Tandem repeats of Allium fistulosum associated with major chromosomal landmarks.
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.
Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. kirovez@gmail.com.|Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. kirovez@gmail.com.|Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium. kirovez@gmail.com.
Ilya V
IV
Kirov
Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.|Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.
Anna V
AV
Kiseleva
Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium.
Katrijn
K
Van Laere
Faculty of Medicine and Health Sciences, Center of Medical Genetics, Ghent University, Ghent, Belgium.
Nadine
N
Van Roy
Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. ludmila.khrustaleva19@gmail.com.|Department of Genetics, Biotechnology and Plant Breeding, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. ludmila.khrustaleva19@gmail.com.
Ludmila I
http://orcid.org/0000-0002-0614-4641
LI
Khrustaleva
D000490:Allium / Q000235:genetics*; D002871:Chromosome Banding; D032461:Chromosomes, Plant; D003001:Cloning, Molecular; D017343:Genes, Plant; D006570:Heterochromatin / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D017404:In Situ Hybridization, Fluorescence; D008856:Microscopy, Fluorescence; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000235:genetics; D011003:Ploidies; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences / Q000235:genetics*
D006570:Heterochromatin; D015345:Oligonucleotide Probes
Allium fistulosum; Allium wakegi; FISH; Heterochromatin; Pachytene; Pericentromeric region; Satellite DNA