Genetic mapping of centromeres in the nine Citrus clementina chromosomes using half-tetrad analysis and recombination patterns in unreduced and haploid gametes

BMC Plant Biology

Volumn 15, Issue 1, 2015, Pages

  Aleza, Pablo ^a   Cuenca, José ^a   Hernández, María ^a   Juárez, José ^a   Navarro, Luis ^a   Ollitrault, Patrick ^a,b  

^a INSTITUTO VALENCIANO DE INVESTIGACIONES AGRARIAS IVIA   (Spain)

^b UMR AGAP   (France)

Author keywords

Chromosome interference; Clementine; Genetic recombination; Physical location; Second division restitution; Triploid

Indexed keywords

CITRUS; CITRUS CLEMENTINA; CITRUS RETICULATA;

GENETIC MARKER;

CENTROMERE; CHROMOSOMAL MAPPING; CITRUS; CONFIDENCE INTERVAL; CROSS BREEDING; CROSSING OVER; FLOWER; GENETIC MARKER; GENETIC RECOMBINATION; GENETICS; HAPLOIDY; HETEROZYGOTE; METABOLISM; PLANT CHROMOSOME; PROCEDURES;

CENTROMERE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CITRUS; CONFIDENCE INTERVALS; CROSSES, GENETIC; CROSSING OVER, GENETIC; GENETIC MARKERS; GERM CELLS, PLANT; HAPLOIDY; HETEROZYGOTE; RECOMBINATION, GENETIC;

EID: 84928237629     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-015-0464-y     Document Type: Article

References (83)

1. Hall AE, Keith KC, Hall SE, Copenhaver GP, Preuss D. The rapidly evolving field of plant centromeres. Curr Opin Plant Biol. 2004;7:108-14.
2. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin X, et al. Genetic definition and sequence analysis of Arabidopsis centromeres. Science. 1999;286(5449):2468-74.
3. Ma J, Wing RA, Bennetzen JL, Jackson SA. Plant Centromere organization: a dynamic structure with conserved functions. Trends Genet. 2007;23(3):134-9.
4. Jiang J, Birchler JA, Parrot WA, Dawe RK. A molecular view of plant centromeres. Trends Plant Sci. 2003;8(12):570-5.
5. Houben A, Schubert I. DNA and proteins of plant centromeres. Curr Opin Plant Biol. 2003;6:554-60.
6. Nie H, Li Q, Zhao X, Kong L. Genetic positioning of centromeres through half-tetrad analysis in gynogenetic diploid families of the Zhikong Scallop (Chlamysfarreri). Mar Biotechnol. 2013;15:1-15.
7. Singh K, Ishii T, Parco A, Huang N, Brar DS, Khush GS. Centromere mapping and orientation of the molecular linkage map of rice (Oryzasativa L). PNAS. 1996;93:6163-8.
8. Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, Krieg F, et al. A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchusmykiss) with presumptive coverage of all chromosome arms. BMC Genomics. 2006;7:302.
9. Park TH, Kim JB, Hutten RCB, van Eck HJ, Jacobsen E, Visser RGE. Genetic positioning of centromeres using half-tetrad analysis in a 4x-2x cross population of potato. Genetics. 2007;176:85-94.
10. Copenhaver GP, Keith KC, Preuss D. Tetrad analysis in higher plants. a budding technology. Plant Physiol. 2000;124:7-15.
11. Harlan JR, De Wet JMJ. On O. Winge and a prayer: the origins of polyploidy. Botan Rev. 1975;41:361-90.
12. Bretagnolle F, Thompson JD. Gametes with the somatic chromosome number: mechanisms of their formation and role in the evolution of autopolyploid plants. New Phytol. 1995;129:1-22.
13. Ramsey J, Schemske DW. Pathways, mechanisms, and rates of polyploidy formation in flowering plants. Annu Rev Ecol Syst. 1998;29:467-501.
14. Ramsey J, Schemske DW. Neopolyploidy in flowering plants. Annu Rev Ecol Syst. 2002;33:589-639.
15. Tavoletti S, Bingham ET, Yandell BS, Veronesi F, Osborn TC. Half tetrad analysis in alfalfa using multiple restriction fragment length polymorphism markers. Proc Natl Acad Sci U S A. 1996;93:10918-22.
16. Rhoades MM, Dempsey E. Induction of chromosome doubling at meiosis by the elongate gene in maize. Genetics. 1966;54(2):505-22.
17. Mendiburu AO, Peloquin SJ. Gene-centromere mapping by 4x-2x matings in potatoes. Theor Appl Genet. 1979;54:177-80.
18. Veilleux R. Diploid and polyploid gametes in crop plants: mechanisms of formation and utilization in plant breeding. Plant Breed Rev. 1985;3:253-88.
19. Carputo D, Barone A, Frusciante L. 2n gemetes in the potato: essential ingredients for breeding and germplasm transfer. Theor Appl Genet. 2000;101:805-13.
20. Ramanna MS, Jacobsen E. Relevance of sexual polyploidization for crop improvement-a review. Euphytica. 2003;133:3-18.
21. Esen A, Soost RK. Unexpected triploids in citrus: their origin, identification and possible use. J Hered. 1971;62:329-33.
22. Geraci G, De Pasquale F, Tusa N. Percentages of spontaneous triploids in progenies of diploid lemons and mandarins. In: Grierson W, editor. Proceedings of Second International Citrus Congress. International Society of Citriculture, vol. 2. 1977. p. 596-7.
23. Bastiaanssen HJM, Van Den Berg PMMM, Lindhout P, Jacobsen E, Ramanna MS. Postmeiotic restitution in 2n-egg formation of diploid potato. Heredity. 1998;81:20-7.
24. Cuenca J, Froelicher Y, Aleza P, Juarez J, Navarro L, Ollitrault P. Multilocus half-tetrad analysis and centromere mapping in citrus: evidence of SDR mechanism for 2n megagametophyte production and partial chiasma interference in mandarin cv 'Fortune'. Heredity. 2011;107:462-70.
25. Douches DS, Quiros CF. Genetic strategies to determine the mode of 2n egg formation in diploid potatoes. Euphytica. 1988;38(3):247-60.
26. Luro F, Maddy F, Ollitrault P, Rist D. Identification of 2n gamete parental origin and mode of nuclear restitution of spontaneous triploid citrus hybrids. In: Proceedings of 9th International Citrus Congress. Orlando: International Society of Citriculture; 2000. p. 168-9. 3-7 December.
27. Crespel L, Gudin S. Evidence for the production of unreduced gametes by tetraploid Rosa hybrida L. Euphytica. 2003;133:65-9.
28. Kauffman EJ, Gestl EE, Kim DJ, Walker C, Hite JM, Yan G, et al. Microsatellite-centromere mapping in the Zebrafish (Daniorerio). Genomics. 1995;30:337-41.
29. Bastiaanssen HJM, Ramanna MS, Sawor Z, Mincione A, Steen A, Jacobsen E. Pollen markers for gene-centromere mapping in diploid potato. Theor Appl Genet. 1996;93:1040-7.
30. FAOSTAT [ http://faostat.fao.org/site/567/DesktopDefault.aspx?PageID=567#ancor ]
31. Ollitrault P, Terol J, Chen C, Federici CT, Lotfy S, Hippolyte I, et al. A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genomics. 2012;13:593.
32. Wu AG, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol. 2014;32:656-62.
33. Aleza P, Juárez J, Hernández M, Pina JA, Ollitrault P, Navarro L. Recovery and characterization of a Citrus clementina Hort ex Tan Clemenules haploid plant selected to establish the reference whole Citrus genome sequence. BMC Plant Biol. 2009;9:110.
34. Ollitrault P, Dambier D, Luro F, Froelicher Y. Ploidy manipulation for breeding seedless triploid citrus. Plant Breed Rev. 2008;30:323-52.
35. Aleza P, Juárez J, Cuenca J, Ollitrault P, Navarro L. Recovery of citrus triploid hybrids by embryo rescue and flow cytometry from 2x X 2x sexual hybridisation and its application to extensive breeding programs. Plant Cell Rep. 2010;29:1023-34.
36. Chen C, Lyon MT, O'Malley D, Federici CT, Gmitter J, Grosser JW, et al. Origin and frequency of 2n gametes in Citrus sinensis x Poncirus trifoliata and their reciprocal crosses. Plant Sci. 2008;174:1-8.
37. Ollitrault P, Terol J, Garcia-Lor A, Bérard A, Chauveau A, Froelicher Y, et al. SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genomics. 2012;10:13-3.
38. Esselink GD, Nybom H, Vosman B. Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting-peak ratios) method. Theor Appl Genet. 2004;109:402-8.
39. Cuppen E. Genotyping. by allele-specific amplification (KASPar). Cold Spring Harb Protoc 2007; 172-173. doi: 10.1101/pdb.prot4841.
40. Cuenca J, Aleza P, Vicent A, Brunel D, Ollitrault P, Navarro L. Genetically based location from triploid populations and gene ontology of a 3.3-Mb genome region linked to alternaria brown spot resistance in citrus reveal clusters of resistance genes. PLoS One. 2013;8(10):e76755.
41. Zhao H, Speed TP. Statistical analysis of ordered tetrads. Genetics. 1998;150:459-72.
42. Griffiths A, Miller J, Suzuki D, Lewontin R, Gelbart W. An Introduction to Genetic Analysis. 6th ed. New York, USA: W. H. Freeman and Company; 1996.
43. Zhao H, Speed TP. Statistical analysis of half-tetrads. Genetics. 1998;150:473-85.
44. Lander ES, Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989;121:185-99.
45. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;3:403-10.
46. Esen A, Soost RK. Precocious development and germination of spontaneous triploid seeds in citrus. J Hered. 1973;64:147-54.
47. Geraci G, Esen A, Soost RK. Triploid progenies from 2x-2x crosses of citrus cultivars. J Hered. 1975;66:177-8.
48. Esen A, Soost RK, Geraci G. Genetic evidence for the origin of diploid megagametophytes in Citrus. J Hered. 1979;70:5-8.
49. Wakana A, Iwamasa M, Uemoto S. Seed development in relation to ploidy of zygotic embryo and endosperm in polyembryonic Citrus. Proc Int Soc Citricult. 1981;1:135-9.
50. Soost R. Breeding citrus-genetics and nucellarembryony. In: Abbott AJ, Atkin R, editors. Improving Vegetatively Propagated Crops. London: Academic Press; 1987. p. 83-110.
51. Ferrante SP, Lucretti S, Reale S, De Patrizio A, Abbate L, Tusa N, et al. Assessment of the origin of new citrus tetraploid hybrids (2n = 4x) by means of SSR markers and PCR based dosage effects. Euphytica. 2010;173:223-33.
52. Errico A, Cammareri M, Conicella C. Meiotic nuclear restitution mechanisms in a triploid lily. Caryologia. 2005;58(4):367-73.
53. Brownfield L, Kohler C. Unreduced gamete formation in plants: mechanisms and prospects. J Exp Bot. 2011;62:1659-68.
54. Barone A, Gebhardt C, Frusciante L. Heterozygosity in 2n gametes of potato evaluated by RFLP markers. Theor Appl Genet. 1995;91(1):98-104.
55. Vorsa N, Rowland LJ. Estimation of 2n megagametophyteheterozygosity in a diploid blueberry (Vacciniumdarrowi Camp) clone using RAPDs. J Hered. 1997;88(5):423-6.
56. Dewitte A, Van Laere K, Van Huylenbroeck J. Use of 2n fametes in plant breeding. In: Ibrokhim Y, editor. Plant Breeding. Abdurakhmonov: InTech; 2011. p. 59-88.
57. Douches DS, Maas DL. Comparison of FDR and SDR derived tetraploid progeny from 2x x 4x crosses using haploids of Solanumtuberosum L. that produce mixed modes of 2n eggs. Theor Appl Genet. 1998;97:1307-13.
58. Mok DWS, Peloquin SJ. Three mechanisms of 2n pollen formation in diploid potatoes. Can J Genet Cytol. 1975;17:217-25.
59. Kidane-Mariam HM, Arndt GC, Macaso-Khwaja AC, Peloquin SJ. Comparisons between 4x × 2x hybrid and open-pollinated true potato seed families. Potato Res. 1985;28:35-42.
60. David JL, Boudec P, Gallais A. Quantitative genetics of 4x-2x hybrid populations with First-Division Restitution and 2nd-Division Restitution 2n gametes produced by diploid parents. Genetics. 1995;139(4):1797-803.
61. Buso JA, Boiteux LS, Tai GCC, Peloquin SJ. Chromosome regions between centromeres and proximal crossovers are the physical sites of major effect loci for yield in potato: genetic analysis employing meiotic mutants. PNAS. 1999;96(4):1773-8.
62. Zhu C, Sun Y, Yu X, Tong J. Centromere localization for bighead carp (Aristichthysnobilis) through Half-Tetrad analysis in diploid gynogenetic families. PLoS One. 2013;8(12):e82950.
63. Zhao H, Speed TP, McPeek MS. Statistical analysis of crossover interference using the chi-square model. Genetics. 1995;139:1045-56.
64. Zhao H, Speed TP. On genetic map functions. Genetics. 1996;142:1369-77.
65. Werner JE, Douches DS, Freyre R. Use of half-tetrad analysis to discriminate between 2 types of 2n egg formation in a potato haploid. Genome. 1992;35:741-5.
66. Teuscher F, Brockmann GA, Rudolph PE, Swalve HH, Guiard V. Models for chromatid interference with applications to recombination data. Genetics. 2000;156:1449-60.
67. Giraut L, Falque M, Drouaud J, Pereira L, Martin OC, Mézard C. Genome-Wide crossover distribution in arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. Plos Genetics 2011, doi:10.1371/journal.pgen.1002354.
68. Drouaud J, Mercier R, Chelysheva L, Berard A, Falque M, Martin O, et al. Sex-specific crossover distributions and variations in interference level along Arabidopsis thaliana chromosome 4. PLoS Genet. 2007;3:e106.
69. Lian J, Yin Y, Oliver-Bonet M, Liehr T, Ko E, Turek P, et al. Variation in crossover interference levels on individual chromosomes from human males. Hum Mol Genet. 2008;17(17):2583-94.
70. Broman KW, Rowe LB, Churchill GA, Paigen K. Crossover interference in the mouse. Genetics. 2002;160:1123-31.
71. Levan A, Fredga K, Sandberg AA. Nomenclature for centromeric position on chromosomes. Hereditas. 1964;52:201-20.
72. Dobzhansky T. Translocations involving the third and fourth chromosomes of Drosophila melanogaster. Genetics. 1930;15:347-99.
73. Sherman JD, Stack SM. Two-dimensional spreads of synaptonemal complexes from solanaceous plants VI high-resolution recombination nodule map for tomato (Lycopersiconesculentum). Genetics. 1995;141:683-708.
74. Gill SK, Gill BS, Endo TR, Taylor T. Identification and high-density mapping of gene-rich regions in chromosome group I of wheat. Genetics. 1996;144:1883-91.
75. Haupt W, Fischer TC, Winderl S, Fransz P, Torres-Ruiz RA. The centromere1 (CEN1) region of Arabidopsis thaliana: architecture and functional impact of chromatin. Plant J. 2001;27:285-96.
76. Chen M, Prestin G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, et al. An integrated physical and genetic map of the rice genome. Plant Cell. 2002;14(3):537-45.
77. Anderson LK, Doyle GG, Brigham B, Carter J, Hooker KD, Lai A, et al. High resolution crossover maps for each bivalent of Zea mays using recombination nodules. Genetics. 2003;165:849-65.
78. Talbert PB, Henikoff S. Centromeres convert but don't cross. PLoS Biol. 2010;8:e1000326. doi:1000310.1001371/journal.pbio.1000326.
79. Wang G, Zhang X, Jin W. An overview of plant centromeres. J Genet Genomics. 2009;36(9):529-37. doi: 10.1016/S1673-8527(08)60144-7.
80. Sandhu D, Gill K. Gene-containing regions of wheat and the other grass genomes. Plant Physiol. 2002;128:803-11.
81. Erayman M, Sandhu D, Sidhu D, Dilbirligi M, Baenziger PS, Gill KS. Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res. 2004;32(12):3546-65.
82. Tian Z, Rizzon C, Du J, Zhu L, Bennetzen JL, Jackson SA, et al. Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res. 2009;19(12):2221-30.
83. Liu Z, Yue W, Li D, Wang R, Kong X, Lu K, et al. Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres. Chromosoma. 2008;117:445-56.