Analysis of genetic property of phenotypic plasticity evolution in asian cultivated and wild rice with special reference to year environments in one of the northern-limit regions of rice cultivation

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.

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.

BackgroundChloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.ResultsA total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.ConclusionsThe chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0129-y) contains supplementary material, which is available to authorized users.

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.

Activity and composition of the methanogenic archaeal community in soil vegetated with wild versus cultivated rice

Gene flow between cultivated and wild rice is considered to be the origin of weedy rice, a threat to rice production in Thailand since 2001. The present study determined the degree of cross compatibility between four cultivated rice (Oryza sativa) varieties, namely, two high yielding varieties, CNT1 and SPR1 and two pure lined traditional varieties, KDML105 and RD6, and two common wild rice biotypes (O. rufipogon) from Kanchanaburi (KC) and Nakorn Nayok (NY). The hybrid progeny in the F1 and F2 generations were characterized for selected traits. The cultivated and wild rice cross fertilized with different degrees of compatibility between different parents, with higher seed set in crosses involving the high yield varieties than with the traditional varieties. The F 1 hybrids were mostly fertile, exhibiting wild traits of spikelet awning, seed shattering, and red pericarp with hybrid vigour in panicle size from crosses between cultivated and NY wild rice, followed by transgressive segregation in the same characteristics in the F 2's. Genotypic effects of the cultivated and wild rice parents were shown in segregation of flowering time, culm length, and seed shattering of the F 2 plants. Segregation of seed shattering pattern in the F 2 differed between the wild rice parents; offspring of NY shattered their seed completely, while some of those of KC did not all shatter their seed. Genotypic effects of the wild and cultivated rice parents, especially in those traits important to survival and dispersal, suggest a range of possible recombinations that may need to be considered in effective control of the weedy rice and for the conservation of wild rice in situ.

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.

Co-evolutionary associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties

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.

Genome-wide characterization and functional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)

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.

Summary Post‐pollination competition is reported here in cultivated rice (Oryza sativa) and a perennial wild rice (O. rufipogon) to investigate the occurrence of crop‐to‐wild gene flow. Wild and cultivated rice (variety Minghui‐63) were grown in a common garden in Hunan province, China, and crop‐specific genetic markers were used to detect hybridization following hand‐pollinations. Using 11 sequential pollination treatments, the effects of the relative timing of pollination on the success of foreign pollen was investigated. Foreign pollen from the crop resulted in lower pollen germination, fewer pollen tubes per style, and a significant reduction of seed set, demonstrating a disadvantage of foreign pollen even in the absence of pollen competition. When 1 : 1 pollen mixtures were applied, only 2% of the resulting seeds were hybrids, revealing a much stronger disadvantage of foreign pollen when competing with conspecific pollen. Testing the effects of the relative timing of pollination on the success of foreign pollen suggested that conspecific pollen is often more successful than foreign pollen. Nonetheless, hybridization is possible following the deposition of pollen mixtures, especially when foreign pollen arrives earlier than conspecific pollen. Pollen competition between wild and cultivated rice could slow the rate of crop‐to‐wild gene flow, but even if pollen competition was ubiquitous it would not prevent gene flow from the crop.

This shade house study examined the effect of competition on the growth performance of cultivated (Oryza sativa) and wild (Oryza punctata) rice species in Kenya. Growth was assessed for the two species, grown together and separately, by measuring plant height and tiller number through the growing season, and flag leaf area and above and below-ground biomass at the end of the growing season.O. punctata grew to a higher final height (116.00 ± 13.63 cm) attained higher tiller number (9 tillers /plant) and accumulated more biomass (16.68 ± 0.50 g ) than O. sativa while O. sativa attained a higher flag leaf area (35.00 ± 0.67 cm2 ) than O. punctata (P<0.05). For both species, interspecific competition was detected as a reduction in flag leaf area, (1.4 and 2.5 cm2) for O. punctata and O. sativarespectively. Flag leaf area is known to relate directly to grain yield. It was concluded that O. punctata is a better competitor than O. sativa (P<0.05) as it had more aggressive vegetative growth, less reduction in flag leaf area, attained higher final plant height and phytomass and matured faster than O. sativa. Key words: Competition, growth, Oryza sativa, Oryza punctata, cultivated rice, wild rice.

Phenotypic plasticity is an adaptive mechanism adopted by plants in response to environmental heterogeneity. Cultivated and wild species adapt in contrasting environments; however, it is not well understood how genetic changes responsible for phenotypic plasticity were involved in crop evolution. We investigated the genetic control of phenotypic plasticity in Asian cultivated (Oryza sativa) and wild rice (O. rufipogon) under 5 environmental conditions (2 nutrient and 3 density levels). Quantitative trait locus (QTL) analysis was conducted for traits affecting plant architecture and biomass production. By analysing the phenotypic means, QTLs of large effects were detected as a cluster on chromosome 7 under all the environmental conditions investigated; this might have contributed to transitions of plant architecture during domestication, as reported previously. Multiple QTLs of plasticity were also found within this QTL cluster, demonstrating that allele-specific environmental sensitivity might control plasticity. Furthermore, QTLs controlling plasticity without affecting phenotypic means were also identified. The mode of action and direction of allele effects of plasticity QTLs varied depending on the traits and environmental signals. These findings confirmed that cultivated and wild rice show distinctive genetic differentiation for phenotypic plasticity, which might have contributed to adaptation under contrasting environmental heterogeneity during the domestication of rice.

Common wild rice (Oryza rufipogon Griff.), known as the ancestor of Asian cultivated rice (Oryza sativa L.), is the most important germplasm for rice improvement. The first male sterility gene was found in the wild rice, and introduced to the cultivated rice, which launched the fast development of the high‐yielding hybrid rice. Other agronomically beneficial traits in the wild rice, such as rice tungro virus resistance, bacterial leaf blight (Xa21 gene) resistance and acid sulfate soil tolerance, have played important roles in rice breeding. China has the northernmost distribution area of wild rice possessing great genetic diversity. However, most of the populations of this species have disappeared in China over the last three decades, mainly caused by habitat loss, fragmentation and other human disturbances. Unfortunately, the decline of existing populations still continues. In the present study, we reviewed studies on genetic diversity and conservation of this wild rice in China, concentrating on population structure, pollen competition, pollen/gene flow from cultivated rice to wild rice, and ecological restoration in relation to in situ conservation. The relatively high genetic diversity of populations of O. rufipogon in China suggests that there is great value for conservation. Considerable gene flow from cultivated rice to wild rice may alter the genetic structure of natural populations of O. rufipogon and eventually lead to its genetic erosion. Pollen competition between wild and cultivated rice has caused a low rate of crop‐to‐wild gene flow, but it does not completely prevent gene flow from the crop. Effective isolation measures should be undertaken in the regions where in situ conservation of O. rufipogon is carried out. Reintroduction is an important alternative for the in situ conservation of wild rice species. As wild rice is an important genetic resource, both in situ and ex situ conservation strategies are needed.