Genomic relationships among sixteen species of Avena based on (ACT)₆ trinucleotide repeat FISH

Abstract

Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and their assignment to physical chromosomes. Genomic and species relationships among 16 species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT) probes. The Am1 oligonucleotide probe was particularly enriched in the C genomes, whereas the (ACT) trinucleotide repeat probe showed a diverse distribution of hybridization patterns in the A, AB, C, AC, and ACD genomes but might not be present in the B and D genomes. The hybridization pattern of Avena sativa was very similar to that of A. insularis, indicating that this species most likely originated from A. insularis as a tetraploid ancestor. Although the two FISH probes failed to identify relationships of more species, this proof-of-concept approach opens the way to the use of FISH probes in assigning other signature elements from genomic sequence to physical chromosomes.

New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum

“…Most of the signals produced were located at the centrometic or petricentromeric regions (Figs 1 and 2). These results were consistent with previous studies [32][33][34], and implied that Avena genomes contain more repetitive sequences in the centromeric regions of the chromosome than in intercalary parts, as has been found in many other plants [24,36,41]. Signal numbers produced by these three SSR probes varied, with (AAC) 5 producing the most hybridization signals, followed by (CAG) 5 .…”

“…ND-FISH uses synthesized oligonucleotide sequences as probes, and performs FISH analysis under non-denaturing conditions, thus substantially simplifying the procedure [30]. It has been widely used for cytogenetic studies in barley [27,31], wheat [28], and rye [28], but less often for oat [32][33][34][35].…”

Physical Map of FISH 5S rDNA and (AG3T3)3 Signals Displays Chimonanthus campanulatus R.H. Chang & C.S. Ding Chromosomes, Reproduces its Metaphase Dynamics and Distinguishes Its Chromosomes

“…[65], 1–4 μM in Rubus L. species [68], 1.82–2.75 μM in Berberis diaphana Maxim. [69], 4.03–7.21 μM in Piptanthus concolor Harrow ex Craib [62], 4–13 μM in Avena sativa L. [70], and 9–13 μM in Triticum aestivum L. ‘Chinese Spring’ [71]. In our unpublished works, chromosome lengths were recorded to be 0.97–2.16 μM in Juglans regia L., 0.98–2.65 μM in Juglans sigillata Dode, 1.13–2.41 μM in Firmiana platanifolia (L. f.) Marsili, 1.12–2.49 μM in Koelreuteria bipinnata Franch., 1.31–1.43 μM in Robinia pseudoacacia L., 1.44–5.28 μM in Podocarpus macrophyllus (Thunb.)…”

Cytogenetic events in the endosperm of amphiploidAvena maroccana×A. longiglumis

“…Using a probe of A. eriantha (Cp genome), Nikoloudakis and Katsiotis (2015) determined four major C/A terminal translocations in the root tissue of a triploid hybrid A. magna × A. longiglumis. In A. maroccana (synonym A. magna), the number of such translocations was determined as six by using oligo-probes (Fominaya et al 1995;Luo et al 2018b) and as eight by using genomic DNA (Leggett et al 1994) or oligo-Am1 probe (Luo et al 2018a). The translocations were tiny and terminal or sub-terminal.…”