants. Academic Press, 1996;211-228.
136. Brummer EC, Bouton JH, Kochert G. Development of an RFLP map in diploid alfalfa. Theor Appl Genet 1993;86:329-332.
137. Kiss GB, Kereszt A, Kiss P, Endre G. Colormapping: A non-mathematical procedure for genetic mapping. Acta Biol Hun 1998;49:125-142.
138. Echt CS, Kidwel, KK, Knap SJ, Osborn TC, McCoy TJ. Linkage mapping in diploid alfalfa (Medicago sativa). Genome 1994;37:61-71.
139. Brouwer DJ, Osborn TC. A molecular marker linkage map of tetraploid alfalfa (Medicago sativa). Theor Appl Genet 1999;99:1194-1200.
140. Kaló P, Endre G, Zimányi L, Csanádi G, Kiss GB. Construction of an improved linkage map diploid alfalfa (Medicago Sativa). Theor Appl Genet 2000;100:641-657.
141. 2 populations. Theor Appl Genet 1995;95:81-98.
142. Landau-Ellis D, Angermuller S, Shoemaker R, Gresshoff P. The genetic locus controlling supernodulation in soybean (Glycine max L.) co-segregate tightly with a cloned molecular marker. Molec Gen Genet 1991;228:221-226.
143. Sauer J. Historical Geography of Crop Plants: A Select Roster Boca Raton, FL: CRC Press, 1993.
144. Wilson FD, Menzel MY. Kenaf (Hibiscus cannabinus), roselle (Hibiscus sabdariffa). Econ Bot 1964;18:80-91.
145. Beasley JO. Meiotic chromosome behaviour in species hybrids, haploids, and induced polyploids of Gossypium. Genetics 1942;27:25-54.
146. Endrizzi JE, Ramsay G. Monosomes and telosomes for 18 of the 26 chromosomes of Gossypium hirsutum. Can J Genet Cytol 1979;21:531-536.
147. Reinisch AJ, Dong J-M, Brubaker C, Stelly D, Wendel J, Paterson AH. A detailed RFLP map of cotton (Gossypium hirsutum x G. barbadense) chromosome organization and evolution in disomic polyploid genome. Genetics 1994;138:824-847.
148. Reyes-Valdes M, Stelly DM. A maximum likelihood algorithm for genome mapping of cytogenetic loci from meiotic configuration data. Proc Natl Acad Sci USA 1995;9824-9828.
149. Paterson AH, Lan TH, Reischmann KP, Chang C, Lin Y-R, Liu S-C, Burow MD, Kowalski SP, Katsar CS, DelMonte TA, Feldmann KA, Schertz KF, Wendel JF. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat Genet 1996;14:380-382.
150. Geever RF, Kattermann F, Endrizzi JE. Analysis of repetitive DNA in three species of Gossypium. Biochem Genet 1989;14:1071-1075.
151. Kellogg EA, Birchler JA. Linking phytogeny and genetics: Zea mays as a tool for phylogenetic studies. Syst Biol 1993;42:415-439.
152. Crepet WL, Feldman GD. The earliest remains of grasses in the fossil record. J. Bot 1991;78:1010-1014.
153. Clark, LG, Zhang W, Wendel JF. 1995. A phytogeny of the grass family (Poaceae) based on ndhF sequence data. Syst. Bot. 1995;20:436-460.
154. Chapman GP. The Biology of Grasses. Salisbury, UK: CAB international, 1996.
155. Bonierbale MW, Plaisted RL, Tanksley SD. RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 1988;120:1095-1103.
156. Helenjaris T, Slocum M, Wright S, Schaefer A, Nienhuis J. Construction of genetic map in maize and tomato using restriction fragment length polymorphisms. Theor Appl Genet 1986;72:761-769.
157. McCouh S. Toward a plant genomics initiative: Thoughts on the value of cross-species and cross-genera comparisons in the grasses. Proc Natl Acad Sci USA 1998;95(5):1983-1985.
158. Van Deynze AE, Sorrells ME, Park WD, Ayres NM, Fu H, Cartinhour SW, Paul E, McCouch SR. Anchor probes for comparative mapping of grass genera. Theor Appl Genet 1998;97:356-369.
159. Devos KM, Gale MD. The genetic maps of wheat and their potential in wheat breeding. Outlook Agric 1993;22:93-99.
160. Liu YG, Kawalski SP, Lan T-H, Feldmann KA, Paterson AH, genome-wide high resolution mapping by recurrent intermating, using Arabidopsis thaliana as a model. Genetics 1996;142:247-258.
161. Van Deynze AE, Dubcovsky J, Gill KS, et al. Molecular genetic maps for chromosome 1 in Triticeae species and their relation to chromosomes in rice and oats. Genome 1995;38:47-59.
162. Nelson JC, Sorrells ME, Van Deynze AE, et al. Molecular mapping of wheat. Major genes and rearrangements in homeologus group 4, 5 and 7. Genetics 1995;141:721-731.
163. Roeder M, Ganal M. Wheat Microsatellites - Development and Use in Gene Mapping and Germplasm Analysis. Rice genome forum VIII, Ibaraki Japan, 2000.
164. Heun M, Kennedy AE, Anderson JA, et al. Construction of restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 1991;34:437-447.
165. Sherman JD, Fenwick AL, Namuth DM, et al. A barley RFLP map: alignment of three barley maps and comparisons to Gramineae species. Theor Appl Genet 1995;91:681-690.
166. Ulrich SE, Genomics and malting quality of barley: A North America perspective. Abstract, Plant and Animal Genome Meeting VIII, San Diego Calif, 2000.
167. Naranjo T, Roca P, Goicoechea PG, et al. Arm Homoelogy of wheat and rye chromosomes. Genome 1987;29:873-882.
168. Rognli OA, Devos KM, Chinoy CN, et al. RFLP mapping of rye chromosome 7R reveals a highly translocated chromosome relative to wheat. Genome 1992;35:1026-1031.
169. Sasaki T. The rice genome project in Japan. Proc Natl Acad Sci USA 1998;95(5):2027-2028.
170. Umehara Y, Inagaki A, Tanoue H, et al. Construction and characterization of a rice YAC library for physical mapping. Molecular Breeding 1995;1:79-89.
171. Wang GL, Holsten TE, Song WY, et al. Construction of a rice bacterial artificial chromosome library and identification of clones linked to the Xa-21 disease resistance locus. Plant J 1995;7:525-533.
172. Zhang HB, Choi S, Woo SS, et al. Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Poster 276. Plant Genome III. San Diego Calif. Jan 15-19, 1995.
173. Wu J, Shimokawa T, Maehara T, Koike K, Umehara Y, Matsumoto T. Mapping Rice ESTs on YAC. Towards the establishment of comprehensive gene expression map. Rice genome 1997;6(1):2-3.
174. Yamamoto K, Sasaki T. Large scale EST sequencing in rice. Plant Molecular Biology 1997;35:135-144.
175. Shul GH, The genotypes of maize. Am Nat 1911;45:234-252
176. Creighton HS, McClintock B. A correlation of cytological and genetical crossing-over in Zea mays. Proc Natl Acad Sci USA 1931;17:492-497.
177. McClintock B. Mutable loci in maize. Carnegie Inst Wash 1948;47:21-36.
178. Burr B, Burr F, Thompson KH, Albertsen MC, Stuber CW. Gene mapping with recombinant inbreds in maize. Genetics 1988;118:519-526.
179. Beavis WD, Grant D. A linkage map based on information from four F2 populations of maize. Theor Appl Genet 1991;82:636-644.
180. Gardiner J, Coe EH, Melia-Hancock S, Hoisington DA, Chao S. Development of core RFLP map in maize using immortalized F2 population. Genetics 1993;134:917-930.
181. Polacco ML, Hancock D, Byrne P, Yerk-Davis G, Coe EH. Maize DB, an internet gateway to map-based information and tools. Proc Plant Genome IV, San Diego, Calif, 1996:108.
182. Davis GL, McMullen MD, Baysdorfer C, Musket T, Grant D, Staebell M, Xu G, Polacco M, Koster L, Melia-Hancock S, Houchins K, Chao S, Coe EH-Jr. A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 1999;152:1137-1172.
183. Kellogg EA. Relationships of cereal crops and other grasses. Proc Natl Acad Sci USA 1998;95:2005-2010.
184. Foote T, Roberts M, Kurata N, Sasaki T, Moore G. Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat. Genetics 1997;147:801-807
185. Springer PS, Edwards KJ, Bennetzen JL. DNA class organization on maize Adh1 yeast artificial chromosome. Proc Natl Acad Sci USA 1994;91:863-867.
186. Whitkus R, Doebley J, Lee M. Comparative genome mapping of sorghum and maize. Genetics 1992;132:119-130.
187. Ribaut J-M, Hoisington D. Current progress and approaches toward understanding the genes involved in drought tolerance in maize. Rice genome forum VIII, Ibaraki, Japan, 2000.
188. Rami J-F, Dufour P, Trouche G, Fliedel G, Mestres C, Davrieux F, Blanchard P, Hamon P. Quantitative trait loci for grain quality, productivity, morphological and agronomical traits in sorghum (Sorghum bicolor L. Moench). Theor Appl Genet 1998;97:605-616.
189. Binelli GL, Gianfanceschi L, Pe ME, Taramino G, Busso C, Stenhouse J, Ottaviano E. Similarity of maize and sorghum genomes as revealed by maize RFLP probes. Theor Appl Genet 1992;84:10-16.
190. Chittenden LM, Schertz KF, Lin YR, Wing RA, Paterson AH. A detailed RFLP map of Sorghum bicolor x S. propinquum, suitable for high-density mapping suggests ancestral duplication of sorghum chromosomes or chromosomal segments. Theor Appl Genet 1994;87:925-933.
191. Pereira MG, Lee M, Bramel Cox PJ, Woodman W, Doebley JF, Whitkus R. Construction of an RFLP map in sorghum and comparative mapping in maize. Genome 1994;37:236-243.
192. Koester RP, Sisco PH, Stuber CW. Identification of quantitative trait loci controlling days to flowering and plant height in two near isogenic lines of maize. Crop Sci 1993;33:1209-1216.
193. Chopra S, Brendel V, Zhang J, Axtell JD, Peterson T. Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor. Proc Natl Acad Sci USA 1999;96(26):15330-15335.
194. Bennetzen JL, SanMiguel P, Chen M, Tikhono A, Francki M, Zoya Avramova Z. Grass genomes. Proc Natl Acad Sci USA 1998;95(5):1975-1978.
195. Watson L, Clifford HT, Dallwitz MJ. The classification of the Poaceae: subfamilies and supertribes. Aust. J. Bot. 1985;33:433-484.
196. Clayton WD, Renvoize SA: Genera Graminum. Grasses of the World. KewBulletin Additional Series XIII, Royal Botanical Gardens, Kew, Her Majesty's Stationery Office, London, 1986.
197. Stebbins GL. Variation and evolution in plants. New York: Columbia University Press, 1950;495-520.
198. Soltis PS, Doyle JJ, Soltis DE. Molecular data and polyploid evolution in plants. In: Soltis PS, Soltis DE, Doyle JJ (eds). Molecular Systematics of Plants. New York, NY: Chapman and Hall, 1992;177-210.
199. Ritter E, Gebhart C, Salamini F. Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 1990;125:645-654.
200. Burnquist WB. Development and application of restriction fragment length polymorphism technology in sugarcane (Saccharum spp.) breeding. Ph.D. dissertation, Cornell University, Ithaca NY, 1991.
201. Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD. The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 1992;83:294-300.
202. Aljanabi SM, Honeycutt RJ, McClelland M, Sobral BWS. A genetic linkage map of Saccharum spontaneum (L.) 'SES 208'. Genetics, 1993;134:1249-1260.
203. Da Silva JG, Sorrels ME, Burnquist WL, Tanksley SD. RFLP linkage map of Saccharum spontaneum. Genome 1993;36:782-791.
204. Da Silva JG, Honeycutt RJ, Burnquist W, Aljanabi SM, Sorrels ME, Tanksley SD, Sobral BWS. Saccharum spontaneum L. 'SES 208' genetic linkage map combining RFLP and PCR-based markers, Mol Breed 1995;1:165-179.
205. Grivet L, D'Hont A, Roques D, Feldmann P, Lanaud C, Glaszmann JC. RFLP mapping in cultivated sugarcane (Saccharum spp.): Genome organization in a highly polyploid and aneuploid interspecific hybrid. Genetics 1996;142:987-1000.
206. Aljanabi SM, McClelland M, Peterson C, Sobral BWS. Phylogenetic analysis of organellar DNA sequence in the Saccharinae: Andropogoneae Theor Appl Genet 1993;88:933-944.
207. Grivet L, D'Hont A, Dufour P, Hamon P, Rouqes D, Glaszmann JC. Comparative genome mapping of sugarcane with other species within the Andropogoneae tribe. Heredity 1994;73:500-508.
208. Vettore AL, Kemper EL, Da Silva FR, Arruda P. Towards discovering the sugarcane genes. Plant and Animal Genome, San Diego, Calif, 2000.
209. Casu RE, Dimmock CM, Thomas MA, Grof CP, McIntyre L, Manners JM. Functional genomics for sucrose accumulation gene discovery in sugarcane. Plant and Animal Genome VIII, San Diego, Calif. 2000.
210. Pimental D, Harvey C, Resosudarmo P, Sinclair K, Kurz D, and others. Environmental and economic costs of soil erosion and conservation benefits. Science 1995;267:1117-1123.
211. Henry Rj. Practical Application of Plant Molecular Biology. Chapman & Hall, 1997.
212. Openshaw SJ, Jarboe SG, Beavis WD. Marker-assisted selection in backcross breeding. Analysis of Molecular Data Symposium. 1994 Aug 5-6; Corvallis, OR. Madison, WI: Crop Science Society of America.
213. Young ND, Tanksley SD. Graphic-based whole genome selection using RFLPs. In: Helentjaris T and Burr B (eds). Development and Application of molecular markers to problems in plant Genetics. Cold Spring Harbor, New York: Cold spring Harbor Laboratory Press, 1989;39-57.
214. Lee M. DNA markers and plant breeding programs. Advanc Agron 1995;55:265-344.
215. Shands HL, Wiesner LE. Use of Plant Introductions in Cultivar Development, Part 1. In: Shands HL and Wiesner LE (eds). Madison, WI: Crop Science Society of America, 1991.
216. Tanksley SD, Nelson JC. Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 1996;92:(2)191-203.
217. Bliss FA. Utilization of vegetable germplasm. Hortscience 1981;16:(2)129-132.
218. Rasmusson DC, Phillips RL. Plant breeding progress and genetic diversity from de novo variation and elevated epistasis. Crop Sci 1997;37:(2)303-331.
219. Stuber CW, Polacco M, Senior ML. Synergy of empirical breeding, marker-assisted selection, and genomics to increase crop yield potential. Crop Sci 1999;39:(6)1571-1583
220. Smith JSC, Smith OS. Fingerprinting crop varieties. Advances in agronomy 1992;47:85-140.
221. Ajmone-Marsan P, Monferdini G, Ludwig W, Melchinger A, Franceschini P, Pagnotto G, Motto M. In an elite cross of maize a major quantitative trait locus controls one-fourth of the genetic variation for grain yield. Thero Appl Genet 1995;90:415-424.
222. Barua UM, Chalmers KJ, Thomas WTB, Hackett CA. Molecular mapping of genes determining height, time to heading and growth habit in barley (Hordeum vulgare). Genome 1993;36:1080-1087.
223. Pereira MG, Lee M. Identification of genomic regions affecting plant height in sorghum and maize. Theor Appl Genet 1995;90:380-388.
224. Ohmori T, Murata M, Moyoyoshi F. Identification of RAPD markers linked to the Tm-2 locus in tomato. Theor Appl Genet 1995;90:307-311.
225. Oh J, Fredriksen RA, Magill CW. Identification of molecular markers linked to head smut resistance gene (Shs) in sorghum by RFLP and RAPD analyses. Phytopathology 1994;84:830-833.
226. Hittalmani S, Foolad MR, Mew T, Rodriguez RL, Huang N. Development of a PCR-based marker to identify rice blast resistance gene, Pi-2(t), in segregating population. Theor Appl Genet 1995;91:9-14.
227. Nari S, Bentur JS, Prasada Rao U, Mohan M. DNA markers tightly linked to a gall midge resistance gene (Gm2) are potentially useful for marker-aided selection in rice breeding. Theor Appl Genet 1995;91:68-73.
228. Lawson WR, Henry RJ, Kochman JK, Kong GA. Genetic diversity in sunflower (Helianthus annus L.) as reveled by Random Amplified Polymorphic DNA analysis. Australian Journal of Agricultural Research 1994;45:1319-1327.
229. pat-1) on chromosome 1 of B. patellaris. Theor Appl Genet 1995;90:885-891.
230. Marshall A, Hudgson J. DNA chips: An array of possibilities. Nature Biotechnology 1998;16:27-31.
231. Schafer AJ, Hawkins JR. DNA variation and the future of human genetics. Nature Biotechnology 1998;16:33-39.
232. Mashal RD, Sklar J. Practical methods of mutation detection. Current Opinion in Gednet Dev 1996;6:275-280.