Strong Photoperiod Sensitivity Research Articles

Incorporation of Photoperiod Insensitivity and High-Yield Genes into an Indigenous Rice Variety from Myanmar, Paw San Hmwe

Paw San Hmwe (PSH) is an indigenous rice variety from Myanmar with a good taste, a pleasant fragrance, and excellent elongation ability during cooking. However, its low yield potential and strong photoperiod sensitivity reduce its productivity, and it is vulnerable to climate changes during growth. To improve the photoperiod insensitivity, yield, and plant stature of PSH, the high-yield genes Grain number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP), together with the photoperiod insensitivity trait, were introgressed into PSH via marker-assisted backcross breeding and phenotype selection. For the photoperiod insensitivity trait, phenotypic selection was performed under long-day conditions during the dry season. After foreground selection of Gn1a and WFP via simple sequence repeat genotyping, genotyping-by-sequencing was conducted to validate the introgression of target genes and determine the recurrent parent genome recovery of the selected lines. The improved lines were insensitive to photoperiod, and the Gn1a and WFP introgression lines showed significantly higher numbers of primary panicle branches and spikelets per panicle than the recurrent parent, with comparative similarity in cooking and eating qualities. This study successfully improved PSH by decreasing its photoperiod sensitivity and introducing high-yield genes via marker-assisted selection. The developed lines can be used for crop rotation and double-season cropping of better-quality 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.

Minor-effect QTL for heading date detected in crosses between indica rice cultivar Teqing and near isogenic lines of IR24

Identification of quantitative trait loci (QTL) having small effects on heading date (HD) is important for fine-tuning flowering time in rice (Oryza sativa L.). In this study, minor-effect QTL for HD were identified using five segregating rice populations, including a recombinant inbred line population derived from crosses between indica cultivar Teqing and near isogenic lines of IR24, and four populations derived from residual heterozygotes identified in the original population. HD data from these populations were obtained in multiple years or at two locations with different photoperiods. A total of 11 QTL were detected; they had small additive effects ranging from 0.21 to 1.63days. The QTL were all detected in different populations, locations and/or years, having consistent allelic effects across experiments and a stable magnitude across years at the same location. These QTL, and other minor-effect QTL that have been cloned or fine-mapped, generally do not have strong photoperiod sensitivity, and thus can be used in a wide range of eco-geographical conditions. Seven of the 11 QTL were different from those that have been cloned or fine-mapped, providing new candidates for gene cloning and marker-assisted breeding. Allelic effects of QTL corresponding to those that had been cloned or fine-mapped, were much smaller in this study than previously reported. The results supported the assumption that qualitative and quantitative genes may be different alleles at the same loci, suggesting that it may be promising to identify minor-effect QTL from major heading date genes/QTL that have been cloned.

Casein kinases I and 2α phosphorylate oryza sativa pseudo-response regulator 37 (OsPRR37) in photoperiodic flowering in rice.

Flowering time (or heading date) is controlled by intrinsic genetic programs in response to environmental cues, such as photoperiod and temperature. Rice, a facultative short-day (SD) plant, flowers early in SD and late in long-day (LD) conditions. Casein kinases (CKs) generally act as positive regulators in many signaling pathways in plants. In rice, Heading date 6 (Hd6) and Hd16 encode CK2α and CKI, respectively, and mainly function to delay flowering time. Additionally, the major LD-dependent floral repressors Hd2/Oryza sativa Pseudo-Response Regulator 37 (OsPRR37; hereafter PRR37) and Ghd7 also confer strong photoperiod sensitivity. In floral induction, Hd16 acts upstream of Ghd7 and CKI interacts with and phosphorylates Ghd7. In addition, Hd6 and Hd16 also act upstream of Hd2. However, whether CKI and CK2α directly regulate the function of PRR37 remains unclear. Here, we use in vitro pull-down and in vivo bimolecular fluorescence complementation assays to show that CKI and CK2α interact with PRR37. We further use in vitro kinase assays to show that CKI and CK2α phosphorylate different regions of PRR37. Our results indicate that direct posttranslational modification of PRR37 mediates the genetic interactions between these two protein kinases and PRR37. The significance of CK-mediated phosphorylation for PRR37 and Ghd7 function is discussed.

Rayada specialty: the forgotten resource of elite features of rice.

Crop domestication and thereafter gradual selection or directional breeding have narrowed the genetic diversity of elite varieties and even promoted gathering of deleterious mutations in their stress response mechanisms, whereas local ecotypes, landraces and wild relatives still growing on native environment and preferences keep the genetic diversities for features like stress tolerance. Rayada is such an exceptional ecotype, variant of typical deepwater rice, completely endemic to certain areas of Madhumati river tracts of Bangladesh and still shares some features of wild rices. Multiple physiological features of Rayadas are distinctly different from typical deepwater rice. Tolerance to prolonged flood, submergence and cold are special features along with strong photoperiod sensitivity and lack of dormancy. Moreover, longer root system and prompt recovery capacity make it as an elite resource of stress tolerance. However, it has long been neglected because of mainly its long life cycle and poor yield. This review examines the specialty of Rayada rice and the potential use of its unique traits.

A two-step approach to quantify photothermal effects on pre-flowering rice phenology

Decreasing water availability for rice based systems resulted in the introduction of water saving production systems such as aerobic rice and alternate wetting–drying technology. To further improve resource use efficiency in these systems, water management should be attuned to critical growth stages, requiring accurate prediction of crop phenology. Photoperiod-sensitivity of aerobic rice genotypes complicates the estimation of the parameters characterising phenological development and hence impairs predictions. To overcome this complication, we followed a two-step approach: (1) the photoperiod response was determined in growth chambers, through a reciprocal transfer experiment with variable day length, conducted at a fixed temperature, and consecutively, (2) the temperature response was studied by combining the obtained photoperiod parameters with data from field experiments. All four aerobic rice genotypes tested exhibited strong photoperiod-sensitivity. Durations of basic vegetative phase (BVP) i.e. when plants are still insensitive to photoperiod, photoperiod-sensitive phase (PSP), and post-PSP (PPP) varied among genotypes. The temperature response of the genotypes was explored by combining phenological observations in the reciprocal transfer experiment with observations in two field experiments. The temperature range in the field experiments was too narrow to obtain convergence to a unique set of temperature response parameters, regardless whether a bilinear or a beta model was used. Sensitivity analysis however provided clear arguments in support of the recent doubts on the validity of a commonly used set of cardinal temperatures for rice phenology. Using standard cardinal temperatures, the rate of development at temperatures below 31°C was overestimated. This finding stresses the need for experiments on rice phenology under a wider range of temperatures.

Breeding strategies for optimum heading date using genotypic information in rice

Heading date (HD) is a key trait for the adaptation of rice cultivar to a specific growing region. Here, we report conventional and marker-assisted breeding strategies using genetic information related to the determination of HD, where the breeding objectives were to avoid the delayed heading common in indica × japonica hybrids, to increase the efficiency in selecting hybrid rice combinations having a suitable growth duration, and to develop cultivars with target growth duration by quantitative trait locus (QTL) pyramiding. The allelic constitution at the major HD loci was determined for a set of 109 leading Chinese rice cultivars by crossing them with HD tester lines. It was shown that the late heading in indica × japonica hybrids can be overcome by replacing the strong photoperiod-sensitivity allele Se-1 n with Se-1 e . A breeding strategy to enable the selection of hybrid combinations with suitable growth duration was proposed, based on HD genotypic information in rice. Meanwhile, a QTL analysis for HD was conducted over five years based on a recombinant inbred line population, derived from two parents Asominori (japonica) and IR24 (indica). Four QTLs, located on chromosomes 2, 3, 6, and 8, respectively, could be detected in all five years, indicating they were stably expressed QTL. According to this QTL information, and taking Asominori as an example, the HD genotypes for improving the growth duration were designed, and the best breeding selection schemes were determined by use of a genetic breeding simulation tool. Results obtained in this study demonstrate that genetic information related to HD can make a significant contribution to rice breeding.

Phenological characters and genetic divergence in aromatic rices

Phenological properties of rice cultivars determine their yield potential, local agronomic suitability and ability to escape from drought and natural calamities. This study was conducted to assess the genetic diversity of aromatic rice genotypes on the basis of phenological characters. 40 genotypes composed of 32 local aromatic, 5 exotic aromatic and three non-aromatic rice cultivars were used in the experiment. Multivariate analysis grouped the genotypes into 6 clusters. In discriminant function analysis (DFA) function 1 and function 2 together absorbed 99.9% of total dispersion. The most contributing characters participated in the clustering were growth duration, flowering duration, basic vegetative phase (BVP) and relative photoperiod sensitivity. Inter-cluster D2 value was the maximum between cluster i and iii and minimum was found between ii and iv. Cluster i and ii possessed the majority of genotypes having shorter BVP and strong photoperiod sensitivity. Therefore these genotypes can be used in the objective type of breeding programme and also for successful crop production in the post flood situation especially in the disaster-prone countries of south Asia.

Genetic analyses of heading date of Japonica rice cultivars from Northeast China

Northeast regions of China (38–55°N latitude) play an important role in Japonica rice planting. Heading dates of 10 Japonica rice cultivars native to the Northeast of China were investigated and their sensitivities to photoperiod and temperature were analyzed. The results showed that these Japonica rice cultivars were insensitive to photoperiod but strongly sensitive to temperature, i.e. a high temperature can markedly shorten the heading date. Genetic analyses were conducted on these 10 cultivars using a set of heading date tester lines. All these Japonica cultivars carried a dominant early heading gene Ef-1, and most of these cultivars carried the photoperiod insensitivity allele e 1 , and two types of alleles were presented at the Se-1 locus, including recessive photoperiod insensitivity gene Se-1 e and dominant strong photoperiod-sensitivity (PS) gene Se-1 n . The PS of these cultivars carrying E 1 or Se- 1 n can be repressed or weakened by Ef-1 and the recessive allele hd2 they carried. These results provided a reasonable explanation to the adaptability of Japonica rice to the high latitude environment of the Northeast China, and could be useful for breeding new cultivars well adapted to the high latitude regions and expanding the rice cultivation range.

Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar ‘Nona Bokra’

Many rice cultivars that originated from lower-latitude regions exhibit a strong photoperiod sensitivity (PS) and show extremely late heading under long-day conditions. Under natural day-length conditions during the cropping season in Japan, the indica rice cultivar 'Nona Bokra' from India showed extremely late heading (202 days to heading) compared to the japonica cultivar 'Koshihikari' (105 days), from Japan. To elucidate the genetic factors associated with such extremely late heading, we performed quantitative trait locus (QTL) analyses of heading date using an F(2) population and seven advanced backcross progeny (one BC(1)F(2) and six BC(2)F(2)) derived from a cross between 'Nona Bokra' and 'Koshihikari'. The analyses revealed 12 QTLs on seven chromosomes. The 'Nona Bokra' alleles of all QTLs contributed to an increase in heading date. Digenic interactions were rarely observed between QTLs. Based on the genetic parameters of the QTLs, such as additive effects and percentage of phenotypic variance explained, these 12 QTLs are likely generate a large proportion of the phenotypic variation observed in the heading dates between 'Nona Bokra' and 'Koshihikari'. Comparison of chromosomal locations between heading date QTLs detected in this study and QTLs previously identified in 'Nipponbare' x 'Kasalath' populations revealed that eight of the heading date QTLs were recognized nearby the Hd1, Hd2, Hd3a, Hd4, Hd5, Hd6, Hd9, and Hd13. These results suggest that the strong PS in 'Nona Bokra' was generated mainly by the accumulation of additive effects of particular alleles at previously identified QTLs.

Inheritance of photoperiod‐sensitivity genes controlling flower initiation in sorghum, Sorghum bicolor Moench

AbstractThe existence of a sorghum (Sorghum bicolor Moench) photoperiod sensitivity gene has been proposed to account for postponing flower initiation until Tentaka and Kazetachi meet with short daylengths below 12.5 h. To investigate the inheritance of this gene, three parental varieties, F1, F2, BC1F1 and BC1F2 populations of Tentaka and Kazetachi were evaluated for days‐to‐emergence of flag leaf (DEFL) under the field condition of long daylength (>13 h) and minimum temperatures over 20°C for at least 51 days after sowing in 1999, 2000 and 2001. The F1 hybrids, Tentaka (MS79 × Chohin232) and Kazetachi (MS138 × Chohin232), showed strong photoperiod sensitivity and very late DEFL, in spite of the photoperiod insensitivity of their parental varieties. In two different F2 populations, the segregation of early, middle and late plants for DEFL fitted in with the expected ratio of 7 : 30 : 27 under the three genes hypothesis, TtD1d1D2d2 for Tentaka and Kazetachi. Additionally, the expected ratio of early : middle : late (1 : 2 : 1) was observed in the segregation of BC1F1 of Tentaka × Chohin232 and Kazetachi × Chohin232 in 2000. These results suggest that two photoperiod sensitivity genes, D1 and D2 which show complementary dominant effects, are existent and the flowering phenotype of Tentaka and Kazetachi are expressed by the interactive operation both of a dominant thermo‐sensitivity gene (T) and complementary dominant photoperiod sensitivity genes (D1, D2), that is, the genotype TtD1d1D2d2.

Photothermal responses of O. sativa and O. glaberrima varieties and interspecific progenies from West Africa

Rice is an increasingly important cereal in West Africa, where it is grown in a wide range of hydrological conditions in high rainfall, humid forest to low rainfall, savanna agro-ecological zones. In order to identify cultivars that are well adapted to these diverse environments, and the traits that are needed in new cultivars to ensure adaptation, the effects of photoperiod and temperature on duration from emergence to flowering ( f) need to be quantified. The objectives of this study were: to phenotype duration to flowering of a diverse set of rice cultivars representing types grown in West Africa using data from carefully selected photothermal controlled environments (CEs); to examine how basic vegetative phase (BVP) and photoperiod-sensitivity varied among the different species and ecotypes; and to assess the usefulness of this simplified approach for characterising genotypes and lines for plant breeding and association and functional genomics. Twenty-two genotypes of rice representing the diversity found in West Africa, and including Oryza sativa indica and japonica, Oryza glaberrima and O. sativa×O. glaberrima progenies, were grown in a controlled environment (CE) under flooded (lowland) and free-drained (upland) hydrologies at 11 and 13 h photoperiods combined with mean temperatures of 22 and 28 °C. A simple model describing f in terms of a BVP, photoperiod-sensitive phase (PSP) and post-PSP was used to analyse variation in f. Hydrology had no effect on f but did affect plant height in some genotypes. Flowering occurred earliest in the 11 h photoperiod regimes (between 41 and 87 days after emergence (DAE)) and latest at 13 h/22 °C (between 68 and >150 days). The earliest genotypes to flower were all O. glaberrima and these all had a very short BVP (mean 276 °C days: T b=10 °C) but were strongly photoperiod-sensitive (mean PSP 364 °C days h −1). In contrast traditional O. sativa japonica cultivars were all late flowering due to a long BVP (mean 1006 °C days) and strong photoperiod-sensitivity (mean 342 °C days h −1). Improved japonicas, indicas and O. sativa×O. glaberrima progenies all had shorter BVPs (447–662 °C days) than traditional japonicas. Photoperiod-sensitivity was also less in the progenies and improved japonicas (about 200 °C days h −1). There were good correlations between values for BVP and PSP estimated in CE and the field ( r=0.86 and 0.68, respectively). We conclude that diverse genotypes can be successfully phenotyped for f using a simple model and three or four carefully chosen photoperiod and temperature regimes in a CE facility.

イネ品種Kasalathの感光性遺伝子座E<SUB>1</SUB>座およびSe-1座に関する遺伝子分析

The indica rice cultivar Kasalath (KA) has been extensively used as a model cultivar in the molecular genetics of rice in Japan. To advance our knowledge of the nrolecular genetics of heading thrre in rice, we performed a genetic analysis of KA with special reference to two major photoperiod sensitivity loci, E1 and Se-1. We also discussed the relationships of these two loci with the five QTLs (Hd-1∼Hd-5) that Yano et al.(1995) identified using the progenies from the cross‘KA × the Japanese japonica cultivar Nipponbare'.The F1 and F2 generations from the crosses ‘11 heading time tester lines × KA' were subjected to genetic analyses. The Rc (brown pericarp and seed coat) and Pgi-2 (phosphoglucose isomerase-2) Ioci were used as linkage markers of the E1 and Se-1 Ioci, respectively. Experimental results showed that KA carries a new photoperiod sensitivity allele E1 k(t) and a photoperiod insensitivity allele Se-1e. The E1k(t) proved to stimulate the photoperiod sensitivity of rice more than a strong photoperiod sensitivity allele E1. Based on the findings of the present study and previous works, we concluded that the E1 and Se-1 Ioci were identical with the Hd-4 and Hd-1 Ioci, respectively.

Trisomic analysis of a strong photoperiod-sensitivity gene E1 in rice (Oryza sativa L.)

Recent genetic analyses on heading-time of rice indicated that almost all the well-adapted varieties in the temperate zone carry a strong photoperiod-sensitivity gene E1, a dominant allele of E1 locus. In order to identify the chromosome on which E1 is located, a trisomic analysis was made using two primary trisomic series originating from the japonica varieties, Nipponbare and Kinmaze, respectively. The Nipponbare and Kinmaze series were crossed with heading-time tester lines, EG0 and EG3, respectively, both of which did not carry the E1. The F2 populations for chromosome 1, 2, and 3 could not be analyzed due to lack of seed. All the other F2 populations showed distinct segregation into early-type and late-type plants caused by the E1 locus segregation, which suggested that the trisomic analysis for E1 locus could be efficiently made. Both disomic and trisomic groups in the F2 population from the cross of the trisomic line for chromosome 7 × EG0 showed a segregation ratio significantly different at the 1% level from a ratio of 1 [e1e1; early]: 3 [E1e1, E1E1; late]. This suggested that E1 was located on chromosome 7. Subsequently, the linkage analysis was made using three morphological marker genes on chromosome 7. It was recognized that E1 was linked to rfs (rolled fine strip gene) and slg (slender glume gene) with recombination values of 16.3 ± 5.88 and 9.1 ± 4.72%, respectively. From these results, it can be concluded that E1 is most likely to be located on chromosome 7.