Hybrid incompatibilities in interspecific crosses between tetraploid wheat and its wild diploid relative Aegilops umbellulata

Effects of cold and methyl jasmonate on the expression of miRNAs and target genes in response to vernalisation in two wheat cultivars (Triticum aestivum L.)

Wheat undergoes significant physiological changes during winter, driven by processes such as cold acclimation and vernalisation that are regulated by gene expression and phytohormones. We investigate the effects of methyl jasmonate (MeJA) and cold treatments on the expression of three specific miRNAs and the associated target genes in Baz spring wheat and Norstar winter wheat using qRT-PCR analysis. Our objective was to examine the impact of MeJA on vernalisation and cold adaptation in these genotypes. Results showed that MeJA had no significant impact on vernalisation and acclimation in Baz, while the compound decreased these traits in Norstar. Additionally, the expression of miRNAs in Norstar was significantly reduced after a 2-day cold treatment, particularly for miR156 and further reduced after 14days for miR172 and miR319 . In contrast, Baz showed varied gene expression responses, with an increase in miRNA levels after the 14-day cold treatment. MeJA combined with a 2-day cold treatment suppressed the expression of SPL , AP2 and MYB3 target genes, with the most pronounced suppression observed in SPL . However, AP2 was induced after 14-day cold treatment in both cultivars. The study highlighted an inverse relationship between miRNAs and target genes under vernalisation conditions, underscoring the complex regulatory interactions between genotype, miRNAs and the associated target genes. Therefore, these findings provide new insights into how MeJA and cold treatments modulate miRNA and gene expression, enhancing our understanding of wheat's adaptive response mechanisms.

Chromosome stability of synthetic Triticum turgidum-Aegilops umbellulata hybrids

BACKGROUND

Unreduced gamete formation during meiosis plays a critical role in natural polyploidization. However, the unreduced gamete formation mechanisms in Triticum turgidum-Aegilops umbellulata triploid F1 hybrid crosses and the chromsome numbers and compostions in T. turgidum-Ae. umbellulata F2 still not known.

RESULTS

In this study, 11 T.turgidum-Ae. umbellulata triploid F1 hybrid crosses were produced by distant hybridization. All of the triploid F1 hybrids had 21 chromosomes and two basic pathways of meiotic restitution, namely first-division restitution (FDR) and single-division meiosis (SDM). Only FDR was found in six of the 11 crosses, while both FDR and SDM occurred in the remaining five crosses. The chromosome numbers in the 127 selfed F2 seeds from the triploid F1 hybrid plants of 10 crosses (no F2 seeds for STU 16) varied from 35 to 43, and the proportions of euploid and aneuploid F2 plants were 49.61% and 50.39%, respectively. In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes. The chromosome loss of the U genome was the highest (26.77%) among the three genomes, followed by that of the B (22.83%) and A (11.81%) genomes, and the chromosome gain for the A, B, and U genomes was 3.94%, 3.94%, and 1.57%, respectively. Of the 21 chromosomes, 7U (16.54%), 5 A (3.94%), and 1B (9.45%) had the highest loss frequency among the U, A, and B genomes. In addition to chromosome loss, seven chromosomes, namely 1 A, 3 A, 5 A, 6 A, 1B, 1U, and 6U, were gained in the aneuploids.

CONCLUSION

In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes, chromsomes, and crosses. In addition to variations in chromosome numbers, three types of chromosome translocations including 3UL·2AS, 6UL·1AL, and 4US·6AL were identified in the F2 plants. Furthermore, polymorphic fluorescence in situ hybridization karyotypes for all the U chromosomes were also identified in the F2 plants when compared with the Ae. umbellulata parents. These results provide useful information for our understanding the naturally occurred T. turgidum-Ae. umbellulata amphidiploids.

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.

Temperature-dependent sugar accumulation in interspecific Capsicum F1 plants showing hybrid weakness

In plants, F₁ hybrids showing hybrid weakness exhibit weaker growth than their parents. The phenotypes of hybrid weakness are often suppressed at certain temperatures. However, it is unclear whether hybrid weakness in Capsicum annuum × C. chinense is temperature-dependent or not. Our study showed that Capsicum hybrid weakness was suppressed at 30 and 35 °C and was induced at 15, 20, and 25 °C. Moreover, we investigated the time course of hybrid weakness in cell death, metabolite content, and gene expression in leaves of plants transferred to 20 °C after growing at 30 °C for 21 days. The expression of pathogen defense-related genes was upregulated at 1 day after transfer to 20 °C (DAT). Cell death was detected at 7 DAT, plant growth had almost stopped since 14 DAT, and sugars were accumulated at 42 DAT in hybrid plants. The study revealed that some sugar transporter genes, which had been upregulated since 7 DAT, were involved in sugar accumulation in Capsicum hybrid weakness. Thus, our results demonstrated that gene expression changes occur first, followed by physiological and morphological changes after induction of hybrid weakness. These responses observed in this study in Capsicum hybrid weakness are likely to be owed to plant defense responses-like reactions.

Leaf chlorosis in Arabidopsis thaliana hybrids is associated with transgenerational decline and imbalanced ribosome number

The interaction of two parental genomes can result in negative outcomes in offspring, also known as hybrid incompatibility. We have previously reported a case in which two recessively interacting alleles result in hybrid chlorosis in Arabidopsis thaliana. A DEAD-box RNA helicase 18 (AtRH18) was identified to be necessary for chlorosis. In this study, we use a sophisticated genetic approach to investigate genes underlying hybrid chlorosis. Sequence comparisons, DNA methylation inhibitor drug treatment and segregation analysis were used to investigate the epigenetic regulation of hybrid chlorosis. Relative rRNA numbers were quantified using real-time quantitative PCR. We confirmed the causality of AtRH18 and provided evidence for the involvement of the promoter region of AtRH18 in the hybrid chlorosis. Furthermore, AtMOM1 from the second parent was identified as the likely candidate gene on chromosome 1. Chlorotic hybrids displayed transgenerational decline in chlorosis, and DNA demethylation experiment restored chlorophyll levels in chlorotic hybrids. Quantification of rRNA indicated that hybrid chlorosis was associated with an imbalance in the ratio of cytosolic and plastid ribosomes. Our findings highlight that the epigenetic regulation of AtRH18 causes hybrid breakdown and provide novel information about the role of AtRH18 in plant development.

Phenylalanine ammonia-lyase and phenolic compounds are related to hybrid lethality in the cross Nicotiana suaveolens×N. tabacum

Hybrid lethality observed in hybrid seedlings between Nicotiana suaveolens and N. tabacum is characterized by browning, initially of the hypocotyls and eventually of entire seedlings. We investigated the mechanism underlying this browning of tissues. A phenylalanine ammonia-lyase (PAL) gene codes an enzyme involved in a pathway producing phenolic compounds related to the browning of plant tissues. The expression of PAL rapidly increased with the induction of hybrid lethality. Phenolic compounds were observed to be accumulated in whole parts of hybrid seedlings. Treatment of hybrid seedlings with L-2-aminooxy-3-phenylpropionic acid (AOPP), an inhibitor for PAL, suppressed browning and decreased the phenolic content of hybrid seedlings. Although programmed cell death (PCD) was involved in hybrid lethality, AOPP treatment also suppressed cell death and enhanced the growth of hybrid seedlings. These results indicated that PAL is involved in hybrid lethality, and phenolic compounds could be the cause of hybrid lethality-associated tissue browning.

Phenotypic effects of the U-genome variation in nascent synthetic hexaploids derived from interspecific crosses between durum wheat and its diploid relative Aegilops umbellulata

Aegilops umbellulata is a wild diploid wheat species with the UU genome that is an important genetic resource for wheat breeding. To exploit new synthetic allohexaploid lines available as bridges for wheat breeding, a total of 26 synthetic hexaploid lines were generated through crossing between the durum wheat cultivar Langdon and 26 accessions of Ae. umbellulata. In nascent synthetic hexaploids with the AABBUU genome, the presence of the set of seven U-genome chromosomes was confirmed with U-genome chromosome-specific markers developed based on RNA-seq-derived data from Ae. umbellulata. The AABBUU synthetic hexaploids showed large variations in flowering- and morphology-related traits, and these large variations transmitted well from the parental Ae. umbellulata accessions. However, the variation ranges in most traits examined were reduced under the AABBUU hexaploid background compared with under the diploid parents. The AABBUU and AABBDD synthetic hexaploids were clearly discriminated by several morphological traits, and an increase of plant height and in the number of spikes and a decrease of spike length were commonly observed in the AABBUU synthetics. Thus, interspecific differences in several morphological traits between Ae. umbellulata and A. tauschii largely affected the basic plant architecture of the synthetic hexaploids. In conclusion, the AABBUU synthetic hexaploid lines produced in the present study are useful resources for the introgression of desirable genes from Ae. umbellulata to common wheat.

HWA1- and HWA2-Mediated Hybrid Weakness in Rice Involves Cell Death, Reactive Oxygen Species Accumulation, and Disease Resistance-Related Gene Upregulation

Hybrid weakness is a type of reproductive isolation in which F₁ hybrids of normal parents exhibit weaker growth characteristics than their parents. F₁ hybrid of the Oryza sativa Indian cultivars ‘P.T.B.7′ and ‘A.D.T.14′ exhibits hybrid weakness that is associated with the HWA1 and HWA2 loci. Accordingly, the aim of the present study was to analyze the hybrid weakness phenotype of the ‘P.T.B.7′ × ‘A.D.T.14′ hybrids. The height and tiller number of the F₁ hybrid were lower than those of either parent, and F₁ hybrid also exhibited leaf yellowing that was not observed in either parent. In addition, the present study demonstrates that SPAD values, an index correlated with chlorophyll content, are effective for evaluating the progression of hybrid weakness that is associated with the HWA1 and HWA2 loci because it accurately reflects degree of leaf yellowing. Both cell death and H₂O₂, a reactive oxygen species, were detected in the yellowing leaves of the F₁ hybrid. Furthermore, disease resistance-related genes were upregulated in the yellowing leaves of the F₁ hybrids, whereas photosynthesis-related genes tended to be downregulated. These results suggest that the hybrid weakness associated with the HWA1 and HWA2 loci involves hypersensitive response-like mechanisms.

An Update of Recent Use of Aegilops Species in Wheat Breeding

Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.

RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat

Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

BACKGROUND

Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited.

RESULTS

To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of Ae. tauschii and barley (Hordeum vulgare L.), which were regarded as virtual chromosomes of Ae. umbellulata. Interestingly, genetic diversity in Ae. umbellulata was higher than in Ae. tauschii, despite the narrow habitat of Ae. umbellulata. Comparative analyses of nucleotide polymorphisms between Ae. umbellulata and Ae. tauschii revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in Ae. umbellulata, with patterns clearly distinct from those in Ae. tauschii.

CONCLUSIONS

The anchored SNPs, covering all chromosomes, provide sufficient genetic markers between Ae. umbellulata accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in Ae. umbellulata.

Two Rye Genes Responsible for Abnormal Development of Wheat⁻Rye Hybrids Are Linked in the Vicinity of an Evolutionary Translocation on Chromosome 6R

The post-zygotic reproductive isolation (RI) in plants is frequently based on the negative interaction of the parental genes involved in plant development. Of special interest is the study of such types of interactions in crop plants, because of the importance of distant hybridization in plant breeding. This study is devoted to map rye genes that are incompatible with wheat, determining the development of the shoot apical meristem in wheat⁻rye hybrids. Linkage analysis of microsatellite loci, as well as genes of embryo lethality (Eml-R1) and hybrid dwarfness (Hdw-R1) was carried out in hybrids of Chinese Spring wheat with recombinant inbred lines as well as interline rye hybrids. Eml-R1 and Hdw-R1 could be mapped proximal and distal of two closely linked EST-SSR markers, Xgrm902 and Xgrm959, on rye chromosome 6R. Both rye genes are located on a segment of chromosome 6R that contains a breakpoint of evolutionary translocation between the ancestral chromosomes of homeologous groups 6 and 3. The obtained results are discussed in relation to genes interacting in developmental pathways as a class of causal genes of RI.