Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types

BMC Plant Biology

Volumn 13, Issue 1, 2013, Pages

  Soto Cerda, Braulio J ^a,b,d   Diederichsen, Axel ^c   Ragupathy, Raja ^a,b   Cloutier, Sylvie ^a,b  

^a UNIVERSITY OF MANITOBA   (Canada)

^b Cereal Research Centre   (Canada)

^c AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^d Agriaquaculture Nutritional Genomic Center Genomics and Bioinformatics Unit   (Chile)

Author keywords

Association mapping; Divergent selection; Fiber flax; Genetic diversity; Linkage disequilibrium; Linseed; Linum usitatissimum; Population structure

Indexed keywords

LINUM USITATISSIMUM;

CELLULOSE; FATTY ACID; MICROSATELLITE DNA; PLANT DNA;

ARTICLE; BIOSYNTHESIS; BREEDING; CELL WALL; CHROMOSOME MAP; CLASSIFICATION; FLAX; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PLANT SEED; XYLEM;

BREEDING; CELL WALL; CELLULOSE; CHROMOSOME MAPPING; DNA, PLANT; EVOLUTION, MOLECULAR; FATTY ACIDS; FLAX; GENETIC VARIATION; MICROSATELLITE REPEATS; PHYLOGENY; SEEDS; SELECTION, GENETIC; XYLEM;

EID: 84877072076     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-13-78     Document Type: Article

References (85)

1. Ragupathy R, Rathinavelu R, Cloutier S. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 2011, 12(1):217. 10.1186/1471-2164-12-217, 3113786, 21554714.
2. Vavilov NI. The origin, variation, immunity and breeding of cultivated plants. Chronica Botanica 1951, 13:1-366.
3. Green AG, Chen Y, Singh SP, Dribnenki JCP. Flax. Compendium of transgenic crop plants 2008, 199-226. Oxford: Blackwell Publishing Ltd, Kole C, Hall TC.
4. Diederichsen A, Ulrich A. Variability in stem fibre content and its association with other characteristics in 1177 flax (Linum usitatissimum L) genebank accessions. Ind Crop Prod 2009, 30(1):33-39.
5. van Zeist W, Bakker-Heeres JAH. Evidence for linseed cultivation before 6000 BC. J Archeol Sci 1975, 2(3):215-219.
6. Przybylski R. Flax oil and high linolenic oils. Bailey's industrial oil and fat products 2001, 281-301. Hoboken: John Wiley & Sons, Inc, Shahidi F, 6.
7. Westcott NA, Muir AD. Flax seed lignan in disease prevention and health promotion. Phytochem Rev 2003, 2003(2):401-417.
8. Cullis C. Oilseeds: Linum. Wild crop relatives: Genomic and breeding resources 2011, 177-189. Berlin: Springer, Cole C.
9. von Kulpa W, Danert S. Zur Systematik von Linum usitatissimum L. Kulturpflanze 1962, 3:341-388.
10. Diederichsen A. Comparison of genetic diversity of flax (Linum usitatissimum L.) between Canadian cultivars and a world collection. Plant Breed 2001, 120(4):360-362.
11. Diederichsen A, Rozhmina TA, Zhuchenko AA, Richards KW. Screening for broad adaptation in 96 flax (Linum usitatissimum L.) accessions under dry and warm conditions in Canada and Russia. Plant Genet Resour Newsl 2006, 146:9-16.
12. Diederichsen A, Raney JP. Seed colour, seed weight and seed oil content in Linum usitatissimum accessions held by Plant Gene Resources of Canada. Plant Breed 2006, 125(4):372-377.
13. Tyson H, Fieldes MA, Cheung C, Starobin J. Isozyme relative mobility (Rm) changes related to leaf position; apparently smooth Rm trends and some implications. Biochem Genet 1985, 23(9-10):641-654.
14. Månsby E, Diaz O, von Bothmer R. Preliminary study of genetic diversity in Swedish flax (Linum usitatissimum). Genet Resour Crop Evol 2000, 47(4):417-424.
15. Spielmeyer W, Green AG, Bittisnish D, Mendham N, Lagudah ES. Identification of quantitative trait loci contributing to Fusarium wilt resistance on an AFLP linkage map of flax (Linum usitatissimum). Theor Appl Genet 1998, 97(4):633-641.
16. Everaert I, De Riek J, De Loose M, Van Waes J, Van Bockstaele E. Most similar variety grouping for distinctness evaluation of flax and linseed (Linum usitatissimum L.) varieties by means of AFLP and morphological data. Plant Var Seed 2001, 14(2):69-87.
17. Fu YB, Diederichsen A, Richards KW, Peterson G. Genetic diversity within a range of cultivars and landraces of flax (Linum usitatissimum L) as revealed by RAPDs. Genet Resour Crop Evol 2002, 49(2):167-174.
18. Fu YB, Rowland GG, Duguid SD, Richards KW. RAPD analysis of 54 North American flax cultivars. Crop Sci 2003, 43(4):1510-1515.
19. Wiesnerová D, Wiesner I. ISSR-based clustering of cultivated flax germplasm is statistically correlated to thousand seed mass. Mol Biotechnol 2004, 26(3):207-213. 10.1385/MB:26:3:207, 15004289.
20. Fu YB. Geographic patterns of RAPD variation in cultivated flax. Crop Sci 2005, 45(3):1084-1091.
21. Diederichsen A, Fu YB. Phenotypic and molecular (RAPD) differentiation of four infraspecific groups of cultivated flax (Linum usitatissimum L. subp. usitatissimum). Genet Resour Crop Evol 2006, 53(1):77-90.
22. Diederichsen A, Fu BF. Flax genetic diversity as the raw material for future success 2008, International conference on flax and other bast plants, [http://www.saskflax.com/documents/fb_papers/51_Diederichsen.pdf].
23. Cloutier S, Niu Z, Datla R, Duguid S. Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet 2009, 119(1):53-63. 10.1007/s00122-009-1016-3, 19357828.
24. Rajwade AV, Arora RS, Kadoo NY, Harsulkar AM, Ghorpade PB, Gupta VS. Relatedness of Indian flax genotypes (Linum usitatissimum L.): an inter-simple sequence repeat (ISSR) primer assay. Mol Biotechnol 2010, 45(2):161-170. 10.1007/s12033-010-9256-7, 20195799.
25. Uysal H, Fu YB, Kurt O, Peterson GW, Diederichsen A, Kusters P. Genetic diversity of cultivated flax (Linum usitatissimum L.) and its wild progenitor pale flax (Linum bienne Mill.) as revealed by ISSR markers. Genet Resour Crop Evol 2010, 57(7):1109-1119.
26. Fu YB. Genetic evidence for early flax domestication with capsular dehiscence. Genet Resour Crop Evol 2011, 58(8):1119-1128.
27. Smỳkal P, Bačová-Kerteszová N, Kalendar R, Corander J, Schulman AH, Pavelek M. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet 2011, 122(7):1385-1397. 10.1007/s00122-011-1539-2, 21293839.
28. Soto-Cerda BJ, Maureira-Butler I, Muñoz G, Rupayan A, Cloutier S. SSR-based population structure, molecular diversity and linkage disequilibrium analysis of a collection of flax (Linum usitatissimum L.) varying for mucilage seed-coat content. Mol Breed 2012, 30(2):875-888.
29. Cloutier S, Miranda E, Ward K, Radovanovic N, Reimer E, Walichnowski A, Datla R, Rowland G, Duguid S, Ragupathy R. Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.). Theor Appl Genet 2012, 125(4):685-694. 10.1007/s00122-012-1860-4, 3405236, 22484296.
30. Diederichsen A. Ex situ collections of cultivated flax (Linum usitatissimum L.) and other species of the genus Linum L. Genet Resour Crop Evol 2007, 54(3):661-678.
31. Kumar S, You FM, Cloutier S. Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics 2012, 13:684. 10.1186/1471-2164-13-684, 3557168, 23216845.
32. Cloutier S, Ragupathy R, Niu Z, Duguid S. SSR-based linkage map of flax (Linum usitatissimum L.) and mapping of QTLs underlying fatty acid composition traits. Mol Breed 2011, 28(4):437-451.
33. Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). Theor Appl Genet 2012, 125(8):1783-1795. 10.1007/s00122-012-1953-0, 3493668, 22890805.
34. Venglat P, Xiang D, Qiu S, Stone SL, Tibiche C, Cram D, Alting-Mees M, Nowak J, Cloutier S, Deyholos M, Bekkaoui F, Sharpe A, Wang E, Rowland G, Selvaraj G, Datla R. Gene expression analysis on flax seed development. BMC Plant Biol 2011, 11:74. 10.1186/1471-2229-11-74, 3107784, 21529361.
35. Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK, Wang J, Deyholos MK. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 2012, 72(3):461-473. 10.1111/j.1365-313X.2012.05093.x, 22757964.
36. Flint-Garcia S, Thornsberry JM, Bukler ES. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 2003, 54:357-374. 10.1146/annurev.arplant.54.031902.134907, 14502995.
37. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Bukler ES. Association mapping: Critical considerations shift from genotyping to experimental design. Plant Cell 2009, 21(8):2194-2202. 10.1105/tpc.109.068437, 2751942, 19654263.
38. Cornuet JM, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 1996, 144(4):2001-2014. 1207747, 8978083.
39. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB. Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 1998, 89(3):238-247. 10.1093/jhered/89.3.238, 9656466.
40. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nature Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
41. Rachinskaya OA, Lemesh VA, Muravenko OV, Yurkevich OY, Guzenko EV, Bol'sheva NL, Bogdanova MV, Samatadze TE, Popov KV, Malyshev SV, Shostak NG, Heller K, Hotyleva LV, Zelenin AV. Genetic polymorphism of flax Linum usitatissimum based on the use of molecular cytogenetic markers. Genetika 2011, 47(1):56-65.
42. Maggioni L, Pavelek M, van Soest LJM, Lipman E. Flax Genetic Resources in Europe. Ad hoc meeting: 7-8 December 2001 2002, Prague: International Plant Genetic Resources Institute.
43. Yu J, Pressoir G, Briggs W, Vroh Bi I, Yamasaki M, Doebley J, McMullen M, Gaut B, Nielsen D, Holland J, Kresovich S, Buckler E. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 2006, 38(2):203-208. 10.1038/ng1702, 16380716.
44. Bernardo R, Romero-Severson J, Ziegle J, Hauser J, Joe L, Hookstra G, Doerge RW. Parental contribution and coefficient of coancestry among maize inbreds: pedigree, RFLP, and SSR data. Theor Appl Genet 2000, 100(3-4):552-556.
45. Roose-Amsaleg C, Cariou-Pham E, Vautrin D, Tavernier R, Solignac M. Polymorphic microsatellite loci in Linum usitatissimum. Mol Ecol Notes 2006, 6(3):796-799.
46. Deng X, Long S, He D, Li X, Wang Y, Liu J, Chen H. Development and characterization of polymorphic microsatellite markers in Linum usitatissimum. J Plant Res 2010, 123(1):119-123. 10.1007/s10265-009-0271-3, 19882206.
47. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 2002, 99(15):9650-9655. 10.1073/pnas.112324299, 124964, 12105270.
48. Yu J, Buckler E. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 2006, 17(2):155-160. 10.1016/j.copbio.2006.02.003, 16504497.
49. Morrell PL, Toleno DM, Lundy KE, Clegg MT. Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 2005, 102:2442-2447. 10.1073/pnas.0409804102, 549024, 15699350.
50. Xiao Y, Cai D, Yang W, Ye W, Younas M, Wu J, Liu K. Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association panel revealed by microsatellites. Theor Appl Genet 2012, 125(3):437-447. 10.1007/s00122-012-1843-5, 22437490.
51. Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE, Paterson AH, Aquadro CF, Kresovich S. Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theor Appl Genet 111(1):23-30.
52. Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, Heath S, Foulley JL, Gautier M. The genome response to artificial selection: a case study in dairy cattle. PLoS ONE 2009, 4(8):e6595. 10.1371/journal.pone.0006595, 2722727, 19672461.
53. Schwarzenbacher H, Dolezal M, Flisikowski K, Seefried F, Wurmser C, Schlötterer C, Fries R. Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle. BMC Genomics 2012, 13:48. 10.1186/1471-2164-13-48, 3305582, 22289501.
54. Shimada Y, Shikano T, Merilä J. A high incidence of selection on physiologically important genes in the three-spined stickleback, Gasterosteus aculeatus. Mol Biol Evol 2011, 28(1):181-193. 10.1093/molbev/msq181, 20660084.
55. He XC, Qin YM, Xu Y, Hu CY, Zhu YX. Molecular cloning, expression profiling, and yeast complementation of 19 β-tubulin cDNAs from developing cotton ovules. J Exp Bot 2008, 59(10):2687-2695. 10.1093/jxb/ern127, 2486464, 18596112.
56. Roach MJ, Deyholos MK. Microarray analysis of developing flax hypocotyls identifies novel transcripts correlated with specific stages of phloem fibre differentiation. Ann Bot 2008, 102(3):317-330. 10.1093/aob/mcn110, 2701801, 18593690.
57. Sexton TR, Henry RJ, Hardwood CE, Thomas DS, McManus LJ, Raymond C, Henson M, Shepherd M. Pectin methyltransferase genes influence solid wood properties of Eucalyptus pilularis. Plant Physiol 2011, 158(1):531-541. 3252102, 22052017.
58. Fenart S, Ndong YP, Duarte J, Rivière N, Wilmer J, van Wuytswinkel O, Lucau A, Cariou E, Neutelings G, Gutierrez L, Chabbert B, Guillot X, Tavernier R, Hawkins S, Thomasset B. Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray. BMC Genomics 2010, 11:592. 10.1186/1471-2164-11-592, 3091737, 20964859.
59. Deng X, Long S, He D, Li X, Wang Y, Hao D, Qiu C, Chen X. Isolation and characterization of polymorphic microsatellite markers from flax (Linum usitatissimum L.). Afr J Biotechnol 2011, 10(5):734-739.
60. Manly BFJ. The statistics of natural selection. Spurious test results due to isolation by distance 1985, 186-195. London: Chapman and Hall.
61. Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX. POPGENE, the user-friendly shareware for population genetic analysis 1997, Molecular biology and biotechnology centre: University of Alberta Press.
62. Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 1973, 70(12):3321-3323. 10.1073/pnas.70.12.3321, 427228, 4519626.
63. Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 2005, 21(9):2128-2129. 10.1093/bioinformatics/bti282, 15705655.
64. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
65. Yunusbayev B, Metspalu M, Järve M, Kutuev I, Rootsi S, Metspalu E, Behar DM, Varendi K, Sahakyan H, Khusainova R, Yepiskoposyan L, Khusnutdinova EK, Underhill PA, Kivisild T, Villems R. The Caucasus as an asymmetric semipermeable barrier to ancient human migrations. Mol Biol Evol 2011, 29(1):359-365.
66. van Berloo R. GGT 2.0: Versatile software for visualization and analysis of genetic data. J Hered 2008, 99(2):232-236. 10.1093/jhered/esm109, 18222930.
67. Peakall R, Smouse PE. GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 2006, 6(1):288-295.
68. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Hum Genet 2000, 67(1):170-181. 10.1086/302959, 1287075, 10827107.
69. Hubisz MJ, Falush D, Stephens M, Pritchard JK. Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 2009, 9(5):1322-1332. 10.1111/j.1755-0998.2009.02591.x, 3518025, 21564903.
70. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005, 14(8):2611-2620. 10.1111/j.1365-294X.2005.02553.x, 15969739.
71. Rosenberg NA. Distruct: a program for the graphical display of population structure. Mol Ecol Notes 2004, 4(1):137-138.
72. Caballero A, Toro MA. Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet 2002, 3(3):289-299.
73. Gutierréz JP, Royo LJ, álvarez I, Goyache F. MolKin v. 2.0: a computer program for genetic analysis of populations using molecular coancentry information. J Hered 2005, 96(6):718-721. 10.1093/jhered/esi118, 16251515.
74. Kalinowski ST. HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 2005, 5(1):187-189.
75. Breseghello F, Sorrells M. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 2006, 172(2):1165-1177. 1456215, 16079235.
76. Watterson GA. The homozygosity test of neutrality. Genetics 1978, 88(2):405-417. 1213809, 17248803.
77. Kauer MO, Dieringer D, Schlötterer C. A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster. Genetics 2003, 165(3):1137-1148. 1462820, 14668371.
78. Beaumont MA, Nichols RA. Evaluating loci for use in the genetic analysis of population structure. Proc Royal Soc Lond B 1996, 263(1377):1619-1626.
79. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 2008, 9:323. 10.1186/1471-2105-9-323, 2515854, 18662398.
80. Excoffier L, Hofer T, Foll M. Detecting loci under selection in a hierarchically structured population. Heredity 2009, 103(4):285-298. 10.1038/hdy.2009.74, 19623208.
81. Excoffier L, Lischer HEL. Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010, 10(3):564-567. 10.1111/j.1755-0998.2010.02847.x, 21565059.
82. Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 2008, 24(5):637-644. 10.1093/bioinformatics/btn013, 18218656.
83. Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 2004, 20(16):2878-2879. 10.1093/bioinformatics/bth315, 15145805.
84. The UniProt Consortium The universal protein resource (UniProt) 2009. Nucleic Acid Res 2009, 37:D169-D174. 2686606, 18836194, The UniProt Consortium.
85. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, Luthe DS, Bridges SM, Burgess SC. AgBase: a functional genomics resource for agriculture. BMC Genomics 2006, 7:229. 10.1186/1471-2164-7-229, 1618847, 16961921.