Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping

Theoretical and Applied Genetics

Volumn 116, Issue 7, 2008, Pages 1015-1026

  An, Chuanfu ^a   Saha, Sukumar ^b   Jenkins, Johnie N ^b   Ma, Din Pow ^c   Scheffler, Brian E ^d   Kohel, Russell J ^e   Yu, John Z ^e   Stelly, David M ^f  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b CROP SCIENCE RESEARCH LABORATORY   (United States)

^c MISSISSIPPI STATE UNIVERSITY   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

^f TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LINKAGE MAPPING; PHYLOGENOMIC CHARACTERIZATION; TETRAPLOID SPECIES;

BIODIVERSITY; BIOMARKERS; CHARACTERIZATION; CHROMOSOMES; COTTON; CROPS; GENE ENCODING; NUCLEOTIDES;

TRANSCRIPTION FACTORS;

TRANSCRIPTION FACTOR;

ARTICLE; CHROMOSOME MAP; COTTON; GENE EXPRESSION REGULATION; GENETICS; GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; ONCOGENE MYB; PHYLOGENY; PLANT CHROMOSOME; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENE EXPRESSION REGULATION, PLANT; GENES, MYB; GENOME, PLANT; GOSSYPIUM; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSCRIPTION FACTORS;

GOSSYPIUM; GOSSYPIUM HIRSUTUM;

EID: 42149125441     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-008-0732-4     Document Type: Article

References (85)

1. An C, Saha S, Jenkins JN, Scheffler BE, Wilkins TA, Stelly DM (2007) Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol Genet Genomics 278:539-553
2. Beecher B, Bowman J, Martin JM, Bettge AD, Morris CF, Blake TK, Giroux MJ (2002) Hordoindolines are associated with a major endosperm-texture QTL in barley (Hordeum vulgare). Genome 45:584-591
3. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yullambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D (2006) CMD: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics 7:132
4. Bundock PC, Henry RJ (2004) Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor Appl Genet 109:543-551
5. Bundock PC, Christopher JT, Eggler P, Ablett G, Henry RJ, Holton TA (2003) Single nucleotide polymorphisms in cytochrome P450 genes from barley. Theor Appl Genet 106:676-682
6. Cedroni ML, Cronn RC, Adams KL, Wilkins TA, Wendel JF (2003) Evolution and expression of MYB genes in diploid and polyploid cotton. Plant Mol Biol 51:313-325
7. Chee PW, Rong J, Williams-Coplin D, Schulze SR, Paterson AH (2004) EST derived PCR-based markers for functional gene homologues in cotton. Genome 47:449-462
8. Chee PW, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005a) Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: I. Fiber elongation. Theor Appl Genet 111:757-763
9. Chee PW, Draye X, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005b) Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length. Theor Appl Genet 111:772-781
10. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3:19
11. Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23:203-207
12. Cronn R, Small RL, Wendel JF (1999) Duplicated genes evolve indenpendently after polyploid formation in cotton. Proc Natl Acad Sci USA 96:14406-14411
13. Cronn R, Cedroni M, Haselkorn T, Grover C, Wendel JF (2002) PCR-mediated recombination in amplification products derived from polyploid cotton. Theor Appl Genet 104:482-489
14. Draye X, Chee PW, Jiang CX, Decanini L, Delmonte TA, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness. Theor Appl Genet 111:764-771
15. Faris JD, Li WL, Liu DJ, Chen PD, Gill BS (1999) Candidate gene analysis of quantitative disease resistance in wheat. Theor Appl Genet 98:219-225
16. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Res 14:1812-1819
17. Frelichowski JE, Palmer MB, Main D, Tomkins JP, Cantrell RG, Stelly DM, Yu J, Kohel RJ, Ulloa M (2006) Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends. Mol Genet Genomics 275:479-491
18. Giroux MJ, Talbert L, Habernicht DK, Lanning S, Hemphill A, Martin JM (2000) Association of puroindoline sequence type and grain hardiness in hard red spring wheat. Crop Sci 40:370-380
19. Glover BJ, Perez-Rodriguez M, Martin C (1998) Development of several epidermal cell types can be specified by the same MYB-related plant transcription factor. Development 125:3497-3508
20. Guo WZ, Ma GJ, Zhu YC, Yi CX, Zhang TZ (2006) Molecular tagging and mapping of quantitative trait loci for lint percentage and morphological marker genes in Upland cotton. J Integr Plant Biol 48:320-326
21. Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, Shi B, Zhang T (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176:527-541
22. 2 performance. Crop Sci 42:1841-1847
23. Hauser MT, Harr B, Schlotterer C (2001) Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular analysis of the candidate gene GLABROUS1. Mol Biol Evol 18:1754-1763
24. He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Feng CD, Stewart JMcD (2005) Mapping QTLs of traits contributing to yield and analysis of genetic effects in tetraploid cotton. Euphytica 144:141-149
25. He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W (2007) QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153:181-197
26. Hsu CY, Jenkins JN, Saha S, Ma DP (2005) Transcriptional regulation of the lipid transfer protein gene LTP3 cotton fiber by a novel MYB protein. Plant Sci 168:167-181
27. Humphries JA, Walker AR, Timmis JN, Orford SJ (2005) Two WD-repeat genes from cotton are functional homologues of the Arabidopsis thaliana TRANSPARENT TESTA GLABRA1 (TTG1) gene. Plant Mol Biol 57:67-81
28. Jenkins JN, McCarty JC, Wu J, Saha S, Gutierrez O, Hayes R, Stelly DM (2007) Genetic effect of thirteen Gossypium barbadense L. chromosome substitution line in topcrosses with Upland cotton cultivars: II. Fiber quality traits. Crop Sci 47:561-570
29. Jiang CX, Wright RJ, El-Zik KM, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:449-4424
30. Kamiya T, Kawabe A, Miyashita NT (2002) Nucleotide polymorphism at Atmyb2 locus of the wild plant Arabidopsis thaliana. Genet Res Camb 80:89-98
31. Kohel RJ, Yu J, Park YH, Lazo GR (2001) Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121:163-172
32. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172-175
33. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163
34. Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum × Gossypium barbadense backcross generations. Crop Sci 45:123-140
35. Lee JJ, Hassan OSS, Gao W, Wei NE, Kohel RJ, Chen XY, Payton P, Sze SH, Stelly DM, Chen ZJ (2006) Developmental and gene expression analysis of a cotton naked seed mutant. Planta 223:418-432
36. Lin Z, He D, Zhang X, Nie Y, Guo X, Feng C, Stewart JMcD (2005) Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD. Plant Breed 124:180-187
37. Liu S, Saha S, Stelly DM, Burr B, Cantrell RG (2000) Chromosomal assignment of microsatellite loci in cotton. J Hered 91:326-332
38. Liu Q, Brubaker CL, Green AG, Marshall DR, Sharp PJ, Singh SP (2001) Evolution of the FAD-2 fatty acid desaturase 5′ UTR intron and the molecular systematics of Gossypium (Malvaceae). Am J Bot 88:92-102
39. Loguercio LL, Zhang JQ, Wilkins TA (1999) Differential regulation of six novel MYB-domain genes defines two distinct expression patterns in allotetraploid cotton (Gossypium hirsutum L.) Mol Gen Genet 261:660-671
40. Mei M, Syed NH, Gao W, Thaxton PM, Smith CW, Stelly DM, Chen ZJ (2004) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280-291
41. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
42. Oppenheimer OG, Hermn PL, Sivakumaran S, Esch J, Marks DM (1991) A myb gene required for leaf trichome differentiation in Arabidopsis is expressed in stipules. Cell 67:483-493
43. Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274:428-441
44. Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ (2003) QTL analysis of genotype × environment interactions affecting cotton fiber quality. Theor Appl Genet 106:384-396
45. Perez-Rodriguez M, Jaffe FW, Butelli E, Glover BJ, Martin C (2005) Development of three different cell types is associated with the activity of a specific MYB transcription factor in the ventral petal of Antirrhinum majus flowers. Development 132:359-370
46. Pflieger S, Lefebvre V, Caranta C, Blattes A, Goffinet B, Palloix A (1999) Disease resistance gene analogs as candidates for QTLs involved in pepper-pathogen interactions. Genome 42:1100-1110
47. Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7:275-291
48. Reinisch AJ, Dong J, Brubaker CL, Stelly DM, Wendel JF, Paterson AH (1994) A detailed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829-847
49. Ren LH, Guo WZ, Zhang TZ (2002) Identification of quantitative trait loci (QTLs) affecting yield and fiber propreties in chromosome 16 in cotton using substitution line. Acta Bot Sin 44:815-820
50. Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu GL (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105-2110
51. Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, Park C, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao X, Zhu L, Paterson AH (2004) A 3347-locus genetic recombinant map of sequence-taged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389-417
52. Rong J, Feltus FA, Waghmare VN, Pierce GJ, Chee PW, Draye X, Saranga Y, Wright RJ, Wilkins TA, May OL, Wayne S, Gannaway JR, Wendel JF, Paterson AH (2007) Meta-analysis of polyploid cotton QTLs shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176:2577-2588
53. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analysis by the coalescent and other methods. Bioinformatics 19:2496-2497
54. Saha S, Jenkins JN, Wu J, McCarty JC, Gutierrez OA, Percy RG, Cantrell RG, Stelly DM (2006a) Effect of chromosome-specific introgression in Upland cotton on fiber and agronomic traits. Genetics 172:1927-1938
55. 1 hybrid hypoaneuploid chromosome substitution series. J Cot Sci 12:263-272
56. Saranga Y, Menz M, Jiang CX, Wright RJ, Yakir D, Paterson AH (2001) Genomic dissection of genotype × environment interactions conferring adaptation of cotton to arid conditions. Genome Res 11:1988-1995
57. Schiefelbein J (2003) Cell-fate specification in the epidermis: a common patterning mechanism in the root and shoot. Curr Opin Plant Biol 6:74-78
58. Schneider K, Schafer-Pregl R, Borchardt DC, Salamini F (2002) Mapping of QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers. Theor Appl Genet 104:1107-1113
59. Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF (2003) Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol Biol Evol 20:633-643
60. Shen X, Guo W, Zhu X, Yuan Y, Yu JZ, Kohel RJ, Zhang T (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed 15:169-181
61. Shen X, Zhang T, Guo W, Zhu X, Zhang X (2006) Mapping fiber and yield QLTs with main, epistatic, and QTL × environment interaction effects in recombinant inbred lines of Upland cotton. Crop Sci 46:61-66
62. Shen X, Guo W, Lu Q, Zhu X, Yuan Y, Zhang T (2007) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155:371-380
63. Small RL, Wendel JF (2002) Differential evolutionary dynamics of duplicated paralogous Adh loci in alloteraploid cotton (Gossypium). Mol Biol Evol 19:597-607
64. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in recently diverged plant group. Am J Bot 85:1301-1315
65. Small RL, Ryburn JA, Wendel JF (1999) Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Mol Biol Evol 16:491-501
66. Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49:431-437
67. Stelly DM, Saha S, Raska DA, Jenkins JN, McCarty JC, Gutierrez OA (2005) Registration of 17 Upland (Gossypium hirsutum) cotton germplasm lines disomic for different G. barbadense chromosome or arm substitutions. Crop Sci 45:2663-2665
68. Suo J, Liang X, Pu L, Zhang Y, Xue Y (2003) Identification of GhMYB109 encoding a R2R3 MYB transcription factor that expressed specifically in fiber initials and elongating fibers of cotton (Gossypium hirsutum L.) BBA-Gene Struct Expr 1630:25-34
69. Szymanski DB, Lloyd AM, Marks MD (2000) Progress in the molecular genetic analysis of trichome initiation and morphogenesis in Arabidopsis. Trends Plant Sci 5:214-219
70. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460
71. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustalx windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
72. ® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen
73. Wang Z, Taramino G, Yang D, Liu G, Tingey SV, Miao GH, Wang GL (2001) Rice ESTs with disease-resistance gene- or defense-response gene-like sequences mapped to regions containing major resistance genes or QTLs. Mol Genet Genomics 265:302-310
74. Wang S, Wang JW, Yu N, Li CH, Luo B, Gou JY, Wang LJ, Chen XY (2004) Control of plant trichome development by a cotton fiber MYB gene. Plant Cell 16:2323-2334
75. Wang B, Guo W, Zhu X, Wu Y, Huang N, Zhang T (2006a) QTL mapping of fiber quality in an elite hybrid derived-RIL population of upland cotton. Euphytica 152:367-378
76. Wang K, Song X, Han Z, Guo W, Yu JZ, Sun J, Pan J, Kohel RJ, Zhang T (2006b) Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping. Theor Appl Genet 113:73-80
77. Wendel JF, Cronn RC (2003) Polyploid and the evolutionary history of cotton. Adv Agron 78:139-186
78. Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719-2733
79. Wu Y, Machado AC, White RG, Llewellyn DJ, Dennis ES (2006) Expression profiling identifies genes expression early during lint fibre initiation in cotton. Plant Cell Physiol 47:107-127
80. Yang SS, Cheung F, Lee JJ, Ha M, Wei NE, Sze SH, Stelly DM, Thaxton P, Triplett B, Town CD, Chen ZJ (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant J 47:761-775
81. Zhang J, Guo W, Zhang T (2002) Molecular linkage mapping of allotetraploid cotton (Gossypium hirsutum L. × Gossypium barbadense L.) with a haploid population. Theor Appl Genet 105:1166-1174
82. Zhang W, Gianibelli MC, Ma W, Rampling L, Gale KR (2003) Identification of SNPs and development of allele-specific PCR markers for γ-gliadin alleles in Triticum aestivum. Theor Appl Genet 107:130-138
83. Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L, Li DM, Pei Y (2005) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.) Euphytica 144:91-99
84. Zhao XP, Si Y, Hanson RE, Crane CF, Price HJ, Stelly DM, Wendel JF, Paterson AH (1998) Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res 8:479-492
85. Zhu YL, Song QJ, Hyten DL, Tassell CPV, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123-1134