Molecular Genetics and Genomics

, Volume 292, Issue 2, pp 453–464 | Cite as

Tandem repeats of Allium fistulosum associated with major chromosomal landmarks

  • Ilya V. KirovEmail author
  • Anna V. Kiseleva
  • Katrijn Van Laere
  • Nadine Van Roy
  • Ludmila I. KhrustalevaEmail author
Original Article


Tandem repeats are often associated with important chromosomal landmarks, such as centromeres, telomeres, subtelomeric, and other heterochromatic regions, and can be good candidates for molecular cytogenetic markers. Tandem repeats present in many plant species demonstrate dramatic differences in unit length, proportion in the genome, and chromosomal organization. Members of genus Allium with their large genomes represent a challenging task for current genetics. Using the next generation sequencing data, molecular, and cytogenetic methods, we discovered two tandemly organized repeats in the Allium fistulosum genome (2n = 2C = 16), HAT58 and CAT36. Together, these repeats comprise 0.25% of the bunching onion genome with 160,000 copies/1 C of HAT58 and 93,000 copies/1 C of CAT36. Fluorescent in situ hybridization (FISH) and C-banding showed that HAT58 and CAT36 associated with the interstitial and pericentromeric heterochromatin of the A. fistulosum chromosomes 5, 6, 7, and 8. FISH with HAT58 and CAT36 performed on A. cepa (2n = 2C = 16) and A. wakegi (2n = 2C = 16), a natural allodiploid hybrid between A. fistulosum and A. cepa, revealed that these repeats are species specific and produced specific hybridization patterns only on A. fistulosum chromosomes. Thus, the markers can be used in interspecific breeding programs for monitoring of alien genetic material. We applied Non-denaturing FISH that allowed detection of the repeat bearing chromosomes within 3 h. A polymorphism of the HAT58 chromosome location was observed. This finding suggests that the rapid evolution of the HAT58 repeat is still ongoing.


Allium fistulosum Allium wakegi FISH Heterochromatin Pachytene Pericentromeric region Satellite DNA 



Fluorescence in situ hybridization


Non-denaturing Fluorescence in situ hybridization


Tandem repeats






Pollen mother cells



We are grateful to Ruth Newman for correction of English in this paper. We thank our students Nataliya Kudryavtseva, Pavel Kornienkov, and Sergey Odintsov for technical assistance. This study was financially supported by a research Grant No. 16-16-10031 from the Russian Science Foundation.


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© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  1. 1.Center of Molecular BiotechnologyRussian State Agrarian University-Moscow Timiryazev Agricultural AcademyMoscowRussia
  2. 2.Department of Genetics, Biotechnology and Plant BreedingRussian State Agrarian University-Moscow Timiryazev Agricultural AcademyMoscowRussia
  3. 3.Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO)MelleBelgium
  4. 4.Faculty of Medicine and Health Sciences, Center of Medical GeneticsGhent UniversityGhentBelgium

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