The role of recently derived FT paralogs in sunflower domestication

Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species

Many species of Sapindaceae, such as lychee, longan, and rambutan, provide nutritious and delicious fruit. Understanding the molecular genetic mechanisms that underlie the regulation of flowering is essential for securing flower and fruit productivity. Most endogenous and exogenous flowering cues are integrated into the florigen encoded by FLOWERING LOCUS T. However, the regulatory mechanisms of flowering remain poorly understood in Sapindaceae. Here, we identified 60 phosphatidylethanolamine-binding protein-coding genes from six Sapindaceae plants. Gene duplication events led to the emergence of two or more paralogs of the FT gene that have evolved antagonistic functions in Sapindaceae. Among them, the FT1-like genes are functionally conserved and promote flowering, while the FT2-like genes likely serve as repressors that delay flowering. Importantly, we show here that the natural variation at nucleotide position - 1437 of the lychee FT1 promoter determined the binding affinity of the SVP protein (LcSVP9), which was a negative regulator of flowering, resulting in the differential expression of LcFT1, which in turn affected flowering time in lychee. This finding provides a potential molecular marker for breeding lychee. Taken together, our results reveal some crucial aspects of FT gene family genetics that underlie the regulation of flowering in Sapindaceae.

A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.

The evolution and functional divergence of FT-related genes in controlling flowering time in Brassica rapa ssp. rapa

KEY MESSAGE

The BrrFT paralogues exhibit distinct expression patterns and play different roles in regulating flowering time, and BrrFT4 competes with BrrFT1 and BrrFT2 to interact with BrrFD proteins. Flowering time is an important agricultural trait for Brassica crops, and early bolting strongly affects the yield and quality of Brassica rapa ssp. rapa. Flowering Locus T paralogues play an important role in regulating flowering time. In this study, we identified FT-related genes in turnip by phylogenetic classification, and four BrrFT homoeologs that shared with high identities with BraFT genes were isolated. The different gene structures, promoter binding sites, and expression patterns observed indicated that these genes may play different roles in flowering time regulation. Further genetic and biochemical experiments showed that as for FT-like paralogues, BrrFT2 acted as the key floral inducer, and BrrFT1 seems to act as a mild 'florigen' protein. However, BrrFT4 acts as a floral repressor and antagonistically regulates flowering time by competing with BrrFT1 and BrrFT2 to bind BrrFD proteins. BrrFT3 may have experienced loss of function via base shift mutation. Our results revealed the potential roles of FT-related genes in flowering time regulation in turnip.

Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia

BACKGROUND

The formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking.

RESULTS

Here, we report the chromosomal-level reference genome of C. japonica through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F1 hybrids between C. japonica and C. chekiangoleosa. We identify two whole-genome duplication events in C. japonica: one is a shared ancient γ event, and the other is revealed to be specific to genus Camellia. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the AGAMOUS loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of C. japonica and C. azalea-a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including GIGANTEA and CONSTANS of the photoperiod pathway, have been disrupted in C. azalea. Furthermore, we reveal that the distinctive expression patterns of FLOWERING LOCUS T can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in GIGANTEA, CONSTANS, and FLOWERING LOCUS T is central to achieve seasonality.

CONCLUSIONS

Through the genomic and comparative genomics characterizations of ornamental Camellia spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.

Insights into flowering mechanisms in apple (Malus × domestica Borkh.) amidst climate change: An exploration of genetic and epigenetic factors

Apple (Malus × domestica Borkh.) holds a prominent position among global temperate fruit crops, with flowering playing a crucial role in both production and breeding. This review delves into the intricate mechanisms governing apple flowering amidst the backdrop of climate change, acknowledging the profound influence of external and internal factors on biennial bearing, flower bud quality, and ultimately, fruit quality. Notably, the challenge faced in major apple production regions is not an inadequacy of flowers but an excess, leading to compromised fruit quality necessitating thinning practices. Climate change exacerbates these challenges, rendering apple trees more susceptible to crop failure due to unusual weather events, such as reduced winter snowfall, early spring cold weather, and hailstorms during flowering and fruit setting. Altered climatic conditions, exemplified by increased spring warming coupled with sub-freezing temperatures, negatively impact developing flower buds and decrease overall crop production. Furthermore, changing winter conditions affect chilling accumulation, disrupting flower development and synchronicity. Although the physiological perception of apple flowering has been reviewed in the past, the genetic, epigenetic, and multi-omics regulatory mechanisms governing floral induction and flowering are still rarely discussed in the case of apple flowering. This article comprehensively reviews the latest literature encompassing all aspects of apple flowering, aiming to broaden our understanding and address flowering challenges while also laying a solid foundation for future research in developing cultivars that are ideally adapted to climate change.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Hormonal Regulation and Stimulation Response of Jatropha curcas L. Homolog Overexpression on Tobacco Leaf Growth by Transcriptome Analysis

The Flowering locus T (FT) gene encodes the florigen protein, which primarily regulates the flowering time in plants. Recent studies have shown that FT genes also significantly affect plant growth and development. The FT gene overexpression in plants promotes flowering and suppresses leaf and stem development. This study aimed to conduct a transcriptome analysis to investigate the multiple effects of Jatropha curcas L. homolog (JcFT) overexpression on leaf growth in tobacco plants. The findings revealed that JcFT overexpression affected various biological processes during leaf development, including plant hormone levels and signal transduction, lipid oxidation metabolism, terpenoid metabolism, and the jasmonic-acid-mediated signaling pathway. These results suggested that the effects of FT overexpression in plants were complex and multifaceted, and the combination of these factors might contribute to a reduction in the leaf size. This study comprehensively analyzed the effects of JcFT on leaf development at the transcriptome level and provided new insights into the function of FT and its homologous genes.

Genomic Resequencing Unravels the Genetic Basis of Domestication, Expansion, and Trait Improvement in Morus Atropurpurea

Mulberry is an economically important plant in the sericulture industry and traditional medicine. However, the genetic and evolutionary history of mulberry remains largely unknown. Here, this work presents the chromosome-level genome assembly of Morus atropurpurea (M. atropurpurea), originating from south China. Population genomic analysis using 425 mulberry accessions reveal that cultivated mulberry is classified into two species, M. atropurpurea and M. alba, which may have originated from two different mulberry progenitors and have independent and parallel domestication in north and south China, respectively. Extensive gene flow is revealed between different mulberry populations, contributing to genetic diversity in modern hybrid cultivars. This work also identifies the genetic architecture of the flowering time and leaf size. In addition, the genomic structure and evolution of sex-determining regions are identified. This study significantly advances the understanding of the genetic basis and domestication history of mulberry in the north and south, and provides valuable molecular markers of desirable traits for mulberry breeding.

CRISPR/Cas9 mutants delineate roles of Populus FT and TFL1/CEN/BFT family members in growth, dormancy release and flowering

Vegetative and reproductive phase change and phenology are economically and ecologically important traits. Trees typically require several years of growth before flowering and, once mature, seasonal control of the transition to flowering and flower development is necessary to maintain vegetative meristems and for reproductive success. Members of two related gene subfamilies, FLOWERING LOCUST (FT) and TERMINAL FLOWER1 (TFL1)/CENTRORADIALIS (CEN)/BROTHER OF FT AND TFL1 (BFT), have antagonistic roles in flowering in diverse species and roles in vegetative phenology in trees, but many details of their functions in trees have yet to be resolved. Here, we used CRISPR/Cas9 to generate single and double mutants involving the five Populus FT and TFL1/CEN/BFT genes. The ft1 mutants exhibited wild-type-like phenotypes in long days and short days, but after chilling, to release dormancy, they showed delayed bud flush and GA3 could compensate for the ft1 mutation. After rooting and generating some phytomers in tissue culture, both cen1 and cen1ft1 mutants produced terminal as well as axillary flowers, indicating that the cen1 flowering phenotype is independent of FT1. The CEN1 showed distinct circannual expression patterns in vegetative and reproductive tissues and comparison with the expression patterns of FT1 and FT2 suggests that the relative levels of CEN1 compared with FT1 and FT2 regulate multiple phases of vegetative and reproductive seasonal development.

Functional characterization of three TERMINAL FLOWER 1-like genes from Platanus acerifolia

KEY MESSAGE

TFL1-like genes of the basal eudicot Platanus acerifolia have conserved roles in maintaining vegetative growth and inhibiting flowering, but may act through distinct regulatory mechanism. Three TERMINAL FLOWER 1 (TFL1)-like genes were isolated and characterized from London plane tree (Platanus acerifolia). All genes have conserved genomic organization and characteristic of the phosphatidylethanolamine-binding protein (PEBP) family. Sequence alignment and phylogenetic analysis indicated that two genes belong to the TFL1 clade, designated as PlacTFL1a and PlacTFL1b, while another one was grouped in the BFT clade, named as PlacBFT. qRT-PCR analysis showed that all three genes primarily expressed in vegetative phase, but the expression of PlacTFL1a was much higher and wider than that of PlacTFL1b, with the latter only detected at relatively low expression levels in apical and lateral buds in April. PlacBFT was mainly expressed in young stems of adult trees followed by juvenile tissues. Ectopic expression of any TFL1-like gene in Arabidopsis showed phenotypes of delayed or repressed flowering. Furthermore, overexpression of PlacTFL1a gene in petunia also resulted in extremely delayed flowering. In non-flowering 35:PlacTFL1a transgenic petunia plants, the FT-like gene (PhFT) gene was significantly upregulated and AP1 homologues PFG, FBP26 and FBP29 were significantly down-regulated in leaves. Yeast two-hybrid analysis indicated that only weak interactions were detected between PlacTFL1a and PlacFDL, and PlacTFL1a showed no interaction with PhFDL1/2. These results indicated that the TFL1-like genes of Platanus have conserved roles in repressing flowering, but probably via a distinct regulatory mechanism.

Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture

Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.

SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture, and drought responses

Allelic variation in the CETS (CENTRORADIALIS, TERMINAL FLOWER 1, SELF PRUNING) gene family controls agronomically important traits in many crops. CETS genes encode phosphatidylethanolamine-binding proteins that have a central role in the timing of flowering as florigenic and anti-florigenic signals. The great expansion of CETS genes in many species suggests that the functions of this family go beyond flowering induction and repression. Here, we characterized the tomato SELF PRUNING 3C (SP3C) gene, and show that besides acting as a flowering repressor it also regulates seed germination and modulates root architecture. We show that loss of SP3C function in CRISPR/Cas9-generated mutant lines increases root length and reduces root side branching relative to the wild type. Higher SP3C expression in transgenic lines promotes the opposite effects in roots, represses seed germination, and also improves tolerance to water stress in seedlings. These discoveries provide new insights into the role of SP paralogs in agronomically relevant traits, and support future exploration of the involvement of CETS genes in abiotic stress responses.

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

Functional diversification and molecular mechanisms of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in horticultural plants

Flowering is an important process in higher plants and is regulated by a variety of factors, including light, temperature, and phytohormones. Flowering restriction has a considerable impact on the commodity value and production cost of many horticultural crops. In Arabidopsis, the FT/TFL1 gene family has been shown to integrate signals from various flowering pathways and to play a key role in the transition from flower production to seed development. Studies in several plant species of the FT/TFL1 gene family have revealed it harbors functional diversity in the regulation of flowering. Here, we review the functional evolution of the FT/TFL1 gene family in horticulture plants and its unique regulatory mechanisms; in addition, the FT/TFL1 family of genes as an important potential breeding target is explored.

The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation

Gene duplications have long been recognized as a contributor to the evolution of genes with new functions. Multiple copies of genes can result from tandem duplication, from transposition to new chromosomes, or from whole-genome duplication (polyploidy). The most common fate is that one member of the pair is deleted to return the gene to the singleton state. Other paths involve the reduced expression of both copies (hypofunctionalization) that are held in duplicate to maintain sufficient quantity of function. The two copies can split functions (subfunctionalization) or can diverge to generate a new function (neofunctionalization). Retention of duplicates resulting from doubling of the whole genome occurs for genes involved with multicomponent interactions such as transcription factors and signal transduction components. In contrast, these classes of genes are underrepresented in small segmental duplications. This complementary pattern suggests that the balance of interactors affects the fate of the duplicate pair. We discuss the different mechanisms that maintain duplicated genes, which may change over time and intersect.

Putting the pea in photoPEAriod

This article comments on:

Williams O, Vander Schoor JK, Butler JB, Ridge S, Sussmilch FC, Hecht VFG, Weller JL. 2022. The genetic architecture of flowering time changes in pea from wild to crop. Journal of Experimental Botany 73,3978–3990.

Passiflora organensis FT/TFL1 gene family and their putative roles in phase transition and floral initiation

Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about the molecular control of phase transition and flower initiation in this species. The florigen agent FLOWERING LOCUS T (FT) interacts with the bZIP protein FLOWERING LOCUS D (FD) to induce flowering in the model species Arabidopsis thaliana. Current models based on research in rice suggest that this interaction is bridged by 14-3-3 proteins. We identified eight FT/TFL1 family members in Passiflora organensis and characterized them by analyzing their phylogeny, gene structure, expression patterns, protein interactions and putative biological roles by heterologous expression in Arabidopsis. PoFT was highest expressed during the adult vegetative phase and it is supposed to have an important role in flowering induction. In contrast, its paralogs PoTSFs were highest expressed in the reproductive phase. While ectopic expression of PoFT in transgenic Arabidopsis plants induced early flowering and inflorescence determinacy, the ectopic expression of PoTSFa caused a delay in flowering. PoTFL1-like genes were highest expressed during the juvenile phase and their ectopic expression caused delayed flowering in Arabidopsis. Our protein-protein interaction studies indicate that the flowering activation complexes in Passiflora might deviate from the hexameric complex found in the model system rice. Our results provide insights into the potential functions of FT/TFL1 gene family members during floral initiation and their implications in the special plant architecture of Passiflora species, contributing to more detailed studies on the regulation of passion fruit reproduction.

Identification of a major locus for flowering pattern sheds light on plant architecture diversification in cultivated peanut

A major gene controls flowering pattern in peanut, possibly encoding a TFL1-like. It was subjected to gain/loss events of a deletion and changes in mRNA expression levels, partly explaining the evolution of flowering pattern in Arachis. Flowering pattern (FP) is a major characteristic differentiating the two subspecies of cultivated peanut (Arachis hypogaea L.). Subsp. fastigiata possessing flowers on the mainstem (MSF) and a sequential FP, whereas subsp. hypogaea lacks MSF and exhibits an alternate FP. FP is considered the main contributor to plant adaptability, and evidence indicates that its diversification occurred during the several thousand years of domestication. However, the genetic mechanism that controls FP in peanut is unknown. We investigated the genetics of FP in a recombinant inbred population, derivatives of an A. hypogaea by A. fastigiata cross. Lines segregated 1:1 for FP, indicating a single gene effect. Using Axiom_Arachis2 SNP-array, FP was mapped to a small segment in chromosome B02, wherein a Terminal Flowering 1-like (AhTFL1) gene with a 1492 bp deletion was found in the fastigiata line, leading to a truncated protein. Remapping FP in the RIL population with the AhTFL1 indel as a marker increased the LOD score from 53.3 to 158.8 with no recombination in the RIL population. The same indel was found co-segregating with the phenotype in two independent EMS-mutagenized M2 families, suggesting a hotspot for gene conversion. Also, AhTFL1 was significantly less expressed in the fastigiata line compared to hypogaea and in flowering than non-flowering branches. Sequence analysis of the AhTFL1 in peanut world collections indicated significant conservation, supporting the putative role of AhTFL1 in peanut speciation during domestication and modern cultivation.

Pathways to de novo domestication of crop wild relatives

Growing knowledge about crop domestication, combined with increasingly powerful gene-editing toolkits, sets the stage for the continual domestication of crop wild relatives and other lesser-known plant species.

Functional Redundancy of FLOWERING LOCUS T 3b in Soybean Flowering Time Regulation

Photoperiodic flowering is an important agronomic trait that determines adaptability and yield in soybean and is strongly influenced by FLOWERING LOCUS T (FT) genes. Due to the presence of multiple FT homologs in the genome, their functions in soybean are not fully understood. Here, we show that GmFT3b exhibits functional redundancy in regulating soybean photoperiodic flowering. Bioinformatic analysis revealed that GmFT3b is a typical floral inducer FT homolog and that the protein is localized to the nucleus. Moreover, GmFT3b expression was induced by photoperiod and circadian rhythm and was more responsive to long-day (LD) conditions. We generated a homozygous ft3b knockout and three GmFT3b-overexpressing soybean lines for evaluation under different photoperiods. There were no significant differences in flowering time between the wild-type, the GmFT3b overexpressors, and the ft3b knockouts under natural long-day, short-day, or LD conditions. Although the downstream flowering-related genes GmFUL1 (a, b), GmAP1d, and GmLFY1 were slightly down-regulated in ft3b plants, the floral inducers GmFT5a and GmFT5b were highly expressed, indicating potential compensation for the loss of GmFT3b. We suggest that GmFT3b acts redundantly in flowering time regulation and may be compensated by other FT homologs in soybean.

FT-like paralogs are repressed by an SVP protein during the floral transition in Phalaenopsis orchid

An SVP protein, PhSVP, bound to the CArG-boxes in the promoter regions of FT-like paralogs and repressed their expression, thus affecting the floral transition in Phalaenopsis orchid. Phalaenopsis is an important ornamental flower native to tropical rain forests. It usually reaches vegetative maturity after 4-5 leaves and, after a juvenile stage, forms a flower spike (inflorescence) from the axillary buds. The PEBP gene family encodes a phosphatidyl-ethanolamine-binding protein (PEBP) domain involved in regulating flowering and other aspects of plant development. Here, we identified eight PEBP family genes in Phalaenopsis and detected the expression patterns of seven of them in various organs. Among them, PhFT1 (Phalaenopsis hybrid FLOWERING LOCUS T1), PhFT3, PhFT5, and PhMFT (Phalaenopsis hybrid MOTHER OF FT AND TFL1) promoted flowering in transgenic Arabidopsis, while PhFT6 inhibited flowering. PhSVP (Phalaenopsis hybrid SHORT VEGETATIVE PHASE), an SVP protein that repressed flowering in Arabidopsis, bound to the CArG-boxes in the promoter regions of PhFT3, PhFT6, and PhMFT in a yeast one-hybrid assay. Additionally, dual-luciferase and transient expression assays showed that PhSVP significantly inhibits the expression of both PhFT3 and PhFT6. Together, our work provides a comprehensive understanding of the PhFT-like genes that can promote or repress flowering, and it suggests strategies for regulating the floral transition in Phalaenopsis that exploit the evolutionary versatility of PhFTs to respond to various signals stimuli.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Enhancing crop diversity for food security in the face of climate uncertainty

Global agriculture is dominated by a handful of species that currently supply a huge proportion of our food and feed. It additionally faces the massive challenge of providing food for 10 billion people by 2050, despite increasing environmental deterioration. One way to better plan production in the face of current and continuing climate change is to better understand how our domestication of these crops included their adaptation to environments that were highly distinct from those of their centre of origin. There are many prominent examples of this, including the development of temperate Zea mays (maize) and the alteration of day-length requirements in Solanum tuberosum (potato). Despite the pre-eminence of some 15 crops, more than 50 000 species are edible, with 7000 of these considered semi-cultivated. Opportunities afforded by next-generation sequencing technologies alongside other methods, including metabolomics and high-throughput phenotyping, are starting to contribute to a better characterization of a handful of these species. Moreover, the first examples of de novo domestication have appeared, whereby key target genes are modified in a wild species in order to confer predictable traits of agronomic value. Here, we review the scale of the challenge, drawing extensively on the characterization of past agriculture to suggest informed strategies upon which the breeding of future climate-resilient crops can be based.

Towards understanding the biological foundations of perenniality

Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials' physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.

Meristem transitions and plant architecture-learning from domestication for crop breeding

Genetic networks that regulate meristem transitions were recurrent targets of selection during crop domestication and allow fine-tuning of plant architecture for improved crop productivity.

Functional homoeologous alleles of CONSTANS contribute to seasonal crop type in rapeseed

Two CO paralogs in Brassica napus were confirmed and shown distinct expression pattern and function in promoting flowering and allelic variation s within BnaCO.A10 were found closely associated with ecotype divergence. CONSTANS (CO) is a key gene that responds to photoperiod and in Arabidopsis can promote flowering under long-day (LD) conditions. Brassica napus L. is a major oil crop and close relative of Arabidopsis, and arose via allopolyploidization from the diploids B. rapa (A genome) and B. oleracea (C genome). In this study, we confirmed that B. napus has two CO genes located on the A10 (BnaCO.A10) and C9 (BnaCO.C9) chromosomes. Significant differences in level and temporal pattern of transcription, as well as in protein function, of these homoeologous may have resulted from sequence variation in the promoter as well as in the coding region. Apart from two insertions of 527 bp and 2002 bp in the promoter of BnaCO.C9 that function as transcriptional enhancers, this gene is otherwise highly conserved in both promoter and coding region. However, BnaCO.A10 was classified into two haplotypes and transgene analysis in Arabidopsis and backcross analysis in rapeseed indicated that the winter-type haplotype had a greater effect in promoting flowering than the spring type. We discuss the contribution of CO alleles to species evolution, and for eco-geographic radiation following crop domestication, alongside scope for managing this locus in future breeding.

Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce

KEY MESSAGE

Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study, the effects of photoperiod and ambient temperature on bolting and flowering regulation were studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI 251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 h) and long (16 h) days and low (20 °C) and high (35 °C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2), and two candidate genes were identified by fine mapping, homology, and gene expression studies. In short days and high temperature conditions, qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8, and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences and were used to design a genetic marker which may be used to identify the late bolting trait.

Overcoming the genetic compensation response of soybean florigens to improve adaptation and yield at low latitudes

The classical soybean (Glycine max) trait long juvenile (LJ) is essentially a reduction in sensitivity to short-day (SD) conditions for induction and completion of flowering, and has been introduced into soybean cultivars to improve yield in tropical environments. However, only one locus, J, is known to confer LJ in low-latitude varieties. Here, we defined two quantitative trait loci contributing to the LJ trait, LJ16.1 and LJ16.2, and identified them as the florigen (FT) homologs FT2a and FT5a, respectively. The two selected florigen variations both delay flowering time under SD conditions by repressing the floral meristem identity gene GmAPETALA1. Single mutants have a relatively subtle effect on flowering time and displayed a substantial genetic compensation response, but this was absent in ft2a ft5a double mutants, which showed an enhanced LJ phenotype that translated to higher yields under SD conditions. A survey of sequence diversity suggests that FT2a and FT5a variants have diverse origins and have played distinct roles as soybean spread to lower latitudes. Our results show that integration of variants in the florigen genes offers a strategy for customizing flowering time to adjust adaptation and improve crop productivity in tropical regions.

A TILLING by sequencing approach to identify induced mutations in sunflower genes

The Targeting Induced Local Lesions in Genomes (TILLING) technology is a reverse genetic strategy broadly applicable to every kind of genome and represents an attractive tool for functional genomic and agronomic applications. It consists of chemical random mutagenesis followed by high-throughput screening of point mutations in targeted genomic regions. Although multiple methods for mutation discovery in amplicons have been described, next-generation sequencing (NGS) is the tool of choice for mutation detection because it quickly allows for the analysis of a large number of amplicons. The aim of the present work was to screen a previously generated sunflower TILLING population and identify alterations in genes involved in several important and complex physiological processes. Twenty-one candidate sunflower genes were chosen as targets for the screening. The TILLING by sequencing strategy allowed us to identify multiple mutations in selected genes and we subsequently validated 16 mutations in 11 different genes through Sanger sequencing. In addition to addressing challenges posed by outcrossing, our detection and validation of mutations in multiple regulatory loci highlights the importance of this sunflower population as a genetic resource.

Diversification in Functions and Expressions of Soybean FLOWERING LOCUS T Genes Fine-Tunes Seasonal Flowering

The proper timing of flowering in response to environmental changes is critical for ensuring crop yields. FLOWERING LOCUS T (FT) homologs of the phosphatidylethanolamine-binding protein family play important roles as floral integrators in many crops. In soybean, we identified 17 genes of this family, and characterized biological functions in flowering for ten FT homologs. Overexpression of GmFT homologs in Arabidopsis revealed that a set of GmFT homologs, including GmFT2a/2b, GmFT3a/3b, and GmFT5a/5b, promoted flowering similar to FT; in contrast, GmFT1a/1b, GmFT4, and GmFT6 delayed flowering. Consistently, expressions of GmFT2a, GmFT2b, and GmFT5a were induced in soybean leaves in response to floral inductive short days, whereas expressions of GmFT1a and GmFT4 were induced in response to long days. Exon swapping analysis between floral activator GmFT2a and floral repressor GmFT4 revealed that the segment B region in the fourth exon is critical for their antagonistic functions. Finally, expression analysis of GmFT2a, GmFT5a, and GmFT4 in soybean accessions exhibiting various flowering times indicated that the mRNA levels of GmFT2a and GmFT5a were higher in early flowering accessions than in late-flowering accessions, while GmFT4 showed the opposite pattern. Moreover, the relative mRNA levels between GmFT2a/GmFT5a and GmFT4 was important in determining day length-dependent flowering in soybean accessions. Taken together, our results suggest that the functions of GmFT homologs have diversified into floral activators and floral repressors during soybean evolution, and the timing of flowering in response to changing day length is determined by modulating the activities of antagonistic GmFT homologs.

Diversity and selection of the continuous-flowering gene, RoKSN, in rose

Blooming seasonality is an important trait in ornamental plants and was selected by humans. Wild roses flower only in spring whereas most cultivated modern roses can flower continuously. This trait is explained by a mutation of a floral repressor gene, RoKSN, a TFL1 homologue. In this work, we studied the origin, the diversity and the selection of the RoKSN gene. We analyzed 270 accessions, including wild and old cultivated Asian and European roses as well as modern roses. By sequencing the RoKSN gene, we proposed that the allele responsible for continuous-flowering, RoKSN^copia, originated from Chinese wild roses (Indicae section), with a recent insertion of the copia element. Old cultivated Asian roses with the RoKSN^copia allele were introduced in Europe, and the RoKSN^copia allele was progressively selected during the 19th and 20th centuries, leading to continuous-flowering modern roses. Furthermore, we detected a new allele, RoKSN^A181, leading to a weak reblooming. This allele encodes a functional floral repressor and is responsible for a moderate accumulation of RoKSN transcripts. A transient selection of this RoKSN^A181 allele was observed during the 19th century. Our work highlights the selection of different alleles at the RoKSN locus for recurrent blooming in rose.

Molecular regulation of plant developmental transitions and plant architecture via PEPB family proteins: an update on mechanism of action

This year marks the 100th anniversary of the experiments by Garner and Allard that showed that plants measure the duration of the night and day (the photoperiod) to time flowering. This discovery led to the identification of Flowering Locus T (FT) in Arabidopsis and Heading Date 3a (Hd3a) in rice as a mobile signal that promotes flowering in tissues distal to the site of cue perception. FT/Hd3a belong to the family of phosphatidylethanolamine-binding proteins (PEBPs). Collectively, these proteins control plant developmental transitions and plant architecture. Several excellent recent reviews have focused on the roles of PEBPs in diverse plant species; here we will primarily highlight recent advances that enhance our understanding of the mechanism of action of PEBPs and discuss critical open questions.

Cotton architecture: examining the roles of SINGLE FLOWER TRUSS and SELF-PRUNING in regulating growth habits of a woody perennial crop

By specifying patterns of determinate and indeterminate growth, FLOWERING LOCUS T/SINGLE FLOWER TRUSS (SFT) and TERMINAL FLOWER 1/SELF-PRUNING (SP) regulate plant architecture. Though well characterized in Arabidopsis, the impacts of these genes on the architectures of diverse crops cultivated in different environments, and their potential to enhance crop productivity and management, are less well addressed. Cotton (Gossypium spp.) is naturally a short-day photoperiodic perennial that is now grown primarily as a day-neutral, annual row crop. Different environments and cultivation practices favor specific growth habits to optimize yield, and in cotton, especially in regions that rely heavily on mechanized harvest, the trend has been to more determinate varieties. Identifying and functionally characterizing SFT and SP homologs in cotton uncovered new aspects of how ratios of indeterminate and determinate growth are balanced, and unraveling their genetic networks emphasized how broadly these gene products affect cotton growth habits.

CaFT-LIKE is a flowering promoter in pepper and functions as florigen in tomato

We identified a pepper late-flowering mutant that is disrupted in the sequence of CaFT-LIKE, the ortholog of tomato SINGLE FLOWER TRUSS (SFT). Heterologous expression in tomato indicated that CaFT-LIKE has a conserved function as a flowering promoter and can rescue the wild-type phenotype of the tomato sft mutant. CaFT-LIKE confers a graft-transmissible signal for flowering initiation in tomato, implicating its function as a florigen. To test the relationship between CaFT-LIKE and FASCICULATE (FA), the ortholog of tomato SELF PRUNING (SP), we constructed the double mutant Caft-like fa. The phenotype of Caft-like fa resembled that of Caft-like, indicating epistasis of Caft-like over fa in controlling flowering time and sympodial shoot structure. To examine the association between the expression pattern of flowering genes and natural variation in flowering time, the expression levels of CaFT-LIKE and the flowering repressor CaAP2 were determined in a panel of early-flowering cultivars and late-flowering landraces and wild accessions. Strong positive and negative correlations between flowering time and expression levels of CaAP2 and CaFT-LIKE, respectively, were observed, indicating that high-expression alleles of CaFT-LIKE and low-expression alleles of CaAP2 were selected for early flowering during pepper domestication and breeding.

TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T

Plants monitor seasonal cues to optimize reproductive success by tuning onset of reproduction and inflorescence architecture. TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) and their orthologs antagonistically regulate these life history traits, yet their mechanism of action, antagonism and targets remain poorly understood. Here, we show that TFL1 is recruited to thousands of loci by the bZIP transcription factor FD. We identify the master regulator of floral fate, LEAFY (LFY) as a target under dual opposite regulation by TFL1 and FT and uncover a pivotal role of FT in promoting flower fate via LFY upregulation. We provide evidence that the antagonism between FT and TFL1 relies on competition for chromatin-bound FD at shared target loci. Direct TFL1-FD regulated target genes identify this complex as a hub for repressing both master regulators of reproductive development and endogenous signalling pathways. Our data provide mechanistic insight into how TFL1-FD sculpt inflorescence architecture, a trait important for reproductive success, plant architecture and yield.

SINGLE FLOWER TRUSS and SELF-PRUNING signal developmental and metabolic networks to guide cotton architectures

Patterns of indeterminate and determinate growth specify plant architecture and influence crop productivity. In cotton (Gossypium hirsutum), SINGLE FLOWER TRUSS (SFT) stimulates the transition to flowering and determinate growth, while its closely related antagonist SELF-PRUNING (SP) maintains meristems in indeterminate states to favor vegetative growth. Overexpressing GhSFT while simultaneously silencing GhSP produces highly determinate cotton with reduced foliage and synchronous fruiting. These findings suggest that GhSFT, GhSP, and genes in these signaling networks hold promise for enhancing 'annualized' growth patterns and improving cotton productivity and management. To identify the molecular programs underlying cotton growth habits, we used comparative co-expression networks, differential gene expression, and phenotypic analyses in cotton varieties expressing altered levels of GhSFT or GhSP. Using multiple cotton and tomato datasets, we identified diverse genetic modules highly correlated with SFT or SP orthologs which shared related Gene Ontologies in different crop species. Notably, altering GhSFT or GhSP levels in cotton affected the expression of genes regulating meristem fate and metabolic pathways. Further phenotypic analyses of gene products involved in photosynthesis, secondary metabolism, and cell wall biosynthesis showed that early changes in GhSFT and GhSP levels profoundly impacted later development in distal tissues. Identifying the molecular underpinnings of GhSFT and GhSP activities emphasizes their broad actions in regulating cotton architecture.

New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation

Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.

Evolutionary Insights into the Nature of Plant Domestication

Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations that are critical for human survival. Darwin used domesticated species as early models for evolution, highlighting their variation and the key role of selection in species differentiation. Over the last two decades, a growing synthesis of plant genetics, genomics, and archaeobotany has led to challenges to old orthodoxies and the advent of fresh perspectives on how crop domestication and diversification proceed. I discuss four new insights into plant domestication - that in general domestication is a protracted process, that unconscious (natural) selection plays a prominent role, that interspecific hybridization may be an important mechanism for crop species diversification and range expansion, and that similar genes across multiple species underlies parallel/convergent phenotypic evolution between domesticated taxa. Insights into the evolutionary origin and diversification of crop species can help us in developing new varieties (and possibly even new species) to deal with current and future environmental challenges in a sustainable manner.

QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants

Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as the training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. The average precision was 0.027 for Arabidopsis and 0.029 for rice. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validated Sorghum bicolor and Setaria viridis models. The S. bicolor model was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. In addition, we applied the S. viridis model and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.

Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants

Plant growth and development, particularly the induction of flowering, are tightly controlled by key regulators in response to endogenous and environmental cues. The FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family of phosphatidylethanolamine-binding protein (PEBP) genes is central to plant development, especially the regulation of flowering time and plant architecture. FT, the long-sought florigen, promotes flowering and TFL1 represses flowering. The balance between FT and TFL1 modulates plant architecture by switching the meristem from indeterminate to determinate growth, or vice versa. Recent studies in a broad range of plant species demonstrated that, in addition to their roles in flowering time and plant architecture, FT/TFL1 family genes participate in diverse aspects of plant development, such as bamboo seed germination and potato tuber formation. In this review, we briefly summarize the evolution of the FT/TFL1 family and highlight recent findings on their conserved and divergent functions in different species.

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.

Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways

Quinoa (Chenopodium quinoa Willd.) is a grain crop grown in the Andes renowned as a highly nutritious plant exhibiting tolerance to abiotic stress such as drought, cold and high salinity. Quinoa grows across a range of latitudes corresponding to differing day lengths, suggesting regional adaptations of flowering regulation. Improved understanding and subsequent modification of the flowering process, including flowering time, ensuring high yields, is one of the key factors behind expansion of cultivation zones and goals of the crop improvement programs worldwide. However, our understanding of the molecular basis of flower initiation and development in quinoa is limited. Here, we use a computational approach to perform genome-wide identification and analysis of 611 orthologues of the Arabidopsis thaliana flowering genes. Conservation of the genes belonging to the photoperiod, gibberellin and autonomous pathways was observed, while orthologues of the key genes found in the vernalisation pathway (FRI, FLC) were absent from the quinoa genome. Our analysis indicated that on average each Arabidopsis flowering gene has two orthologous copies in quinoa. Several genes including orthologues of MIF1, FT and TSF were identified as homologue-rich genes in quinoa. We also identified 459 quinoa-specific genes uniquely expressed in the flower and/or meristem, with no known orthologues in other species. The genes identified provide a resource and framework for further studies of flowering in quinoa and related species. It will serve as valuable resource for plant biologists, crop physiologists and breeders to facilitate further research and establishment of modern breeding programs for quinoa.

Evolutionary processes from the perspective of flowering time diversity

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.

Evolution and Expression of Reproductive Transition Regulatory Genes FT/TFL1 With Emphasis in Selected Neotropical Orchids

Flowering is a rigorously timed and morphologically complex shift in plant development. This change depends on endogenous as well as environmental factors. FLOWERING LOCUS T (FT) integrates several cues from different pathways acting as a flowering promoter. Contrary to the role of FT, its paralog TERMINAL FLOWER 1 (TFL1) delays floral transition. Although FT/TFL1 homologs have been studied in model eudicots and monocots, scarce studies are available in non-model monocots like the Orchidaceae. Orchids are very diverse and their floral complexity is translated into a unique aesthetic display, which appeals the ornamental plant market. Nonetheless, orchid trade faces huge limitations due to their long vegetative phase and intractable indoor flowering seasons. Little is known about the genetic basis that control reproductive transition in orchids and, consequently, manipulating their flowering time remains a challenge. In order to contribute to the understanding of the genetic bases that control flowering in orchids we present here the first broad-scale analysis of FT/TFL1-like genes in monocots with an expanded sampling in Orchidaceae. We also compare expression patterns in three selected species and propose hypotheses on the putative role of these genes in their reproductive transition. Our findings show that FT-like genes are by far more diversified than TFL1-like genes in monocots with six subclades in the former and only one in the latter. Within MonFT1, the comparative protein sequences of MonFT1A and MonFT1B suggest that they could have recruited functional roles in delaying flowering, a role typically assigned to TFL1-like proteins. On the other hand, MonFT2 proteins have retained their canonical motifs and roles in promoting flowering transition. This is also shown by their increased expression levels from the shoot apical meristem (SAM) and leaves to inflorescence meristems (IM) and floral buds (FBs). Finally, TFL1-like genes are retained as single copy and often times are lost. Their loss could be linked to the parallel recruitment of MonFT1A and MonFT1B homologs in delaying flowering and maintaining indeterminacy of the inflorescence meristem. These hypotheses lay the foundation for future functional validation in emerging model orchid species and comparative analyses in orchids with high horticultural potential in the market.

Fertile Tetraploids: New Resources for Future Rice Breeding?

Ploidy manipulation is an efficient technique for the development of novel phenotypes in plant breeding. However, in rice (Oryza sativa L.), severe seed sterility has been considered a barrier preventing cultivation of autotetraploids since the 1930s. Recently, a series of studies identified two fertile autotetraploids, identified herein as the PMeS (Polyploid Meiosis Stability) and Neo-Tetraploid lines. Here, we summarize their characteristics, focusing on the recovery of seed fertility, and discuss potential future directions of study in this area, providing a comprehensive understanding of current progress in the study of fertile tetraploid rice, a classical, but promising, concept for rice breeding.

Defining the Role of the MADS-Box Gene, Zea Agamous-like1, a Target of Selection During Maize Domestication

Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.

Revolutions in agriculture chart a course for targeted breeding of old and new crops

The dominance of the major crops that feed humans and their livestock arose from agricultural revolutions that increased productivity and adapted plants to large-scale farming practices. Two hormone systems that universally control flowering and plant architecture, florigen and gibberellin, were the source of multiple revolutions that modified reproductive transitions and proportional growth among plant parts. Although step changes based on serendipitous mutations in these hormone systems laid the foundation, genetic and agronomic tuning were required for broad agricultural benefits. We propose that generating targeted genetic variation in core components of both systems would elicit a wider range of phenotypic variation. Incorporating this enhanced diversity into breeding programs of conventional and underutilized crops could help to meet the future needs of the human diet and promote sustainable agriculture.

Parallelism and convergence in post-domestication adaptation in cereal grasses

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

De Novo Domestication: An Alternative Route toward New Crops for the Future

Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.