Genomic relationships among sixteen species of Avena based on (ACT)<inf>6</inf> trinucleotide repeat FISH
Citation
Luo, X., Tinker, N.A., Zhou, Y., Wight, C.P., Liu, J., Wan, W., Chen, L., Peng, Y. (2018). Genomic relationships among sixteen species of Avena based on (ACT)6 trinucleotide repeat FISH. Genome, [online] 61(1), 63-70. http://dx.doi.org/10.1139/gen-2017-0132
Plain language summary
Repeat elements are short motifs in DNA that are repeated in tandem. Knowledge of the locations of repeat elements could be very important development of complete genome sequences. In this study used DNA probes (short labelled pieces of DNA) to highlight regions of the oat genome where DNA was most similar to the sequences in the probes. This technique is called “fluorescence in situ hybridization (FISH)”. One of our probes was made from a short repeated sequence of ACT. We also used a previously identified probe called “Am1” that was known to hybridize to specific oat chromosomes. By conducting FISH in cultivated oat as well as in various wild species that are related to oat, we could identify which chromosomes contained these sequences, and which wild relatives were most closely-related to cultivated oat. One important result of this work is that we found that the wild oat species called Avena insularis contained a set of 14 chromosome pairs that are very similar to 14 of the 21 pairs of chromosomes in cultivated oat. Thus, Avena insularis is a strong candidate as a recent ancestor of cultivated oat. This corroborates other recent research where we found similar results using different methods.
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)6 probes. The Am1 oligonucleotide probe was particularly enriched in the C genomes, whereas the (ACT)6 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.