Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm

Genetica

Volumn 136, Issue 3, 2009, Pages 401-417

  Abdurakhmonov, Ibrokhim Y ^a   Saha, Sukumar ^b   Jenkins, Jonnie N ^b   Buriev, Zabardast T ^a   Shermatov, Shukhrat E ^a   Scheffler, Brain E ^c   Pepper, Alan E ^d   Yu, John Z ^e   Kohel, Russell J ^e   Abdukarimov, Abdusattor ^a  

^a S YU YUNUSOV INSTITUTE OF THE CHEMISTRY OF PLANT SUBSTANCES   (Uzbekistan)

^b CROP SCIENCE RESEARCH LABORATORY   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d TEXAS A AND M UNIVERSITY   (United States)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Cotton germplasm; Fiber quality; Genetic diversity; LD based association mapping; Linkage disequilibrium (LD); Simple sequence repeat (SSR) markers

Indexed keywords

GOSSYPIUM HIRSUTUM;

ANALYSIS OF VARIANCE; ARTICLE; CHROMOSOME MAP; COTTON; CYTOLOGY; ENVIRONMENT; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; HISTOLOGY; PHYLOGENY; PLANT GENOME; STATISTICAL MODEL; VARIABLE NUMBER OF TANDEM REPEAT;

ANALYSIS OF VARIANCE; CHROMOSOME MAPPING; ENVIRONMENT; GENETIC MARKERS; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GOSSYPIUM; LINEAR MODELS; LINKAGE DISEQUILIBRIUM; MINISATELLITE REPEATS; PHYLOGENY; POLYMORPHISM, GENETIC;

EID: 67651109034     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-008-9337-8     Document Type: Article

References (95)

1. AM Abdalla OUK Reddy KM El-Zik AE Pepper 2001 Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP Theor Appl Genet 102 222 229 10.1007/s001220051639
2. Abdurakhmonov IY (2007) Exploiting genetic diversity. In: Ethridge D (ed) Plenary presentations and papers. Proceedings of World Cotton Research Conference-4. Lubbock, TX, USA, 10-14 Sept 2007 p 2153
3. IY Abdurakhmonov A Abdukarimov 2008 Application of association mapping to understanding the genetic diversity of plant germplasm resources Int J Plant Genomics 2008 574927
4. IY Abdurakhmonov ZT Buriev S Saha AE Pepper JA Musaev A Almatov 2007 Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum Euphytica 156 141 156 10.1007/s10681-007-9361-2
5. IY Abdurakhmonov FN Kushanov N Djaniqulov ZT Buriev AE Pepper N Fayzieva 2007 The role of induced mutation in conversion of photoperiod dependence in cotton J Hered 98 258 266 10.1093/jhered/esm007
6. RD Ball 2005 Experimental designs for reliable detection of linkage disequilibrium in unstructured random population association studies Genetics 170 859 873 10.1534/genetics.103.024752
7. AT Barnaud Lacombe A Doligez 2006 Linkage disequilibrium in cultivated grapevine, Vitis vinifera L Theor Appl Genet 112 708 716 10.1007/s00122-005- 0174-1
8. A Blenda J Scheffler B Scheffler M Palmer JM Lacape JZ Yu 2006 CMD: a cotton microsatellite database resource for Gossypium genomics BMC Genomics 7 132 10.1186/1471-2164-7-132
9. PJ Bradbury Z Zhang DE Kroon TM Casstevens Y Ramdoss ES Buckler 2007 TASSEL: software for association mapping of complex traits in diverse samples Bioinformatics 23 2633 2635 10.1093/bioinformatics/btm308
10. F Breseghello ME Sorrells 2006 Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars Genetics 172 1165 1177 10.1534/genetics.105.044586
11. CL Brubaker JF Wendel 1994 Re-evaluating the origin of domesticated cotton (Gossypium hirsutum, Malvaceae) using nuclear restriction fragment length polymorphism (RFLP) Am J Bot 81 1309 1326 10.2307/2445407 (Pubitemid 2151314)
12. CL Brubaker AH Paterson JF Wendel 1999 Comparative genetic mapping of allotetraploid cotton and its diploid progenitors Genome 42 184 203 10.1139/gen-42-2-184 (Pubitemid 29294126)
13. ZJ Chen BE Scheffler E Dennis BA Triplett T Zhang W Guo 2007 Toward sequencing cotton (Gossypium) genomes Plant Physiol 145 1303 1310 10.1104/pp.107.107672
14. A Ching KS Caldwell M Jung M Dolan OS Smith S Tingey 2002 SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines BMC Genet 3 1 14 10.1186/1471-2156-3-19
15. KN Conneely M Boehnke 2007 So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests Am J Hum Genet 81 1158 1168 10.1086/522036
16. TW Culp CF Lewis 1973 Breeding methods for improving yield and fiber quality of upland cotton (Gossypium hirsutum) Crop Sci 13 686 689
17. SL Dellaporta J Wood JP Hicks 1983 A plant DNA minipreparation: version II Plant Mol Biol Rep 1 19 21 10.1007/BF02712670
18. L Excoffier P Smouse J Quattro 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data Genetics 131 479 491
19. SA Flint-Garcia JM Thornsberry ES Buckler IV 2003 Structure of linkage disequilibrium in plants Annu Rev Plant Biol 54 357 374 10.1146/annurev.arplant. 54.031902.134907
20. SN Goodman 2001 Of P-values and Bayes: a modest proposal Epidemiology 12 295 297 10.1097/00001648-200105000-00006
21. PK Gupta S Rustgi PL Kulwal 2005 Linkage disequilibrium and association studies in higher plants: present status and future prospects Plant Mol Biol 57 461 485 10.1007/s11103-005-0257-z
22. OA Gutierrez S Basu S Saha JN Jenkins DB Shoemaker CL Cheatham 2002 Genetic distance among selected cotton genotypes and its relationship with F2 performance Crop Sci 42 1841 1847 (Pubitemid 35326216)
23. MT Hamblin SE Mitchell GM White J Gallego R Kukatla RA Wing 2004 Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor Genetics 167 471 483 10.1534/genetics.167.1.471
24. ZG Han W Guo XL Song T Zhang 2004 Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton Mol Genet Genomics 272 308 327 10.1007/s00438-004-1059-8
25. M Hansen T Kraft S Ganestam S Sall NO Nilsson 2001 Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers Genet Res 77 s61 s66 10.1017/S0016672300004857
26. OJ Hardy 2003 Estimation of pairwise relatedness between individuals and characterization of isolation by distance processes using dominant genetic markers Mol Ecol 12 1577 1588 10.1046/j.1365-294X.2003.01835.x
27. OJ Hardy X Vekemans 2002 SpaGeDi: a versatile computer program to analyze spatial genetic structure at the individual or population levels Mol Ecol Notes 2 618 620 10.1046/j.1471-8286.2002.00305.x
28. DH He L Zhong-Xu XL Zhang YC Nie XP Guo CD Feng 2005 Mapping QTLs of traits contributing to yield and analysis of genetic effects in tetraploid cotton Euphytica 144 141 149 10.1007/s10681-005-5297-6
29. DH He ZX Lin XL Zhang YC Nie XP Guo CD Feng 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 10.1007/s10681-006-9254-9
30. PM Hollingsworth RA Ennos 2004 Neighbor joining trees, dominant markers and population genetic structure Heredity 92 490 498 10.1038/sj.hdy.6800445
31. Holsinger KE, Lewis PO (2003) HICKORY: a package for analysis of population genetic data, version 1.0. Department of Ecology and evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
32. KE Holsinger PO Lewis DK Dey 2002 A Bayesian approach to inferring population structure from dominant markers Mol Ecol 11 1157 1164 10.1046/j.1365-294X.2002.01512.x
33. GA Huttley MW Smith M Carrington SJ O'Brien 1999 A scan for linkage disequilibrium across the human genome Genetics 152 1711 1722 (Pubitemid 29370348)
34. MJ Iqbal N Aziz NA Saeed Y Zafar KA Malik 1997 Genetic diversity evaluation of some elite cotton varieties by RAPD analysis Theor Appl Genet 94 139 144 10.1007/s001220050392
35. J Iqbal OUK Reddy KM El-Zik AE Pepper 2001 A genetic bottleneck in the 'evolution under domestication' of Upland cotton Gossypium hirsutum L. examined using DNA fingerprinting Theor Appl Genet 103 547 554 10.1007/PL00002908 (Pubitemid 32897186)
36. H Iwata Y Uga Y Yoshioka K Ebana T Hayashi 2007 Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms Theor Appl Genet 114 1437 1449 10.1007/s00122-007-0529-x
37. SK Kantartzi JM Stewart 2008 Association analysis of fibre traits in Gossypium arboreum accessions Plant Breed 127 173 179 10.1111/j.1439-0523.2008. 01490.x
38. HA Katki 2008 Invited commentary: evidence-based evaluation of P values and Bayes factors Am J Epidemiol 268 384 388 10.1093/aje/kwn148
39. ATW Kraakman RE Niks PMMM Van den Berg P Stam FA Van Eeuwijk 2004 Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars Genetics 168 435 446 10.1534/genetics.104.026831
40. ATW Kraakman F Martinez B Mussiraliev FA van Eeuwijk RE Niks 2006 Linkage disequilibrium mapping of morphological, resistance and other agronomically relevant traits in modern spring barley cultivars Mol Breed 17 41 58 10.1007/s11032-005-1119-8
41. TM Kraft Hansen NO Nilsson 2000 Linkage disequilibrium and fingerprinting in sugar beet Theor Appl Genet 101 323 326 10.1007/s001220051486 (Pubitemid 30656272)
42. L Kruglyak 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes Nat Genet 22 139 144 10.1038/9642
43. JM Lacape TB Nguyen B Courtois JL Belot M Giband JP Gourlot 2005 QTL analysis of cotton fiber quality using multiple Gossypium hirsutum × Gossypium barbadense backcross generations Crop Sci 45 123 140 (Pubitemid 40118381)
44. JM Lacape D Dessauw M Rajab JL Noyer B Hau 2007 Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs Mol Breed 19 45 58 10.1007/s11032-006-9042-1
45. H Lewis 1962 Catastrophic selection as a factor in speciation Evol Int J Org Evol 16 257 271 10.2307/2406275
46. Y Li Y Li K Han Z Wang W Hou Y Zeng 2007 Estimation of multilocus linkage disequilibria in diploid populations with dominant markers Genetics 176 1811 1821 10.1534/genetics.106.068890
47. Z Lin D He X Zhang Y Nie X Guo C Feng 2005 Linkage map construction and mapping QTL for cotton fiber quality using SRAP, SSR and RAPD Plant Breed 124 180 187 10.1111/j.1439-0523.2004.01039.x
48. K Liu SV Muse 2005 PowerMarker: an integrated analysis environment for genetic marker analysis Bioinformatics 21 2128 2129 10.1093/bioinformatics/ bti282
49. S Liu S Saha D Stelly B Burr RG Cantrell 2000 Chromosomal assignment of microsatellite loci in cotton J Hered 91 326 332 10.1093/jhered/91.4.326 (Pubitemid 30457462)
50. S Liu RG Cantrell JCJ [tmp] McCarty JM Stewart 2000 Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions Crop Sci 40 1459 1469
51. KJ Liu M Goodman S Muse JS Smith E Buckler J Doebley 2003 Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites Genetics 165 2117 2128 (Pubitemid 38040295)
52. M Maccaferri MC Sanguineti E Noli R Tuberosa 2005 Population structure and long-range linkage disequilibrium in a drum wheat elite collection Mol Breed 15 271 289 10.1007/s11032-004-7012-z
53. M Malosetti CG van der Linden B Vosman FA van Eeuwijk 2007 A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato Genetics 175 879 889 10.1534/genetics.105.054932
54. LV Malysheva-Otto MW Ganal MS Roder 2006 Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.) BMC Genet 7 6 10.1186/1471-2156-7-6
55. AF [tmp] McRae JC [tmp] McEwan KG Dodds T Wilson AM Crawford J Slate 2002 Linkage disequilibrium in domestic sheep Genetics 160 1113 1122 (Pubitemid 34263474)
56. M Mei NH Syed W Gao PM Thaxton CW Smith DM Stelly 2004 Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium) Theor Appl Genet 108 280 291 10.1007/s00122-003-1433-7
57. KL Mohlke EM Lange TT Valle S Ghosh VL Magnuson K Silander 2001 Linkage disequilibrium between microsatellite markers extends beyond 1 cM on chromosome 20 in Finns Genome Res 11 1221 1226 10.1101/gr.173201
58. M Nei 1973 Analysis of gene diversity in subdivided populations Proc Natl Acad Sci USA 70 3321 3323 10.1073/pnas.70.12.3321
59. M Nordborg JO Borevitz J Bergelson CC Berry J Chory J Hanblad 2002 The extent of linkage disequilibrium in Arabidopsis thaliana Nat Genet 30 90 193 10.1038/ng813
60. M Nordborg TT Hu Y Ishino J Jhaveri C Toomajian H Zheng 2005 The pattern of polymorphism in Arabidopsis thaliana PLoS Biol 3 el96 10.1371/journal.pbio. 0030196
61. Paterson AH, Smith RH (1999) Future horizons: biotechnology of cotton improvement. In: Smith CW, Cothren JT (eds) Cotton: origin, history, technology, and production. Wiley, New York, pp 415-432
62. M Pillay GO Myers 1999 Genetic diversity in cotton assessed by variation in ribosomal RNA genes and AFLP markers Crop Sci 39 1881 1886
63. S Preetha TS Raveendren 2008 Molecular marker technology in cotton Biotechnol Mol Biol Rev 3 032 045
64. Pritchard JK, Wen W (2004) Documentation for Structure software. The University of Chicago Press, Chicago
65. JK Pritchard M Stephens P Donnelly 2000 Inference of population structure using multi-locus genotype data Genetics 155 945 959 (Pubitemid 30397141)
66. A Rafalski M Morgante 2004 Corn and humans: recombination and linkage disequilibrium in two genomes of similar size Trends Genet 20 103 111 10.1016/j.tig.2003.12.002
67. DL Remington JM Thornsberry Y Matsuoka LM Wilson SR Whitt J Doebley 2001 Structure of linkage disequilibrium and phenotypic associations in the maize genome Proc Natl Acad Sci USA 98 11479 11484 10.1073/pnas.201394398
68. J Reynolds BS Weir CC Cockerham 1983 Estimation for the coancestry coefficient: basis for a short-term genetic distance Genetics 105 7767 7779
69. D Rungis D Llewellyn ES Dennis BR Lyon 2005 Simple sequence repeat (SSR) markers reveal low levels of polymorphism between cotton (Gossypium hirsutum L.) cultivars J Agric Res 56 301 307 10.1071/AR04190
70. M Saitou N Nei 1987 The neighbor joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
71. PG Sand 2007 A lesson not learned: allele misassignment Behav Brain Funct 3 65 10.1186/1744-9081-3-65
72. Schneider S, Roessll D, Excoffier L (2000) ARLEQUIN: a software for population genetics data analysis, version 2.0. Genetics and Biometry Laboratory, Department of Anthropology, Geneva, Switzerland, University of Geneva
73. TG Schulze FJ [tmp] McMahon 2002 Genetic association mapping at the crossroad: which test and why? Overview and practical guidelines Am J Med Genet 114 1 11 10.1002/ajmg.10042
74. X Shen W Guo X Zhu Y Yuan JZ Yu RJ Kohel 2005 Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers Mol Breed 15 169 181 10.1007/s11032-004-4731-0
75. B Stich AE Melchinger M Frisch HP Maurer M Heckenberger JC Reif 2005 Linkage disequilibrium in European elite maize germplasm investigated with SSRs Theor Appl Genet 111 723 730 10.1007/s00122-005-2057-x
76. B Stich HP Maurer AE Melchinger M Frisch M Heckenberger JR van der Voort 2006 Comparison of linkage disequilibrium in elite European maize inbred lines using AFLP and SSR markers Mol Breed 17 217 226 10.1007/s11032-005-5296-2
77. JD Storey R Tibshirani 2003 Statistical significance for genome-wide experiments Proc Natl Acad Sci USA 100 9440 9445 10.1073/pnas.1530509100
78. Swofford DL (2002) Phylogenetic analysis using parsimony (and other methods). Sinauer, Sunderland
79. V Tatineni RG Canlrell DD Davis 1996 Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPD Crop Sci 36 186 192
80. MI Tenaillon MC Sawkins AD Long RL Gaut JF Doebley BS Gaut 2001 Patterns of DNA sequence polymorphism along chromosome 1 of maize (Xea mays ssp. mays L.) Proc Natl Acad Sci USA 98 9161 9166 10.1073/pnas.151244298
81. JM Thornsberry MM Goodman J Doebley S Kresovich D Nielsen ES Buckler 2001 Dwarf 8 polymorphisms associate with variation in flowering time Nat Genet 28 286 289 10.1038/90135
82. L Tommasini T Schnurbusch D Fossati F Mascher B Keller 2007 Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties Theor Appl Genet 115 697 708 10.1007/s00122-007-0601-6
83. B Wang W Guo X Zhu Y Wu N Huang T Zhang 2006 QTL mapping of fiber quality in an elite hybrid derived-RIL population of Upland cotton Euphytica 152 367 378 10.1007/s10681-006-9224-2
84. BS Weir CC Cockerham 1984 Estimating F statistics for the analysis of population structure Evol Int J Org Evol 38 1358 1370 10.2307/2408641 (Pubitemid 16277759)
85. KM Weiss AG Clark 2002 Linkage disequilibrium and mapping of human traits Trends Genet 18 19 24 10.1016/S0168-9525(01)02550-1
86. JF Wendel CL Brubaker AE Percival 1992 Genetic diversity in Gossypium hirsutum and the origin of upland cotton Am J Bot 79 1291 1310
87. SR Witt ES Buckler 2003 Using natural allelic diversity to evaluate gene function Methods Mol Biol 236 123 139
88. Young FW, Bann CM (1996) Data analyses with ViSta. In: Fox J, Stine R (eds) Statistical computing environments for social research. Sage Publications, California, pp 207-235
89. J Yu G Pressoir WH Briggs BI Vroh M Yamasaki JF Doebley 2006 A unified mixed-model method for association mapping that accounts for multiple levels of relatedness Nat Genet 38 203 208 10.1038/ng1702
90. K Zhang M Deng T Chen MS Waterman F Sun 2002 A dynamic programming algorithm for haplotype block partitioning Proc Natl Acad Sci USA 99 7335 7339 10.1073/pnas.102186799
91. ZS Zhang YH Xiao M Luo XB Li XY Luo L Hou 2005 Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.) Euphytica 144 91 99 10.1007/s10681-005-4629-x
92. J Zhang Y Lu RG Cantrell E Hughs 2005 Molecular marker diversity and field performance in commercial cotton cultivars evaluated in the Southwestern USA Crop Sci 45 1483 1490 10.2135/cropsci2004.0581
93. HB Zhang Y Li B Wang PW Chee 2008 Recent advances in cotton genomics Int J Plant Genomics 2008 742304
94. K Zhao MJ Aranzana S Kim C Lister C Shindo C Tang 2007 An Arabidopsis example of association mapping in structured samples PLoS Genet 31 e4 10.1371/journal.pgen.0030004
95. YL Zhu QJ Song DL Hyten CP Van Tassell LK Matukumalli DR Grimm 2003 Single-nucleotide polymorphisms in soybean Genetics 163 1123 1134 (Pubitemid 36417952)