Abstract
BackgroundThe identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species.ResultsTandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa.ConclusionsThis new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.
Highlights
The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization
The lowest proportion of chromosome sequence length contributed by tandem repeats (TR) was for chromosome 6D at 1.11 %, and highest proportion of sequence length contributed by TRs was for chromosome 6 C reaching 8.67 % (Figure S1a)
We found that the physical distribution of the probes on AA1 to AA7 chromosomes closely matched their locations revealed by ND-fluorescence in situ hybridization (FISH) on the A genome of A. sativa
Summary
The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. The common oat (Avena sativa L., 2n = 6x = 42, AACC DD) is a temperate crop (annual production of 23 million tons in 2017; http://faostat.fao.org) which is primarily used for livestock feed and partially for human food. It is a food crop recommended by nutritionists because. Identification of the chromosome complements of Avena species has been successfully achieved using fluorescence in situ hybridization (FISH) based on the satellite sequence pAs120a, specific to the A genome, in combination with rDNA probes and the sequence pAm1, satellite DNA specific to the C genome [14, 15]. Establishment of a universal karyotyping nomenclature system for each individual oat chromosome pair would be of enormous benefit to Avena researchers
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