Unveiling the Genomes of Wild Wheat Relatives: Dissecting the S, U, M and C Genomes of Aegilops into Complete Sets of Separate Chromosomes

The S, U, M and C genomes are present in 20 out of 23 species of genus Aegilops. The species may provide new alleles for wheat breeding to sustain yield and quality under extreme conditions. However, the introgression of favorable traits from wild relatives to wheat is hampered by poor knowledge of their genomes and scarcity of molecular tools. The application of genomics tools to chromosomes simplifies genome analysis by reducing sample  complexity and has been used in wheat to obtain shotgun sequences, to develop markers and to construct sequence-ready physical maps. Chromosome genomics relies on the ability to purify chromosomes via flow cytometric sorting. However, discrimination of individual chromosomes based on DNA fluorescence alone requires differences in size between chromosomes, a condition which is not frequently met in plants. Chromosome discrimination can be improved after fluorescent labelling by in situ hybridization in suspension (FISHis) those DNA repeats, which are distributed unevenly among the chromosomes. Here we report on biparametric analysis and sorting chromosomes from diploid Ae. speltoides, Ae. umbellulata, Ae. comosa and Ae. caudata. Bivariate flow karyotypes were obtained after the analysis of DAPI-stained and FISHis-labelled chromosomes and the content of flow-sorted chromosome populations was determined. The results showed that S, U, M and C genomes could be dissected into pure fractions of separate chromosomes (1S-7S, 84.4-99.2%; 1U-7U, 88.7-98.9%; 1M-7M, 62.6-98.4%; 1C-7C, 80.09-97.9%). Purified chromosome fractions provide an attractive resource to investigate the structure and evolution of Aegilops genomes and deliver molecular tools for wheat introgression breeding.