Genetic mapping of the apospory-specific genomic region in Pennisetum squamulatum using retrotransposon-based molecular markers

Theoretical and Applied Genetics

Volumn 119, Issue 2, 2009, Pages 199-212

  Huo, Heqiang ^a   Conner, Joann A ^a   Ozias Akins, Peggy ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOSPORY-SPECIFIC GENOMIC REGIONS; ASEXUAL REPRODUCTION; BACTERIAL ARTIFICIAL CHROMOSOMES; GENETIC LINKAGE; GENETIC MAP; GENETIC MAPPING; GENOMIC REGIONS; HIGH-RESOLUTION GENETIC MAPPING; LINKAGE GROUPS; LONG TERMINAL REPEATS; MAP-BASED CLONING; MOLECULAR MARKER; OPEN READING FRAME; PCR PRODUCTS; PRIMER COMBINATIONS; RETROTRANSPOSON; SCAR MARKERS; SEQUENCE CHARACTERIZED AMPLIFIED REGIONS; SINGLE-DOSE; SPECIFIC PRIMERS;

CLONING;

MAPPING;

ARTICLE; ASEXUAL REPRODUCTION; CHROMOSOME MAP; DNA SEQUENCE; GENETIC LINKAGE; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; LONG TERMINAL REPEAT; PEARL MILLET; PHYLOGENY; PLANT GENOME; RETROPOSON; SOUTHERN BLOTTING;

BLOTTING, SOUTHERN; CHROMOSOME MAPPING; GENETIC MARKERS; GENOME, PLANT; LINKAGE (GENETICS); PENNISETUM; PHYLOGENY; POLYMORPHISM, GENETIC; REPRODUCTION, ASEXUAL; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; TERMINAL REPEAT SEQUENCES;

BACTERIA (MICROORGANISMS); PENNISETUM GLAUCUM; PENNISETUM SQUAMULATUM;

EID: 67650455971     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-009-1029-y     Document Type: Article

References (77)

1. A Acquadro E Portis A Moglia F Magurno S Lanteri 2006 Retrotransposon-based S-SAP as a platform for the analysis of genetic variation and linkage in globe artichoke Genome 49 1149 1159 (Pubitemid 46270178)
2. ML Ainouche A Baumel A Salmon G Yannic 2003 Hybridization, polyploidy and speciation in Spartina (Poaceae) New Phytol 161 165 172 (Pubitemid 38047057)
3. Y Akiyama JA Conner S Goel DT Morishige JE Mullet WW Hanna P Ozias-Akins 2004 High-resolution physical mapping in Pennisetum squamulatum reveals extensive chromosomal heteromorphism of the genomic region associated with apomixis Plant Physiol 134 1733 1741 (Pubitemid 38527380)
4. Y Akiyama WW Hanna P Ozias-Akins 2005 High-resolution physical mapping reveals that the apospory-specific genomic region (ASGR) in Cenchrus ciliaris is located on a heterochromatic and hemizygous region of a single chromosome Theor Appl Genet 111 1042 1051 (Pubitemid 41434114)
5. E Albertini A Porceddu F Ferranti L Reale G Barcaccia B Romano M Falcinelli 2001 Apospory and parthenogenesis may be uncoupled in Poa pratensis: a cytological investigation Sex Plant Reprod 14 213 217 (Pubitemid 34018135)
6. Arabidopsis Genome Initiative 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796 815
7. Asker SE, Jerling L (1992) Apomixis in plants. CRC Press, Boca Raton, pp 5-19
8. ZV Avramova 2002 Heterochromatin in animals and plants. Similarities and differences Plant Physiol 129 40 49 (Pubitemid 34527306)
9. M Berenyi T Gichuki J Schmidt K Burg 2002 Ty1-copia retrotransposon-based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato Theor Appl Genet 105 862 869 (Pubitemid 36080315)
10. RA Bicknell AM Koltunow 2004 Understanding apomixis: recent advances and remaining conundrums Plant Cell 16 Suppl S228 S245
11. A Bonin E Bellemain P Bronken Eidesen F Pompanon C Brochmann P Taberlet 2004 How to track and assess genotyping errors in population genetics studies Mol Ecol 13 3261 3273 (Pubitemid 39415663)
12. A Bouck R Peeler ML Arnold SR Wessler 2005 Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers Genetics 171 1289 1303 (Pubitemid 43234860)
13. A Bousios I Saldana-Oyarzabal AG Valenzuela-Zapata C Wood SR Pearce 2007 Isolation and characterization of Ty1-copia retrotransposon sequences in the blue agave (Agave tequilana Weber var. azul) and their development as SSAP markers for phylogenetic analysis Plant Sci 172 291 298 (Pubitemid 46073268)
14. E Boyko R Kalendar V Korzun J Fellers A Korol AH Schulman BS Gill 2002 A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function Plant Mol Biol 48 767 790 (Pubitemid 34415984)
15. JG Carman 1997 Asynchronous expression of duplicate genes in angiosperms may cause apomixis, bispory, tetraspory, and polyembryony Biol J Linn Soc 61 51 94 (Pubitemid 27274765)
16. AS Catanach SK Erasmuson E Podivinsky BR Jordan R Bicknell 2006 Deletion mapping of genetic regions associated with apomixis in Hieracium Proc Natl Acad Sci USA 103 18650 18655 (Pubitemid 44913465)
17. JA Conner S Goel G Gunawan M Cordonnier-Pratt VE Johnson C Liang H Wang LH Pratt JE Mullet J DeBarry L Yang JL Bennetzen PE Klein P Ozias-Akins 2008 Sequence analysis of BAC clones from the apospory-specific genomic region (ASGR) of Pennisetum and Cenchrus Plant Physiol 147 1 16
18. HK Dooner L He 2008 Maize genome structure variation: interplay between retrotransposon polymorphisms and genic recombination Plant Cell 20 249 258 (Pubitemid 352844010)
19. M Dujardin W Hanna 1989 Crossability of pearl millet with wild Pennisetum species Crop Sci 29 77 80
20. TH Ellis SJ Poyser MR Knox AV Vershinin MJ Ambrose 1998 Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea Mol Gen Genet 260 9 19 (Pubitemid 28502216)
21. AJ Flavell E Dunbar R Anderson SR Pearce R Hartley A Kumar 1992 Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants Nucleic Acids Res 20 3639 3644
22. AJ Flavell SR Pearce JS Heslop-Harrison A Kumar 1997 The evolution of Ty1-copia group retrotransposons in eukaryote genomes Genetica 100 185 195 (Pubitemid 28034766)
23. S Goel Z Chen JA Conner Y Akiyama WW Hanna P Ozias-Akins 2003 Delineation by fluorescence in situ hybridization of a single hemizygous chromosomal region associated with aposporous embryo sac formation in Pennisetum squamulatum and Cenchrus ciliaris Genetics 163 1069 1082 (Pubitemid 36417948)
24. S Goel Z Chen Y Akiyama JA Conner M Basu G Gualtieri WW Hanna P Ozias-Akins 2006 Comparative physical mapping of the apospory-specific genomic region in two apomictic grasses: Pennisetum squamulatum and Cenchrus ciliaris Genetics 173 389 400 (Pubitemid 43800210)
25. D Grimanelli O Leblanc DG De Leon Y Savidan 1995 Apomixis expression in maize-Tripsacum hybrid derivatives and the implications regarding its control and potential for manipulation Apomixis Newsl 8 35 37
26. D Grimanelli O Leblanc E Espinosa E Perotti DG De Leon Y Savidan 1998 Mapping diplosporous apomixis in tetraploid Tripsacum: one gene or several genes? Heredity 80 33 39 (Pubitemid 28110983)
27. D Grimanelli O Leblanc E Perotti U Grossniklaus 2001 Developmental genetics of gametophytic apomixis Trends Genet 17 597 604 (Pubitemid 32918302)
28. U Grossniklaus GA Nogler PJ van Dijk 2001 How to avoid sex: the genetic control of gametophytic apomixis Plant Cell 13 1491 1498
29. RW Jessup BL Burson GB Burow YW Wang C Chang Z Li AH Paterson MA Hussey 2002 Disomic inheritance, suppressed recombination, and allelic interactions govern apospory in buffelgrass as revealed by genome mapping Crop Sci 42 1688 1694 (Pubitemid 35022037)
30. AM Koltunow RA Bicknell AM Chaudhury 1995 Apomixis: molecular strategies for the generation of genetically identical seeds without fertilization Plant Physiol 108 1345 1352
31. A Kumar JL Bennetzen 1999 Plant retrotransposons Annu Rev Genet 33 479 532 (Pubitemid 30083131)
32. A Kumar H Hirochika 2001 Applications of retrotransposons as genetic tools in plant biology Trends Plant Sci 6 127 134 (Pubitemid 33146316)
33. P Labombarda A Busti ME Caceres F Pupilli S Arcioni 2002 An AFLP marker tightly linked to apomixis reveals hemizygosity in a portion of the apomixis-controlling locus in Paspalum simplex Genome 45 513 519 (Pubitemid 34443858)
34. GJ Lightbourn JG Jelesko RE Veilleux 2007 Retrotransposon-based markers from potato monoploids used in somatic hybridization Genome 50 492 501 (Pubitemid 47236500)
35. Z Liu Y Wang Y Shen W Guo S Hao B Liu 2004 Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia Plant Mol Biol 54 571 582 (Pubitemid 39174909)
36. Q Lou J Chen 2007 Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits Genome 50 802 810 (Pubitemid 350144747)
37. LH Madsen E Fukai S Radutoiu CK Yost N Sandal L Schauser J Stougaard 2005 LORE1, an active low-copy-number TY3-gypsy retrotransposon family in the model legume Lotus japonicus Plant J 44 372 381 (Pubitemid 43919867)
38. O Manninen R Kalendar J Robinson AH Schulman 2000 Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley Mol Gen Genet 264 325 334 (Pubitemid 30831537)
39. T Meeûs F Prugnolle P Agnew 2007 Asexual reproduction: genetics and evolutionary aspects Cell Mol Life Sci 64 1355 1367
40. Nogler GA (1984) Gametophytic apomixis. In: Johri BM (ed) Embryology of angiosperms. Springer, Berlin, pp 475-518
41. RD Noyes LH Rieseberg 2000 Two independent loci control agamospermy (apomixis) in the triploid flowering plant Erigeron annuus Genetics 155 379 390 (Pubitemid 30257137)
42. P Ozias-Akins 2006 Apomixis: developmental characteristics and genetics Crit Rev Plant Sci 25 199 214
43. P Ozias-Akins EL Lubbers WW Hanna JW McNay 1993 Transmission of the apomictic mode of reproduction in Pennisetum: Co-inheritance of the trait and molecular markers Theor Appl Genet 85 632 638
44. P Ozias-Akins D Roche WW Hanna 1998 Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes Proc Natl Acad Sci USA 95 5127 5132
45. P Ozias-Akins Y Akiyama WW Hanna 2003 Molecular characterization of the genomic region linked with apomixis in Pennisetum/Cenchrus Funct Integr Genomics 3 94 104 (Pubitemid 40796207)
46. R Panstruga R Buschges P Piffanelli P Schulze-Lefert 1998 A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome Nucleic Acids Res 26 1056 1062 (Pubitemid 28291662)
47. SR Pearce C Stuart-Rogers MR Knox A Kumar TH Ellis AJ Flavell 1999 Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies Plant J 19 711 717
48. SR Pearce M Knox TH Ellis AJ Flavell A Kumar 2000 Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum Mol Gen Genet 263 898 907
49. F Pompanon A Bonin E Bellemain P Taberlet 2005 Genotyping errors: causes, consequences and solutions Nat Rev Genet 6 847 859
50. A Porceddu E Albertini G Barcaccia M Falcinelli 2002 Linkage mapping in apomictic and sexual Kentucky bluegrass (Poa pratensis L.) genotypes using a two-way pseudotestcross strategy based on AFLP and SAMPL markers Theor Appl Genet 104 273 280 (Pubitemid 36065054)
51. A Porceddu E Albertini G Barcaccia G Marconi FB Bertoli F Veronesi 2002 Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L Mol Genet Genomics 267 107 114 (Pubitemid 34251589)
52. RA Queen BM Gribbon C James P Jack AJ Flavell 2004 Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat Mol Genet Genomics 271 91 97 (Pubitemid 38299689)
53. DL Remington RW Whetten BH Liu DM O'Malley 1999 Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda Theor Appl Genet 98 1279 1292 (Pubitemid 29323999)
54. D Roche J Conner A Budiman D Frisch R Wing W Hanna P Ozias-Akins 2002 Construction of BAC libraries from two apomictic grasses to study the microcolinearity of their apospory-specific genomic regions Theor Appl Genet 104 804 812 (Pubitemid 36053157)
55. Sambrook J, Russell DW (2001) Molecular cloning, 3rd edn. Cold Spring Harbor Laboratory Press, New York
56. VJ Sant MN Sainani R Sami-Subbu PK Ranjekar VS Gupta 2000 Ty1-copia retrotransposon-like elements in chickpea genome: their identification, distribution and use for diversity analysis Gene 257 157 166 (Pubitemid 30774694)
57. AM Sanz SG Gonzalez NH Syed MJ Suso CC Saldana AJ Flavell 2007 Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers Mol Genet Genomics 278 433 441 (Pubitemid 47437687)
58. A Schneider SA Walker S Poyser M Sagan TH Ellis JA Downie 1999 Genetic mapping and functional analysis of a nodulation-defective mutant (sym19) of pea (Pisum sativum L.) Mol Gen Genet 262 1 11 (Pubitemid 29423896)
59. Schulman AH, Flavell AJ, Ellis N (2004) The application of LTR retrotransposons as molecular markers in plants. In: Miller WJ, Capy P (eds) Mobile genetic elements: protocols and genomic applications. Humana Press, Totowa, pp 145-173
60. RJ Scott 2007 Polyspermy in apomictic Crataegus: yes and no New Phytol 173 227 229
61. C Spillane A Steimer U Grossniklaus 2001 Apomixis in agriculture: the quest for clonal seeds Sex Plant Reprod 14 179 187 (Pubitemid 34018130)
62. C Spillane MD Curtis U Grossniklaus 2004 Apomixis technology development-virgin births in farmers' fields? Nat Biotechnol 22 687 691 (Pubitemid 38702823)
63. A Suoniemi J Tanskanen AH Schulman 1998 Gypsy-like retrotransposons are widespread in the plant kingdom Plant J 13 699 705 (Pubitemid 28178496)
64. NH Syed S Sureshsundar MJ Wilkinson BS Bhau JJ Cavalcanti AJ Flavell 2005 Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.) Theor Appl Genet 110 1195 1202 (Pubitemid 40689312)
65. NH Syed AP Sorensen R Antonise C van de Wiel CG van der Linden W vant Westende DA Hooftman HC den Nijs AJ Flavell 2006 A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers Theor Appl Genet 112 517 527 (Pubitemid 43081595)
66. SM Tam C Mhiri A Vogelaar M Kerkveld SR Pearce MA Grandbastien 2005 Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR Theor Appl Genet 110 819 831 (Pubitemid 40534165)
67. The Rice Chromosome 10 Sequencing Consortium 2003 In-depth view of structure, activity, and evolution of rice chromosome 10 Science 300 1566 1569
68. PJ van Dijk J van Damme 2000 Apomixis technology and the paradox of sex Trends Plant Sci 5 81 84
69. PJ van Dijk IC Tas M Falque T Bakx-Schotman 1999 Crosses between sexual and apomictic dandelions (Taraxacum). II. The breakdown of apomixis Heredity 83 715 721 (Pubitemid 30044775)
70. ® 3.0, Software for the calculation of genetic linkage maps, 3rd edn. Plant Research International, Wageningen
71. S Venturi L Dondini P Donini S Sansavini 2006 Retrotransposon characterisation and fingerprinting of apple clones by S-SAP markers Theor Appl Genet 112 440 444 (Pubitemid 43081587)
72. P Vos R Hogers M Bleeker M Reijans T van de Lee M Hornes A Frijters J Pot J Peleman M Kuiper 1995 AFLP: a new technique for DNA fingerprinting Nucleic Acids Res 23 4407 4414
73. DF Voytas MP Cummings A Koniczny FM Ausubel SR Rodermel 1992 Copia-like retrotransposons are ubiquitous among plants Proc Natl Acad Sci USA 89 7124 7128
74. R Waugh K McLean AJ Flavell SR Pearce A Kumar BB Thomas W Powell 1997 Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP) Mol Gen Genet 253 687 694
75. KK Wu W Burnquist ME Sorrells TL Tew PH Moore SD Tanksley 1992 The detection and estimation of linkage in polyploids using single-dose restriction fragments Theor Appl Genet 83 294 300
76. BA Young RT Sherwood EC Bashaw 1979 Cleared-pistil and thick-sectioning techniques for detecting aposporous apomixis in grasses Can J Bot 57 1668 1672
77. GX Yu RP Wise 2000 An anchored AFLP- and retrotransposon-based map of diploid Avena Genome 43 736 749