Molecular karyotypes of H. bogdanii Wilensky, 1918 (2n = 14), and H. brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28), were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat) motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of H. bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in H. brevisubulatum. Although the distribution of repeats in the chromosomes of H. brevisubulatum is different from that of H. bogdanii, similar patterns between the two species imply that the autopolyploid origin of H. brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation. Molecular karyotypes of H. bogdanii Wilensky, 1918 (2n = 14), and H. brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28), were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat) motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of H. bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in H. brevisubulatum. Although the distribution of repeats in the chromosomes of H. brevisubulatum is different from that of H. bogdanii, similar patterns between the two species imply that the autopolyploid origin of H. brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation.

Polyploidy plays an important role in the adaptation and speciation of plants. The alteration of karyotype is a significant event during polyploidy formation. The Medicago sativa complex includes both diploid (2n = 2× = 16) and tetraploid (2n = 2× = 32) subspecies. The tetraploid M. ssp. sativa was regarded as having a simple autopolyploid origin from diploid ssp. caerulea, whereas the autopolyploid origin of tetraploid ssp. falcata from diploid form ssp. falcata is still in doubt. In this study, detailed comparative cytogenetic analysis between diploid to tetraploid species, as well as genomic affinity across different species in the M. sativa complex, were conducted based on comparative mapping of 11 repeated DNA sequences and two rDNA sequences by a fluorescence in situ hybridization (FISH) technique. FISH patterns of the repeats in diploid subspecies caerulea were highly similar to those in tetraploid subspecies sativa. Distinctly different FISH patterns were first observed in diploid ssp. falcata, with only centromeric hybridizations using centromeric and multiple region repeats and a few subtelomeric hybridizations using subtelomeric repeats. Tetraploid subspecies falcata was unexpectedly found to possess a highly variable karyotype, which agreed with neither diploid ssp. falcata nor ssp. sativa. Reconstruction of chromosome-doubling process of diploid ssp. caerulea showed that chromosome changes have occurred during polyploidization process. The comparative cytogenetic results provide reliable evidence that diploid subspecies caerulea is the direct progenitor of tetraploid subspecies sativa. And autotetraploid ssp. sativa has been suggested to undergo a partial diploidization by the progressive accumulation of chromosome structural rearrangements during evolution. However, the tetraploid subspecies falcata is far from a simple autopolyploid from diploid subspecies falcata although no obvious morphological change was observed between these two subspecies.

A molecular cytogenetic investigation was conducted on plants of the allohexaploid species Elymus nutans with varying fertility on the Qinghai-Tibet Plateau. Molecular karyotyping revealed that chromosome variants were distributed unevenly among genomes and among different homologue chromosomes in each genome. The plants with varying fertility exhibited significantly higher numbers of chromosome variants than did the normal fertility samples, although both kinds of plants showed the same pattern of high-to-low polymorphism from the Y to St and H genomes. Heterozygosis and karyotype heterozygosity in the plants with varying fertility were 3- and 13-fold higher than those in normal samples, respectively. Significant negative correlations were found not only between seed setting rates and total genome heterozygosity but also between seed setting rates and heterozygosity of each genome in the plants of varying fertility. Chromosome pairing analysis was performed using genomic in situ hybridization in selected plants of different fertility levels. The pairing of chromosomes at meiotic metaphase I was mostly bivalent, although univalent, trivalent, quadrivalent, and other polyvalents also occurred; in addition, chromosome configuration forms and frequencies varied among the studied samples. ANOVA results showed that the average number of ring bivalents in the Y genome was significantly higher than those in the St and H genomes. Significant positive correlations between pollen grain fertility and ring bivalent number were found in the St and H genomes but not in the Y genome. Furthermore, chromosome configuration parameters (total bivalents, numbers of ring and rod bivalents) were found to be significantly correlated with heterozygosity and seed setting rates in the St and H genomes, respectively, but not in the Y genome. It was inferred that the seed setting rate and pollen grain fertility in E. nutans are strongly influenced by the heterozygosity of each genome, but the Y genome differs from the St and H genomes due to chromosome pair alterations. The St and H genomes may contain more chromosome structural variations than the Y genome in E. nutans.

Elymus species, belonging to Triticeae tribe, is a tertiary gene pool for improvement of major cereal crops. Elymus sibiricus, a tetraploid with StH genome, is a typical species in the genus Elymus, which is widely utilized as a high-quality perennial forage grass in template regions. In this study, we report the construction of a chromosome-scale reference assembly of E. sibiricus line Gaomu No. 1 based on PacBio HiFi reads and chromosome conformation capture. Subgenome St and H were well phased by assisting with kmer and subgenome-specific repetitive sequence. The total assembly size was 6.929 Gb with a contig N50 of 49.518 Mb. In total, 89,800 protein-coding genes were predicted. The repetitive sequences accounted for 82.49% of the genome in E. sibiricus. Comparative genome analysis confirmed a major species-specific 4H/6H reciprocal translocation in E. sibiricus. The E. sibiricus assembly will be much helpful to exploit genetic resource of StH species in genus Elymus, and provides an important tool for E. sibiricus domestication.