Cultivated Rice Research Articles

Essential residues in diterpene synthases for biosynthesis of oryzalexins A-F in rice phytoalexin.

Cultivated rice (Oryza sativa) produces a variety of diterpenoid-type phytoalexins. Diterpene synthase genes that are responsible for the biosynthesis of momilactones, phytocassanes, and oryzalexins have been identified in O. sativa cv. Nipponbare. OsKSL10 (Os12t0491800 in RAP and LOC_Os12g30824 in MSU) was previously identified as an enzyme catalyzing the conversion of ent-copalyl diphosphate to ent-sandaracopimaradiene for the production of oryzalexins A to F. Our previous study on Oryza rufipogon, a wild progenitor of Asian cultivated rice, showed that both OrKSL10 and OrKSL10ind from O. rufipogon accessions W1943 and W0106, respectively, closely related to the japonica and indica subspecies, converted ent-copalyl diphosphate to ent-miltiradiene. Thus, the functional conversion of ent-miltiradiene synthase into ent-sandaracopimaradiene synthase is implied to have occurred through natural amino acid mutations, the details of which have not been elucidated. In this study, we show that introduction of A654G substitution into OrKSL10 significantly alters its function into more closely resembling that of OsKSL10. Moreover, double substitution V546I/A654G almost completely converts the function of OrKSL10 into that of OsKSL10. On the other hand, the reversed substitution I546V/G654A was insufficient to convert the function of OsKSL10 into OrKSL10, indicating the introduction of additional substitution S522I is required for the functionality of OsKSL10. Lastly, point mutations atthe 654A residue in OrKSL10 suggest that hydrophobic side chains atthis position have a negative influence on the production of ent-sandaracopimaradiene.

Assessment of outcrossing potential between cultivated and weedy rice under alternate wetting and drying irrigation management

AbstractIn recent years, water conservation efforts in rice production have necessitated the use of reduced irrigation input systems such as alternate wetting and drying (AWD) as a substitute to conventional continuous flood‐irrigated systems (FLD), but little is known about the role of AWD in altering outcrossing potentials between cultivated rice and weedy rice (WR). In the United States, rice growers often control WR by cultivating varieties that possess herbicide resistance. However, an ongoing concern with such technology is hybridization or outcrossing between herbicide‐resistant rice cultivars and WR over time. Such outcrossing may result in transferring of herbicide resistance with increased occurrence of herbicide‐resistant WR ecotypes and reduction in the efficacy of herbicide management. This study compared and quantified outcrossing rates between two Clearfield rice varieties (CL142AR and CL261) that are herbicide resistant and two common WR genotypes, strawhull (SH) and blackhull (BH), under FLD and AWD management. Outcrossing was evident in all four genotype combinations (i.e., CL142AR or CL261 cultivated rice and SH or BH weedy rice) in both FLD and AWD; however, outcrossing rates with CL261 averaged about 6.5 times lower than those with CL142AR. Additional analysis revealed that higher outcrossing rates were associated with increased synchrony of flowering times and closer vertical proximity of panicles of WR to CL142AR than with CL261. AWD irrigation reduced outcrossing in SH weedy rice, suggesting that reduced outcrossing of SH weedy rice might be an additional benefit from AWD irrigation management.

Isolation of endophytic fungi from wild rice species for disease management and growth promotion in cultivated rice (Oryza sativa L.)

ABSTRACT The focus of plant health management is shifting from synthetic chemicals to bio-agents, and endophytes are beneficial for this purpose. In the present study, we isolated eleven endophytic fungi from seven wild rice species. Independent treatment of endophytic fungi in rice showed significant improvements in plant growth, higher tillering and percent fertility, panicle number/hill and filled grain number in endophyte-inoculated plants compared to control plants. Growth promotion activities of two endophytes Curvularia lunata (NRRI EF-11) and Hypocreals sp. (NRRI EF-8) were recorded with increased rice yield. These isolates also exhibited higher plant growth promoting chemicals namely, Indole acetic acid (IAA) and Inorganic phosphate (IP) which was realised into better growth promotion in rice. The biocontrol efficacy of endophytic fungi was highest in NRRI EF-11among all isolates as indicated by inhibition of radial growth of pathogens by 76.98–77.06% and in NRRI EF-8 by 74.81–76.61%, which is due to higher production of prussic acid. Defense induction was confirmed by analyzing the expression of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) defense enzymes, where expression of CAT, POD and SOD increased by 19.44–25.86, 2.70–3.16, 11.14–12.95 Units g−1 in treated NRRI EF-11 plants and 18.39–25.84, 2.16–2.94, 10.96–12.62 Units g−1 in treated NRRI EF-8 plants, respectively. These two endophytes have the potentiality to manage crop health in a sustainable way.

Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice

Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.

Comparative Study on the Bacterial Community of Cultivated and Uncultivated Rice Field Soils

A study was conducted to determine the changes in bacterial micro flora of soil in relation fallowing (abandonment) in rice fields. Soil samples from two paddy fields at Kumarakom region, southwest part of Kuttanad, Kerala, one field with paddy cultivation and the other fallowed, was subjected to the study. A total of 15 bacterial species, 8 from the cultivated field only, 6 from the fallowed field only and 1 common to both fields were isolated and identified in the study. The bacterial community in the soil of uncultivated field are entirely shifted from field where rice has been cultivated continuously. The persistent occurrence encountered in the cultivated field isolates were Bacillus megaterium, Pseudomonas aeroginosa and Klebsiella oxytoca while that in the abandoned field were of E coli followed by higher incidence of (80%) Enterobacter aerogenes and Citrobacter freundii. Under rice cultivation, soil pH, EC and bacterial density were generally higher than that in uncultivated soils while organic carbon in the soil was consistently lower than that in uncultivated soils. The study reveals the importance of bacteria in maintaining the health of a habitat and confirm that soil quality deteriorates over long-term fallowing.

Metal and Pesticide Assessments of Imported and Locally Cultivated Rice (Oryza sativa) in Senegal

Identifying heavy metal and pesticide contaminants is an essential step in assessing the health indicators of rice cultivation and consumption in Africa. Information on the contaminant levels of the imported and cultivated rice consumed in Senegal seems lacking. In this study, we assessed heavy metals, pesticides, ash, and protein in rice using rice samples from India, Thailand, South America, Vietnam, and China. Arsenic, Pb, Cd, Ni, Cu, Mo, Co, Cr, and Al are usually found in the soils used for rice cultivation in northern Senegal. While the heavy metal levels measured in soils were above the threshold limit, only Pb, Cd, and Al were found in cultivated rice. In all the analyzed rice samples from each country, there were certain amounts of Pb, As Al, and Cd. The concentration ranges in the six countries were as follows: 0.635–1.165 mg kg−1 for Pb, 0.047–0.438 mg kg−1 for As, 2.22–95.54 mg kg−1 for Al, and 0.002–0.082 mg kg−1 for Cd. The protein content in cultivated rice in Senegal was 7.31 mg kg−1, while the average from the imported rice ranged between 6.42% and 7.32%. The humidity levels in imported rice ranged between 11.12% and 12.95%. The fat content for the rice from six countries ranged between 0.22% and 0.67%, and the ash content ranged between 0.23% and 0.48%. These results allowed for the determination of the carbohydrate concentration, which varied between 79.18% and 80.82%. Indeed, freshly harvested rice grains typically contain around 80% carbohydrates. We noticed the presence of pesticides in all rice samples. The levels of three pesticides (total Pyrethrin, Bensulfuron-methyl, Propanyl, and 2,4D) were found to be beyond their maximum residue limits (MRLs) from the Codex Alimentarius, whereas deltamethrin was found to be below its MRL. This study indicates the presence of heavy metals carcinogenic to humans (Al, As, Cd, and Pb). Additionally, this study reveals the presence of deltamethrin, which is classified as probably carcinogenic to humans (Group 1), and 2,4-dichlorophenoxyacetic acid, which is classified as possibly carcinogenic to humans (Group 2B).

Influence of natural and artificial selection on the yield differences among progeny derived from crossing between subspecies in cultivated rice

Extended natural and artificial selection have introduced pronounced differences throughout the genomes, morphological traits, and geographical distributions of the two predominant rice strains, Oryza sativa Xian/indica (XI) and O. sativa Geng/japonica (GJ). However, the unique roles of natural and artificial selection in strain differentiation remain uncharacterized. Therefore, we independently produced advanced inbreeding populations in typical GJ- and XI-cultivated areas, beginning from the F2 generation. We utilized pedigree and bulk-selective methods to characterize artificial and natural selection, respectively. Our examination uncovered preferences between artificial and natural selection. Artificial selection was favored by individuals with increased grain count per panicle but reduced panicle number, while natural selection favored traits like greater panicle number, reduced grains per panicle, and higher thousand-grain weight, especially in the XI cultivation areas. Notably, in the XI regions, natural selection produced a preference for wider grains, indicating that the elongated grains in XI rice may be caused by artificial rather than natural selection. Using de novo assembly of a high-quality parental genome, we observed an increased prevalence of the GJ genotype in GJ areas compared to XI areas, segregation distortion in the advanced inbreeding population could be attributed to loci regulating hybrid sterility. Notably, the semi-dwarf allele sd1-d, linked to the “Green Revolution”, was not favored in either selection paradigm in northern areas, possibly due to its disadvantages on grain yield per plant and NH4+ uptake rate. Our study offers novel perspectives into the contributions of natural and artificial selection to the divergence between XI and GJ subspecies.

Comprehensive identification and analysis of DUF640 genes associated with rice growth

Protein domains with conserved amino acid sequences and uncharacterized functions are called domains of unknown function (DUF). The DUF640 gene family plays a crucial role in plant growth, particularly in light regulation, floral organ development, and fruit development. However, there exists a lack of systematic understanding of the evolutionary relationships and functional differentiation of DUF640 within the Oryza genus. In this study, 61 DUF640 genes were identified in the Oryza genus. The expression of DUF640s is induced by multiple hormonal stressors including abscisic acid (ABA), cytokinin (CK), ethylene (ETH), and indole-3-acetic acid (IAA). Specifically, OiDUF640-10 expression significantly increased after ETH treatment. Transgenic experiments showed that overexpressing OiDUF640-10 lines were sensitive to ETH, and seedling length was obstructed. Evolutionary analysis revealed differentiation of the OiDUF640-10 gene in O. sativa ssp. indica and japonica varieties, likely driven by natural selection during the domestication of cultivated rice. These results indicate that OiDUF640-10 plays a vital role in the regulation of rice seedling length.

Design of a delivery vehicle chitosan-based self-assembling: controlled release, high hydrophobicity, and safe treatment of plant fungal diseases

BackgroundTraditional pesticides are poorly water-soluble and suffer from low bioavailability. N-succinyl chitosan (NSCS) is a water-soluble chitosan derivative, has been recently used to encapsulate hydrophobic drugs to improve their bioavailability. However, it remains challenging to synthesize pesticides of a wide variety of water-soluble drugs and to scale up the production in a continuous manner.ResultsA synthetic method for preparing water-soluble nanopesticides with a polymer carrier was applied. The bioactive molecule BTL-11 was loaded into hollow NSCS to promote drug delivery, improve solubility and anti-fungal activity. The synthesized nanopesticides had well controlled sizes of 606 nm and the encapsulation rate was 80%. The release kinetics, drug toxicity and drug activity were further evaluated. The inhibitory activity of nanopesticides against Rhizoctonia solani (R. solani) was tested in vivo and in vitro. In vivo against R. solani trials revealed that BTL-11 has excellent control efficiency for cultivated rice leaf and sheath was 79.6 and 76.5%, respectively. By contrast, for BTL-11@NSCS NPs, the anti-fungal ability was strongly released and afforded significant control efficiencies of 85.9 and 81.1%. Those effects were significantly better than that of the agricultural fungicide azoxystrobin (51.5 and 66.5%). The proposed mechanism was validated by successfully predicting the synthesis outcomes.ConclusionsThis study demonstrates that NSCS is a promising biocompatible carrier, which can enhance the efficacy of pesticides, synergistically improve plant disease resistance, protect crop growth, and can be used for the delivery of more insoluble pesticides.Graphical

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process.

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Harnessing weedy rice as functional food and source of novel traits for crop improvement.

A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.

A Synthetic Microbiome Based on Dominant Microbes in Wild Rice Rhizosphere to Promote Sulfur Utilization

Sulfur (S) is one of the main components of important biomolecules, which has been paid more attention in the anaerobic environment of rice cultivation. In this study, 12 accessions of rice materials, belonging to two Asian rice domestication systems and one African rice domestication system, were used by shotgun metagenomics sequencing to compare the structure and function involved in S cycle of rhizosphere microbiome between wild and cultivated rice. The sulfur cycle functional genes abundances were significantly different between wild and cultivated rice rhizosphere in the processes of sulfate reduction and other sulfur compounds conversion, implicating that wild rice had a stronger mutually-beneficial relationship with rhizosphere microbiome, enhancing sulfur utilization. To assess the effects of sulfate reduction synthetic microbiomes, Comamonadaceae and Rhodospirillaceae, two families containing the genes of two key steps in the dissimilatory sulfate reduction, aprA and dsrA respectively, were isolated from wild rice rhizosphere. Compared with the control group, the dissimilatory sulfate reduction in cultivated rice rhizosphere was significantly improved in the inoculated with different proportions groups. It confirmed that the synthetic microbiome can promote the S-cycling in rice, and suggested that may be feasible to construct the synthetic microbiome step by step based on functional genes to achieve the target functional pathway. In summary, this study reveals the response of rice rhizosphere microbial community structure and function to domestication, and provides a new idea for the construction of synthetic microbiome.

Transcription factor encoding gene OsC1 regulates leaf sheath color through anthocyanidin metabolism in Oryza rufipogon and Oryza sativa

Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath). In this study, we identified and characterized a well-known MYB transcription factor, OsC1, through phenotypic (leaf sheath color) and metabolic (metabolite profiling) genome-wide association studies (pGWAS and mGWAS) in 160 common wild rice (O. rufipogon) and 151 cultivated (O. sativa) rice varieties. Transgenic experiments demonstrated that biosynthesis and accumulation of cyanidin-3-Galc, cyanidin 3-O-rutinoside and cyanidin O-syringic acid, as well as purple pigmentation in leaf sheath were regulated by OsC1. A total of 25 sequence variations of OsC1 constructed 16 functional haplotypes (higher accumulation of the three anthocyanidin types within purple leaf sheath) and 9 non-functional haplotypes (less accumulation of anthocyanidins within green leaf sheath). Three haplotypes of OsC1 were newly identified in our germplasm, which have potential values in functional genomics and molecular breeding of rice. Gene-to-metabolite analysis by mGWAS and pGWAS provides a useful and efficient tool for functional gene identification and omics-based crop genetic improvement.

Integrated environmental and genomic analysis reveals the drivers of fine‐scale divergence and local adaptation in northern populations of two wild rice species in China

Societal Impact StatementCrop wild relatives represent precious genetic resources for crop improvement. Investigating their local adaptation to marginal environments is important for the utilization of wild genetic resources. Oryza officinalis and Oryza granulata are wild relatives of cultivated rice and possess genes that convey resistance to insects, disease, and tolerance to shade and drought. The northern edge for the distribution of these two lies in China where populations are facing habitat destruction. This study found that the northern marginal populations of both species have adapted to local conditions, with specific implications for the conservation and utilization of wild rice.Summary O. officinalis and O. granulata, wild relatives of cultivated rice, represent important gene reservoirs with the potential to improve rice with respect to insect resistance and stress tolerance. However, the northern marginal populations of these two species in China are facing habitat destruction. Here, we investigated the genetic diversity and divergence of northern marginal populations of O. officinalis and O. granulata. The genomic variation of two species was examined by whole‐genome sequencing on 357 individuals. Generalized dissimilarity modeling was applied to investigate the effects of geographic and environmental isolation on population differentiation. Genetic‐environment association analysis and genome‐wide FST outlier scans were used to identify environmentally driven signals of selection. The marginal populations of both species exhibited low genetic diversity and obvious genetic differentiation stemmed from the joint effects of isolation by geographic distance and the environment. Both genomes exhibited specific signals of adaptation to cold environments in the north. Investigation of the divergence and adaptation of marginal populations of O. officinalis and O. granulata will help us to determine how wild rice can adapt to local environments, thus allowing for the development of scientific conservation policies and the identification of new genetic resources for rice with improved resistance.

Demography as a confounding factor to explain highly diverged loci between cultivated and wild rice

AbstractThe domestication of rice increases the divergence between cultivated rice and its wild progenitor because of artificial selection. However, it remains unknown whether highly diverged loci in rice can be explained by neutral demographic scenarios alone. In this study, we genotyped 45 InDels (insertion/deletion) in two subspecies of Asian cultivated rice (Oryza sativa ssp. japonica and Oryza sativa ssp. indica) and their wild progenitor (O. rufipogon/O. nivara). Among them, 17 loci are highly diverged (FST > 0.4) between rice cultivars and their ancestor. We performed coalescent-based simulations on neutral demographic scenarios and found that neutral demography alone could explain the polymorphic profiles on those highly diverged loci between cultivated and wild rice. Therefore, more signatures of selection should be considered when detecting artificial selection in rice.

Gene Flow Between the Wild Rice Species (Oryza longistaminata) and Two Varieties of Cultivated Rice (Oryza sativa) in Kilombero District, Tanzania

The direction and rate of gene flow between the perennial wild rice species, O. longistaminata and cultivated rice, O. sativa was investigated using nine Microsatellite (SSR) markers. The study involved characterization of parental lines of two cultivated rice varieties and O. longistaminata and their F1 progenies. Presence of crop-specific alleles in the wild species or vice-versa was used as an indicator of occurrence of gene flow between the two species. The study revealed that gene flow between O. longistaminata and each of the two varieties of O. sativa occurs naturally. The direction of gene flow was mainly from the cultivated to wild species. The rate (frequency) of gene flow was higher from cultivated (O. sativa) to wild rice (O. longistaminata) than from O. longistaminata to O. sativa and varied with cultivated rice variety. Higher rate of gene flow from cultivated to wild species could be due to floral structure and out-crossing nature of the wild species (O. longistaminata). Gene flow between O. longistaminata and O. sativa is likely to change genetic integrity of natural populations of the two species in areas where they occur sympatrically. However, isolation by distance can help to control gene flow between these species.

Physiological Responses to Salt Stress at the Seedling Stage in Wild (Oryza rufipogon Griff.) and Cultivated (Oryza sativa L.) Rice

Domesticated rice Oryza sativa L. is a major staple food worldwide, and the cereal most sensitive to salinity. It originated from the wild ancestor Oryza rufipogon Griff., which was reported to possess superior salinity tolerance. Here, we examined the morpho-physiological responses to salinity stress (80 mM NaCl for 7 days) in seedlings of an O. rufipogon accession and two Italian O. sativa genotypes, Baldo (mildly tolerant) and Vialone Nano (sensitive). Under salt treatment, O. rufipogon showed the highest percentage of plants with no to moderate stress symptoms, displaying an unchanged shoot/root biomass ratio, the highest Na+ accumulation in roots, the lowest root and leaf Na+/K+ ratio, and highest leaf relative water content, leading to a better preservation of the plant architecture, ion homeostasis, and water status. Moreover, O. rufipogon preserved the overall leaf carbon to nitrogen balance and photosynthetic apparatus integrity. Conversely, Vialone Nano showed the lowest percentage of plants surviving after treatment, and displayed a higher reduction in the growth of shoots rather than roots, with leaves compromised in water and ionic balance, negatively affecting the photosynthetic performance (lowest performance index by JIP-test) and apparatus integrity. Baldo showed intermediate salt tolerance. Being O. rufipogon interfertile with O. sativa, it resulted a good candidate for pre-breeding towards salt-tolerant lines.

Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.).

Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.

The MAT1 locus is required for microconidia-mediated sexual fertility in the rice blast fungus.

Rice blast fungus (Pyricularia oryzae) is a heterothallic ascomycete that causes the most destructive disease in cultivated rice worldwide. This fungus reproduces sexually and asexually, and its mating type is determined by the MAT1 locus, MAT1-1 or MAT1-2. Interestingly, most rice-infecting field isolates show a loss of female fertility, but the MAT1 locus is highly conserved in female-sterile isolates. In this study, we performed a functional analysis of MAT1 using the CRISPR/Cas9 system in female- and male-fertile isolates and female-sterile (male-fertile) isolates. Consistent with a previous report, MAT1 was essential for sexual reproduction but not for asexual reproduction. Meanwhile, deletion mutants of MAT1-1-1, MAT1-1-2, and MAT1-1-3 exhibited phenotypes different from those of other previously described isolates, suggesting that the function of MAT1-1 genes and/or their target genes in sexual reproduction differs among strains or isolates. The MAT1 genes, excluding MAT1-2-6, retained their functions even in female-sterile isolates, and deletion mutants lead to loss or reduction of male fertility. Although MAT1 deletion did not affect microconidia (spermatia) production, microconidia derived from the mutants could not induce perithecia formation. These results indicated that MAT1 is required for microconidia-mediated male fertility in addition to female fertility in P. oryzae .

Constitutively expressed small heat shock protein LsHsp21.5 not only enhances heat tolerance but also helps to maintain reproduction in female Laodelphax striatellus.

Coping with stressful conditions and maintaining reproduction are two key biological processes that affect insect population dynamics. Small heat shock proteins (sHSPs) are involved in the stress response and the development of insects. The sHsp gene Laodelphax striatellus (Hemiptera: Delphacidae) sHsp 21.5 (LsHsp21.5) showed constitutive, stage- and organ-specific expression in L. striatellus, a pest that damages cultivated rice in east Asia. The expression of LsHsp21.5 was highest in the ovary, with 43.60, 12.99 and 1.45 time higher expression here than in the head, gut and female fat bodies, respectively. The expression of this gene was weakly affected by heat or cold shock. The gene provided in vitro protection against heat damage to malate dehydrogenase and in vivo protection against heat stress in Escherichia coli (Enterobacteriales: Enterobacteriaceae) BL21(DE3) and L. striatellus. Moreover, L. striatellus reproduction decreased by 1.85 times when the expression of LsHsp21.5 was inhibited by RNA interference. The expression of some genes related to reproduction, such as the homologous gene of chorion protein, also declined. These results suggest that LsHsp21.5 expression not only protects other proteins against stress but also helps maintain the stable expression of some reproduction-related genes under non-stressful conditions, with impacts on L. striatellus fecundity.