Photoperiod Sensitivity In Rice Research Articles

Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice (Oryza sativa L.).

The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.

Flowering time and photoperiod sensitivity in rice: Key players and their interactions identified.

Flowering time and photoperiod sensitivity in rice: Key players and their interactions identified.

The Basic Vegetative Phase and Photoperiod Sensitivity Index as the Major Criteria for Indigenous Upland Rice Production in Thailand under Unpredictable Conditions

Indigenous upland rice (Oryza sativa L.) is an important staple food for people. The productivity of upland rice is generally lower than lowland rice since crop yield depends on the amount of rainfall. Climate change is a major problem in rice production due to the unpredictable rainfall. The flowering time, maturity days, growth duration, and photoperiod sensitivity in rice are important for determining productivity. Therefore, in this study, indigenous upland rice germplasm was classified according to their flowering-related traits in the basic vegetative phase (BVP), photoperiod sensitivity index (PSI), grain yield (GY), and yield components. The results reveal that the BVP ranges from 12 to 76 days (mainly less than 30 days) while the PSI ranges from −0.14 to 0.89. Classification of the three groups was based on the PSI: 24 insensitivities (G1; PSI = −0.14–0.30), 214 weakly sensitive (G2; PSI = 0.31–0.70), and 63 strongly sensitive (G3; PSI = 0.71–0.89). Grain yield showed different correlations with day to flowering (DTF), PSI, and BVP in each group. The results suggest that the selection criteria were not only based on GY and DTF but also PSI and BVP. The new ideotypes for upland rice selection under unpredictable conditions such as rainfall and light duration are weakly sensitive (PSI range 0.30–0.60), low BVP (20–30 days), and less than 105 days of DTF, such as ULR189, ULR039, ULR036, ULR403, ULR364, ULR342, and ULR245 genotypes.

Overexpression of a methyl-CpG-binding protein gene OsMBD707 leads to larger tiller angles and reduced photoperiod sensitivity in rice

BackgroundMethyl-CpG-binding domain (MBD) proteins play important roles in epigenetic gene regulation, and have diverse molecular, cellular, and biological functions in plants. MBD proteins have been functionally characterized in various plant species, including Arabidopsis, wheat, maize, and tomato. In rice, 17 sequences were bioinformatically predicted as putative MBD proteins. However, very little is known regarding the function of MBD proteins in rice.ResultsWe explored the expression patterns of the rice OsMBD family genes and identified 13 OsMBDs with active expression in various rice tissues. We further characterized the function of a rice class I MBD protein OsMBD707, and demonstrated that OsMBD707 is constitutively expressed and localized in the nucleus. Transgenic rice overexpressing OsMBD707 displayed larger tiller angles and reduced photoperiod sensitivity—delayed flowering under short day (SD) and early flowering under long day (LD). RNA-seq analysis revealed that overexpression of OsMBD707 led to reduced photoperiod sensitivity in rice and to expression changes in flowering regulator genes in the Ehd1-Hd3a/RFT1 pathway.ConclusionThe results of this study suggested that OsMBD707 plays important roles in rice growth and development, and should lead to further studies on the functions of OsMBD proteins in growth, development, or other molecular, cellular, and biological processes in rice.

Strong photoperiod sensitivity is controlled by cooperation and competition among Hd1, Ghd7 and DTH8 in rice heading.

Summary Rice (Oryza sativa) is a short‐day (SD) plant originally having strong photoperiod sensitivity (PS), with SDs promoting and long days (LDs) suppressing flowering. Although the evolution of PS in rice has been extensively studied, there are few studies that combine the genetic effects and underlying mechanism of different PS gene combinations with variations in PS.We created a set of isogenic lines among the core PS‐flowering genes Hd1, Ghd7 and DTH8 using CRISPR mutagenesis, to systematically dissect their genetic relationships under different day‐lengths. We investigated their monogenic, digenic, and trigenic effects on target gene regulation and PS variation.We found that Hd1 and Ghd7 have the primary functions for promoting and repressing flowering, respectively, regardless of day‐length. However, under LD conditions, Hd1 promotes Ghd7 expression and is recruited by Ghd7 and/or DTH8 to form repressive complexes that collaboratively suppress the Ehd1‐Hd3a/RFT1 pathway to block heading, but under SD conditions Hd1 competes with the complexes to promote Hd3a/RFT1 expression, playing a tradeoff relationship with PS flowering. Natural allelic variations of Hd1, Ghd7 and DTH8 in rice populations have resulted in various PS performances.Our findings reveal that rice PS flowering is controlled by crosstalk of two modules – Hd1–Hd3a/RFT1 in SD conditions and (Hd1/Ghd7/DTH8)–Ehd1–Hd3a/RFT1 in LD conditions – and the divergences of these genes provide the basis for rice adaptation to broad regions.

Ghd8 controls rice photoperiod sensitivity by forming a complex that interacts with Ghd7

BackgroundFlowering time is one of the most important agronomic characteristics that ultimately determine yield potential and eco-geographical adaptation in crops. Ghd8 and Ghd7, two major flowering genes, have similar functions and large pleiotropic effects in controlling the heading date, plant height and grain yield of rice. However, these gene interactions at the genetic and molecular levels have not been determined to date.ResultsIn this study, we investigated the genetic interaction between Ghd8 and Ghd7 by using a set of near-isogenic lines and a panel of natural germplasm accessions in rice. We found that Ghd8 affected multiple agronomic traits in a functional Ghd7-dependent manner. Both functional Ghd8 and Ghd7 are pivotal for rice photoperiod sensitivity controlled by Hd1 and Hd3a. GHD8 could form a heterotrimeric complex with HD1 and OsHAP5b to activate the transcription of Ghd7 by binding directly to the promoter region of Ghd7, which contains the CCAAT-box motif.ConclusionsThe results of this study help to elucidate the genetic and molecular bases of Ghd8 and Ghd7 interactions, indicating that Ghd8 acts upstream of Ghd7 to activate its transcription, which inhibits Hd3a expression and thus affects flowering time and rice adaptation.

OsGI controls flowering time by modulating rhythmic flowering time regulators preferentially under short day in rice

Day length is one of the most important factors that determine flowering time. In this study, we report that a mutation in OsGI reduced the photoperiod sensitivity in rice, resulting in flowering at 91 d after germination (DAG) under short days (SD) and 103 DAG under long days (LD). Transcript levels for flowering regulators that show diurnal rhythmic expression were significantly decreased in the osgi mutants under SD, but chromatin remodeling factor genes were not significantly changed. However, expression by those flowering regulators was not significantly altered in the osgi mutants under LD. Transcript levels for Ghd7 were lower in the mutants compared with the WT before 35 DAG, but higher afterward. These results suggested that OsGI differentially modulates Ghd7 as plants develop. The temporal expression pattern of OsGI was similar under SD and LD. Transcript levels for OsGI peaked at 30 DAG before gradually declining to a minimum at 55 DAG, where they then remained constant until flowering occurred. This developmental regulation of OsGI appears to be the main reason for its affecting photoperiod sensitivity strongly under SD but only weakly under LD.

The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice.

Plants commonly rely on photoperiodism to control flowering time. Rice development before floral initiation is divided into two successive phases: the basic vegetative growth phase (BVP, photoperiod-insensitive phase) and the photoperiod-sensitive phase (PSP). The mechanism responsible for the transition of rice plants into their photoperiod-sensitive state remains elusive. Here, we show that se13, a mutation detected in the extremely early flowering mutant X61 is a nonsense mutant gene of OsHY2, which encodes phytochromobilin (PΦB) synthase, as evidenced by spectrometric and photomorphogenic analyses. We demonstrated that some flowering time and circadian clock genes harbor different expression profiles in BVP as opposed to PSP, and that this phenomenon is chiefly caused by different phytochrome-mediated light signal requirements: in BVP, phytochrome-mediated light signals directly suppress Ehd2, while in PSP, phytochrome-mediated light signals activate Hd1 and Ghd7 expression through the circadian clock genes' expression. These findings indicate that light receptivity through the phytochromes is different between two distinct developmental phases corresponding to the BVP and PSP in the rice flowering process. Our results suggest that these differences might be involved in the acquisition of photoperiod sensitivity in rice.

Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice.

Success of modern agriculture relies heavily on breeding of crops with maximal regional adaptability and yield potentials. A major limiting factor for crop cultivation is their flowering time, which is strongly regulated by day length (photoperiod) and temperature. Here we report identification and characterization of Days to heading 7 (DTH7), a major genetic locus underlying photoperiod sensitivity and grain yield in rice. Map-based cloning reveals that DTH7 encodes a pseudo-response regulator protein and its expression is regulated by photoperiod. We show that in long days DTH7 acts downstream of the photoreceptor phytochrome B to repress the expression of Ehd1, an up-regulator of the "florigen" genes (Hd3a and RFT1), leading to delayed flowering. Further, we find that haplotype combinations of DTH7 with Grain number, plant height, and heading date 7 (Ghd7) and DTH8 correlate well with the heading date and grain yield of rice under different photoperiod conditions. Our data provide not only a macroscopic view of the genetic control of photoperiod sensitivity in rice but also a foundation for breeding of rice cultivars better adapted to the target environments using rational design.

Mechanisms of Photoperiod in Regulation of Rice Flowering

A study on the photoperiodic control of flower in rice is advancing and rice has become an example of short day plant. Many genes used in flowering time determination in rice have been identified by many methods. The conclusion from these molecular studies is a remarkable conservation of genes which play an important role in the control of flowering time in rice. The rice photoperiod sensitivity gene Hd3a was originally detected as a heading date related quantitative trait locus found on chromosome 6 of rice. High resolution linkage mapping of Hd3a was carried using a huge segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasalath. Researchers revealed that there are three (3) pathways for the day length regulation of flowering in rice, short day activation pathway and long day suppression pathway lastly the long day activation pathway. Some genes where used in multiple pathways and others are specific to a particular pathway. There regulation also depends on the developmental stages. Rice may be an ideal plant to study the night break effect on flowering. In the near future there would be a need for better understanding of the control of flowering in rice at the genetic level.

Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day‐length response

The alteration of photoperiod sensitivity has let breeders diversify flowering time in Oryza sativa (rice) and develop cultivars adjusted to a range of growing season periods. Map-based cloning revealed that the rice flowering-time quantitative trait locus (QTL) Heading date 16 (Hd16) encodes a casein kinase-I protein. One non-synonymous substitution in Hd16 resulted in decreased photoperiod sensitivity in rice, and this substitution occurred naturally in an old rice cultivar. By using near-isogenic lines with functional or deficient alleles of several rice flowering-time genes, we observed significant digenetic interactions between Hd16 and four other flowering-time genes (Ghd7, Hd1, DTH8 and Hd2). In a near-isogenic line with the weak-photoperiod-sensitivity allele of Hd16, transcription levels of Ehd1, Hd3a, and RFT1 increased under long-day conditions, and transcription levels of Hd3a and RFT1 decreased under short-day conditions. Expression analysis under continuous light and dark conditions showed that Hd16 was not likely to be associated with circadian clock regulation. Biochemical characterization indicated that the functional Hd16 recombinant protein specifically phosphorylated Ghd7. These results demonstrate that Hd16 acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response as a result of the phosphorylation of Ghd7.

RNAi knockdown of rice SE5 gene is sensitive to the herbicide methyl viologen by the down-regulation of antioxidant defense

Plant heme oxygenase (HO) catalyzes the oxygenation of heme to biliverdin, carbon monoxide (CO), and free iron (Fe(2+))-and Arabidopsis and rice (Oryza sativa) HOs are involved in light signaling. Here, we identified that the rice PHOTOPERIOD SENSITIVITY 5 (SE5) gene, which encoded a putative HO with high similarity to HO-1 from Arabidopsis (HY1), exhibited HO activity, and localized in the chloroplasts. Rice RNAi mutants silenced for SE5 were generated and displayed early flowering under long-day conditions, consistent with phenotypes of the null mutation in SE5 gene reported previously (se5 and s73). The herbicide methyl viologen (MV), which produces reactive oxygen species (ROS), was applied to determine whether SE5 regulates oxidative stress response. Compared with wild-type, SE5 RNAi transgenic plants aggravated seedling growth inhibition, chlorophyll loss and ROS overproduction, and decreased the transcripts of some representative antioxidative genes. By contrast, administration of exogenous CO partially rescued corresponding MV hypersensitivity in the SE5 RNAi plants. Alleviation of seed germination inhibition, chlorophyll loss and ROS overproduction, as well as the induction of antioxidant defense were further observed when SE5 or HY1 was overexpressed in transgenic Arabidopsis plants, indicating that SE5 may be useful for molecular breeding designed to improve plant tolerance to oxidative stress.

The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis.

The CO (CONSTANS) gene of Arabidopsis has an important role in the regulation of flowering by photoperiod. CO is part of a gene family with 17 members that are subdivided into three classes, termed Group I to III here. All members of the family have a CCT (CO, CO-like, TOC1) domain near the carboxy terminus. Group I genes, which include CO, have two zinc finger B-boxes near the amino terminus. Group II genes have one B-box, and Group III genes have one B-box and a second diverged zinc finger. Analysis of rice (Oryza sativa) genomic sequence identified 16 genes (OsA-OsP) that were also divided into these three groups, showing that their evolution predates monocot/dicot divergence. Eight Group I genes (HvCO1-HvCO8) were isolated from barley (Hordeum vulgare), of which two (HvCO1 and HvCO2) were highly CO like. HvCO3 and its rice counterpart (OsB) had one B-box that was distantly related to Group II genes and was probably derived by internal deletion of a two B-box Group I gene. Sequence homology and comparative mapping showed that HvCO1 was the counterpart of OsA (Hd1), a major determinant of photoperiod sensitivity in rice. Major genes determining photoperiod response have been mapped in barley and wheat (Triticum aestivum), but none corresponded to CO-like genes. Thus, selection for variation in photoperiod response has affected different genes in rice and temperate cereals. The peptides of HvCO1, HvCO2 (barley), and Hd1 (rice) show significant structural differences from CO, particularly amino acid changes that are predicted to abolish B-box2 function, suggesting an evolutionary trend toward a one-B-box structure in the most CO-like cereal genes.

Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice.

The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. High-resolution linkage mapping of Hd3 was performed using a large segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasalath. To determine the genotype of Hd3, we employed progeny testing under natural field and short-day conditions. As a result, two tightly linked loci, Hd3a and Hd3b, were identified in the Hd3 region. Nearly-isogenic lines for Hd3a and Hd3b were selected from progeny using marker-assisted selection. The inheritance mode of both Hd3a and Hd3b was found to be additive. Analysis of daylength response in nearly-isogenic lines of Hd3a and Hd3b showed that the Kasalath allele at Hd3a promotes heading under short-day conditions while that at Hd3b causes late heading under long-day and natural field conditions.

Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2.

Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica variety Nipponbare and the indica variety Kasalath. To isolate a gene at Hd6, we used a large segregating population for the high-resolution and fine-scale mapping of Hd6 and constructed genomic clone contigs around the Hd6 region. Linkage analysis with P1-derived artificial chromosome clone-derived DNA markers delimited Hd6 to a 26.4-kb genomic region. We identified a gene encoding the alpha subunit of protein kinase CK2 (CK2 alpha) in this region. The Nipponbare allele of CK2 alpha contains a premature stop codon, and the resulting truncated product is undoubtedly nonfunctional. Genetic complementation analysis revealed that the Kasalath allele of CK2 alpha increases days-to-heading. Map-based cloning with advanced backcross progeny enabled us to identify a gene underlying a quantitative trait locus even though it exhibited a relatively small effect on the phenotype.

Mapping quantitative trait loci associated with days to flowering and photoperiod sensitivity in rice (Oryza sativa L.)

This study was undertaken to identify putative quantitative trait loci (QTLs) associated with days to flowering (DTF) and photoperiod response in rice. A population of 143 recombinant inbred lines derived from a cross between CO39 and Moroberekan was grown under greenhouse conditions and exposed to two different photoperiod regimes. DTF of individual plants was evaluated under 10 h and 14 h day lengths, and loci associated with photoperiod sensitivity were identified based on the delay in flowering under the 14 h photoperiod (DTF at 14 h minus DTF at 10 h). An RFLP data set consisting of 127 markers provided the basis for the QTL analysis. Both single marker and interval analysis were used and interactions between putative QTLs were estimated based on two-way ANOVA. Out of 15 QTLs associated with DTF, only 4 were identified as influencing the response to photoperiod. Interactions between flowering QTLs indicated the complex nature of the control of flowering in rice. The effectiveness of using a single recombinant inbred population to study a variety of complex phenotypes is discussed in relation to practical plant breeding.

Dissection of a major QTL for photoperiod sensitivity in rice: its association with a gene expressed in an age-dependent manner

A proposed major quantitative trait locus (QTL) for photoperiod sensitivity on chromosome 6 in rice was examined by introducing a chromosomal segment from a sensitive line into an insensitive one. The crossing experiments showed that a range of variation in heading date occurred in the later generations and that the region might contain at least a major gene and two additional recessive genes controlling photoperiod sensitivity. Gene mapping experiments showed that the major gene was Se-1 and that a recessive gene (tentatively named se-pat) was loosely linked to it. The responses to photoperiods were examined among the different genotypes under natural and controlled conditions. The two genes acted additively on the degree of photoperiod sensitivity. However, se-pat plants showed a response to photoperiods that differed from that of the other sensitive lines; a short-day treatment at the seedling stage delayed heading in the former plants, suggesting that the manner of its expression was age-dependent. A recessive gene similar to se-pat seemed to be widely distributed in wild and cultivated rice, suggesting that the gene complex in the region plays a significant role in response to photoperiod.

The effect of photoperiod on interval between panicle initiation and flowering in rice

An understanding of response of crops to photoperiod is essential for accurate prediction of their phenological development. This study aimed to determine whether photoperiod influences the duration from panicle initiation (PI) to flowering in rice ( Oryza sativa L.). In a greenhouse experiment, plants of 12 cultivars were grown under three short-day (SD) conditions 10, 11 and 12 h day −1 or under three long-day (LD) conditions 13, 14, and 15 h day −1 until PI, after which half of the plants at SD were transferred to a 3-h longer photoperiod and half of the plants at LD were moved to a 3-h shorter photoperiod. Duration from PI to flowering was positively correlated with the photoperiod experienced after PI; the effect of a 3-h change in photoperiod varied from negligible in some cases to more than 10 days in others. No consistent carryover effect of photoperiod before PI on the PI-to-flowering duration was detected. As expected, the total main-culm leaf number was influenced by photoperiod before PI, but not thereafter. Although the leaf number varied greatly both among cultivars and among pre-PI photoperiods, the number of unexpanded leaves at PI was nearly constant, with an average of about three leaves. This study further supports the earlier experimental finding that rice photoperiod sensitivity continues some days after PI, suggesting the inadequacy of the assumption in crop simulation model CERES-Rice that the PI-to-flowering duration is influenced only by a carryover effect of pre-PI photoperiod.

Genetics of photoperiod sensitivity in rice

A single-gene pair, designatedSe se, determines the sensitivity of rice varieties to the photoperiod.

A gene for photoperiod sensitivity in rice linked with apiculus colour.

LACK of appreciation of the importance of length of day in determining the onset of flowering has vitiated much of the earlier work on the inheritance of age in rice. No genetic analysis of photoperiod response in this plant has yet been published. In the past two years, I have investigated the inheritance of photoperiod sensitivity. The Ceylon pure line, Vellai Ilankalayan 28061, which blooms approximately one hundred days after sowing, and is relatively insensitive to the photoperiod, was crossed with the Burma lines, MLYC 401 and HMC 12, which have, in the short days of the North-East Monsoon season, about the same sowing-to-flowering interval as the former, but are, to a high degree, sensitive to the photoperiod. The annual variation in length of day in Ceylon (lat. 5° 55′–9° 50′ N.) is less than one hour, but this variation exerts a profound influence on the flowering of the sensitive varieties. The growing of segregating progenies in the long days of the South-West Monsoon season makes the separation of sensitive and day-neutral forms possible. The parents and the F1 and F2 generations were sown at the same time, namely, May 1, 1952, at the Rice Research Station, Batalagoda. The mean intervals from sowing to panicle emergence for the parents and the F1 are shown in Table 1.