Genome evolution during bread wheat formation unveiled by the distribution dynamics of SSR sequences on chromosomes using FISH

Abstract

Background During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic regions of chromosomes, are the effective marker for tracing the genomic DNA sequence variations. However, to date the distribution dynamics of SSRs on chromosomes of bread wheat and its donors, including diploid and tetraploid Triticum urartu, Aegilops speltoides, Aegilops tauschii, Triticum turgidum ssp. dicocoides, reflecting the genome evolution events during bread wheat formation had not been comprehensively investigated. Results The genome evolution was studied by comprehensively comparing the distribution patterns of (AAC)n, (AAG)n, (AGC)n and (AG)n in bread wheat Triticum aestivum var. Chinese Spring and its progenitors T. urartu, A. speltoides, Ae. tauschii, wild tetroploid emmer wheat T. dicocoides, and cultivated emmer wheat T. dicoccum. Results indicated that there are specific distribution patterns in different chromosomes from different species for each SSRs. They provided efficient visible markers for identification of some individual chromosomes and SSR sequence evolution tracing from the diploid progenitors to hexaploid wheat. During wheat speciation, the SSR sequence expansion occurred predominately in the centromeric and pericentromeric regions of B genome chromosomes accompanied by little expansion and elimination on other chromosomes. This result indicated that the B genome might be more sensitive to the “genome shock” and more changeable during wheat polyplodization. Conclusions During the bread wheat evolution, SSRs including (AAC)n, (AAG)n, (AGC)n and (AG)n in B genome displayed the greatest changes (sequence expansion) especially in centromeric and pericentromeric regions during the polyploidization from Ae. speltoides S genome, the most likely donor of B genome. This work would enable a better understanding of the wheat genome formation and evolution and reinforce the viewpoint that B genome was originated from S genome.

Cytogenetic evidence supports Avena insularis being closely related to hexaploid oats

“…In contrast, mixed SSRs in a cluster would be amplified jointly. The present results suggest that an SSR combination need not necessarily be arranged in the same way on all chromosomes of an Avena species, as suggested by other authors [47,51,39]. Interestingly, the clusters integrating repeats of different SSRs, for example, AAC, ATC and ACG, were clearly maintained in specific chromosomes of the tetraploid species and hexaploids, suggesting the existence of a close relationship among these chromosomes (Figs 3 and 5).…”

“…Together with other genome information, this reveals features of Avena chromosome organization. For example, oligonucleotides containing motifs such as AAG, ACG or ATC in Triticum and Hordeum produce strong hybridization signals on the chromosomes of their different genomes, in agreement with estimates of the SSR frequencies (51,52,53,68]. However, the high SSR frequencies in hexaploid oat genomes [42,44] are in clear disagreement with the paucity of SSR-FISH signals described here.…”

“…Comparative SSR-FISH karyotyping has been performed with many different grass species, including wheat [47,51], barley [52,53] and Avena species [39, 54-58,]. These studies differed in the number of species and SSRs analyzed, although all of them confirmed the validity of the strategy for karyotyping Avena chromosomes and detecting modifications in the chromosome structure among diploid and polyploid species.…”

Cytogenetic evidence supports Avena insularis being closely related to hexaploid oats

“…In contrast, mixed SSRs in a cluster would be amplified jointly. The present results suggest that an SSR combination need not necessarily be arranged in the same way on all chromosomes of an Avena species, as suggested by other authors [40,49,53]. Interestingly, the clusters integrating repeats of different SSRs, for example, AAC, ATC and ACG, were clearly maintained in specific chromosomes of the tetraploid species and hexaploids, suggesting the existence of a close relationship among these chromosomes (Figs 3 and 5).…”

“…Comparative SSR-FISH karyotyping has been performed with many different grass species, including wheat [49,53], barley [54,55] and Avena species [33,40,[56][57][58][59]. These studies differed in the number of species and SSRs analyzed, although all of them confirmed the validity of the strategy for karyotyping Avena chromosomes and detecting modifications in the chromosome structure among diploid and polyploid species.…”