Advertisement

Theoretical and Applied Genetics

, Volume 129, Issue 3, pp 535–545 | Cite as

High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion

  • Ludmila Khrustaleva
  • Jiming Jiang
  • Michael J. Havey
Original Article

Abstract

Key message

Tyramide FISH was used to locate relatively small genomic amplicons from molecular markers linked to Ms locus onto onion chromosome 2 near the centromere, a region of relatively low recombination.

Abstract

Fluorescence in situ hybridization (FISH) has not been readily exploited for physical mapping of molecular markers in plants due to the technical challenge of visualizing small single-copy probes. Signal amplification using tyramide (tyr) FISH can increase sensitivity up to 100-fold. We used tyr-FISH to physically locate molecular markers tightly linked to the nuclear male-fertility (Ms) restoration locus of onion onto mitotic metaphase, pachytene, and super-stretched pachytene chromosomes. Relatively short genomic amplicons (846–2251 bp) and a cDNA clone (666 bp) were visualized in 9–42 % of observed cells. The markers were assigned to proximal locations close to the centromere on the long arm of chromosome 2, a region of lower recombination, revealing that tightly linked markers may be physically distant from Ms. This result explains why several labs have identified molecular markers tightly linked to the Ms locus after screening relatively few DNA clones or primers and segregating progenies. Although these markers are still useful for marker-aided selection, our results indicate that map-based cloning of Ms will likely be difficult due to reduced recombination near this gene.

Keywords

Cytoplasmic Male Sterility Restriction Fragment Length Polymorphism Mitotic Metaphase Pachytene Chromosome Mitotic Metaphase Chromosome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We gratefully acknowledge the support of a research fellowship to LK (IIE Grantee ID 68130146) from the Fulbright-Hayes Program.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Disclaimer

Names are necessary to report factually on available data; however, the U.S. Department of Agriculture (USDA) neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.

References

  1. Albini SM, Jones GH (1988) Synaptonemal complex spreading in Allium cepa and Allium fistulosum. II. Pachytene observations: the SC karyotype and the correspondence of late recombination nodules and chiasmata. Genome 30:399–410. doi: 10.1139/g88-069 CrossRefGoogle Scholar
  2. Anderson LK, Stack SM, Fox MH, Zhang C (1985) The relationship between genome size and synaptonemal complex length in higher plants. Expl Cell Res 156:367–377. doi: 10.1016/0014-4827(85)90544-0 CrossRefGoogle Scholar
  3. Anderson LK, Doyle GG, Brigham B, Carter J, Hooker KD, Lai A, Rice M, Stack SM (2003) High-resolution crossover maps for each bivalent of Zea mays using recombination nodules. Genetics 165:849–865PubMedCentralPubMedGoogle Scholar
  4. Bang H, Kim S, Park SO, Yoo KS, Patil BS (2013) Development of a codominant CAPS marker linked to the Ms locus controlling fertility restoration in onion (Allium cepa L.). Sci Hortic 153:42–49. doi: 10.1016/j.scienta.2013.01.020 CrossRefGoogle Scholar
  5. Bennett MD, Leitch IJ (2012) Plant DNA C-values database (release 6.0, Dec. 2012) http://www.kew.org/cvalues/
  6. Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001) Toward a cytological characterization of the rice genome. Genome Res 11:2133–2141. doi: 10.1101/gr.194601 PubMedCentralCrossRefPubMedGoogle Scholar
  7. Cheng ZK, Buell CR, Wing RA, Jiang JM (2002) Resolution of fluorescence in situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chrom Res 10:379–387. doi: 10.1023/A:1016849618707 CrossRefPubMedGoogle Scholar
  8. Cho KS, Hong SY, Kwon YS, Woo JG, Moon JY, Ryu SY, Park HG (2005) Selection of maintainer line in open-pollinated onion (Allium cepa L. cv. “Manchuhwang”) using SCAR marker linked to cytoplasmic male sterile factor. Korean J Breed 37:133–137. doi: 10.1590/S0103-90162010000200015 Google Scholar
  9. Cho KS, Yang TJ, Hong SY, Kwon YS, Woo JG, Park HG (2006) Determination of cytoplasmic male sterile factors in onion (Allium cepa L.) using PCR-RFLP and SNP markers. Mol Cells 21:411–417PubMedGoogle Scholar
  10. Danilova T, Birchler J (2008) Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity and banding paint development. Chromosoma 117:345–356. doi: 10.1007/s00412-008-0151-y CrossRefPubMedGoogle Scholar
  11. Danilova TV, Friebe B, Gill BS (2012) Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 121:597–611. doi: 10.1007/s00412-012-0384-7 CrossRefPubMedGoogle Scholar
  12. Danilova TV, Friebe B, Gill BS (2014) Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet 127:715–730. doi: 10.1007/s00122-013-2253-z PubMedCentralCrossRefPubMedGoogle Scholar
  13. de Courcel A, Veder F, Boussac J (1989) DNA polymorphism in Allium cepa cytoplasms and its implications concerning the origin of onions. Theor Appl Genet 77:793–798. doi: 10.1007/bf00268328 CrossRefPubMedGoogle Scholar
  14. de Jong H (2003) Visualizing DNA domains and sequences by microscopy: a fifty-year history of molecular cytogenetics. Genome 46:943–946. doi: 10.1139/g03-107 CrossRefPubMedGoogle Scholar
  15. de Jong H, Fransz P, Zabel P (1999) High resolution FISH in plants—technique and application. Trend Plant Sci 4:258–263. doi: 10.1016/S1360-1385(99)01436-3 CrossRefGoogle Scholar
  16. de Vries JN (1990) Onion chromosome nomenclature and homoeology relationships—workshop report. Euphytica 49:1–3. doi: 10.1007/bf00024124 CrossRefGoogle Scholar
  17. Engelke T, Terefe D, Tatlioglu T (2003) A PCR-based marker system monitoring CMS-(S), CMS-(T) and (N)-cytoplasm in the onion (Allium cepa L.). Theor Appl Genet 107:162–167. doi: 10.1007/s00122-003-1230-3 PubMedGoogle Scholar
  18. Figueroa DM, Bass HW (2010) A historical and modern perspective on plant cytogenetics. Brief Funct Genom 9:95–102. doi: 10.1093/bfgp/elp058 CrossRefGoogle Scholar
  19. Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen C, Dean C, Zabel P, Bisseling T, Jones GH (2000) Integrated cytogenetic map of chromosome arm 4S of A.thaliana: structural organization of heterochromatic knob and centromere region. Cell 100:367–376. doi: 10.1016/s1369-5266(00)80013-8 CrossRefPubMedGoogle Scholar
  20. Gökçe AF, Havey MJ (2002) Linkage equilibrium among tightly linked RFLPs and the Ms locus in open-pollinated onion populations. J Amer Soc Hort Sci 127:944–946Google Scholar
  21. Gökçe AF, McCallum J, Sato Y, Havey MJ (2002) Molecular tagging of the Ms locus in onion. J Amer Soc Hort Sci 127:576–582Google Scholar
  22. Haupt W, Fischer TC, Winderl S, Fransz P, Torres-Ruiz RA (2001) The centromere1 (CEN1) region of Arabidopsis thaliana: architecture and functional impact of chromatin. Plant J 27:285–296. doi: 10.1046/j.1365-313x.2001.01087.x CrossRefPubMedGoogle Scholar
  23. Havey MJ (1993) A putative donor of S-cytoplasm and its distribution among open-pollinated populations of onion. Theor Appl Genet 86:128–134. doi: 10.1007/bf00223817 CrossRefPubMedGoogle Scholar
  24. Havey MJ (1995) Identification of cytoplasms using the polymerase chain reaction to aid in the extraction of maintainer lines from open-pollinated populations of onion. Theor Appl Genet 90:263–268. doi: 10.1007/bf00222212 CrossRefPubMedGoogle Scholar
  25. Havey MJ (2004) The use of cytoplasmic male sterility for hybrid seed production. In: Daniel H, Chase C (eds) Molecular biology and biotechnology of plant organelles. Kluwer Academic Publishers, The Netherlands, pp 623–634CrossRefGoogle Scholar
  26. Havey MJ (2013) Single nucleotide polymorphisms in linkage disequilibrium with the male-fertility restoration (Ms) locus of onion. J Amer Soc Hort Sci 138:306–309Google Scholar
  27. Holford P, Croft J, Newbury H (1991) Differences between and possible origins of the cytoplasms found in fertile and male-sterile onions (Allium cepa L.). Theor Appl Genet 82:737–744. doi: 10.1007/bf00227319 PubMedGoogle Scholar
  28. Hou Y, Miao J, Liu B, Yang Y, Zhang Y, Tahara Y, Meng Q, He Q, Kitano H, Wu X (2012) The expression of pectin methylesterase in onion flower buds is associated with the dominant male-fertility restoration allele. Plant Breed 131:211–216. doi: 10.1111/j.1439-0523.2011.01907.x CrossRefGoogle Scholar
  29. Iovene M, Wielgus SM, Simon PW, Buell CR, Jiang JM (2008) Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics 180:1307–1317. doi: 10.1534/genetics.108.093179 PubMedCentralCrossRefPubMedGoogle Scholar
  30. Jiang J, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068. doi: 10.1139/g06-076 CrossRefPubMedGoogle Scholar
  31. Jones A, Clarke A (1943) Inheritance of male sterility in the onion and the production of hybrid seed. Proc Amer Soc Hort Sci 43:189–194Google Scholar
  32. Jones HA, Davis GN (1944) Inbreeding and heterosis and their relation to the development of new varieties of onions. US Dept Agr Tech Bul No 874, Washington, p 28Google Scholar
  33. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467. doi: 10.1159/000084979 CrossRefPubMedGoogle Scholar
  34. Karafiátová M, Bartoš J, Kopecký D, Ma L, Sato K, Houben A, Stein N, Doležel J (2013) Mapping nonrecombining regions in barley using multicolor FISH. Chrom Res 21:9380. doi: 10.1007/s10577-013-9380-x CrossRefGoogle Scholar
  35. Khan WA, Rogan PK, Knoll JHM (2014) Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes. Mol Cytogenet 7:70. doi: 10.1186/s13039-014-0070-y PubMedCentralCrossRefPubMedGoogle Scholar
  36. Khan WA, Rogan PK, Knoll JHM (2015) Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes. Mol Cytogenet 8:65. doi: 10.1186/s13039-015-0159-y PubMedCentralCrossRefPubMedGoogle Scholar
  37. Khrustaleva LI, Kik C (2001) Localization of single copy T-DNA insertion in transgenic shallots (Allium cepa L.) by using ultra-sensitive FISH with tyramide signal amplification. Plant J 25:699–707. doi: 10.1046/j.1365-313x.2001.00995.x CrossRefPubMedGoogle Scholar
  38. Khrustaleva LI, de Melo PE, van Heusden AW, Kik C (2005) The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid Allium population. Genetics 169:1673–1685. doi: 10.1534/genetics.104.038687 PubMedCentralCrossRefPubMedGoogle Scholar
  39. Kim S (2014) A codominant molecular marker in linkage disequilibrium with a restorer-of-fertility gene (Ms) and its application in reevaluation of inheritance of fertility restoration in onions. Mol Breed 34:769–778. doi: 10.1007/s11032-014-0073-8 CrossRefGoogle Scholar
  40. Kim S, Lee E, Cho DY, Han T, Bang H, Patil BS, Ahn YK, Yoon M (2009) Identification of a novel chimeric gene, orf725, and its use in development of a molecular marker for distinguishing among three cytoplasm types in onion (Allium cepa L.). Theor Appl Genet 118:433–441. doi: 10.1007/s00122-008-0909-x CrossRefPubMedGoogle Scholar
  41. Kirov I, Divashuk M, Van Laere K, Soloviev A, Khrustaleva L (2014a) An easy ‘‘SteamDrop’’ method for high quality plant chromosome preparation. Mol Cytogenet 7:21. doi: 10.1186/1755-8166-7-21 PubMedCentralCrossRefPubMedGoogle Scholar
  42. Kirov I, Van Laere K, De Riek J, De Keyser E, Van Roy N, Khrustaleva L (2014b) Anchoring linkage groups of the Rosa genetic map to physical chromosomes with tyramide-FISH and EST-SNP markers. PLoS One 9(4):e95793. doi: 10.1371/journal.pone.0095793 PubMedCentralCrossRefPubMedGoogle Scholar
  43. Kirov IV, Van Laere K, Khrustaleva LI (2015) High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa. BMC Genet 16:74. doi: 10.1186/s12863-015-0233-9 PubMedCentralCrossRefPubMedGoogle Scholar
  44. Koo D-H, Jiang J (2009) Supper-stretched pachytene chromosomes for fluorescence in situ hybridization mapping and immunodetection of DNA methylation. Plant J 59:509–516. doi: 10.1111/j.1365-313x.2009.03881.x CrossRefPubMedGoogle Scholar
  45. Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation break points. Genetics 154:397–412PubMedCentralPubMedGoogle Scholar
  46. Lamb JC, Danilova T, Bauer MJ, Meyer JM, Holland JJ, Jensen MD, Birchler JA (2007) Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 175:1047–1058. doi: 10.1534/genetics.106.065573 PubMedCentralCrossRefPubMedGoogle Scholar
  47. Lilly JW, Havey MJ (2001) Sequence analysis of a chloroplast intergenic spacer for phylogenetic estimates and a PCR-based polymorphism detecting mixtures of male-fertile and male-sterile cytoplasmic onion. Theor Appl Genet 102:78–82. doi: 10.1007/s001220051620 CrossRefGoogle Scholar
  48. Liu Z, Wang D, Feng J, Seiler GJ, Cai X, Jan CC (2013) Diversifying sunflower germplasm by integration and mapping of a novel male fertility restoration gene. Genetics 193:727–737. doi: 10.1534/genetics.112.146092 PubMedCentralCrossRefPubMedGoogle Scholar
  49. Martin W, McCallum J, Shigyo M, Jakse J, Kuhl JC, Yamane N, Sink KC, Town CD, Havey MJ (2005) Genetic mapping of expressed sequences in onion and in silico comparisons show scant colinearity with rice. Mol Genet Genom 274:197–204. doi: 10.1007/s00438-005-0007-6 CrossRefGoogle Scholar
  50. Park J, Bang H, Cho DY, Yoon MK, Patil BS, Kim S (2013) Construction of high-resolution linkage map of the Ms locus, a restorer-of-fertility gene in onion (Allium cepa L.). Euphytica 192:267–278. doi: 10.1007/s10681-012-0851-5 CrossRefGoogle Scholar
  51. Pedersen C, Linde-Laursen I (1995) The relationship between physical and genetic distances at the Hor1 and Hor2 loci of barley estimated by two-colour fluorescent in situ hybridization. Theor App Genet 91:941–946. doi: 10.1007/bf00223904 Google Scholar
  52. Perez R, de Bustos A, Jouve N, Cuadrado A (2009) Localization of Rad50, a single-copy gene, on group 5 chromosomes of wheat, using a FISH protocol employing Tyramide for signal amplification (Tyr-FISH). Cytogenet Genome Res 125:321–328. doi: 10.1159/000235938 CrossRefPubMedGoogle Scholar
  53. Raap A, van de Corput M, Vervenne R, van Gijlswijk R, Tanke H, Wiegant J (1995) Ultra-sensitive FISH using peroxidase-mediated deposition of biotin- or fluorochrome-tyramides. Hum Mol Genet 4:529–534. doi: 10.1093/hmg/4.4.529 CrossRefPubMedGoogle Scholar
  54. Reeves A, Tear J (2000) MicroMeasure for Windows.Version 3.3. http://www.colostate.edu/Depts/Biology/MicroMeasure. Accessed 20 Feb 2015
  55. Romanov D, Divashuk M, Havey MJ, Khrustaleva L (2015) Tyramide-FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa L. Genome. doi: 10.1139/gen-2015-0019 PubMedGoogle Scholar
  56. Sambrook J, Russell DW (1989) Molecular cloning: A laboratory manual, vol 1. Cold Spring Harbor Press, New York, pp 33–162Google Scholar
  57. Sanz MJ, Loarce Y, Ferrer E, Fominaya A (2012) Use of tyramide-fluorescence in situ hybridization and chromosome microdissection for ascertaining homology relationships and chromosome linkage group associations in oats. Cytogenet Genome Res 136:145–156. doi: 10.1159/000335641 CrossRefPubMedGoogle Scholar
  58. Sato Y (1998) PCR amplification of CMS-specific mitochondrial nucleotide sequences to identify cytoplasmic genotypes of onion (Allium cepa L.). Theor Appl Genet 96:367–370. doi: 10.1007/s001220050750 CrossRefPubMedGoogle Scholar
  59. Satoh Y, Nagai M, Mikami M, Kinoshita T (1993) The use of mitochondrial DNA polymorphism in the classification of individual plants by cytoplasmic genotypes. Theor Appl Genet 86:345–348. doi: 10.1007/bf00222100 PubMedGoogle Scholar
  60. Sherman JD, Stack SM (1995) Two-dimensional spreads of synaptonemal complexes from Solanaceous plants. VI. High resolution recombination nodule map for tomato (Lycopersicon esculentum). Genetics 141:683–708PubMedCentralPubMedGoogle Scholar
  61. Speel EJM, Hopman AHN, Komminoth P (1999) Amplification methods to increase the sensitivity of in situ hybridization: play CARD(S). J Histochem Cytochem 47:281–288. doi: 10.1177/002215549904700302 CrossRefPubMedGoogle Scholar
  62. Stephens JL, Brown SE, Lapitan NLV, Knudson DL (2004) Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47:179–189. doi: 10.1139/g03-084 CrossRefPubMedGoogle Scholar
  63. Sugiyama S, Yoshino T, Kanahara H, Shichiri M, Fukushi D, Ohtani T (2004) Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy. Anal Biochem 324:39–44. doi: 10.1016/j.ab.2003.09.026 CrossRefPubMedGoogle Scholar
  64. Suzuki G, Ura A, Saito N, Do GS, Seo BB, Yamamoto M, Mukai Y (2001) BAC FISH analysis in Allium cepa. Genes Genet Syst 76:251–255. doi: 10.1266/ggs.76.251 CrossRefPubMedGoogle Scholar
  65. Szinay D, Chang SB, Khrustaleva L, Peters S, Schijlen E, Bai Y, Stiekema WJ, van Ham RC, de Jong H, Klein Lankhorst RM (2008) High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. Plant J 56:627–637. doi: 10.1111/j.1365-313x.2008.03626.x CrossRefPubMedGoogle Scholar
  66. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB (1992) High-density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160PubMedCentralPubMedGoogle Scholar
  67. van Gijlswijk RPM, Zijlmans HJMA, Wiegant J, Bobrow MN, Erickson TJ, Adler KE, Tanke HJ, Raap AK (1997) Fluorochrome-labeled Tyramides: use in immunocytochemistry and fluorescence in situ hybridization. J Histochem Cytochem 45:375–382. doi: 10.1177/002215549704500305 CrossRefPubMedGoogle Scholar
  68. von Kohn C, Kiełkowska A, Havey MJ (2013) Sequencing and annotation of the chloroplast DNAs of normal (N) male-fertile and male-sterile (S) cytoplasms of onion and single nucleotide polymorphisms distinguishing these cytoplasms. Genome 56:737–742. doi: 10.1139/gen-2013-0182 CrossRefGoogle Scholar
  69. Werner JE, Endo TR, Gill BS (1992) Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci USA 89:11307–11311. doi: 10.1073/pnas.89.23.11307 PubMedCentralCrossRefPubMedGoogle Scholar
  70. Yamashita K-I, Takatori Y, Tashiro Y (2005) Chromosomal location of a pollen fertility-restoring gene, Rf, for CMS in Japanese bunching onion (Allium fistulosum L.) possessing the cytoplasm of A. galanthum Kar. Et Kir. revealed by genomic in situ hybridization. Theor Appl Genet 111:15–22. doi: 10.1007/s00122-005-1941-8 CrossRefPubMedGoogle Scholar
  71. Yang YY, Huo YM, Miao J, Liu BJ, Kong SP, Gao LM, Liu C, Wang ZB, Tahara Y, Kitano H, Wu X (2013) Identification of two SCAR markers co-segregated with the dominant Ms and recessive ms alleles in onion (Allium cepa L.). Euphytica 190:267–277. doi: 10.1007/s10681-012-0842-6 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Ludmila Khrustaleva
    • 1
  • Jiming Jiang
    • 2
  • Michael J. Havey
    • 3
  1. 1.Center of Molecular Biotechnology, Department of Genetics and BiotechnologyRussian State Agrarian University-Timiryazev Agricultural AcademyMoscowRussia
  2. 2.Department of HorticultureUniversity of WisconsinMadisonUSA
  3. 3.USDA-ARS and Department of HorticultureUniversity of WisconsinMadisonUSA

Personalised recommendations