Flower opening time (FOT) trait variability in wild rice species for heat stress resilience

Flower opening time (FOT) is affected by genetic and environmental factors, but little is known about the effect of light and dark conditions on FOT in cereal crops. FOT of an indica rice cultivar, IR64, and its near-isogenic line carrying a QTL for an early-morning flowering trait (IR64+qEMF3) were investigated in a natural-light and temperature-controlled small greenhouse by exposing either the panicle or stem or both plant organs to different light and dark conditions. FOT did not change in either genotype when panicles were exposed to light. A large difference in FOT was found between genotypes when panicles were exposed to dark conditions; no flower opening was observed in IR64, whereas flower opening was delayed but observed in IR64+qEMF3. These results suggest that the panicle is the organ that perceives light for flower opening in both genotypes, whereas the light requirement to reach flower opening was quite different between genotypes. Flower opening of IR64 occurred concomitantly with elongation of anther filament in the light after the dark treatment stopped, whereas approximately half of flowering of IR64+qEMF3 resulted in apparent cleistogamy even during dark treatment. An extended duration of the dark treatment until 1730H (30–50 min before sunset) made FOT of IR64 spikelets on the next day shifted to a time as early as that of IR64+qEMF3, with significant advancement of FOT compared to the control IR64 spikelets. Our results indicated that different flowering responses to light and dark conditions exist between IR64 and IR64+qEMF3. These findings provide clues for understanding the unique genetic controls of flowering in an EMF line in rice. This study also showed evidence that artificial light environments can shift the FOT of IR64 to that of IR64+qEMF3.

Rice is susceptible to heat stress at flowering, where temperatures above 33 °C during anthesis causes spikelet sterility. Heat-induced spikelet sterility at flowering is associated with reduction in grain yield. So far only N22 has been used as universal donor for heat stress. One of the major traits employed in N22 in mitigating the impact of high temperature is the early morning flowering (EMF). Hence, the present study was designed to identify novel donors from the indigenous landraces of rice available at TNAU. The physiological basis of flower opening time (FOT) showed early flowering lines had higher transpiration rate coupled with low photosynthetic rate and stomatal conductance during anthesis. The transpiration rate also led to a reduction in panicle temperatures in these lines. It was concluded that at the time of anthesis, the panicle temperatures were 24 °C and less which led to advanced FOT. The results revealed that among the 21 lines, seven landraces, namely Thatan samba, Panamara samba, Thooyamali, Norungan, Mattikar, Sornavari and Seakar, flowering (9.30 to 10.00 IST). Hence, the lines Thatan samba, Panamara samba which flowered before 9.40 IST can be used as potential donors of EMF trait to develop heat-tolerant varieties.

To safeguard global food security against rapid population growth and a warming world, the effective genetic improvement of cereals is imperative. Flower opening time (FOT) critically affects the seed setting rate. In this study, we identified a gene, EARLY-MORNING FLOWERING 3 (EMF3), in which single-nucleotide substitutions strongly modulate FOT in rice in a semi-dominant manner, resulting in wide variation in FOT from earlier to later FOT than the wild-type. EMF3 knock-out mutants showed significantly reduced FOT synchrony and disrupted anther dehiscence, leading to fertilisation failure. EMF3 encodes a plasma membrane-localised polypeptide of 723 amino acids with an armadillo repeat fold and four transmembrane segments. Furthermore, EMF3 is specifically expressed in the anthers starting from nighttime on the day of flowering, with substantial impacts on the transcriptomes of both anther and lodicule, which suggested an exclusive role of EMF3 in flowering events. Modifying EMF3 alleles of O. sativa enabled the adjustment of FOT among Oryza species and subspecies, potentially facilitating cross-fertilisation by overcoming one of the major challenges of inter-specific hybridisation to exploit heterosis. Introducing the EMF3 alleles with the earlier FOT into popular rice cultivars resulted in flowering at an earlier time of day when the temperature was cooler, efficiently increasing seed setting rate under heat stress. This discovery unveils the novel mechanism of anther control of flower opening time through the EMF3 gene, while also enabling the use of EMF3 alleles in breeding strategies for efficient fertilisation for increasing hybrid rice seed production and mitigating future heat-stress damage at flowering.

Rice is most susceptible to heat and drought stress at flowering stage, but flowering characteristics under drought stress are not well characterized. This study investigated flowering characteristics of rice genotypes contrasting in their flower opening time (FOT) and level of drought tolerance. Near-isogenic lines for the early-morning flowering trait (IR64+ qEMF3) and for drought tolerance (IR87707-445-B-B-B), and their recurrent parent cultivar (IR64) were used. IR64+ qEMF3 had stable earlier FOT than IR64 and IR87707-445-B-B-B under drought stress conditions. Drought stress occasionally affects FOT depending on genotype. The number of open spikelets was higher in IR87707-445-B-B-B than in IR64 and IR64+ qEMF3, and the difference among genotypes increased as the rice plants were subjected to more severe stress levels. Panicle temperature increased under drought stress conditions and was similar among genotypes when it was measured at the same time of day, demonstrating that earlier FOT in IR64+ qEMF3 must be beneficial to avoid heat stress at flowering under drought stress conditions. However, IR64+ qEMF3 did not exhibit drought avoidance, as evidenced by the root mass at depth. To assess the potential for the EMF trait to complement ongoing drought breeding efforts, heat tolerance among 13 advanced drought breeding lines and released cultivars was tested. Wide variation in heat tolerance at flowering was observed and, notably, none of the 13 lines possessed the EMF trait. This study therefore proposes that a breeding strategy that transfers the EMF trait into drought tolerant lines could enhance the resilience of rice spikelets to the combined stresses of heat and drought at flowering. Abbreviations: Analysis of variance (ANOVA), dry season (DS), early-morning flowering (EMF), flower opening time (FOT), near-isogenic line (NIL), panicle water potential (PWP), quantitative trait locus (QTL), wet season (WS)

Flower opening time (FT) is a critical factor for seed production in hybrid rice. To unravel the genetic basis of FT, a recombinant inbred (RI) line population including 184 lines was developed from the cross between a japonica variety Nipponbare and an early FT mutant (eft). A genetic linkage map was constructed using 70 SSR and 123 InDel markers, covering a total length of 1753.3 cM of the genome. The FT of both parents and RI lines was measured by the traditional grading scale method and a new time-interval method in two environments, i.e., Hainan (HN) and Hangzhou (HZ). A total of seven FT-related quantitative trait loci (QTLs) distributing on 4 chromosomes were detected in HN and HZ. qFT1b and qFT12 could be detected in both environments. The time-interval FT in Hangzhou allowed us to detect one more QTL (qFT-9) than the grading scale method. qFT1a is a major QTL explaining more than 60% of the total phenotypic variations in FT. Although FT had a positive correlation with heading date in Hangzhou (r = 0.16), no common QTL was detected for them, suggesting that FT and heading date are under different genetic controls. These discoveries may help to understand the genetics of flower opening time in rice and be useful for breeding early FT rice to facilitate hybrid seed production in the near future.

A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5-2.0 h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource.

BackgroundMagnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that enable it to resist pathogen invasion. Although wild rice represents a major resource for disease resistance, relative to current cultivated rice varieties, no prior studies have compared the immune and transcriptional responses in the roots of wild and cultivated rice to M. oryzae.ResultsIn this study, we showed that M. oryzae could act as a typical root-infecting pathogen in rice, in addition to its common infection of leaves, and wild rice roots were more resistant to M. oryzae than cultivated rice roots. Next, we compared the differential responses of wild and cultivated rice roots to M. oryzae using RNA-sequencing (RNA-seq) to unravel the molecular mechanisms underlying the enhanced resistance of the wild rice roots. Results indicated that both common and genotype-specific mechanisms exist in both wild and cultivated rice that are associated with resistance to M. oryzae. In wild rice, resistance mechanisms were associated with lipid metabolism, WRKY transcription factors, chitinase activities, jasmonic acid, ethylene, lignin, and phenylpropanoid and diterpenoid metabolism; while the pathogen responses in cultivated rice were mainly associated with phenylpropanoid, flavone and wax metabolism. Although modulations in primary metabolism and phenylpropanoid synthesis were common to both cultivated and wild rice, the modulation of secondary metabolism related to phenylpropanoid synthesis was associated with lignin synthesis in wild rice and flavone synthesis in cultivated rice. Interestingly, while the expression of fatty acid and starch metabolism-related genes was altered in both wild and cultivated rice in response to the pathogen, changes in lipid acid synthesis and lipid acid degradation were dominant in cultivated and wild rice, respectively.ConclusionsThe response mechanisms to M. oryzae were more complex in wild rice than what was observed in cultivated rice. Therefore, this study may have practical implications for controlling M. oryzae in rice plantings and will provide useful information for incorporating and assessing disease resistance to M. oryzae in rice breeding programs.

With the rapidly development of transgenic rice and increasing environmental release, escape of foreign genes through pollen into wild relatives happens possible, the potential ecological effects may become more and more attention. In this study, Cry1Ac/CpTI bivalent transgenic insect-resistant genes from cultivated rice introgressing into common wild rice ( Oryza rufipogon Griff) were carried out to generate F 1 and their offspring of F 2 , F 3 , F 4 and F 5 , as well as backcross progenies, BC 1 F 1 and BC 1 F 2 , and also inheritance and expression of foreign genes in wild rice offspring were analyzed in order to clarify whether or not escape of foreign genes from the transgenic cultivated rice might be stable inheritance and expression in the wild relatives of rice. The results showed that exogenous gene copy number in the wild rice offspring was completely identical to the gene donor of cultivated rice. The insertion loci of foreign genes in common wild rice were also quite stable. The expression patterns and expression levels of insecticidal protein Cry1Ac in the different generations of wild rice were almost consistent to that of their gene donor of cultivated rice. This study illustrated that foreign genes of transgenic rice once escaping into wild relatives might be introgressing into other rice cultivar and wild relatives of rice, The foreign genes can be stable inherited and expressed, which imply that GM rice escape of foreign genes from GM rice into closely related species might exist potential ecological risk.

Soil salinity is a major constraint that affects plant growth and development. Rice is a staple food for more than half of the human population but is extremely sensitive to salinity. Among the several known mechanisms, the ability of the plant to exclude cytosolic Na+ is strongly correlated with salinity stress tolerance in different plant species. This exclusion is mediated by the plasma membrane (PM) Na+/H+ antiporter encoded by Salt Overly Sensitive (SOS1) gene and driven by a PM H+-ATPase generated proton gradient. However, it is not clear to what extent this mechanism is operational in wild and cultivated rice species, given the unique rice root anatomy and the existence of the bypass flow for Na+. As wild rice species provide a rich source of genetic diversity for possible introgression of abiotic stress tolerance, we investigated physiological and molecular basis of salinity stress tolerance in Oryza species by using two contrasting pairs of cultivated (Oryza sativa) and wild rice species (Oryza alta and Oryza punctata). Accordingly, dose- and age-dependent Na+ and H+ fluxes were measured using a non-invasive ion selective vibrating microelectrode (the MIFE technique) to measure potential activity of SOS1-encoded Na+/H+ antiporter genes. Consistent with GUS staining data reported in the literature, rice accessions had (~4–6-fold) greater net Na+ efflux in the root elongation zone (EZ) compared to the mature root zone (MZ). Pharmacological experiments showed that Na+ efflux in root EZ is suppressed by more than 90% by amiloride, indicating the possible involvement of Na+/H+ exchanger activity in root EZ. Within each group (cultivated vs. wild) the magnitude of amiloride-sensitive Na+ efflux was higher in tolerant genotypes; however, the activity of Na+/H+ exchanger was 2–3-fold higher in the cultivated rice compared with their wild counterparts. Gene expression levels of SOS1, SOS2 and SOS3 were upregulated under 24 h salinity treatment in all the tested genotypes, with the highest level of SOS1 transcript detected in salt-tolerant wild rice genotype O. alta (~5–6-fold increased transcript level) followed by another wild rice, O. punctata. There was no significant difference in SOS1 expression observed for cultivated rice (IR1-tolerant and IR29-sensitive) under both 0 and 24 h salinity exposure. Our findings suggest that salt-tolerant cultivated rice relies on the cytosolic Na+ exclusion mechanism to deal with salt stress to a greater extent than wild rice, but its operation seems to be regulated at a post-translational rather than transcriptional level.

BackgroundRice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined.ResultsIn the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together.ConclusionsThis study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.

Rice (Oryza sativa L.) is one of the most important crops in the world and a basic food source for about two-thirds of the population. It has been grown in the tropics and sub-tropics probably for thousands of years. Owing to the fast growing world population, there is a high demand for increased and improved rice production. Wild relatives of cultivated rice, the related A genome species, carry a vast genetic diversity and are a significant resource for rice improvement. Recent advances in both molecular breeding programmes and next-generation sequencing have potential for application in genetic improvement of elite rice lines with valuable traits from wild rice species. Numerous genes have already been transferred from wild species into selected rice lines and new varieties have been released for commercial use. Very recently two distinct groups of wild rice have been discovered in northern Queensland. They could be new Australian wild rice species and represent novel gene reservoirs in rice. These populations have remained isolated from the great genetic impact of the domesticated rice populations from Asia. The characterisation, collection and conservation of this wild genetic resource may be critical for global food security. The focus of this study was, firstly, the characterisation of the novel Australian wild rice relatives in terms of their relationship with other Oryza species, including the cultivars, using full chloroplast sequence as well as nuclear genome regions; secondly, creating genomic resources of these wild rice relatives by means of whole genome sequencing and generating reference genomes for the two novel Australian wild rice taxa. The draft genomes generated were used for whole genome characterization studies including phylogenetic reconstruction with high resolution, divergence time estimation, structural descriptions, gene annotation, and repeat content exploration. The evolutionary inference results revealed that northern Australia might be the centre of diversity of the A genome Oryza and highlighted the need for better understanding and exploitation of these populations.

BackgroundRice, which serves as a staple food for more than half of the world’s population, is very susceptible to the pathogenic fungus, Magnaporthe oryzae. However, common wild rice (Oryza rufipogon), which is the ancestor of Asian cultivated rice (O. sativa), has significant potential as a genetic source of resistance to M. oryzae. Recent studies have shown that the domestication of rice has altered its relationship to symbiotic arbuscular mycorrhizae. A comparative response of wild and domestic rice inhabited by mycorrhizae to infection by M. oryzae has not been documented.ResultsIn the current study, roots of wild and cultivated rice colonized with the arbuscular mycorrhizal (AM) fungus (AMF) Rhizoglomus intraradices were used to compare the transcriptomic responses of the two species to infection by M. oryzae. Phenotypic analysis indicated that the colonization of wild and cultivated rice with R. intraradices improved the resistance of both genotypes to M. oryzae. Wild AM rice, however, was more resistant to M. oryzae than the cultivated AM rice, as well as nonmycorrhizal roots of wild rice. Transcriptome analysis indicated that the mechanisms regulating the responses of wild and cultivated AM rice to M. oryzae invasion were significantly different. The expression of a greater number of genes was changed in wild AM rice than in cultivated AM rice in response to the pathogen. Both wild and cultivated AM rice exhibited a shared response to M. oryzae which included genes related to the auxin and salicylic acid pathways; all of these play important roles in pathogenesis-related protein synthesis. In wild AM rice, secondary metabolic and biotic stress-related analyses indicated that the jasmonic acid synthesis-related α-linolenic acid pathway, the phenolic and terpenoid pathways, as well as the phenolic and terpenoid syntheses-related mevalonate (MVA) pathway were more affected by the pathogen. Genes related to these pathways were more significantly enriched in wild AM rice than in cultivated AM rice in response to M. oryzae. On the other hand, genes associated with the ‘brassinosteroid biosynthesis’ were more enriched in cultivated AM rice.ConclusionsThe AMF R. intraradices-colonized rice plants exhibited greater resistance to M. oryzae than non-AMF-colonized plants. The findings of the current study demonstrate the potential effects of crop domestication on the benefits received by the host via root colonization with AMF(s), and provide new information on the underlying molecular mechanisms. In addition, results of this study can also help develop guidelines for the applications of AMF(s) when planting rice.

To clarify the inter- and intraspecific variations of floral traits in rice, we investigated eleven traits related to pistil, stamen and glume using 128 Asian cultivated rice (Oryza sativa L.) accessions including 72 Indica and 56 Japonica type accessions, and 53 wild rice (O. rufipogon Griff.) accessions including 32 perennial and 21 annual ecotype accessions. We examined the results from three specific levels: intraspecific variation between perennial and annual ecotypes of wild rice, interspecific variation between cultivated rice and wild rice, and intraspecific variation between Indica and Japonica type cultivars. The annual wild rice accessions exhibited a shorter stigma and anther than the perennial wild rice ones. The cultivated rice accessions showed a lower stigma exsertion, shorter stigma, shorter anther, and thicker and wider lemma and palea than the wild rice accessions. These floral traits of cultivated rice are considered to play an important role in selfing and high seed production. None of the floral traits showed distinct differences between the Indica and Japonica type accessions in cultivated rice, although the Indica type accessions tended to display a slenderer stigma and glume than the Japonica type accessions. It is suggested that the varietal differentiation into the Indica and Japonica types is not likely to be related to genetic variations of floral traits. We clarified the differences in floral traits between annual and perennial ecotypes of wild rice, between cultivated rice and wild rice, and between the Indica and Japonica type cultivars, and discussed the relationship between genetic variations of floral traits and domestication and varietal differentiation in rice.

Genes in evolution: the control of diversity and speciation