Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data

Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving in diverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, including one from T. timopheevii and one from Thinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at the Vrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be an efficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.

Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat

KEY MESSAGE

PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

KEY MESSAGE

Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F₁ hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.

Wild emmer wheat, the progenitor of modern bread wheat, exhibits great diversity in the VERNALIZATION1 gene

Wild emmer wheat is an excellent reservoir of genetic variability that can be utilized to improve cultivated wheat to address the challenges of the expanding world population and climate change. Bearing this in mind, we have collected a panel of 263 wild emmer wheat (WEW) genotypes across the Fertile Crescent. The genotypes were grown in different locations and phenotyped for heading date. Genome-wide association mapping (GWAS) was carried out, and 16 SNPs were associated with the heading date. As the flowering time is controlled by photoperiod and vernalization, we sequenced the VRN1 gene, the most important of the vernalization response genes, to discover new alleles. Unlike most earlier attempts, which characterized known VRN1 alleles according to a partial promoter or intron sequences, we obtained full-length sequences of VRN-A1 and VRN-B1 genes in a panel of 95 wild emmer wheat from the Fertile Crescent and uncovered a significant sequence variation. Phylogenetic analysis of VRN-A1 and VRN-B1 haplotypes revealed their evolutionary relationships and geographic distribution in the Fertile Crescent region. The newly described alleles represent an attractive resource for durum and bread wheat improvement programs.

Contemplation on wheat vernalization

Vernalization is a period of low non-freezing temperatures, which provides the competence to flower. This mechanism ensures that plants sown before winter develop reproductive organs in more favourable conditions during spring. Such an evolutionary mechanism has evolved in both monocot and eudicot plants. Studies in monocots, represented by temperate cereals like wheat and barley, have identified and proposed the VERNALIZATION1 (VRN1) gene as a key player in the vernalization response. VRN1 belongs to MADS-box transcription factors and is expressed in the leaves and the apical meristem, where it subsequently promotes flowering. Despite substantial research advancement in the last two decades, there are still gaps in our understanding of the vernalization mechanism. Here we summarise the present knowledge of wheat vernalization. We discuss VRN1 allelic variation, review vernalization models, talk VRN1 copy number variation and devernalization phenomenon. Finally, we suggest possible future directions of the vernalization research in wheat.