Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa)

A sorghum gigantea mutant attenuates florigen gene expression and delays flowering time

GIGANTEA (GI) is a conserved plant-specific gene that modulates a range of environmental responses in multiple plant species, including playing a key role in photoperiodic regulation of flowering time. The C4 grass Sorghum bicolor is an important grain and subsistence crop, animal forage, and cellulosic biofuel feedstock that is tolerant of abiotic stresses and marginal soils. To understand sorghum flowering time regulatory networks, we characterized the sbgi-ems1 nonsense mutant allele of the sorghum GIGANTEA (SbGI) gene from a sequenced M4 EMS-mutagenized BTx623 population. sbgi-ems1 plants flowered later than wild type siblings under both long-day or short-day photoperiods. Delayed flowering in sbgi-ems1 plants accompanied an increase in node number, indicating an extended vegetative growth phase prior to flowering. sbgi-ems1 plants had reduced expression of floral activator genes SbCO and SbEHD1 and downstream FT-like florigen genes SbFT, SbCN8, and SbCN12. Therefore, SbGI plays a role in regulating SbCO and SbEHD1 expression that serves to accelerate flowering. SbGI protein physically interacts with the sorghum FLAVIN-BINDING, KELCH REPEAT, F-BOX1-like (SbFFL) protein, a conserved flowering-associated blue light photoreceptor, and the SbGI-SbFFL interaction is stimulated by blue light. This work demonstrates that SbGI is an activator of sorghum flowering time upstream of florigen genes under short- and long-day photoperiods, likely in association with the activity of the blue light photoreceptor SbFFL.

SIGNIFICANCE STATEMENT

This study elucidates molecular details of flowering time networks for the adaptable C4 cereal crop Sorghum bicolor, including demonstration of a role for blue light sensing in sorghum GIGANTEA activity. This work validates the utility of a large publicly available sequenced EMS-mutagenized sorghum population to determine gene function.

Molecular and genetic pathways for optimizing spikelet development and grain yield

The spikelet is a unique structure of inflorescence in grasses that generates one to many flowers depending on its determinate or indeterminate meristem activity. The growth patterns and number of spikelets, furthermore, define inflorescence architecture and yield. Therefore, understanding the molecular mechanisms underlying spikelet development and evolution are attractive to both biologists and breeders. Based on the progress in rice and maize, along with increasing numbers of genetic mutants and genome sequences from other grass families, the regulatory networks underpinning spikelet development are becoming clearer. This is particularly evident for domesticated traits in agriculture. This review focuses on recent progress on spikelet initiation, and spikelet and floret fertility, by comparing results from Arabidopsis with that of rice, sorghum, maize, barley, wheat, Brachypodium distachyon, and Setaria viridis. This progress may benefit genetic engineering and molecular breeding to enhance grain yield.

Environmental Signal-Dependent Regulation of Flowering Time in Rice

The transition from the vegetative to the reproductive stage of growth is a critical event in the lifecycle of a plant and is required for the plant’s reproductive success. Flowering time is tightly regulated by an internal time-keeping system and external light conditions, including photoperiod, light quality, and light quantity. Other environmental factors, such as drought and temperature, also participate in the regulation of flowering time. Thus, flexibility in flowering time in response to environmental factors is required for the successful adaptation of plants to the environment. In this review, we summarize our current understanding of the molecular mechanisms by which internal and environmental signals are integrated to regulate flowering time in Arabidopsis thaliana and rice (Oryza sativa).

Indel marker analysis of putative stress-related genes reveals genetic diversity and differentiation of rice landraces in peninsular Thailand

Genetic assessment of rice landraces is important for germplasm evaluation and genetic resource utilization. Rice landraces in peninsular Thailand have adapted to unique environmental stresses over time and have great significance as a genetic resource for crop improvement. In this study, rice landraces derived from rice research centers and farmers from different areas of peninsular Thailand were genetically assessed using 16 polymorphic InDel markers from putative stress-related genes. A total of 36 alleles were obtained. The average PIC value was 0.27/marker. The F_ST varied from 0.46 to 1.00. Genetic diversity was observed both within and between populations. AMOVA indicated that genetic variations occurred mainly between populations (70%) rather than within populations (30%). The dendrogram, population structure, and PCoA scatter plot clearly demonstrated the differentiation of the two major groups, i.e., landraces from upland and lowland rice ecosystems. The unique alleles of Indel1922, -2543, -6746, -7447 and -8538, which lie in genes encoding putative WAX2, heavy metal-associated domain-containing protein, GA20ox2, PTF1, and PLETHORA2, respectively, were only found in rice from upland ecosystems. Putative WAX2, GA20ox2, and PLETHORA2 are likely related to drought and salt stress. Our findings demonstrate the diversity of landraces in peninsular Thailand. The preservation of these landraces should be facilitated with effective markers to maintain all variant alleles and to protect the genetic diversity. Indel1922, -2543, -6746, -7447 and -8538 have the potential to differentiate upland rice from lowland rice. Furthermore, Indel1922, -6746 and -8538 might be effective markers for drought and salt tolerance.

In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods

Japonica rice has become increasingly popular in China owing to its superior grain quality. Over the past decades, "indica to japonica" projects have been proposed to promote cultivation of japonica rice in low latitudes in China. Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region. The key obstacle for introducing elite mid-latitude japonica varieties to low latitudes is the severe shortening of growth period of the japonica varieties due to their sensitivity to low-latitude short photoperiod and high temperature. Here we report development of new japonica rice with prolonged basic vegetative growth (BVG) periods for low latitudes by targeted editing the Early heading date 1 (Ehd1) gene. Using CRISPR/Cas9 system, we generated both frame-shift and/or in-frame deletion mutants in four japonica varieties, Nipponbare, Longdao16, Longdao24, and Xiushui134. When planting at low-latitude stations, the frame-shift homozygous lines exhibited significantly longer BVG periods compared with wild-types. Interestingly, we observed that minor deletion of the first few residues within the receiver domain could quantitatively impair the function of Ehd1 on activation of Hd3a and RFT1, resulting in an intermediate-long BVG period phenotype in the homozygous in-frame deletion ehd1 lines. Field investigation further showed that, both the in-frame and frame-shift lines exhibited significantly improved yield potential compared with wild-types. Our study demonstrates an effective approach to rapid breeding of elite japonica varieties with intermediate-long and long BVG periods for flexible cropping systems in diverse areas or under different seasons in southern China, and other low-latitude regions.

Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population

A whole genome bin map was developed for a MAGIC population. Association studies for heading date at bin level exhibited powerful QTL mapping and identified favorable alleles. The presumed advantages of multiparent advanced generation intercross (MAGIC) population in quantitative trait locus (QTL) mapping were not fully utilized in the previous studies in which genome-wide association studies (GWAS) were conducted at only single nucleotide polymorphism level. In this study, we genotyped a rice four-way MAGIC population of 247 F₇ lines and their parents by sequencing. A total of 5934 bins with an average length of 65 kb were constructed and covered 97% of the genome. The MAGIC population showed low population structure and balanced parental contributions. A bin-based GWAS for heading date identified 4 QTLs in three environments. Three major QTLs were mapped exactly to the bins where the major heading date genes DTH3, Ghd7.1 and Ghd8 were located. Multiple comparisons showed that different parental alleles had varied genetic effects. Like DTH3, the alleles of the Guichao 2/YJSM, IR34 and Cypress had larger, intermediate and no effects, respectively. Based on comparative sequencing of 8 known heading date genes undetected in this MAGIC population, only Ghd7 exhibited diverse function among parents. The failure in Ghd7 mapping was well explained by its interaction with Hd1 because Ghd7 had no effects on heading date when combined with the nonfunctional hd1 carried by all four parents. Overall, bin-based GWAS have more mapping power and higher resolution with a MAGIC population and provide favorable alleles to breeders. The use of more diversified parents is encouraged to develop a MAGIC population for detecting more QTLs for important agronomical traits.

Genome-wide association analyses reveal the genetic basis of combining ability in rice

Combining ability is a measure for selecting elite parents and predicting hybrid performance in plant breeding. However, the genetic basis of combining ability remains unclear and a global view of combining ability from diverse mating designs is lacking. We developed a North Carolina II (NCII) population of 96 Oryza sativa and four male sterile lines to identify parents of greatest value for hybrid rice production. Statistical analyses indicated that general combining ability (GCA) and specific combining ability (SCA) contributed variously to different agronomic traits. In a genome-wide association study (GWAS) of agronomic traits, GCA and SCA, we identified 34 significant associations (P < 2.39 × 10^-7 ). The superior alleles of GCA loci (Ghd8, GS3 and qSSR4) accumulated in parental lines with high GCA and explained 30.03% of GCA variance in grain yield, indicating that molecular breeding of high GCA parental lines is feasible. The distinct distributions of these QTLs contributed to the differentiation of parental GCA in subpopulations. GWAS of SCA identified 12 more loci that showed dominance on corresponding agronomic traits. We conclude that the accumulation of superior GCA and SCA alleles is an important contributor to heterosis and QTLs that greatly contributed to combining ability in our study would accelerate the identification of elite inbred lines and breeding of super hybrids.

Genome-wide association study of pre-harvest sprouting tolerance using a 90K SNP array in common wheat (Triticum aestivum L.)

Three major loci for pre-harvest sprouting tolerance (PHST) were mapped on chromosomes 1AL, 3BS, and 6BL, and two CAPS and one dCAPS markers were validated. Sixteen lines with favorable alleles and increased PHST were identified. Pre-harvest sprouting (PHS) significantly affects wheat grain yield and quality. In the present study, the PHS tolerance (PHST) of 192 wheat varieties (lines) was evaluated by assessment of field sprouting, seed germination index, and period of dormancy in different environments. A high-density Illumina iSelect 90K SNP array was used to genotype the panel. A genome-wide association study (GWAS) based on single- and multi-locus mixed linear models was used to detect loci for PHST. The single-locus model identified 23 loci for PHST (P < 0.0001) and explained 6.0-18.9% of the phenotypic variance. Twenty loci were consistent with known quantitative trait loci (QTLs). Three single-nucleotide polymorphism markers closely linked with three major loci (Qphs.ahau-1A, Qphs.ahau-3B, and Qphs.ahau-6B) on chromosomes 1AL, 3BS, and 6BL, respectively, were converted to two cleaved amplified polymorphic sequences (CAPS) and one derived-CAPS markers, and validated in 374 wheat varieties (lines). The CAPS marker EX06323 for Qphs.ahau-6B co-segregated with a novel major QTL underlying PHST in a recombinant inbred line population raised from the cross Jing 411 × Wanxianbaimaizi. Linear regression showed a clear dependence of PHST on the number of favorable alleles. Sixteen varieties showing an elevated degree of PHST were identified and harbored more than 16 favorable alleles. The multi-locus model detected 39 marker-trait associations for PHST (P < 0.0001), of which five may be novel. Six loci common to the two models were identified. The combination of the two GWAS methods contributes to efficient dissection of the complex genetic mechanism of PHST.

Genetic Interactions Among Ghd7, Ghd8, OsPRR37 and Hd1 Contribute to Large Variation in Heading Date in Rice

BACKGROUND

Heading date is crucial for rice reproduction and geographic expansion. Many heading date genes are sensitive to photoperiod and jointly regulate flowering time in rice. However, it is not clear how these genes coordinate rice heading.

RESULTS

Here, we performed a genetic interaction analysis among four major rice heading date genes Ghd7, Ghd8, OsPRR37/Ghd7.1 (hereafter PRR37) and Hd1 in the near-isogenic background under both natural long-day (NLD) and natural short-day (NSD) conditions. The 4-gene segregating population exhibited a large heading date variation with more than 95 days under NLD and 42 days under NSD conditions. Tetragenic, trigenic and digenic interactions among these four genes were observed under both conditions but more significant under NLD conditions. In the functional Hd1 backgrounds, the strongest digenic interaction was Ghd7 by Ghd8 under NLD but was Ghd7 by PRR37 under NSD conditions. Interestingly, PRR37 acted as a flowering suppressor under NLD conditions, while it functioned alternatively as an activator or a suppressor under NSD conditions depending on the status of the other three genes. Based on the performances of 16 homozygous four-gene combinations, a positive correlation between heading date and spikelets per panicle (SPP) was found under NSD conditions, but changed to a negative correlation when heading date was over 90 days under NLD conditions.

CONCLUSIONS

These results demonstrate the importance of genetic interactions in the rice flowering regulatory network and will help breeders to select favorable combinations to maximize rice yield potential for different ecological areas.

A key variant in the cis-regulatory element of flowering gene Ghd8 associated with cold tolerance in rice

Variations in the gene promoter play critical roles in the evolution of important adaptive traits in crops, but direct links of the regulatory mutation to the adaptive change are not well understood. Here, we examine the nucleotide variations in the promoter region of a transcription factor (Ghd8) that control grain number, plant height and heading date in rice. We find that a dominant promoter type of subspecies japonica displayed a high activity for Ghd8 expression in comparison with the one in indica. Transgenic analyses revealed that higher expression levels of Ghd8 delayed heading date and enhanced cold tolerance in rice. Furthermore, a single-nucleotide polymorphism (T1279G) at the position −1279 bp that locates on the potential GA-responsive motif in the Ghd8 promoter affected the expression of this gene. The 1279 T variant has elevated expression of Ghd8, thus conferring increased cold tolerance of rice seedlings. Nucleotide diversity analysis revealed that the approximately 25-kb genomic region surrounding Ghd8 in the subspecies japonica was under significant selection pressure. Our findings demonstrate that the join effects of the regulatory and coding variants largely contribute to the divergence of japonica and indica and increase the adaptability of japonica to the cold environment.

A transcription factor coordinating internode elongation and photoperiodic signals in rice

In several plant species, inflorescence formation is accompanied by stem elongation. Both processes are accelerated in rice upon perception of shortening days. Here, we show that PREMATURE INTERNODE ELONGATION 1 (PINE1), encoding a rice zinc-finger transcription factor, reduces the sensitivity of the stem to gibberellin (GA). The florigens reduce PINE1 expression to increase stem responsiveness to GA and promote flowering. These data indicate the existence of a regulatory network coordinating flowering and GA-dependent growth.

Lessons from natural variations: artificially induced heading date variations for improvement of regional adaptation in rice

New strategy of breeding by modulating key heading date gene Ehd1 to enhance the variations of heading date regardless of genetic background for better adaptation to local environment in rice. Flowering time (or heading date) is an important quantitative trait in rice (Oryza sativa) that determines its adaptation to specific cultivation areas and growing seasons. However, breeding of flowering time is currently relying on laborious selections and combinations of different alleles of various genes. Here, we cloned a cis-variant allele of Ehd1 that regulated not only heading date but also yield potential. Genetic analysis revealed that Ehd1 acted downstream of Ghd7 as a negative regulator of yield potential, and expression divergence of Ehd1 negatively correlates with phenotype variations including heading date and grain yield. Moreover, regardless of genetic background, manipulations of the expression of a single gene, Ehd1, are sufficient for recreating beneficial heading date variations which could be subjected to the selection of best suitable lines for local environment conditions. Beyond a deeper understanding of transcriptional control of quantitative traits, this study provided an effective and flexible strategy for breeding rice cultivars to maximize grain production for any region of cultivation.

Beyond heading time: FT-like genes and spike development in cereals

This article comments on: Shaw LM, Lyu B, Turner R, Li C, Chen F, Han X, Fu D, Dubcovsky J. 2018. FLOWERING LOCUS T2 regulates spike development and fertility in temperate cereals. Journal of Experimental Botany 70, 193–204.

Loss-of-Function Alleles of Heading date 1 (Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region

Adaptation of temperate japonica rice varieties to tropical regions is impeded by extremely early flowering probably due to photoperiod change from long to short. However, constant breeding efforts led to development of temperate japonica varieties adapted to tropical/subtropical regions, but the genetic factor underlying this is still elusive. We analyzed the 45 diverse rice accessions and 12 tropical-adapted temperate japonica lines for the allele types of seven major flowering genes Hd1, OsPPR37, DTH8, Ghd7, Ehd1, RFT1, and Hd3a and flowering time under three different field conditions in temperate and tropical locations. The accessions originated from the tropical/subtropical regions preferred the non-functional alleles of Hd1 and not other flowering genes. The genetic effect analysis of each gene showed that only the functional Hd1 caused early flowering in the tropical location. All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate japonica varieties. These results indicate that the functional Hd1 alleles of temperate japonica varieties induced extremely early flowering in the tropics and the non-functional hd1 alleles brought about the adaptation of temperate japonica rice to tropical regions.

Systems model-guided rice yield improvements based on genes controlling source, sink, and flow

A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.

Genes Contributing to Domestication of Rice Seed Traits and Its Global Expansion

Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for the natural survival of wild rice such as seed dormancy and shattering have become favorable ones for human consumption due to the loss-of-function mutations in the genes that are underlying these traits. As a consequence, many genes that are related to these kinds of traits have been fixed with favorable alleles in modern cultivars by artificial selection. After domestication, Oryza sativa cultivars gradually spread to temperate and cool regions from the tropics and subtropics due to the loss of their photoperiod sensitivity. In this paper, we review the characteristics of domestication-related seed traits and heading dates in rice, including the key genes controlling these traits, the differences in allelic diversity between wild rice and cultivars, the geographic distribution of alleles, and the regulatory pathways of these traits. A comprehensive comparison shows that these genes contributed to rice domestication and its global expansion. In addition, these traits have also experienced parallel evolution by artificial selection on the homologues of key genes in other cereals.

Novel α-Tubulin Mutations Conferring Resistance to Dinitroaniline Herbicides in Lolium rigidum

The dinitroaniline herbicides (particularly trifluralin) have been globally used in many crops for selective grass weed control. Consequently, trifluralin resistance has been documented in several important crop weed species and has recently reached a level of concern in Australian Lolium rigidum populations. Here, we report novel mutations in the L. rigidum α-tubulin gene which confer resistance to trifluralin and other dinitroaniline herbicides. Nucleotide mutations at the highly conserved codon Arg-243 resulted in amino acid substitutions of Met or Lys. Rice calli transformed with the mutant 243-Met or 243-Lys α-tubulin genes were 4- to 8-fold more resistant to trifluralin and other dinitroaniline herbicides (e.g., ethalfluralin and pendimethalin) compared to calli transformed with the wild type α-tubulin gene from L. rigidum. Comprehensive modeling of molecular docking predicts that Arg-243 is close to the trifluralin binding site on the α-tubulin surface and that replacement of Arg-243 by Met/Lys-243 results in a spatial shift of the trifluralin binding domain, reduction of trifluralin-tubulin contacts, and unfavorable interactions. The major effect of these substitutions is a significant rise of free interaction energy between α-tubulin and trifluralin, as well as between trifluralin and its whole molecular environment. These results demonstrate that the Arg-243 residue in α-tubulin is a determinant for trifluralin sensitivity, and the novel Arg-243-Met/Lys mutations may confer trifluralin resistance in L. rigidum.

Genetic interaction involving photoperiod-responsive Hd1 promotes early flowering under long-day conditions in rice

Although flowering in rice has been extensively investigated, few studies focused on genetic interactions. Flowering evaluation of two recombinant inbred line (RIL) populations involving photo-insensitive rice cultivars, Bengal and Cypress, and a weedy rice accession, PSRR-1, under natural long-day (LD) conditions, revealed six to ten quantitative trait loci (QTLs) and a major QTL interaction. In addition to the validation of several previously cloned genes using an introgression lines (IL) population of PSRR-1, a few novel QTLs were also discovered. Analysis of the marker profiles of the advanced backcross lines revealed that Hd1 allele of PSRR-1 was responsible for the photoperiodic response in the near-isogenic lines (NILs) developed in both cultivar backgrounds. Based on the phenotypic and genotypic data of the NILs, and NIL mapping population and the transcript abundance of key flowering pathway genes, we conclude that Hd1 and its interaction with a novel gene other than Ghd7 play an important role in controlling flowering under LD conditions. Our study demonstrates the important role of genetic interaction that regulates flowering time in rice and the need for further investigation to exploit it for breeding adaptable rice varieties.

Alternative functions of Hd1 in repressing or promoting heading are determined by Ghd7 status under long-day conditions

Previous studies suggested that Hd1 promoted heading under short-day conditions (SD) and delayed heading under long-day conditions (LD). However in this study, Hd1 was demonstrated to consistently promote heading date in Zhenshan 97 (ZS97) background by upregulating Ehd1, Hd3a and RFT1 expression under both SD and LD. While the high photoperiod sensitivity of Hd1 was observed in Minghui 63 (MH63) background, with heading being suppressed in LD but promoted in SD. Comparative analysis of two sets of near isogenic lines of Hd1 in MH63 and ZS97 backgrounds indicated that the alternative functions of Hd1 in promoting or suppressing heading under LD are dependent on the previously cloned flowering repressor gene Ghd7. The interaction between proteins Ghd7 and Hd1 occurred through binding of the CCT domain of Ghd7 to the transcription-activating domain of Hd1, resulting in suppression of Ehd1 and florigen gene expression. The involvement of the transcription-activating domain of Hd1 in this protein-protein interaction probably blocked or weakened its transcriptional activity. These findings suggest that Hd1 alone essentially acts as a promoter of heading date, and the protein interaction between Ghd7 and Hd1 determines photoperiod sensitivity and integrated Hd1-mediated and Ehd1-mediated flowering pathways in rice.

The DTH8-Hd1 Module Mediates Day-Length-Dependent Regulation of Rice Flowering

Photoperiodic flowering is one of the most important pathways to govern flowering in rice (Oryza sativa), in which Heading date 1 (Hd1), an ortholog of the Arabidopsis CONSTANS gene, encodes a pivotal regulator. Hd1 promotes flowering under short-day conditions (SD) but represses flowering under long-day conditions (LD) by regulating the expression of Heading date 3a (Hd3a), the FLOWERING LOCUS T (FT) ortholog in rice. However, the molecular mechanism of how Hd1 changes its regulatory activity in response to day length remains largely unknown. In this study, we demonstrated that the repression of flowering in LD by Hd1 is dependent on the transcription factor DAYS TO HEADING 8 (DTH8). Loss of DTH8 function results in the activation of Hd3a by Hd1, leading to early flowering. We found that Hd1 directly interacts with DTH8 and that the formation of the DTH8-Hd1 complex is necessary for the transcriptional repression of Hd3a by Hd1 in LD, implicating that the switch of Hd1 function is mediated by DTH8 in LD rather than in SD. Furthermore, we revealed that DTH8 associates with the Hd3a promoter to modulate the level of H3K27 trimethylation (H3K27me3) at the Hd3a locus. In the presence of the DTH8-Hd1 complex, the H3K27me3 level was increased at Hd3a, whereas loss of DTH8 function resulted in decreased H3K27me3 level at Hd3a. Taken together, our findings indicate that, in response to day length, DTH8 plays a critical role in mediating the transcriptional regulation of Hd3a by Hd1 through the DTH8-Hd1 module to shape epigenetic modifications in photoperiodic flowering.

Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes

Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes.

Many plant species flower in response to changes in day length and can be categorized depending on their requirements for long or short days. Rice has tropical origins and normally flowers in response to shortening days. However, artificial selection operated by ancient farmers or modern breeders adapted rice cultivation to several environments, including those typical of temperate regions characterized by long days during the cropping season. Modifications of the genetic network controlling flowering that are causal to such expansion have been the subject of extensive studies, but the full complement of genes that regulate it and the molecular bases of their activity remains unknown. We took advantage of germplasm cultivated in Europe—and highly adapted to flower under long days–to isolate widespread variants of the HEADING DATE 1 (Hd1) gene that limits flowering in temperate areas, and showed that such variants are non-functional and unable to prevent long day flowering. We identified the DNA changes causing the gene to be non-functional and used such mutant alleles as tools to demonstrate that Hd1 can bind a specific DNA sequence in the promoter of a florigenic rice gene. Mining genetic diversity becomes thus instrumental to define the molecular properties of regulatory pathways.

The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals

Flowering is the result of the coordination between genetic information and environmental cues. Gene regulatory networks have evolved in plants in order to measure diurnal and seasonal variation of day length (or photoperiod), thus aligning the reproductive phase with the most favorable season of the year. The capacity of plants to discriminate distinct photoperiods classifies them into long and short day species, depending on the conditions that induce flowering. Plants of tropical origin and adapted to short day lengths include rice, maize, and sorghum, whereas wheat and barley were originally domesticated in the Fertile Crescent and are considered long day species. In these and other crops, day length measurement mechanisms have been artificially modified during domestication and breeding to adapt plants to novel areas, to the extent that a wide diversity of responses exists within any given species. Notwithstanding the ample natural and artificial variation of day length responses, some of the basic molecular elements governing photoperiodic flowering are widely conserved. However, as our understanding of the underlying mechanisms improves, it becomes evident that specific regulators exist in many lineages that are not shared by others, while apparently conserved components can be recruited to novel functions during evolution.

Development and validation of KASP assays for genes underpinning key economic traits in bread wheat

We developed and validated a robust marker toolkit for high-throughput and cost-effective screening of a large number of functional genes in wheat. Functional markers (FMs) are the most valuable markers for crop breeding programs, and high-throughput genotyping for FMs could provide an excellent opportunity to effectively practice marker-assisted selection while breeding cultivars. Here we developed and validated kompetitive allele-specific PCR (KASP) assays for genes that underpin economically important traits in bread wheat including adaptability, grain yield, quality, and biotic and abiotic stress resistances. In total, 70 KASP assays either developed in this study or obtained from public databases were validated for reliability in application. The validation of KASP assays were conducted by (a) comparing the assays with available gel-based PCR markers on 23 diverse wheat accessions, (b) validation of the derived allelic information using phenotypes of a panel comprised of 300 diverse cultivars from China and 13 other countries, and (c) additional testing, where possible, of the assays in four segregating populations. All KASP assays being reported were significantly associated with the relevant phenotypes in the cultivars panel and bi-parental populations, thus revealing potential application in wheat breeding programs. The results revealed 45 times superiority of the KASP assays in speed than gel-based PCR markers. KASP has recently emerged as single-plex high-throughput genotyping technology; this is the first report on high-throughput screening of a large number of functional genes in a major crop. Such assays could greatly accelerate the characterization of crossing parents and advanced lines for marker-assisted selection and can complement the inflexible, high-density SNP arrays. Our results offer a robust and reliable molecular marker toolkit that can contribute towards maximizing genetic gains in wheat breeding programs.

CONSTANS-like 9 (COL9) delays the flowering time in Oryza sativa by repressing the Ehd1 pathway

Flowering or heading is one of most important agronomic traits in rice. It has been characterized that CONSTANS (CO) and CONSTANS-like (COL) proteins are critical flowering regulators in response to photoperiodic stress in plants. We have previously identified that the COL family member OsCOL9 can positively enhance the rice blast resistance. In the present study, we aimed to explore the functional role of OsCOL9 in modulating the photoperiodic flowering. Our data showed that overexpression of OsCOL9 delayed the flowering time under both short-day (SD) and long-day (LD) conditions, leading to suppressed expressions of EHd1, RFT and Hd3a at the mRNA Level. OsCOL9 expression exhibited two types of circadian patterns under different daylight conditions, and it could delay the heading date by suppressing the Ehd1 photoperiodic flowering pathway. In contrast, the expressions of previously reported flowering regulators were not significantly changed in OsCOL9 transgenic plants, indicating that OsCOL9 functioned independently of other flowering pathways. In addition, OsCOL9 served as a potential yield gene, and its deficiency reduced the grain number of main panicle in plants. Furthermore, yeast two-hybrid assay indicated that OsCOL9 physically interacted with Receptor for Activated C-kinase 1 (OsRACK1). Rhythmic pattern analysis suggested that OsRACK1 responded to the change of daylight, which was regulated by the circadian clock. Taken together, our results revealed that OsCOL9 could delay the flowering time in rice by repressing the Ehd1 pathway.

Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice

Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.

Homodimerization of Ehd1 Is Required to Induce Flowering in Rice

In plants, flowering time is elaborately controlled by various environment factors. Ultimately, florigens such as FLOWERING LOCUS T (FT) or FT-like molecules induce flowering. In rice (Oryza sativa), Early heading date 1 (Ehd1) is a major inducer of florigen gene expression. Although Ehd1 is highly homologous to the type-B response regulator (RR) family in the cytokinin signaling pathway, its precise molecular mechanism is not well understood. In this study, we showed that the C-terminal portion of the protein containing the GARP DNA-binding (G) domain can promote flowering when overexpressed. We also observed that the N-terminal portion of Ehd1, carrying the receiver (R) domain, delays flowering by inhibiting endogenous Ehd1 activity. Ehd1 protein forms a homomer via a 16-amino acid region in the inter domain between R and G. From the site-directed mutagenesis analyses, we demonstrated that phosphorylation of the Asp-63 residue within the R domain induces the homomerization of Ehd1, which is crucial for Ehd1 activity. A type-A RR, OsRR1, physically interacts with Ehd1 to form a heterodimer. In addition, OsRR1-overexpressing plants show a late-flowering phenotype. Based on these observations, we conclude that OsRR1 inhibits Ehd1 activity by binding to form an inactive complex.

Functional Inactivation of Putative Photosynthetic Electron Acceptor Ferredoxin C2 (FdC2) Induces Delayed Heading Date and Decreased Photosynthetic Rate in Rice

Ferredoxin (Fd) protein as unique electron acceptor, involved in a variety of fundamental metabolic and signaling processes, which is indispensable for plant growth. The molecular mechanisms of Fd such as regulation of electron partitioning, impact of photosynthetic rate and involvement in the carbon fixing remain elusive in rice. Here we reported a heading date delay and yellowish leaf 1 (hdy1) mutant derived from Japonica rice cultivar “Nipponbare” subjected to EMS treatment. In the paddy field, the hdy1 mutant appeared at a significantly late heading date and had yellow-green leaves during the whole growth stage. Further investigation indicated that the abnormal phenotype of hdy1 was connected with depressed pigment content and photosynthetic rate. Genetic analysis results showed that the hdy1 mutant phenotype was caused by a single recessive nuclear gene mutation. Map-based cloning revealed that OsHDY1 is located on chromosome 3 and encodes an ortholog of the AtFdC2 gene. Complementation and overexpression, transgenic plants exhibited the mutant phenotype including head date, leaf color and the transcription levels of the FdC2 were completely rescued by transformation with OsHDY1. Real-time PCR revealed that the expression product of OsHDY1 was detected in almost all of the organs except root, whereas highest expression levels were observed in seeding new leaves. The lower expression levels of HDY1 and content of iron were detected in hdy1 than WT’s. The FdC2::GFP was detected in the chloroplasts of rice. Real-time PCR results showed that the expression of many photosynthetic electron transfer related genes in hdy1 were higher than WT. Our results suggest that OsFdC2 plays an important role in photosynthetic rate and development of heading date by regulating electron transfer and chlorophyll content in rice.