GmCOL1a and GmCOL1b Function as Flowering Repressors in Soybean Under Long-Day Conditions

More than flowering: CONSTANS plays multifaceted roles in plant development and stress responses

Plants have evolved a remarkable ability to sense and respond to changes in photoperiod, allowing adjustments to their growth and development based on seasonal and environmental cues. The floral transition is a pivotal stage in plant growth and development, signifying a shift from vegetative to reproductive growth. CONSTANS (CO), a central photoperiodic response factor conserved in various plants, mediates day-length signals to control the floral transition, although its mechanisms of action vary among plants with different day-length requirements. In addition, recent studies have uncovered roles for CO in organ development and stress responses. These pleiotropic roles in model plants and crops make CO a potentially fruitful target for molecular breeding aimed at modifying crop agronomic traits. This review systematically traces research on CO, from its discovery and functional studies to the exploration of its regulatory mechanisms and newly discovered functions, providing important insight into the roles of CO and laying a foundation for future research.

Genome-wide association study revealed some new candidate genes associated with flowering and maturity time of soybean in Central and West Siberian regions of Russia

The duration of flowering and maturity is an important agricultural trait determining the suitability of a variety for cultivation in the target region. In the present study, we used genome-wide association analysis (GWAS) to search for loci associated with soybean flowering and maturity in the Central and West Siberian regions of Russia. A field experiment was conducted in 2021/2022 at two locations (Orel and Novosibirsk). A germplasm collection of 180 accessions was genotyped using SoySNP50K Illumina Infinium Bead-Chip. From the initial collection, we selected 129 unrelated accessions and conducted GWAS on this dataset using two multi-locus models: FarmCPU and BLINK. As a result, we identified 13 loci previously reported to be associated with duration of soybean development, and 17 new loci. 33 candidate genes were detected in these loci using analysis of co-expression, gene ontology, and literature data, with the best candidates being Glyma.03G177500, Glyma.13G177400, and Glyma.06G213100. These candidate genes code the Arabidopis orthologs TOE1 (TARGET OF EAT 1), SPL3 (SQUAMOSA PROMOTER BINDING PROTEIN LIKE 3), the DELLA protein, respectively. In these three genes, we found haplotypes which may be associated with the length of soybean flowering and maturity, providing soybean adaptation to a northern latitudes.

Editing the nuclear localization signals of E1 and E1Lb enables the production of tropical soybean in temperate growing regions

Soybean is a typical short-day crop, and most commercial soybean cultivars are restricted to a relatively narrow range of latitudes due to photoperiod sensitivity. Photoperiod sensitivity hinders the utilization of soybean germplasms across geographical regions. When grown in temperate regions, tropical soybean responds to prolonged day length by increasing the vegetative growth phase and delaying flowering and maturity, which often pushes the harvest window past the first frost date. In this study, we used CRISPR/LbCas12a to edit a North American subtropical soybean cultivar named 06KG218440 that belongs to maturity group 5.5. By designing one gRNA to edit the nuclear localization signal (NLS) regions of both E1 and E1Lb, we created a series of new germplasms with shortened flowering time and time to maturity and determined their favourable latitudinal zone for cultivation. The novel partial function alleles successfully achieve yield and early maturity trade-offs and exhibit good agronomic traits and high yields in temperate regions. This work offers a straightforward editing strategy to modify subtropical and tropical soybean cultivars for temperate growing regions, a strategy that could be used to enrich genetic diversity in temperate breeding programmes and facilitate the introduction of important crop traits such as disease tolerance or high yield.

Genome-wide identification and expression analysis of the CONSTANS-like family in potato (Solanum tuberosum L.)

The CONSTANS-like (COL) gene plays important roles in plant growth, development, and abiotic stress. A total of 15 COL genes are unevenly distributed on eight chromosomes in the potato genome. The amino acid length of the family members was 347-453 aa, the molecular weight was 38.65-49.92 kD, and the isoelectric point was 5.13-6.09. The StCOL family can be divided into three subfamilies by evolutionary tree analysis, with conserved motifs and similar gene structure positions in each subfamily. The analysis of promoter cis-acting elements showed 17 cis-acting elements related to plant hormones, stress, and light response. Collinearity analysis of COL genes of tomato, potato, and Arabidopsis showed that 13 StCOL genes in the different species may have a common ancestor. A total of 10 conserved motifs and six kinds of post-translational modifications in the 15 StCOL proteins were identified. The 15 StCOL genes exhibit a genomic structure consisting of exons and introns, typically ranging from two to four in number. The results showed that 10 genes displayed significant expression across all potato tissues, while the remaining five genes were down-expressed in potato transcriptome data. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis exhibited differential expression of 8 StCOL genes in the potato leaves and tubers at different growth stages, as well as 7 StCOL genes under 2°C treatment conditions. These results suggested that the StCOL gene family may play an important role in regulating potato tuberization and responding to cold stress.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants

As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.

Molecular breeding for improvement of photothermal adaptability in soybean

Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01406-z.

Natural variation of FKF1 controls flowering and adaptation during soybean domestication and improvement

Soybean (Glycine max) is a major source of protein and edible oil world-wide and is cultivated in a wide range of latitudes. However, it is extremely sensitive to photoperiod, which influences flowering time, maturity, and yield, and severely limits soybean latitude adaptation. In this study, a genome-wide association study (GWAS) identified a novel locus in accessions harboring the E1 allele, called Time of flowering 8 (Tof8), which promotes flowering and enhances adaptation to high latitude in cultivated soybean. Gene functional analyses showed that Tof8 is an ortholog of Arabidopsis FKF1. We identified two FKF1 homologs in the soybean genome. Both FKF1 homologs are genetically dependent on E1 by binding to E1 promoter to activate E1 transcription, thus repressing FLOWERING LOCUS T 2a (FT2a) and FT5a transcription, which modulate flowering and maturity through the E1 pathway. We also demonstrate that the natural allele FKF1b^H3 facilitated adaptation of soybean to high-latitude environments and was selected during domestication and improvement, leading to its rapid expansion in cultivated soybean. These findings provide novel insights into the roles of FKF1 in controlling flowering time and maturity in soybean and offer new means to fine-tune adaptation to high latitudes and increase grain yield.

Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean

Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.

Photoperiod controls plant seed size in a CONSTANS-dependent manner

Photoperiodic plants perceive changes in day length as seasonal cues to orchestrate their vegetative and reproductive growth. Although it is known that the floral transition of photoperiod-sensitive plants is tightly controlled by day length, how photoperiod affects their post-flowering development remains to be clearly defined, as do the underlying mechanisms. Here we demonstrate that photoperiod plays a prominent role in seed development. We found that long-day (LD) and short-day (SD) plants produce larger seeds under LD and SD conditions, respectively; however, seed size remains unchanged when CONSTANS (CO), the central regulatory gene of the photoperiodic response pathway, is mutated in Arabidopsis and soybean. We further found that CO directly represses the transcription of AP2 (a known regulatory gene of seed development) under LD conditions in Arabidopsis and SD conditions in soybean, thereby controlling seed size in a photoperiod-dependent manner, and that these effects are exerted through regulation of the proliferation of seed coat epidermal cells. Collectively, our findings reveal that a crucial regulatory cascade involving CO-AP2 modulates photoperiod-mediated seed development in plants and provide new insights into how plants with different photoperiod response types perceive seasonal changes that enable them to optimize their reproductive growth.

The genetic basis of high-latitude adaptation in wild soybean

In many plants, flowering time is influenced by daylength as an adaptive response. In soybean (Glycine max) cultivars, however, photoperiodic flowering reduces crop yield and quality in high-latitude regions. Understanding the genetic basis of wild soybean (Glycine soja) adaptation to high latitudes could aid breeding of improved cultivars. Here, we identify the Tof4 (Time of flowering 4) locus, which encodes by an E1-like protein, E1La, that represses flowering and enhances adaptation to high latitudes in wild soybean. Moreover, we found that Tof4 physically associates with the promoters of two important FLOWERING LOCUS T (FT2a and FT5a) and with Tof5 to inhibit their transcription under long photoperiods. The effect of Tof4 on flowering and maturity is mediated by FT2a and FT5a proteins. Intriguingly, Tof4 and the key flowering repressor E1 independently but additively regulate flowering time, maturity, and grain yield in soybean. We determined that weak alleles of Tof4 have undergone natural selection, facilitating adaptation to high latitudes in wild soybean. Notably, over 71.5% of wild soybean accessions harbor the mutated alleles of Tof4 or a previously reported gain-of-function allele Tof5^H2, suggesting that these two loci are the genetic basis of wild soybean adaptation to high latitudes. Almost no cultivated soybean carries the mutated tof4 allele. Introgression of the tof4-1 and Tof5^H2 alleles into modern soybean or editing E1 family genes thus represents promising avenues to obtain early-maturity soybean, thereby improving productivity in high latitudes.

Altered regulation of flowering expands growth ranges and maximizes yields in major crops

Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.

GIGANTEA orthologs, E2 members, redundantly determine photoperiodic flowering and yield in soybean

Soybean (Glycine max L.) is a typical photoperiod-sensitive crop, such that photoperiod determines its flowering time, maturity, grain yield, and phenological adaptability. During evolution, the soybean genome has undergone two duplication events, resulting in about 75% of all genes being represented by multiple copies, which is associated with rampant gene redundancy. Among duplicated genes, the important soybean maturity gene E2 has two homologs, E2-Like a (E2La) and E2-Like b (E2Lb), which encode orthologs of Arabidopsis GIGANTEA (GI). Although E2 was cloned a decade ago, we still know very little about its contribution to flowering time and even less about the function of its homologs. Here, we generated single and double mutants in E2, E2La, and E2Lb by genome editing and determined that E2 plays major roles in the regulation of flowering time and yield, with the two E2 homologs depending on E2 function. At high latitude regions, e2 single mutants showed earlier flowering and high grain yield. Remarkably, in terms of genetic relationship, genes from the legume-specific transcription factor family E1 were epistatic to E2. We established that E2 and E2-like proteins form homodimers or heterodimers to regulate the transcription of E1 family genes, with the homodimer exerting a greater function than the heterodimers. In addition, we established that the H3 haplotype of E2 is the ancestral allele and is mainly restricted to low latitude regions, from which the loss-of-function alleles of the H1 and H2 haplotypes were derived. Furthermore, we demonstrated that the function of the H3 allele is stronger than that of the H1 haplotype in the regulation of flowering time, which has not been shown before. Our findings provide excellent allelic combinations for classical breeding and targeted gene disruption or editing.

Expression Patterns of Key Genes in the Photoperiod and Vernalization Flowering Pathways in Lilium longiflorum with Different Bulb Sizes

Lilium longiflorum is a wild Lilium, and its flowering transition requires a long period of cold exposure to meet the demand of vernalization. The responses of different sized bulbs to cold exposure and photoperiod are different, and the floral transition pathways of small and large bulbs are different. In this study, small and large bulbs were placed in cold storage for different weeks and then cultured at a constant ambient temperature of 25 °C under long day (LD) and short day (SD) conditions. Then, the flowering characteristics and expression patterns of key genes related to the vernalization and photoperiod pathways in different groups were calculated and analyzed. The results showed that the floral transition of Lilium longiflorum was influenced by both vernalization and photoperiod, that vernalization and LD conditions can significantly improve the flowering rate of Lilium longiflorum, and that the time from planting to visible flowering buds’ appearance was decreased. The flowering time and rate of large bulbs were greatly influenced by cold exposure, and the vernalization pathway acted more actively at the floral transition stage. The floral transition of small bulbs was affected more by the photoperiod pathway. Moreover, it was speculated that cold exposure may promote greater sensitivity of the small bulbs to LD conditions. In addition, the expression of LlVRN1, LlFKF1, LlGI, LlCO5, LlCO7, LlCO16, LlFT1, LlFT3 and LlSOC1 was high during the process of floral transition, and LlCO13, LlCO14 and LlCO15 were highly expressed in the vegetative stage. The expression of LlCO13 and LlCO14 was different under different lighting conditions, and the flowering induction function of LlCO9 and LlFT3 was related to vernalization. Moreover, LlFKF1, LlGI, LlCO5, LlCO16, LlSOC1 and LlFT2 were involved in the entire growth process of plants, while LlCO6, LlCO16 and LlFT1 are involved in the differentiation and formation of small bulblets of plants after the inflorescence stage, and this process is also closely related to LD conditions. This study has great significance for understanding the molecular mechanisms of the vernalization and photoperiod flowering pathways of Lilium longiflorum.

Current overview on the genetic basis of key genes involved in soybean domestication

Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.

The Conserved and Specific Roles of the LUX ARRHYTHMO in Circadian Clock and Nodulation

LUX ARRHYTHMO (LUX) plays a key role in circadian rhythms and flowering. Here, we identified the MtLUX gene which is the putative ortholog of LUX in Medicago truncatula. The roles of MtLUX, in both the nodulation belowground and leaf movement aboveground, were investigated by characterizing a loss-of-function mtlux mutant. MtLUX was required for the control of flowering time under both long-day and short-day conditions. Further investigations showed that the early flowering in the mtlux mutant was correlated with the elevated expression level of the MtFTa1 gene but in a CO-like independent manner. MtLUX played a conserved role in the regulatory interactions with MtLHY, MtTOC1, and MtPRR genes, which is similar to those in other species. Meanwhile, the unexpected functions of MtLUX were revealed in nodule formation and nyctinastic leaf movement, probably through the indirect regulation in MtLHY. Its participation in nodulation is of interest in the context of functional conservation and the neo-functionalization of the products of LUX orthologs.

CONSTANS Polymorphism Modulates Flowering Time and Maturity in Soybean

CONSTANS (CO) plays a critical role in the photoperiodic flowering pathway. However, the function of soybean CO orthologs and the molecular mechanisms in regulating flowering remain largely unknown. This study characterized the natural variations in CO family genes and their association with flowering time and maturity in soybeans. A total of 21 soybean CO family genes (GmCOLs) were cloned and sequenced in 128 varieties covering 14 known maturity groups (MG 0000-MG X from earliest to latest maturity). Regarding the whole genomic region involving these genes, GmCOL1, GmCOL3, GmCOL8, GmCOL9, GmCOL10, and GmCOL13 were conserved, and the remaining 15 genes showed genetic variation that was brought about by mutation, namely, all single-nucleotide polymorphisms (SNPs) and insertions-deletions (InDels). In addition, a few genes showed some strong linkage disequilibrium. Point mutations were found in 15 GmCOL genes, which can lead to changes in the potential protein structure. Early flowering and maturation were related to eight genes (GmCOL1/3/4/8/13/15/16/19). For flowering and maturation, 11 genes (GmCOL2/5/6/14/20/22/23/24/25/26/28) expressed divergent physiognomy. Haplotype analysis indicated that the haplotypes of GmCOL5-Hap2, GmCOL13-Hap2/3, and GmCOL28-Hap2 were associated with flowering dates and soybean maturity. This study helps address the role of GmCOL family genes in adapting to diverse environments, particularly when it is necessary to regulate soybean flowering dates and maturity.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean

The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.

Flowering process in soybean under water deficit conditions: A review on genetic aspects

Soybean is a key crop in many countries, being used from human food to the animal industry due to its nutritional properties. Financially, the grain chain moves large sums of money into the economy of producing countries. However, like other agricultural commodities around the world, it can have its final yield seriously compromised by abiotic environmental stressors, like drought. As flowers imply in pods and in grains inside it to minimize damages caused by water restriction, researchers have focused on understanding flowering-process related genes and their interactions. Here a review dedicated to the soybean flowering process and gene network involved in it is presented, describing gene interactions and how genes act in this complex mechanism, also ruled by environmental triggers such as day-light and circadian cycle. The objective was to gather information and insights on the soybean flowering process, aiming to provide knowledge useful to assist in the development of drought-tolerant soybean lines, minimizing losses due to delays or anticipation of flowering and, consequently, restraining financial and productivity losses.

Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Soybean (Glycine max) serves as a major source of protein and edible oils worldwide. The genetic and genomic bases of the adaptation of soybean to tropical regions remain largely unclear. Here, we identify the novel locus Time of Flowering 16 (Tof16), which confers delay flowering and improve yield at low latitudes and determines that it harbors the soybean homolog of LATE ELONGATED HYPOCOTYL (LHY). Tof16 and the previously identified J locus genetically additively but independently control yield under short-day conditions. More than 80% accessions in low latitude harbor the mutations of tof16 and j, which suggests that loss of functions of Tof16 and J are the major genetic basis of soybean adaptation into tropics. We suggest that maturity and yield traits can be quantitatively improved by modulating the genetic complexity of various alleles of the LHY homologs, J and E1. Our findings uncover the adaptation trajectory of soybean from its temperate origin to the tropics.

Haplotype variations of major flowering time genes in quinoa unveil their role in the adaptation to different environmental conditions

Response to photoperiod is of major importance in crop production. It defines the adaptation of plants to local environments. Quinoa is a short-day plant which had been domesticated in the Andeans regions. We wanted to understand the adaptation to long-day conditions by studying orthologues of two major flowering time regulators of Arabidopsis, FLOWERING LOCUS T (FT) and CONSTANS (CO) in quinoa accessions with contrasting photoperiod response. By searching the quinoa reference genome sequence, we identified 24 FT and six CO homologs. CqFT genes displayed remarkably different expression patterns between long- and short-day conditions, whereas the influence of the photoperiod on CqCOL expressions was moderate. Cultivation of 276 quinoa accessions under short- and long-day conditions revealed great differences in photoperiod sensitivity. After sequencing their genomes, we identified large sequence variations in 12 flowering time genes. We found non-random distribution of haplotypes across accessions from different geographical origins, highlighting the role of CqFT and CqCOL genes in the adaptation to different day-length conditions. We identified five haplotypes causing early flowering under long days. This study provides assets for quinoa breeding because superior haplotypes can be assembled in a predictive breeding approach to produce well-adapted early flowering lines under long-day photoperiods.

Molecular mechanisms for the photoperiodic regulation of flowering in soybean

Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean (Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.

A flowering time locus dependent on E2 in soybean

Soybean [Glycine max (L.) Merrill] is very sensitive to changes in photoperiod as a typical short-day plant. Photoperiodic flowering influences soybean latitudinal adaptability and yield to a considerable degree. Identifying new quantitative trait loci (QTLs) controlling flowering time is a powerful initial approach for elucidating the mechanisms underlying flowering time and adaptation to different latitudes in soybean. In this study, we developed a Recombinant Inbred Lines (RILs) population and recorded flowering time under natural long-day conditions. We also constructed a high-density genetic map by genotyping-by-sequencing and used it for QTL mapping. In total, we detected twelve QTLs, four of which are stable and named by qR1-2, qR1-4, qR1-6.1, and qR1-10, respectively. Among these four QTLs, qR1-4 and qR1-6.1 are novel. QTL mapping in two sub-populations classified by the genotype of the maturity locus E2, genetic interaction evaluation between E2 and qR1-2, and qRT-PCR indicated that E2 has an epistatic effect on qR1-2, and that causal gene of qR1-2 acts upstream of E2. We presumed the most likely candidate genes according to the resequencing data and briefly analyzed the geographic distributions of these genes. These findings will be beneficial for our understanding of the mechanisms underlying photoperiodic flowering in soybean, contribute to further investigate of E2, and provide genetic resources for molecular breeding of soybean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01224-1.

Ancient relaxation of an obligate short-day requirement in common bean through loss of CONSTANS-like gene function

Common bean (Phaseolus vulgaris L.) is a major global food staple and source of dietary protein that was domesticated independently in Mexico and Andean South America. Its subsequent development as a crop of importance worldwide has been enabled by genetic relaxation of the strict short-day requirement typical of wild forms, but the genetic basis for this change is not well understood. Recently, a loss of photoperiod sensitivity was shown to result from mutations in the phytochrome photoreceptor gene Ppd/PHYA3 that arose independently within the two major domesticated lineages. Here, we define a second major photoperiod sensitivity locus, at which recessive alleles associate with deleterious mutations affecting the CONSTANS-like gene COL2. A wider survey of sequence variation in over 800 diverse lines, including wild, landrace, and domesticated accessions, show that distinct col2 haplotypes are associated with early flowering in Andean and Mesoamerican germplasm. The relative frequencies and distributions of COL2 and PHYA3 haplotypes imply that photoperiod adaptation developed in two phases within each gene pool: an initial reduction in sensitivity through impairment of COL2 function and subsequent complete loss through PHYA3. Gene expression analyses indicate that COL2 functions downstream of PHYA3 to repress expression of FT genes and may function in parallel with PvE1, the bean ortholog of a key legume-specific flowering repressor. Collectively, these results define the molecular basis for a key phenological adaptation, reveal a striking convergence in the naturally replicated evolution of this major crop, and further emphasize the wider evolutionary lability of CONSTANS effects on flowering time control.

Allelic characterization and protein structure analysis reveals the involvement of splice site mutation for growth habit differences in Lablab purpureus (L.) Sweet

BACKGROUND

Interrelationship between growth habit and flowering played a key role in the domestication history of pulses; however, the actual genes responsible for these traits have not been identified in Indian bean. Determinate growth habit is desirable due to its early flowering, photo-insensitivity, synchronous pod maturity, ease in manual harvesting and short crop duration. The present study aimed to identify, characterize and validate the gene responsible for growth habit by using a candidate gene approach coupled with sequencing, multiple sequence alignment, protein structure prediction and binding pocket analysis.

RESULTS

Terminal flowering locus was amplified from GPKH 120 (indeterminate) and GNIB-21 (determinate) using the primers designed from PvTFL1y locus of common bean. Gene prediction revealed that the length of the third and fourth exons differed between the two alleles. Allelic sequence comparison indicated a transition from guanine to adenine at the end of the third exon in GNIB 21. This splice site single-nucleotide polymorphism (SNP) was validated in germplasm lines by sequencing. Protein structure analysis indicated involvement of two binding pockets for interaction of terminal flowering locus (TFL) protein with other proteins.

CONCLUSION

The splice site SNP present at the end of the third exon of TFL locus is responsible for the transformation of shoot apical meristem into a reproductive fate in the determinate genotype GNIB 21. The splice site SNP leads to absence of 14 amino acids in mutant TFL protein of GNIB 21, rendering the protein non-functional. This deletion disturbed previously reported anion-binding pocket and secondary binding pocket due to displacement of small β-sheet away from an external loop. This finding may enable the modulation of growth habit in Indian bean and other pulse crops through genome editing.

Modulation of evening complex activity enables north-to-south adaptation of soybean

Soybean, a typical short-day crop, is sensitive to photoperiod, which is a major limiting factor defining its north-to-south cultivation range. The long-juvenile (LJ) trait is controlled primarily by the J locus which has been used for decades by soybean breeders to delay flowering and improve grain yield in tropical regions. The J gene encodes an ortholog of the Arabidopsis Evening Complex (EC) component EARLY FLOWERING 3 (ELF3). To identify modifiers of J, we conducted a forward genetic screen and isolated a mutant (eoj57) that in combination with j has longer flowering delay compared with j single mutant plants. Map-based cloning and genome re-sequencing identified eoj57 (designated as GmLUX2) as an ortholog of the Arabidopsis EC component LUX ARRHYTHMO (LUX). To validate that GmLUX2 is a modifier of J, we used trans-complementation and identified a natural variant allele with a similar phenotype. We also show that GmLUX2 physically interacts with GmELF3a/b and binds DNA, whereas the mutant and natural variant are attenuated in both activities. Transcriptome analysis shows that the GmLUX2-GmELF3a complex co-regulates the expression of several circadian clock-associated genes and directly represses E1 expression. These results provide mechanistic insight into how GmLUX2-GmELF3 controls flowering time via synergistic regulation of gene expression. These novel insights expand our understanding of the regulation of the EC complex, and facilitate the development of soybean varieties adapted for growth at lower latitudes.

High-Temperature Conditions Promote Soybean Flowering through the Transcriptional Reprograming of Flowering Genes in the Photoperiod Pathway

Global warming has an impact on crop growth and development. Flowering time is particularly sensitive to environmental factors such as day length and temperature. In this study, we investigated the effects of global warming on flowering using an open-top Climatron chamber, which has a higher temperature and CO2 concentration than in the field. Two different soybean cultivars, Williams 82 and IT153414, which exhibited different flowering times, were promoted flowering in the open-top Climatron chamber than in the field. We more specifically examined the expression patterns of soybean flowering genes on the molecular level under high-temperature conditions. The elevated temperature induced the expression of soybean floral activators, GmFT2a and GmFT5a as well as a set of GmCOL genes. In contrast, it suppressed floral repressors, E1 and E2 homologs. Moreover, high-temperature conditions affected the expression of these flowering genes in a day length-independent manner. Taken together, our data suggest that soybean plants properly respond and adapt to changing environments by modulating the expression of a set of flowering genes in the photoperiod pathway for the successful production of seeds and offspring.

The Candidate Photoperiod Gene MtFE Promotes Growth and Flowering in Medicago truncatula

Flowering time influences the yield and productivity of legume crops. Medicago truncatula is a reference temperate legume that, like the winter annual Arabidopsis thaliana, shows accelerated flowering in response to vernalization (extended cold) and long-day (LD) photoperiods (VLD). However, unlike A. thaliana, M. truncatula appears to lack functional homologs of core flowering time regulators CONSTANS (CO) and FLOWERING LOCUS C (FLC) which act upstream of the mobile florigen FLOWERING LOCUS T (FT). Medicago truncatula has three LD-induced FT-like genes (MtFTa1, MtFTb1, and MtFTb2) with MtFTa1 promoting M. truncatula flowering in response to VLD. Another photoperiodic regulator in A. thaliana, FE, acts to induce FT expression. It also regulates the FT transport pathway and is required for phloem development. Our study identifies a M. truncatula FE homolog Medtr6g444980 (MtFE) which complements the late flowering fe-1 mutant when expressed from the phloem-specific SUCROSE-PROTON SYMPORTER 2 (SUC2) promoter. Analysis of two M. truncatula Tnt1 insertional mutants indicate that MtFE promotes flowering in LD and VLD and growth in all conditions tested. Expression of MtFTa1, MtFTb1, and MtFTb2 are reduced in Mtfe mutant (NF5076), correlating with its delayed flowering. The NF5076 mutant plants are much smaller than wild type indicating that MtFE is important for normal plant growth. The second mutant (NF18291) displays seedling lethality, like strong fe mutants. We searched for mutants in MtFTb1 and MtFTb2 identifying a Mtftb2 knock out Tnt1 mutant (NF20803). However, it did not flower significantly later than wild type. Previously, yeast-two-hybrid assays (Y2H) suggested that Arabidopsis FE interacted with CO and NUCLEAR FACTOR-Y (NF-Y)-like proteins to regulate FT. We found that MtFE interacts with CO and also M. truncatula NF-Y-like proteins in Y2H experiments. Our study indicates that despite the apparent absence of a functional MtCO-like gene, M. truncatula FE likely influences photoperiodic FT expression and flowering time in M. truncatula via a partially conserved mechanism with A. thaliana.

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.

From graph topology to ODE models for gene regulatory networks

A gene regulatory network can be described at a high level by a directed graph with signed edges, and at a more detailed level by a system of ordinary differential equations (ODEs). The former qualitatively models the causal regulatory interactions between ordered pairs of genes, while the latter quantitatively models the time-varying concentrations of mRNA and proteins. This paper clarifies the connection between the two types of models. We propose a property, called the constant sign property, for a general class of ODE models. The constant sign property characterizes the set of conditions (system parameters, external signals, or internal states) under which an ODE model is consistent with a signed, directed graph. If the constant sign property for an ODE model holds globally for all conditions, then the ODE model has a single signed, directed graph. If the constant sign property for an ODE model only holds locally, which may be more typical, then the ODE model corresponds to different graphs under different sets of conditions. In addition, two versions of constant sign property are given and a relationship between them is proved. As an example, the ODE models that capture the effect of cis-regulatory elements involving protein complex binding, based on the model in the GeneNetWeaver source code, are described in detail and shown to satisfy the global constant sign property with a unique consistent gene regulatory graph. Even a single gene regulatory graph is shown to have many ODE models of GeneNetWeaver type consistent with it due to combinatorial complexity and continuous parameters. Finally the question of how closely data generated by one ODE model can be fit by another ODE model is explored. It is observed that the fit is better if the two models come from the same graph.

Single-base deletion in GmCHR5 increases the genistein-to-daidzein ratio in soybean seed

Novel mutant alleles related to isoflavone content are useful for breeding programs to improve the disease resistance and nutritional content of soybean. However, identification of mutant alleles from high-density mutant libraries is expensive and time-consuming because soybean has a large, complicated genome. Here, we identified the gene responsible for increased genistein-to-daidzein ratio in seed of the mutant line F333ES017D9. For this purpose, we used a time- and cost-effective approach based on selective genotyping of a small number of F₂ plants showing the mutant phenotype with nearest-neighboring-nucleotide substitution-high-resolution melting analysis markers, followed by alignment of short reads obtained by next-generation sequencing analysis with the identified locus. In the mutant line, GmCHR5 harbored a single-base deletion that caused a change in the substrate flow in the isoflavone biosynthetic pathway towards genistein. Mutated GmCHR5 was expressed at a lower level during seed development than wild-type GmCHR5. Ectopic overexpression of GmCHR5 increased the production of daidzein derivatives in both the wild-type and mutant plants. The present strategy will be useful for accelerating identification of mutant alleles responsible for traits of interest in agronomically important crops.

A Soybean Deletion Mutant That Moderates the Repression of Flowering by Cool Temperatures

Ambient growing temperature and photoperiod are major environmental stimuli that summer annual crops use to adjust their reproductive phenology so as to maximize yield. Variation in flowering time among soybean (Glycine max) cultivars results mainly from allelic diversity at loci that control photoperiod sensitivity and FLOWERING LOCUS T (FT) orthologs. However, variation in the thermal regulation of flowering and its underlying mechanisms are poorly understood. In this study, we identified a novel mutant (ef1) that confers altered thermal regulation of flowering in response to cool ambient temperatures. Mapping analysis with simple sequence repeat (SSR) markers located the mutation in the upper part of chromosome 19, where no QTL for flowering has been previously reported. Fine-mapping and re-sequencing revealed that the mutation was caused by deletion of a 214 kbp genomic region that contains 11 annotated genes, including CONSTANS-LIKE 2b (COL2b), a soybean ortholog of Arabidopsis CONSTANS. Comparison of flowering times under different photo-thermal conditions revealed that early flowering in the mutant lines was most distinct under cool ambient temperatures. The expression of two FT orthologs, FT2a and FT5a, was dramatically downregulated by cool temperature, but the magnitude of the downregulation was lower in the mutant lines. Cool temperatures upregulated COL2b expression or delayed peak expression, particularly at the fourth trifoliate-leaf stage. Intriguingly, they also upregulated E1, a soybean-specific repressor of FT orthologs. Our results suggest that the ef1 mutation is involved in thermal regulation of flowering in response to cool ambient temperature, and the lack of COL2b in the mutant likely alleviates the repression of flowering by cool temperature. The ef1 mutant can be used as a novel gene resource in breeding soybean cultivars adapted to cool climate and in research to improve our understanding of thermal regulation of flowering in soybean.

Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication

Adaptive changes in plant phenology are often considered to be a feature of the so-called 'domestication syndrome' that distinguishes modern crops from their wild progenitors, but little detailed evidence supports this idea. In soybean, a major legume crop, flowering time variation is well characterized within domesticated germplasm and is critical for modern production, but its importance during domestication is unclear. Here, we identify sequential contributions of two homeologous pseudo-response-regulator genes, Tof12 and Tof11, to ancient flowering time adaptation, and demonstrate that they act via LHY homologs to promote expression of the legume-specific E1 gene and delay flowering under long photoperiods. We show that Tof12-dependent acceleration of maturity accompanied a reduction in dormancy and seed dispersal during soybean domestication, possibly predisposing the incipient crop to latitudinal expansion. Better understanding of this early phase of crop evolution will help to identify functional variation lost during domestication and exploit its potential for future crop improvement.

Light- and temperature-entrainable circadian clock in soybean development

In plants, the spatiotemporal expression of circadian oscillators provides adaptive advantages in diverse species. However, the molecular basis of circadian clock in soybean is not known. In this study, we used soybean hairy roots expression system to monitor endogenous circadian rhythms and the sensitivity of circadian clock to environmental stimuli. We discovered in experiments with constant light and temperature conditions that the promoters of clock genes GmLCLb2 and GmPRR9b1 drive a self-sustained, robust oscillation of about 24-h in soybean hairy roots. Moreover, we demonstrate that circadian clock is entrainable by ambient light/dark or temperature cycles. Specifically, we show that light and cold temperature pulses can induce phase shifts of circadian rhythm, and we found that the magnitude and direction of phase responses depends on the specific time of these two zeitgeber stimuli. We obtained a quadruple mutant lacking the soybean gene GmLCLa1, LCLa2, LCLb1, and LCLb2 using CRISPR, and found that loss-of-function of these four GmLCL orthologs leads to an extreme short-period circadian rhythm and late-flowering phenotype in transgenic soybean. Our study establishes that the morning-phased GmLCLs genes act constitutively to maintain circadian rhythmicity and demonstrates that their absence delays the transition from vegetative growth to reproductive development.

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.)

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Identification of quantitative trait loci associated with flowering time in perilla using genotyping-by-sequencing

Understanding the transition to the reproductive period is important for crop breeding. This information can facilitate the production of novel varieties that are better adapted to local environments or changing climatic conditions. Here, we report the development of a high-density linkage map based on genotyping-by-sequencing (GBS) for the genus perilla. Through GBS library construction and Illumina sequencing of an F₂ population, a total of 9607 single-nucleotide polymorphism (SNP) markers were developed. The ten-group linkage map of 1309.39 cM contained 2518 markers, with an average marker density of 0.56 cM per linkage group (LG). Using this map, a total of six QTLs were identified. These quantitative trait loci (QTLs) are associated with three traits related to flowering time: days to visible flower bud, days to flowering, and days to maturity. Ortholog analysis conducted with known genes involved in the regulation of flowering time among different crop species identified GI, CO and ELF4 as putative perilla orthologs that are closely linked to the QTL regions associated with flowering time. These results provide a foundation that will be useful for future studies of flowering time in perilla using fine mapping, and marker-assisted selection for the development of new varieties of perilla.

Characterization of Two Growth Period QTLs Reveals Modification of PRR3 Genes During Soybean Domestication

Soybean yield is largely dependent on growth period. We characterized two growth period quantitative trait loci, Gp11 and Gp12, from a recombinant inbred population generated from a cross of wild (W05) and cultivated (C08) soybean. Lines carrying Gp11C08 and Gp12C08 tend to have a shorter growth period and higher expression of GmFT2a and GmFT5a. Furthermore, multiple interval mapping suggests that Gp11 and Gp12 may be genetically interacting with the E2 locus. This is consistent with the observation that GmFT2a and GmFT5a are activated by Gp11C08 and Gp12C08 at ZT4 in the recessive e2 but not the dominant E2 background. Gp11 and Gp12 are duplicated genomic regions each containing a copy of the soybean ortholog of PSEUDO RESPONSE REGULATOR 3 (GmPRR3A and GmPRR3B). GmPRR3A and GmPRR3B from C08 carry mutations that delete the CCT domain in the encoded proteins. These mutations were selected during soybean improvement and they alter the subcellular localization of GmPRR3A and GmPRR3B. Furthermore, GmPRR3A and GmPRR3B can interact with TOPLESS-related transcription factors, suggesting that they function in a transcription repressor complex. This study addresses previously unexplored components of the genetic network that probably controls the growth period of soybean and puts these loci into context with the well-characterized growth period-regulating E loci.

Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean

Photoperiodic flowering, a plant response to seasonal photoperiod changes in the control of reproductive transition, is an important agronomic trait that has been a central target of crop domestication and modern breeding programs. However, our understanding about the molecular mechanisms of photoperiodic flowering regulation in crop species is lagging behind. To better understand the regulatory gene networks controlling photoperiodic flowering of soybeans, we elucidated global gene expression patterns under different photoperiod regimes using the near isogenic lines (NILs) of maturity loci (E loci). Transcriptome signatures identified the unique roles of the E loci in photoperiodic flowering and a set of genes controlled by these loci. To elucidate the regulatory gene networks underlying photoperiodic flowering regulation, we developed the network inference algorithmic package CausNet that integrates sparse linear regression and Granger causality heuristics, with Gaussian approximation of bootstrapping to provide reliability scores for predicted regulatory interactions. Using the transcriptome data, CausNet inferred regulatory interactions among soybean flowering genes. Published reports in the literature provided empirical verification for several of CausNet's inferred regulatory interactions. We further confirmed the inferred regulatory roles of the flowering suppressors GmCOL1a and GmCOL1b using GmCOL1 RNAi transgenic soybean plants. Combinations of the alleles of GmCOL1 and the major maturity locus E1 demonstrated positive interaction between these genes, leading to enhanced suppression of flowering transition. Our work provides novel insights and testable hypotheses in the complex molecular mechanisms of photoperiodic flowering control in soybean and lays a framework for de novo prediction of biological networks controlling important agronomic traits in crops.

Photoperiod response-related gene SiCOL1 contributes to flowering in sesame

BACKGROUND

Sesame is a major oilseed crop which is widely cultivated all around the world. Flowering, the timing of transition from vegetative to reproductive growth, is one of the most important events in the life cycle of sesame. Sesame is a typical short-day (SD) plant and its flowering is largely affected by photoperiod. However, the flowering mechanism in sesame at the molecular level is still not very clear. Previous studies showed that the CONSTANS (CO) gene is the crucial photoperiod response gene which plays a center role in duration of the plant vegetative growth.

RESULTS

In this study, the CO-like (COL) genes were identified and characterized in the sesame genome. Two homologs of the CO gene in the SiCOLs, SiCOL1 and SiCOL2, were recognized and comprehensively analyzed. However, sequence analysis showed that SiCOL2 lacked one of the B-box motifs. In addition, the flowering time of the transgenic Arabidopsis lines with overexpressed SiCOL2 were longer than that of SiCOL1, indicating that SiCOL1 was more likely to be the potential functional homologue of CO in sesame. Expression analysis revealed that SiCOL1 had high expressed levels before flowering in leaves and exhibited diurnal rhythmic expression in both SD and long-day (LD) conditions. In total, 16 haplotypes of SiCOL1 were discovered in the sesame collections from Asia. However, the mutated haplotypes did not express under both SD and LD conditions and was regarded as a nonfunctional allele. Notably, the sesame landraces from high-latitude regions harboring nonfunctional alleles of SiCOL1 flowered much earlier than landraces from low-latitude regions under LD condition, and adapted to the northernmost regions of sesame cultivation. The result indicated that sesame landraces from high-latitude regions might have undergone artificial selection to adapt to the LD environment.

CONCLUSIONS

Our results suggested that SiCOL1 might contribute to regulation of flowering in sesame and natural variations in SiCOL1 were probably related to the expansion of sesame cultivation to high-latitude regions. The results could be used in sesame breeding and in broadening adaptation of sesame varieties to new regions.

Identification, characterization and gene expression analyses of important flowering genes related to photoperiodic pathway in bamboo

Background

Bamboo is an important member of the family Poaceae and has many inflorescence and flowering features rarely observed in other plant groups. It retains an unusual form of perennialism by having a long vegetative phase that can extend up to 120 years, followed by flowering and death of the plants. In contrast to a large number of studies conducted on the annual, reference plants Arabidopsis thaliana and rice, molecular studies to characterize flowering pathways in perennial bamboo are lacking. Since photoperiod plays a crucial role in flower induction in most plants, important genes involved in this pathway have been studied in the field grown Bambusa tulda, which flowers after 40-50 years.

Results

We identified several genes from B. tulda, including four related to the circadian clock [LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1 (TOC1), ZEITLUPE (ZTL) and GIGANTEA (GI)], two circadian clock response integrators [CONSTANS A (COA), CONSTANS B (COB)] and four floral pathway integrators [FLOWERING LOCUS T1, 2, 3, 4 (FT1, 2, 3, 4)]. These genes were amplified from either gDNA and/or cDNA using degenerate as well as gene specific primers based on homologous sequences obtained from related monocot species. The sequence identity and phylogenetic comparisons revealed their close relationships to homologs identified in the temperate bamboo Phyllostachys edulis. While the four BtFT homologs were highly similar to each other, BtCOA possessed a full-length B-box domain that was truncated in BtCOB. Analysis of the spatial expression of these genes in selected flowering and non-flowering tissue stages indicated their possible involvement in flowering. The diurnal expression patterns of the clock genes were comparable to their homologs in rice, except for BtZTL. Among multiple BtCO and BtFT homologs, the diurnal pattern of only BtCOA and BtFT3, 4 were synchronized in the flower inductive tissue, but not in the non-flowering tissues.

Conclusion

This study elucidates the photoperiodic regulation of bamboo homologs of important flowering genes. The finding also identifies copy number expansion and gene expression divergence of CO and FT in bamboo. Further studies are required to understand their functional role in bamboo flowering.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4571-7) contains supplementary material, which is available to authorized users.

Loss of Function of the E1-Like-b Gene Associates With Early Flowering Under Long-Day Conditions in Soybean

Photoperiod response of flowering determines plant adaptation to different latitudes. Soybean, a short-day plant, has gained the ability to flower under long-day conditions during the growing season at higher latitudes, mainly through dysfunction of phytochrome A genes (E3 and E4) and the floral repressor E1. In this study, we identified a novel molecular genetic basis of photoperiod insensitivity in Far-Eastern Russian soybean cultivars. By testcrossing these cultivars with a Canadian cultivar Harosoy near-isogenic line for a recessive e3 allele, followed by association tests and fine mapping, we determined that the insensitivity was inherited as a single recessive gene located in an 842-kb interval in the pericentromeric region of chromosome 4, where E1-Like b (E1Lb), a homoeolog of E1, is located. Sequencing analysis detected a single-nucleotide deletion in the coding sequence of the gene in insensitive cultivars, which generated a premature stop codon. Near-isogenic lines (NILs) for the loss-of-function allele (designated e1lb) exhibited upregulated expression of soybean FLOWERING LOCUS T (FT) orthologs, FT2a and FT5a, and flowered earlier than those for E1Lb under long-day conditions in both the e3/E4 and E3/E4 genetic backgrounds. These NILs further lacked the inhibitory effect on flowering by far-red light-enriched long-day conditions, which is mediated by E4, but not that of red-light-enriched long-day conditions, which is mediated by E3. These findings suggest that E1Lb retards flowering under long-day conditions by repressing the expression of FT2a and FT5a independently of E1. This loss-of-function allele can be used as a new resource in breeding of photoperiod-insensitive cultivars, and may improve our understanding of the function of the E1 family genes in the photoperiod responses of flowering in soybean.

Photoperiodism dynamics during the domestication and improvement of soybean

Soybean (Glycine max) is a facultative short-day plant with a sensitive photoperiod perception and reaction system, which allows it to adjust its physiological state and gene regulatory networks to seasonal and diurnal changes in environmental conditions. In the past few decades, soybean cultivation has spread from East Asia to areas throughout the world. Biologists and breeders must now confront the challenge of understanding the molecular mechanism of soybean photoperiodism and improving agronomic traits to enable this important crop to adapt to geographical and environmental changes. In this review, we summarize the genetic regulatory network underlying photoperiodic responses in soybean. Genomic and genetic studies have revealed that the circadian clock, in conjunction with the light perception pathways, regulates photoperiodic flowering. Here, we provide an annotated list of 844 candidate flowering genes in soybean, with their putative biological functions. Many photoperiod-related genes have been intensively selected during domestication and crop improvement. Finally, we describe recent progress in engineering photoperiod-responsive genes for improving agronomic traits to enhance geographic adaptation in soybean, as well as future prospects for research on soybean photoperiodic responses.

Fragaria vesca CONSTANS controls photoperiodic flowering and vegetative development

According to the external coincidence model, photoperiodic flowering occurs when CONSTANS (CO) mRNA expression coincides with light in the afternoon of long days (LDs), leading to the activation of FLOWERING LOCUS T (FT). CO has evolved in Brassicaceae from other Group Ia CO-like (COL) proteins which do not control photoperiodic flowering in Arabidopsis. COLs in other species have evolved different functions as floral activators or even as repressors. To understand photoperiodic development in the perennial rosaceous model species woodland strawberry, we functionally characterized FvCO, the only Group Ia COL in its genome. We demonstrate that FvCO has a major role in the photoperiodic control of flowering and vegetative reproduction through runners. FvCO is needed to generate a bimodal rhythm of FvFT1 which encodes a floral activator in the LD accession Hawaii-4: a sharp FvCO expression peak at dawn is followed by the FvFT1 morning peak in LDs indicating possible direct regulation, but additional factors that may include FvGI and FvFKF1 are probably needed to schedule the second FvFT1 peak around dusk. These results demonstrate that although FvCO and FvFT1 play major roles in photoperiodic development, the CO-based external coincidence around dusk is not fully applicable to the woodland strawberry.

Evolution of photoperiod sensing in plants and algae

Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review.

Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield

Soybean is a major legume crop originating in temperate regions, and photoperiod responsiveness is a key factor in its latitudinal adaptation. Varieties from temperate regions introduced to lower latitudes mature early and have extremely low grain yields. Introduction of the long-juvenile (LJ) trait extends the vegetative phase and improves yield under short-day conditions, thereby enabling expansion of cultivation in tropical regions. Here we report the cloning and characterization of J, the major classical locus conferring the LJ trait, and identify J as the ortholog of Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). J depends genetically on the legume-specific flowering repressor E1, and J protein physically associates with the E1 promoter to downregulate its transcription, relieving repression of two important FLOWERING LOCUS T (FT) genes and promoting flowering under short days. Our findings identify an important new component in flowering-time control in soybean and provide new insight into soybean adaptation to tropical regions.

Molecular mechanisms of flowering under long days and stem growth habit in soybean

Precise timing of flowering is critical to crop adaptation and productivity in a given environment. A number of classical E genes controlling flowering time and maturity have been identified in soybean [Glycine max (L.) Merr.]. The public availability of the soybean genome sequence has accelerated the identification of orthologues of Arabidopsis flowering genes and their functional analysis, and has allowed notable progress towards understanding the molecular mechanisms of flowering in soybean. Great progress has been made particularly in identifying genes and modules that inhibit flowering in long-day conditions, because a reduced or absent inhibition of flowering by long daylengths is an essential trait for soybean, a short-day (SD) plant, to expand its adaptability toward higher latitude environments. In contrast, the molecular mechanism of floral induction by SDs remains elusive in soybean. Here we present an update on recent work on molecular mechanisms of flowering under long days and of stem growth habit, outlining the progress in the identification of genes responsible, the interplay between photoperiod and age-dependent miRNA-mediated modules, and the conservation and divergence in photoperiodic flowering and stem growth habit in soybean relative to other legumes, Arabidopsis, and rice (Oryza sativa L.).

Soybean domestication: the origin, genetic architecture and molecular bases

Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.

A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog

FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.