Discovery of UPSTREAM of FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) in Gladiolus ×Hybridus, G. Dalenii

Background. Gladiolus is a geophytic floricultural crop cultivated for cut flower and garden ornamental uses. Monocotyledonous flower crops have few, if any, flowering genes identified. Ornamental geophytes such as gladiolus, lily, tulip and daffodil are examples of floral crops that are currently being investigated to understand the flowering pathway. While the flower genes and environmental / hormonal factors leading to flowering are established in Arabidopsis, the lack of identified flowering genes in economically important ornamental geophytic crops, such as gladiolus, is critical to further genetic research. Thus, the importance of such an ornamental crop that relies on flowers (flowering) for economic purposes encourages researchers to discover the flowering genes to breed vigorous, flowering cultivars. The understanding of the flowering mechanisms in the flowering pathway is also of paramount importance. Results. Herein we show the discovery of UPSTREAM OF FLOWERING LOCUS C (UFC) and FLOWERING LOCUS C EXPRESSOR (FLX) genes in Gladiolus ×hybridus and G. dalenii. The UFC gene is adjacent to FLOWERING LOCUS C (FLC) which is a floral repressor in many temperate species. The FLX gene upregulates FRIGIDA (FRI) which upregulates FLC expression. Discovery of both genes is a step forward in finding the FLC gene in gladiolus, provided they are linked. Seventeen gladiolus genotypes, consisting of early flowering and commercial cultivars, were discovered to possess the UFC gene, consisting of four exons in two allelic forms. The sequenced UFC gene, when translated into its amino acid sequence and set in pair-alignment to other species, has up to 57% in amino acid identity to Musa acuminata. The UFC protein ranges in identity with pair-alignment to other monocot species, also with 57% amino acid identity to M. acuminata. The FLX gene in gladiolus has 3/5 (60%) exons in common relative to Ananas comosus, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the three exons shows an overall ~65% identity of FLX to A. comosus. The UFC protein consists of a conserved domain, DUF966, which is higher in identity (86%) and pair-alignment with Elaeis guineensis. Conclusions. The two newly-discovered genes in gladiolus, UFC and FLX, provide insight to further our understanding of the flowering mechanism, flowering pathway genes, and vernalization response in ornamental geophytes. This knowledge will be valuable for gladiolus breeders and geneticists to finding the FLC gene, identify segregating seedlings for both UFC and FLX, and aid in marker assisted selection for flowering gene expression.

Transcriptional Controls for Early Bolting and Flowering in Angelica sinensis

The root of the perennial herb Angelica sinensis is a widely used source for traditional Chinese medicines. While the plant thrives in cool-moist regions of western China, early bolting and flowering (EBF) for young plants significantly reduces root quality and yield. Approaches to inhibit EBF by changes in physiology during the vernalization process have been investigated; however, the mechanism for activating EBF is still limited. Here, transcript profiles for bolted and unbolted plants (BP and UBP, respectively) were compared by transcriptomic analysis, expression levels of candidate genes were validated by qRT-PCR, and the accumulations of gibberellins (GA1, GA4, GA8, GA9 and GA20) were also monitored by HPLC-MS/MS. A total of over 72,000 unigenes were detected with ca. 2600 differentially expressed genes (DEGs) observed in the BP compared with UBP. While various signaling pathways participate in flower induction, it is genes associated with floral development and the sucrose pathway that are observed to be coordinated in EBF plants, coherently up- and down-regulating flowering genes that activate and inhibit flowering, respectively. The signature transcripts pattern for the developmental pathways that drive flowering provides insight into the molecular signals that activate plant EBF.

Epigenomic Regulatory Mechanism of Flowering in Apple Demonstrated in Two Varieties with Contrasted Flowering Behaviors

Background: Flowering is the necessary condition and yield basis for woody fruits in their life cycle. Although there has been considerable interest in the regulatory mechanisms underlying floral induction and flowering, the associated epigenetic modifications remain relatively uncharacterized. Results: We identified the genome-wide of DNA methylation changes and the transcriptional responses in axillary bud of ‘Qinguan’ (QA) and ‘Fuji’ (FA) varieties with contrasted flowering behaviors. The DNA methylations were19.35%, 62.96% and 17.68% for FA, and 19.64%, 62.49% and 17.86% for QA in the CG, CHG and CHH contexts, respectively. Number of hypermethylated or hypomethylated DMRs in different regions were contributed to significantly up/downregulated gene expression. DNA methylation can positively or negatively regulate gene expression based on the CG, CHG and CHH contexts in different regions. Additionally, the huge differences in transcription of MIKCc-Type MADS-box genes, and multiple flowering genes in multiple flowering pathways (i.e., light, age, GA and sugar) by changing DNA methylation, contributed to contrasted flowering behaviors in both QA and FA. Specifically, the floral meristem identify genes (i.e., FT, LEAFY, AP1 and SOC1) were significantly higher expression in QA than FA, but the floral repressor (i.e., SVP, AGL15, and AGL18) had an opposite result. Significant differences in multiple hormone levels were due to DEGs and their DMRs in their synthesis pathways, leading to both contrasted axillary bud outgrowth and flowering behaviors. Conclusions: The whole-genome bisulfite sequencing (BS) libraries of QA and FA with diverse flowering capabilities have been constructed for finding whole-genome cytosine methylation profiles. The RNA sequencing of QA and FA and diverse flowering capabilities have been combined together to identify the gene expression patterns and the correlation with their methylation states so that we can better understand the epigenetic regulation mechanisms of floral induction and formation in apple.

Fine-Tuning Florigen Increases Field Yield Through Improving Photosynthesis in Soybean

Crop yield has been maintaining its attraction for researchers because of the demand of global population growth. Mutation of flowering activators, such as florigen, increases plant biomass at the expense of later flowering, which prevents crop maturity in the field. As a result, it is difficult to apply flowering activators in agriculture production. Here, we developed a strategy to utilize florigen to significantly improve soybean yield in the field. Through the screening of transgenic lines of RNAi-silenced florigen homologs in soybean (Glycine-max-Flowering Locus T Like, GmFTL), we identified a line, GmFTL-RNAi#1, with minor changes in both GmFTL expression and flowering time but with notable increase in soybean yield. As expected, GmFTL-RNAi#1 matured normally in the field and exhibited markedly high yield over multiple locations and years, indicating that it is possible to reach a trade-off between flowering time and high yield through the fine-tuning expression of flowering activators. Further studies uncovered an unknown mechanism by which GmFTL negatively regulates photosynthesis, a substantial source of crop yield, demonstrating a novel function of florigen. Thus, because of the highly conserved functions of florigen in plants and the classical RNAi approach, the findings provide a promising strategy to harness early flowering genes to improve crop yield.

Comparative evolution of vegetative branching in sorghum

Tillering and secondary branching are two plastic traits with high agronomic importance, especially in terms of the ability of plants to adapt to changing environments. We describe a quantitative trait analysis of tillering and secondary branching in two novel BC1F2 populations totaling 246 genotypes derived from backcrossing two Sorghum bicolor x S. halepense F1 plants to a tetraploidized S. bicolor. A two-year, two-environment phenotypic evaluation in Bogart, GA and Salina, KS permitted us to identify major effect and environment specific QTLs. Significant correlation between tillering and secondary branching followed by discovery of overlapping sets of QTLs continue to support the developmental relationship between these two organs and suggest the possibility of pleiotropy. Comparisons with two other populations sharing S. bicolor BTx623 as a common parent but sampling the breadth of the Sorghum genus, increase confidence in QTL detected for these two plastic traits and provide insight into the evolution of morphological diversity in the Eusorghum clade. Correspondence between flowering time and vegetative branching supports other evidence in suggesting a pleiotropic effect of flowering genes. We propose a model to predict biomass weight from plant architecture related traits, quantifying contribution of each trait to biomass and providing guidance for future breeding experiments.

Characterization of Flowering Genes of Arabidopsis thaliana for Mirror Repeats

A variety of simple DNA repeats are enriched in the eukaryotic genomes. Recent studies have proven their importance in understanding genome organization and function, especially how genomes evolve using them as mutational hotspots during DNA replication. Mirror repeat sequences, the most underrated subset of this class of repeats, are now gaining importance because of their probable involvement in developing several genetic diseases in humans. These repeats typically adopt H-DNA conformations in both in-vitro and in-vivo conditions. On the other end, plants were still not analyzed for their presence or distribution and whether they are responsible for causing diseases in them or not. The present study aims to extract mirror repeats in the flowering genes of Arabidopsis thaliana. To this end, we have deployed FPCB (FASTA-PARALLEL COMPLEMENT-BLAST), an efficacious and quick method to extract perfect and degenerate mirror repeat sequences through pattern matching of alignments with user-defined algorithmic parameters. All the analyzed genes were reported to have quite high densities of mirror sequences. A total of 93 unique mirror repeats of significant lengths were extracted in the analyzed genes.

Transcriptome analysis of flowering regulation by sowing date in Japonica Rice (Oryza sativa L.)

Hybrid japonica cultivars, such as the Yongyou series, have shown high yield potential in the field in both the early and late growing seasons. Moreover, understanding the responses of rice flowering dates to temperature and light is critical for improving yield performance. However, few studies have analyzed flowering genes in high-yielding japonica cultivars. Based on the five sowing date experiments from 2019 to 2020, select the sensitive cultivar Yongyou 538 and the insensitive cultivar Ninggeng 4 and take their flag leaves and panicles for transcriptome analysis. The results showed that compared with sowing date 1 (6/16), after the sowing date was postponed (sowing date 5, 7/9), 4480 and 890 differentially expressed genes (DEGs) were detected in the leaves and panicles in Ninggeng 4, 9275 and 2475 DEGs were detected in the leaves and panicles in Yongyou 538, respectively. KEGG pathway analysis showed that both Ninggeng 4 and Yongyou 538 regulated rice flowering through the plant circadian rhythm and plant hormone signal transduction pathways. Gene expression analysis showed that Os01g0566050 (OsELF3-2), Os01g0182600 (OsGI), Os11g0547000 (OsFKF1), Os06g0275000 (Hd1), and Os09g0513500 (FT-1) were expressed higher and Os02g0771100 (COP1-1) was expressed lower in Yongyou 538 compared with Ninggeng 4 as the climate conditions changed, which may be the key genes that regulate the flowering process with the change of temperature and light resources in sensitive cultivar Yongyou 538 in the late season.

Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice

A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.