Genetic differentiation and post-glacial establishment of the geographical distribution in Aegilops caudata L

Discrepancy of flowering time between genetically close sublineages of Aegilops umbellulata Zhuk

Aegilops umbellulata Zhuk., a wild diploid wheat-related species, has been used as a genetic resource for several important agronomic traits. However, its genetic variations have not been comprehensively studied. We sequenced RNA from 114 accessions of Ae. umbellulata to evaluate DNA polymorphisms and phenotypic variations. Bayesian clustering and phylogenetic analysis based on SNPs detected by RNA sequencing revealed two divergent lineages, UmbL1 and UmbL2. The main differences between them were in the sizes of spikes and spikelets, and culm diameter. UmbL1 is divided into two sublineages, UmbL1e and UmbL1w. These genetic differences corresponded to geographic distributions. UmbL1e, UmbL1w, and UmbL2 are found in Turkey, Iran/Iraq, and Greece, respectively. Although UmbL1e and UmbL1w were genetically similar, flowering time and other morphological traits were more distinct between these sublineages than those between the lineages. This discrepancy can be explained by the latitudinal and longitudinal differences in habitats. Specifically, latitudinal clines of flowering time were clearly observed in Ae. umbellulata, strongly correlated with solar radiation in the winter season. This observation implies that latitudinal differences are a factor in differences in the flowering times of Ae. umbellulata. Differences in flowering time could influence other morphological differences and promote genetic divergence between sublineages.

Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops

Background

Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops.

Results

Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and A^m-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.

Conclusions

RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae)

During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross-species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next-generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross-genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter- and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.

Genetic structure of Aegilops cylindrica Host in its native range and in the United States of America

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae. markgrafii (Greuter) Hammer. and Ae. tauschii Coss. presumably along the Fertile Crescent, where the geographic distributions of its diploid progenitors overlap. However, the center of genetic diversity of this species now encompasses a larger area including northern Iraq, eastern Turkey, and Transcaucasia. Although the majority of accessions of Ae. cylindrica (87%) had D-type plastomes derived from Ae. tauschii, accessions with C-type plastomes (13%), derived from Ae. markgrafii, were also observed. This corroborates a previous study suggesting the dimaternal origin of Ae. cylindrica. Model-based and genetic distance-based clustering using both chloroplast and nuclear markers indicated that Ae. tauschii ssp. tauschii contributed one of its D-type plastomes and its D genome to Ae. cylindrica. Analysis of genetic structure using nuclear markers suggested that Ae. cylindrica accessions could be grouped into three subpopulations (arbitrarily named N-K1, N-K2, and N-K3). Members of the N-K1 subpopulation were the most numerous in its native range and members of the N-K2 subpopulation were the most common in the USA. Our analysis also indicated that Ae. cylindrica accessions in the USA were derived from a few founder genotypes. The frequency of Ae. cylindrica accessions with the C-type plastome in the USA (approximately 24%) was substantially higher than in its native range of distribution (approximately 3%) and all C-type Ae. cylindrica in the USA except one belonged to subpopulation N-K2. The high frequency of the C-type plastome in the USA may reflect a favorable nucleo-cytoplasmic combination.

Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica

Aegilops cylindrica Host (2n = 4x = 28, genome CCDD) is an allotetraploid formed by hybridization between the diploid species Ae. tauschii Coss. (2n = 2x = 14, genome DD) and Ae. markgrafii (Greuter) Hammer (2n = 2x = 14, genome CC). Previous research has shown that Ae. tauschii contributed its cytoplasm to Ae. cylindrica. However, our analysis with chloroplast microsatellite markers showed that 1 of the 36 Ae. cylindrica accessions studied, TK 116 (PI 486249), had a plastome derived from Ae. markgrafii rather than Ae. tauschii. Thus, Ae. markgrafii has also contributed its cytoplasm to Ae. cylindrica. Our analysis of chloroplast and nuclear microsatellite markers also suggests that D-type plastome and the D genome in Ae. cylindrica were closely related to, and were probably derived from, the tauschii gene pool of Ae. tauschii. A determination of the likely source of the C genome and the C-type plastome in Ae. cylindrica was not possible.

Genome relationships in the genus Dasypyrum (Gramineae)

To elucidate the genome relationships in the genus Dasypyrum and the ancestry of tetraploid D. breviaristatum, two cytotypes of D. breviaristatum and D. villosum were reciprocally crossed with one another. Chromosome pairing at the first metaphase of meiosis and fertility were examined in the F1 hybrids and the parental plants. The mean pairing configuration and mean arm pairing frequency in D. villosum-D. breviaristatum (2x) hybrids were 11.12I + 1.44II per cell and 0.107, respectively, and they were almost completely sterile. In D. breviaristatum (4x)-D. breviaristatum (2x) hybrid, up to seven trivalents were formed, and the mean pairing configuration was 3.38I + 3.20II + 3.74III + 0.005IV per cell. The mean arm pairing frequency and relative affinity calculated in that F1 hybrid were 0.915 and 0.641, respectively. Seven bivalents and seven univalents were characteristically formed in D. villosum-D. breviaristatum (4x) hybrids. Based on the present results, we clearly concluded that the genome of diploid D. breviaristatum is distantly related to the genome V of D. villosum, and that these two species have different basic genomes. We, therefore, proposed the symbol Vb for the haploid genome of diploid cytotype of D. breviaristatum. Moreover, we concluded that tetraploid D. breviaristatum is an autotetraploid with doubled sets of the genomes homologous with that of diploid D. breviaristatum, and we proposed the genome constitution VbVb for the haploid genome set of tetraploid cytotype of D. breviaristatum. Furthermore, from the chromosome pairing in the F1 hybrids involving Moroccan and Greek accessions, it was suggested that complicated rearrangements of chromosome structure have occurred in tetraploid D. breviaristatum in its natural populations across the entire distribution area.

Variation and geographical distribution of the genotypes controlling the diagnostic spike morphology of two varieties of Aegilops caudata l

Aegilops caudata L. is an annual wild relative of wheat distributed over the northeastern Mediterranean basin. It consists of two taxonomic varieties, var. typica with awnless lateral spikelets and var.polyathera with awned lateral spikelets. To clarify the variation and the geographical distribution of the genotypes controlling the diagnostic spike morphology of the two taxonomic varieties, three crossing experiments were carried out. First, two varieties collected from nine sympatric populations in the Aegean islands were crossed reciprocally. All of the F1 hybrids were var. typica and the segregation ratio in the F2 generation was 3 typica: 1 polyathera. Secondly, 13 typica accessions collected from the entire distribution area of the variety were crossed with a common polyathera accession. The F1 hybrids involving eight typica accessions from Greece and West Anatolia were var. typica, while those involving five typica accessions from East Anatolia, Syria and Iraq were var. polyathera. Thirdly, the typica F1 hybrids between the Aegean and the Syrian typica accessions were backcrossed to the latter. Four of the seven BC1F1 plants obtained were var. typica, but the other three were var. polyathera. Based on these results, the following two conclusions were made. First, the awnless lateral spikelets characteristic of var. typica are due to two different genotypes: one is a dominant allele suppressing awn development on lateral spikelets and the other is a recessive allele(s) for awnless lateral spikelets with no dominant suppressor allele. Secondly, the former genotype occurs only in the western region of the distribution area of the species, while the latter occurs in the eastern region. The present results and the recent palaeopalynological evidence also suggested that var. polyathera, with more awns than var. typica, rapidly colonized Central Anatolia from the Levant or East Taurus/Zagros mountains arc after the last glacial period.