Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat

Dissecting the genetic architecture of key agronomic traits in lettuce using a MAGIC population

BACKGROUND

Lettuce is a globally important leafy vegetable that exhibits diverse horticultural types and strong population structure, which complicates genetic analyses. To address this challenge, we develop the first multi-parent, advanced generation inter-cross (MAGIC) population for lettuce using 16 diverse founder lines.

RESULTS

Whole-genome sequencing of the 16 founder lines and 381 inbred progeny reveal minimal population structure, enabling informative genome-wide association studies (GWAS). GWAS of the lettuce MAGIC population identifies numerous loci associated with key agricultural traits, including 51 for flowering time, 11 for leaf color, and 5 for leaf shape. Notably, loss-of-function mutations in the LsphyB and LsphyC genes, encoding phytochromes B and C, dramatically delay flowering in lettuce, which is in striking contrast to many other plant species. This unexpected finding highlights the unique genetic architecture controlling flowering time in lettuce. The wild-type LsTCP4 gene plays critical roles in leaf flatness and its expression level is negatively correlated with leaf curvature. Additionally, a novel zinc finger protein (ZFP) gene is required for the development of lobed leaves; a point mutation leads to its loss of function and consequently converted lobed leaves to non-lobed leaves, as exhibited by most lettuce cultivars.

CONCLUSIONS

The MAGIC population's lack of structure and high mapping resolution enables the efficient dissection of complex traits. The identified loci and candidate genes provide significant genetic resources for improving agronomic performance and leaf quality in lettuce.

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

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

Molecular characterization of a novel photoperiod-insensitive allele Ppd-B1a.3 and its effect on heading date in Chinese wheat (Triticum aestivum) cultivar Qingchun 37

Breeders adjust wheat heading dates to improve regional adaptability and reduce or mitigate yield losses caused by meteorological disasters, pests and diseases. The Ppd-1 genes play a crucial role in determining wheat sensitivity to changes in day-length and serve as key regulators of heading dates once the vernalization requirement is satisfied. In this study, we identified a new allelic variant of the promoter region, Ppd-B1a.3, in the Chinese wheat cultivar Qingchun 37. Compared to the Ppd-B1b.1 (carried by Chihokukomugi), the main mutation sites in Ppd-B1a.3 include a substitution of C with G at the -505-bp, a T base insertion at the -625-bp, a mutation of TCG to GGT at the -632 to -634-bp, and a 163-bp insertion at the -691 bp. Analysis of F2 populations indicated that Ppd-B1a.3 promotes heading and flowering (approximately 6 days earlier in population 1 and 17 days in population 2) under short-day conditions in a greenhouse. However, the evaluation of Ppd-B1a.3's effect under field conditions may be influenced by the copy number of the Ppd-B1 locus inherited from the other parent in the F2 populations. Ppd-B1a.3 disrupts circadian rhythm expression and exhibits a stronger effect on heading and flowering than the three-copy Ppd-B1 allele carried by Jing 411. Origin analysis suggests that Ppd-B1a.3 may have derived from non-native germplasm. These results deepen our understanding of wheat photoperiod genes and provide useful genetic resources for fine-tuning wheat heading dates during breeding.

Historic rewiring of grass flowering time pathways and implications for crop improvement under climate change

Grasses are fundamental to human survival, providing a large percentage of our calories, fuel, and fodder for livestock, and an enormous global carbon sink. A particularly important part of the grass plant is the grain-producing inflorescence that develops in response to both internal and external signals that converge at the shoot tip to influence meristem behavior. Abiotic signals that trigger reproductive development vary across the grass family, mostly due to the unique ecological and phylogenetic histories of each clade. The time it takes a grass to flower has implications for its ability to escape harsh environments, while also indirectly affecting abiotic stress tolerance, inflorescence architecture, and grain yield. Here, we synthesize recent insights into the evolution of grass flowering time in response to past climate change, particularly focusing on genetic convergence in underlying traits. We then discuss how and why the rewiring of a shared ancestral flowering pathway affects grass yields, and outline ways in which researchers are using this and other information to breed higher yielding, climate-proof cereal crops.

Independent genetic factors control floret number and spikelet number in Triticum turgidum ssp

Wheat grain yield is a complex trait resulting from a trade-off among many distinct components. During wheat evolution, domestication events and then modern breeding have strongly increased the yield potential of wheat plants, by enhancing spike fertility. To address the genetic bases of spike fertility in terms of spikelet number per spike and floret number per spikelet, a population of 110 recombinant inbred lines (RILS) obtained crossing a Triticum turgidum ssp. durum cultivar (Latino) and a T. dicoccum accession (MG5323) was exploited. Being a modern durum and a semi-domesticated genotype, respectively, the two parents differ for spike architecture and fertility, and thus the corresponding RIL population is the ideal genetic material to dissect genetic bases of yield components. The RIL population was phenotyped in four environments. Using a high-density SNP genetic map and taking advantage of several genome sequencing available for Triticeae, a total of 94 QTLs were identified for the eight traits considered; these QTLs were further reduced to 17 groups, based on their genetic and physical co-location. QTLs controlling floret number per spikelet and spikelet number per spike mapped in non-overlapping chromosomal regions, suggesting that independent genetic factors determine these fertility-related traits. The physical intervals of QTL groups were considered for possible co-location with known genes functionally involved in spike fertility traits and with yield-related QTLs previously mapped in tetraploid wheat. The most interesting result concerns a QTL group on chromosome 5B, associated with spikelet number per spike, since it could host genes still uncharacterized for their association to spike fertility. Finally, we identified two different regions where the trade-off between fertility related traits and kernel weight is overcome. Further analyses of these regions could pave the way for a future identification of new genetic loci contributing to fertility traits essential for yield improvement in durum wheat.

The H3K4 demethylase JMJ1 is required for proper timing of flowering in Brachypodium distachyon

Flowering is a key developmental transition in the plant life cycle. In temperate climates, flowering often occurs in response to the perception of seasonal cues such as changes in day-length and temperature. However, the mechanisms that have evolved to control the timing of flowering in temperate grasses are not fully understood. We identified a Brachypodium distachyon mutant whose flowering is delayed under inductive long-day conditions due to a mutation in the JMJ1 gene, which encodes a Jumonji domain-containing protein. JMJ1 is a histone demethylase that mainly demethylates H3K4me2 and H3K4me3 in vitro and in vivo. Analysis of the genome-wide distribution of H3K4me1, H3K4me2, and H3K4me3 in wild-type plants by chromatin immunoprecipitation and sequencing combined with RNA sequencing revealed that H3K4m1 and H3K4me3 are positively associated with gene transcript levels, whereas H3K4me2 is negatively correlated with transcript levels. Furthermore, JMJ1 directly binds to the chromatin of the flowering regulator genes VRN1 and ID1 and affects their transcription by modifying their H3K4me2 and H3K4me3 levels. Genetic analyses indicated that JMJ1 promotes flowering by activating VRN1 expression. Our study reveals a role for JMJ1-mediated chromatin modification in the proper timing of flowering in B. distachyon.

Finding the right balance: The enduring role of florigens during cereal inflorescence development and their influence on fertility

Flowering is a vital process in a plant's lifecycle and variation for flowering-time has helped cereals adapt to diverse environments. Much cereal research has focused on understanding how flowering signals, or florigens, regulate the floral transition and timing of ear emergence. However, flowering genes also perform an enduring role during inflorescence development, with genotypes that elicit a weaker flowering signal producing more elaborately branched inflorescences with extra floret-bearing spikelets. While this outcome indicates that variable expression of flowering genes could boost yield potential, further analysis has shown that dampened florigen levels can compromise fertility, negating the benefit of extra grain-producing sites. Here, we discuss ways that florigens contribute to early and late inflorescence development, including their influence on branch/spikelet architecture and fertility. We propose that a deeper understanding of the role for florigens during inflorescence development could be used to balance the effects of florigens throughout flowering to improve productivity.

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.

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

KEY MESSAGE

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

Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon

Synchronizing the timing of reproduction with the environment is crucial in the wild. Among the multiple mechanisms, annual plants evolved to sense their environment, the requirement of cold-mediated vernalization is a major process that prevents individuals from flowering during winter. In many annual plants including crops, both a long and short vernalization requirement can be observed within species, resulting in so-called early-(spring) and late-(winter) flowering genotypes. Here, using the grass model Brachypodium distachyon, we explored the link between flowering-time-related traits (vernalization requirement and flowering time), environmental variation, and diversity at flowering-time genes by combining measurements under greenhouse and outdoor conditions. These experiments confirmed that B. distachyon natural accessions display large differences regarding vernalization requirements and ultimately flowering time. We underline significant, albeit quantitative effects of current environmental conditions on flowering-time-related traits. While disentangling the confounding effects of population structure on flowering-time-related traits remains challenging, population genomics analyses indicate that well-characterized flowering-time genes may contribute significantly to flowering-time variation and display signs of polygenic selection. Flowering-time genes, however, do not colocalize with genome-wide association peaks obtained with outdoor measurements, suggesting that additional genetic factors contribute to flowering-time variation in the wild. Altogether, our study fosters our understanding of the polygenic architecture of flowering time in a natural grass system and opens new avenues of research to investigate the gene-by-environment interaction at play for this trait.

GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1

Precise regulation of flowering time is critical for cereal crops to synchronize reproductive development with optimum environmental conditions, thereby maximizing grain yield. The plant-specific gene GIGANTEA (GI) plays an important role in the control of flowering time, with additional functions on the circadian clock and plant stress responses. In this study, we show that GI loss-of-function mutants in a photoperiod-sensitive tetraploid wheat background exhibit significant delays in heading time under both long-day (LD) and short-day photoperiods, with stronger effects under LD. However, this interaction between GI and photoperiod is no longer observed in isogenic lines carrying either a photoperiod-insensitive allele in the PHOTOPERIOD1 (PPD1) gene or a loss-of-function allele in EARLY FLOWERING 3 (ELF3), a known repressor of PPD1. These results suggest that the normal circadian regulation of PPD1 is required for the differential effect of GI on heading time in different photoperiods. Using crosses between mutant or transgenic plants of GI and those of critical genes in the flowering regulation pathway, we show that GI accelerates wheat heading time by promoting FLOWERING LOCUS T1 (FT1) expression via interactions with ELF3, VERNALIZATION 2 (VRN2), CONSTANS (CO), and the age-dependent microRNA172-APETALA2 (AP2) pathway, at both transcriptional and protein levels. Our study reveals conserved GI mechanisms between wheat and Arabidopsis but also identifies specific interactions of GI with the distinctive photoperiod and vernalization pathways of the temperate grasses. These results provide valuable knowledge for modulating wheat heading time and engineering new varieties better adapted to a changing environment.

MiCOL6, MiCOL7A and MiCOL7B isolated from mango regulate flowering and stress response in transgenic Arabidopsis

The CONSTANS/CONSTANS-Like (CO/COL) family has been shown to play important roles in flowering, stress tolerance, fruit development and ripening in higher plants. In this study, three COL genes, MiCOL6, MiCOL7A and MiCOL7B, which each contain only one CCT domain, were isolated from mango (Mangifera indica), and their functions were investigated. MiCOL7A and MiCOL7B were expressed mainly at 20 days after flowering (DAF), and all three genes were highly expressed during the flowering induction period. The expression levels of the three genes were affected by light conditions, but only MiCOL6 exhibited a clear circadian rhythm. Overexpression of MiCOL6 promoted earlier flowering, while overexpression of MiCOL7A or MiCOL7B delayed flowering compared to that in the control lines of Arabidopsis thaliana under long-day (LD) and short-day (SD) conditions. Overexpressing MiCOL6, MiCOL7A or MiCOL7B in transgenic plants increased superoxide dismutase (SOD) and proline levels, decreased malondialdehyde (MAD) levels, and improved survival under drought and salt stress. In addition, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses showed that the MiCOL6, MiCOL7A and MiCOL7B proteins interact with several stress- and flower-related proteins. This work demonstrates the functions of MiCOL6, MiCOL7A and MiCOL7B and provides a foundation for further research on the role of mango COL genes in flowering regulation and the abiotic stress response.

The TaSOC1-TaVRN1 module integrates photoperiod and vernalization signals to regulate wheat flowering

Wheat needs different durations of vernalization, which accelerates flowering by exposure to cold temperature, to ensure reproductive development at the optimum time, as that is critical for adaptability and high yield. TaVRN1 is the central flowering regulator in the vernalization pathway and encodes a MADS-box transcription factor (TF) that usually works by forming hetero- or homo-dimers. We previously identified that TaVRN1 bound to an MADS-box TF TaSOC1 whose orthologues are flowering activators in other plants. The specific function of TaSOC1 and the biological implication of its interaction with TaVRN1 remained unknown. Here, we demonstrated that TaSOC1 was a flowering repressor in the vernalization and photoperiod pathways by overexpression and knockout assays. We confirmed the physical interaction between TaSOC1 and TaVRN1 in wheat protoplasts and in planta, and further validated their genetic interplay. A Flowering Promoting Factor 1-like gene TaFPF1-2B was identified as a common downstream target of TaSOC1 and TaVRN1 through transcriptome and chromatin immunoprecipitation analyses. TaSOC1 competed with TaVRT2, another MADS-box flowering regulator, to bind to TaVRN1; their coding genes synergistically control TaFPF1-2B expression and flowering initiation in response to photoperiod and low temperature. We identified major haplotypes of TaSOC1 and found that TaSOC1-Hap1 conferred earlier flowering than TaSOC1-Hap2 and had been subjected to positive selection in wheat breeding. We also revealed that wheat SOC1 family members were important domestication loci and expanded by tandem and segmental duplication events. These findings offer new insights into the regulatory mechanism underlying flowering control along with useful genetic resources for wheat improvement.

early maturity 7 promotes early flowering by controlling the light input into the circadian clock in barley

Breeding for variation in photoperiod response is crucial to adapt crop plants to various environments. Plants measure changes in day length by the circadian clock, an endogenous timekeeper that allows plants to anticipate changes in diurnal and seasonal light-dark cycles. Here, we describe the early maturity 7 (eam7) locus in barley (Hordeum vulgare), which interacts with PHOTOPERIOD 1 (Ppd-H1) to cause early flowering under non-inductive short days. We identify LIGHT-REGULATED WD 1 (LWD1) as a putative candidate to underlie the eam7 locus in barley as supported by genetic mapping and CRISPR-Cas9-generated lwd1 mutants. Mutations in eam7 cause a significant phase advance and a misregulation of core clock and clock output genes under diurnal conditions. Early flowering was linked to an upregulation of Ppd-H1 during the night and consequent induction of the florigen FLOWERING LOCUS T1 under short days. We propose that EAM7 controls photoperiodic flowering in barley by controlling the light input into the clock and diurnal expression patterns of the major photoperiod response gene Ppd-H1.

INDETERMINATE1-mediated expression of FT family genes is required for proper timing of flowering in Brachypodium distachyon

The transition to flowering is a major developmental switch in plants. In many temperate grasses, perception of indicators of seasonal change, such as changing day-length and temperature, leads to expression of FLOWERING LOCUS T1 (FT1) and FT-Like (FTL) genes that are essential for promoting the transition to flowering. However, little is known about the upstream regulators of FT1 and FTL genes in temperate grasses. Here, we characterize the monocot-specific gene INDETERMINATE1 (BdID1) in Brachypodium distachyon and demonstrate that BdID1 is a regulator of FT family genes. Mutations in ID1 impact the ability of the short-day (SD) vernalization, cold vernalization, and long-day (LD) photoperiod pathways to induce certain FTL genes. BdID1 is required for upregulation of FTL9 (FT-LIKE9) expression by the SD vernalization pathway, and overexpression of FTL9 in an id1 background can partially restore the delayed flowering phenotype of id1. We show that BdID1 binds in vitro to the promoter region of FTL genes suggesting that ID1 directly activates FTL expression. Transcriptome analysis shows that BdID1 is required for FT1, FT2, FTL12, and FTL13 expression under inductive LD photoperiods, indicating that BdID1 is a regulator of the FT gene family. Moreover, overexpression of FT1 in the id1 background results in rapid flowering similar to overexpressing FT1 in the wild type, demonstrating that BdID1 is upstream of FT family genes. Interestingly, ID1 negatively regulates a previously uncharacterized FTL gene, FTL4, and we show that FTL4 is a repressor of flowering. Thus, BdID1 is critical for proper timing of flowering in temperate grasses.

Phytochromes transmit photoperiod information via the evening complex in Brachypodium

BACKGROUND

Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in adapting barley and wheat to northern latitudes. How monocot plants sense photoperiod and integrate this information into growth and development is not well understood.

RESULTS

We find that phytochrome C (PHYC) is essential for flowering in Brachypodium distachyon. Conversely, ELF3 acts as a floral repressor and elf3 mutants display a constitutive long day phenotype and transcriptome. We find that ELF3 and PHYC occur in a common complex. ELF3 associates with the promoters of a number of conserved regulators of flowering, including PPD1 and VRN1. Consistent with observations in barley, we are able to show that PPD1 overexpression accelerates flowering in short days and is necessary for rapid flowering in response to long days. PHYC is in the active Pfr state at the end of the day, but we observe it undergoes dark reversion over the course of the night.

CONCLUSIONS

We propose that PHYC acts as a molecular timer and communicates information on night-length to the circadian clock via ELF3.

Transcriptomic response for revealing the molecular mechanism of oat flowering under different photoperiods

Proper flowering is essential for the reproduction of all kinds of plants. Oat is an important cereal and forage crop; however, its cultivation is limited because it is a long-day plant. The molecular mechanism by which oats respond to different photoperiods is still unclear. In this study, oat plants were treated under long-day and short-day photoperiods for 10 days, 15 days, 20 days, 25 days, 30 days, 40 days and 50 days, respectively. Under the long-day treatment, oats entered the reproductive stage, while oats remained vegetative under the short-day treatment. Forty-two samples were subjected to RNA-Seq to compare the gene expression patterns of oat under long- and short-day photoperiods. A total of 634-5,974 differentially expressed genes (DEGs) were identified for each time point, while the floral organ primordium differentiation stage showed the largest number of DEGs, and the spikelet differentiation stage showed the smallest number. Gene Ontology (GO) analysis showed that the plant hormone signaling transduction and hormone metabolism processes significantly changed in the photoperiod regulation of flowering time in oat. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Mapman analysis revealed that the DEGs were mainly concentrated in the circadian rhythm, protein antenna pathways and sucrose metabolism process. Additionally, transcription factors (TFs) involved in various flowering pathways were explored. Combining all this information, we established a molecular model of oat flowering induced by a long-day photoperiod. Taken together, the long-day photoperiod has a large effect at both the morphological and transcriptomic levels, and these responses ultimately promote flowering in oat. Our findings expand the understanding of oat as a long-day plant, and the explored genes could be used in molecular breeding to help break its cultivation limitations in the future.

Identification of genetic loci for early maturity in spring bread wheat using the association analysis and gene dissection

Background

Early maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season.

Methods

To reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F2:3 population.

Results

Our data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time.

Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression

Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.

EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time

The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.

PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon

Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.

Sense in sensitivity: difference in the meaning of photoperiod-insensitivity between wheat and barley

The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working in these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities the main gene controlling that response is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley), (ii) the main "insensitive" allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source on confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when doing research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programs and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.

Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations

Plant breeders have indirectly selected for variation at circadian-associated loci in many of the world's major crops, when breeding to increase yield and improve crop performance. Using an eight-parent Multiparent Advanced Generation Inter-Cross (MAGIC) population, we investigated how variation in circadian clock-associated genes contributes to the regulation of heading date in UK and European winter wheat (Triticum aestivum) varieties. We identified homoeologues of EARLY FLOWERING 3 (ELF3) as candidates for the Earliness per se (Eps) D1 and B1 loci under field conditions. We then confirmed a single-nucleotide polymorphism within the coding region of TaELF3-B1 as a candidate polymorphism underlying the Eps-B1 locus. We found that a reported deletion at the Eps-D1 locus encompassing TaELF3-D1 is, instead, an allele that lies within an introgression region containing an inversion relative to the Chinese Spring D genome. Using Triticum turgidum cv. Kronos carrying loss-of-function alleles of TtELF3, we showed that ELF3 regulates heading, with loss of a single ELF3 homoeologue sufficient to alter heading date. These studies demonstrated that ELF3 forms part of the circadian oscillator; however, the loss of all homoeologues was required to affect circadian rhythms. Similarly, loss of functional LUX ARRHYTHMO (LUX) in T. aestivum, an orthologue of a protein partner of Arabidopsis (Arabidopsis thaliana) ELF3, severely disrupted circadian rhythms. ELF3 and LUX transcripts are not co-expressed at dusk, suggesting that the structure of the wheat circadian oscillator might differ from that of Arabidopsis. Our demonstration that alterations to ELF3 homoeologues can affect heading date separately from effects on the circadian oscillator suggests a role for ELF3 in cereal photoperiodic responses that could be selected for without pleiotropic deleterious alterations to circadian rhythms.

Effects of genetic components of plant development on yield-related traits in wheat (Triticum aestivum L.) under stress-free conditions

The dynamics of plant development not only has an impact on ecological adaptation but also contributes to the realization of genetically determined yield potentials in various environments. Dissecting the genetic determinants of plant development becomes urgent due to the global climate change, which can seriously affect and even disrupt the locally adapted developmental patterns. In order to determine the role plant developmental loci played in local adaptation and yield formation, a panel of 188 winter and facultative wheat cultivars from diverse geographic locations were characterized with the 15K Illumina Single Nucleotide Polymorphism (SNP) chip and functional markers of several plant developmental genes and included into a multiseason field experiment. Genome-wide association analyses were conducted on five consecutive developmental phases spanning from the first node appearance to full heading together with various grain yield-related parameters. The panel was balanced for the PPD-D1 photoperiod response gene, which facilitated the analyses in the two subsets of photoperiod-insensitive and -sensitive genotypes in addition to the complete panel. PPD-D1 was the single highest source, explaining 12.1%-19.0% of the phenotypic variation in the successive developmental phases. In addition, 21 minor developmental loci were identified, each one explaining only small portions of the variance, but, together, their effects amounted to 16.6%-50.6% of phenotypic variance. Eight loci (2A_27, 2A_727, 4A_570, 5B_315, 5B_520, 6A_26, 7A_1-(VRN-A3), and 7B_732) were independent of PPD-D1. Seven loci were only detectable in the PPD-D1-insensitive genetic background (1A_539, 1B_487, 2D_649, 4A_9, 5A_584-(VRN-A1), 5B_571-(VRN-B1), and 7B_3-(VRN-B3)), and six loci were only detectable in the sensitive background, specifically 2A_740, 2D_25, 3A_579, 3B_414, 7A_218, 7A_689, and 7B_538. The combination of PPD-D1 insensitivity and sensitivity with the extremities of early or late alleles in the corresponding minor developmental loci resulted in significantly altered and distinct plant developmental patterns with detectable outcomes on some yield-related traits. This study examines the possible significance of the above results in ecological adaptation.

Contemplation on wheat vernalization

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

Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.

Flowering time runs hot and cold

Evidence suggests that anthropogenically-mediated global warming results in accelerated flowering for many plant populations. However, the fact that some plants are late flowering or unaffected by warming, underscores the complex relationship between phase change, temperature, and phylogeny. In this review, we present an emerging picture of how plants sense temperature changes, and then discuss the independent recruitment of ancient flowering pathway genes for the evolution of ambient, low, and high temperature-regulated reproductive development. As well as revealing areas of research required for a better understanding of how past thermal climates have shaped global patterns of plasticity in plant phase change, we consider the implications for these phenological thermal responses in light of climate change.

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

The gene VERNALIZATION1 (VRN1) is a key controller of vernalization requirement in wheat. The genome of hexaploid wheat (Triticum aestivum) harbors three homoeologous VRN1 loci on chromosomes 5A, 5B, and 5D. Structural sequence variants including small and large deletions and insertions and single nucleotide polymorphisms (SNPs) in the three homoeologous VRN1 genes not only play an important role in the control of vernalization requirement, but also have been reported to be associated with other yield related traits of wheat. Here we used single-molecule sequencing of barcoded long-amplicons to assay the full-length sequences (∼13 kbp plus 700 bp from the promoter sequence) of the three homoeologous VRN1 genes in a panel of 192 predominantly European winter wheat cultivars. Long read sequences revealed previously undetected duplications, insertions and single-nucleotide polymorphisms in the three homoeologous VRN1 genes. All the polymorphisms were confirmed by Sanger sequencing. Sequence analysis showed the predominance of the winter alleles vrn-A1, vrn-B1, and vrn-D1 across the investigated cultivars. Associations of SNPs and structural variations within the three VRN1 genes with 20 economically relevant traits including yield, nodal root-angle index and quality related traits were evaluated at the levels of alleles, haplotypes, and copy number variants. Cultivars carrying structural variants within VRN1 genes showed lower grain yield, protein yield and biomass compared to those with intact genes. Cultivars carrying a single vrn-A1 copy and a unique haplotype with a high number of SNPs were found to have elevated grain yield, kernels per spike and kernels per m2 along with lower grain sedimentation values. In addition, we detected a novel SNP polymorphism within the G-quadruplex region of the promoter of vrn-A1 that was associated with deeper roots in winter wheat. Our findings show that multiplex, single-molecule long-amplicon sequencing is a useful tool for detecting variants in target genes within large plant populations, and can be used to simultaneously assay sequence variants among target multiple gene homoeologs in polyploid crops. Numerous novel VRN1 haplotypes and alleles were identified that showed significantly associations to economically important traits. These polymorphisms were converted into PCR or KASP assays for use in marker-assisted breeding.

Major niche transitions in Pooideae correlate with variation in photoperiodic flowering and evolution of CCT domain genes

The external cues that trigger timely flowering vary greatly across tropical and temperate plant taxa, the latter relying on predictable seasonal fluctuations in temperature and photoperiod. In the grass family (Poaceae) for example, species of the subfamily Pooideae have become specialists of the northern temperate hemisphere, generating the hypothesis that their progenitor evolved a flowering response to long days from a short-day or day-neutral ancestor. Sampling across the Pooideae, we found support for this hypothesis, and identified several secondary shifts to day-neutral flowering and one to short-day flowering in a tropical highland clade. To explain the proximate mechanisms for the secondary transition back to short-day-regulated flowering, we investigated the expression of CCT domain genes, some of which are known to repress flowering in cereal grasses under specific photoperiods. We found a shift in CONSTANS 1 and CONSTANS 9 expression that coincides with the derived short-day photoperiodism of our exemplar species Nassella pubiflora. This sets up the testable hypothesis that trans- or cis-regulatory elements of these CCT domain genes were the targets of selection for major niche shifts in Pooideae grasses.

MiR172-APETALA2-like genes integrate vernalization and plant age to control flowering time in wheat

Plants possess regulatory mechanisms that allow them to flower under conditions that maximize reproductive success. Selection of natural variants affecting those mechanisms has been critical in agriculture to modulate the flowering response of crops to specific environments and to increase yield. In the temperate cereals, wheat and barley, the photoperiod and vernalization pathways explain most of the natural variation in flowering time. However, other pathways also participate in fine-tuning the flowering response. In this work, we integrate the conserved microRNA miR172 and its targets APETALA2-like (AP2L) genes into the temperate grass flowering network involving VERNALIZATION 1 (VRN1), VRN2 and FLOWERING LOCUS T 1 (FT1 = VRN3) genes. Using mutants, transgenics and different growing conditions, we show that miR172 promotes flowering in wheat, while its target genes AP2L1 (TaTOE1) and AP2L5 (Q) act as flowering repressors. Moreover, we reveal that the miR172-AP2L pathway regulates FT1 expression in the leaves, and that this regulation is independent of VRN2 and VRN1. In addition, we show that the miR172-AP2L module and flowering are both controlled by plant age through miR156 in spring cultivars. However, in winter cultivars, flowering and the regulation of AP2L1 expression are decoupled from miR156 downregulation with age, and induction of VRN1 by vernalization is required to repress AP2L1 in the leaves and promote flowering. Interestingly, the levels of miR172 and both AP2L genes modulate the flowering response to different vernalization treatments in winter cultivars. In summary, our results show that conserved and grass specific gene networks interact to modulate the flowering response, and that natural or induced mutations in AP2L genes are useful tools for fine-tuning wheat flowering time in a changing environment.

The wild grass Brachypodium distachyon as a developmental model system

The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.

Genome-wide identification of CCT genes in wheat (Triticum aestivum L.) and their expression analysis during vernalization

Numerous CCT genes are known to regulate various biological processes, such as circadian rhythm regulation, flowering, light signaling, plant development, and stress resistance. The CCT gene family has been characterized in many plants but remains unknown in the major cereal wheat (Triticum aestivum L.). Extended exposure to low temperature (vernalization) is necessary for winter wheat to flower successfully. VERNALIZATION2 (VRN2), a specific CCT-containing gene, has been proved to be strongly associated with vernalization in winter wheat. Mutation of all VRN2 copies in three subgenomes results in the eliminated demands of low temperature in flowering. However, no other CCT genes have been reported to be associated with vernalization to date. The present study screened CCT genes in the whole wheat genome, and preliminarily identified the vernalization related CCT genes through expression analysis. 127 CCT genes were identified in three subgenomes of common wheat through a hidden Markov model-based method. Based on multiple alignment, these genes were grouped into 40 gene clusters, including the duplicated gene clusters TaCMF6 and TaCMF8, each tandemly arranged near the telomere. The phylogenetic analysis classified these genes into eight groups. The transcriptome analysis using leaf tissues collected before, during, and after vernalization revealed 49 upregulated and 31 downregulated CCT genes during vernalization, further validated by quantitative real-time PCR. Among the differentially expressed and well-investigated CCT gene clusters analyzed in this study, TaCMF11, TaCO18, TaPRR95, TaCMF6, and TaCO16 were induced during vernalization but decreased immediately after vernalization, while TaCO1, TaCO15, TaCO2, TaCMF8, and TaPPD1 were stably suppressed during and after vernalization. These data imply that some vernalization related CCT genes other than VRN2 may exist in wheat. This study improves our understanding of CCT genes and provides a foundation for further research on CCT genes related to vernalization in wheat.

Identification and characterization of QTL for spike morphological traits, plant height and heading date derived from the D genome of natural and resynthetic allohexaploid wheat

QHd.cau-7D.1 for heading date was delimited into the physical interval of approximately 17.38 Mb harboring three CONSTANS-like zinc finger genes. Spike morphological traits, plant height and heading date play important roles in yield improvement of wheat. To reveal the genetic factors that controlling spike morphological traits, plant height and heading date on the D genome, we conducted analysis of quantitative traits locus (QTL) using 198 F_7:8 recombinant inbred lines (RILs) derived from a cross between the common wheat TAA10 and resynthesized allohexaploid wheat XX329 with similar AABB genomes. A total of 23 environmentally stable QTL on the D sub-genome for spike length (SL), fertile spikelet number per spike (FSN), sterile spikelet number per spike (SSN), total spikelet number per spike (TSN), spike compactness (SC), plant height (PHT) and heading date (HD) were detected, among which eight appeared to be novel QTL. Furthermore, QHd.cau-7D.1 and QPht.cau-7D.2 shared identical confidence interval and were delimited into the physical interval of approximately 17.38 Mb with 145 annotated genes, including three CONSTANS-like zinc finger genes (TraesCS7D02G209000, TraesCS7D02G213000 and TraesCS7D02G220300). This study will help elucidate the molecular mechanism of the seven traits (SL, FSN, SSN, TSN, SC, PHT and HD) and provide a potentially valuable resource for genetic improvement.

Responses of Barley to High Ambient Temperature Are Modulated by Vernalization

Ambient temperatures are increasing due to climate change. Cereal crops development and production will be affected consequently. Flowering time is a key factor for adaptation of small grain cereals and, therefore, exploring developmental responses of barley to rising temperatures is required. In this work, we studied phasic growth, and inflorescence traits related to yield, in eight near isogenic lines of barley (Hordeum vulgare L.) differing at the VRN-H1, VRN-H2 and PPD-H1 genes, representing different growth habits. The lines were grown in contrasting vernalization treatments, under two temperature regimes (18 and 25°C), in long days. Lines with recessive ppd-H1 presented delayed development compared to lines with the sensitive PPD-H1 allele, across the two growth phases considered. High temperature delayed flowering in all unvernalized plants, and in vernalized spring barleys carrying the insensitive ppd-H1 allele, whilst it accelerated flowering in spring barleys with the sensitive PPD-H1 allele. This finding evidenced an interaction between PPD-H1, temperature and vernalization. At the high temperature, PPD-H1 lines in spring backgrounds (VRN-H1-7) yielded more, whereas lines with ppd-H1 were best in vrn-H1 background. Our study revealed new information that will support breeding high-yielding cultivars with specific combinations of major adaptation genes tailored to future climatic conditions.

EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon

The proper timing of flowering, which is key to maximize reproductive success and yield, relies in many plant species on the coordination between environmental cues and endogenous developmental programs. The perception of changes in day length is one of the most reliable cues of seasonal change, and this involves the interplay between the sensing of light signals and the circadian clock. Here, we describe a Brachypodium distachyon mutant allele of the evening complex protein EARLY FLOWERING 3 (ELF3). We show that the elf3 mutant flowers more rapidly than wild type plants in short days as well as under longer photoperiods but, in very long (20 h) days, flowering is equally rapid in elf3 and wild type. Furthermore, flowering in the elf3 mutant is still sensitive to vernalization, but not to ambient temperature changes. Molecular analyses revealed that the expression of a short-day marker gene is suppressed in elf3 grown in short days, and the expression patterns of clock genes and flowering time regulators are altered. We also explored the mechanisms of photoperiodic perception in temperate grasses by exposing B. distachyon plants grown under a 12 h photoperiod to a daily night break consisting of a mixture of red and far-red light. We showed that 2 h breaks are sufficient to accelerate flowering in B. distachyon under non-inductive photoperiods and that this acceleration of flowering is mediated by red light. Finally, we discuss advances and perspectives for research on the perception of photoperiod in temperate grasses.

WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat

Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.

Yield-Related QTL Clusters and the Potential Candidate Genes in Two Wheat DH Populations

In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.

Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.

Natural variation and artificial selection of photoperiodic flowering genes and their applications in crop adaptation

Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information. Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment. The domestication of plants into crops, and later crop expansion and improvement, has often involved selection for early flowering. In this review, we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species. The ancestors of rice (Oryza sativa), maize (Zea mays), soybean (Glycine max), and tomato (Solanum lycopersicum) are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas. Wheat (Triticum aestivum) and barley (Hordeum vulgare) are long-day crops whose photosensitivity is influenced by both latitude and vernalization type. Here, we summarize recent studies about where these crops were domesticated, how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions, and how allelic variants of photoperiodic flowering genes were selected during this process. A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00039-0.

Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals

Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.

Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops

Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.

Evolution: Replicated mutation of COL2 contributed long-day flowering in common bean

The ability to flower without strict daylength constraints has helped spread cultivation of crop plants to new locations. The generation of daylength-insensitive common bean accessions in central and South America involved the repeated selection of mutant alleles for a key transcription factor that suppresses long-day flowering.

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.

Stepwise increases in FT1 expression regulate seasonal progression of flowering in wheat (Triticum aestivum)

Flowering is regulated by genes that respond to changing daylengths and temperature, which have been well studied using controlled conditions; however, the molecular processes underpinning flowering in nature remain poorly understood. Here, we investigate the genetic pathways that coordinate flowering and inflorescence development of wheat (Triticum aestivum) as daylengths extend naturally in the field, using lines that contain variant alleles for the key photoperiod gene, Photoperiod-1 (Ppd-1). We found flowering involves a stepwise increase in the expression of FLOWERING LOCUS T1 (FT1), which initiates under day-neutral conditions of early spring. The incremental rise in FT1 expression is overridden in plants that contain a photoperiod-insensitive allele of Ppd-1, which hastens the completion of spikelet development and accelerates flowering time. The accelerated inflorescence development of photoperiod-insensitive lines is promoted by advanced seasonal expression of floral meristem identity genes. The completion of spikelet formation is promoted by FLOWERING LOCUS T2, which regulates spikelet number and is activated by Ppd-1. In wheat, flowering under natural photoperiods is regulated by stepwise increases in the expression of FT1, which responds dynamically to extending daylengths to promote early inflorescence development. This research provides a strong foundation to improve yield potential by fine-tuning the photoperiod-dependent control of inflorescence development.