Rice Mutant Research Articles

Knockout of a rice K5.2 gene increases Ca accumulation in the grain.

Rice is a staple food for half of the world's population, but it is a poor dietary source of calcium (Ca) due to the low concentration. It is an important issue to boost Ca concentration in this grain to improve Ca deficiency risk, but the mechanisms underlying Ca accumulation are poorly understood. Here, we obtained a rice (Oryza sativa) mutant with high shoot Ca accumulation. The mutant exhibited 26%-53% higher Ca in shoots than did wild-type rice (WT) at different Ca supplies. Ca concentration in the xylem sap was 36% higher in the mutant than in the WT. There was no difference in agronomic traits between the WT and mutant, but the mutant showed 25% higher Ca in the polished grain compared with the WT. Map-based cloning combined with a complementation test revealed that the mutant phenotype was caused by an 18-bp deletion of a gene, OsK5.2, belonging to the Shaker-like K+ channel family. OsK5.2 was highly expressed in the mature region of the roots and its expression in the roots was not affected by Ca levels, but upregulated by low K. Immunostaining showed that OsK5.2 was mainly expressed in the pericycle of the roots. Taken together, our results revealed a novel role for OsK5.2 in Ca translocation in rice, and will be a good target for Ca biofortification in rice.

Identification of biochemical indices for brown spot (Bipolaris oryzae) disease resistance in rice mutants and hybrids.

Brown spot caused by Bipolaris oryzae is a major damaging fungal disease of rice which can decrease the yield and value of produce due to grain discoloration. The objectives of the current study were to investigate and understand the biochemical indices of brown spot disease resistance in rice. A total of 108 genotypes (mutant and hybrid) along with Super Basmati and parent RICF-160 were evaluated against brown spot disease. The genotypes exhibiting resistant and susceptible responses to brown spot disease according to the IRRI standard disease rating scale were screened and selected. To study the biochemical response mechanism, forty five selected genotypes along with Super Basmati and RICF-160 were analyzed using the biochemical markers. The physiological and biochemical analysis provided valuable insights and confirmed the resistance of rice hybrids and mutants against brown spot disease. Positive correlations were observed among stress bio-markers and disease response. Rice genotypes i.e. Mu-AS-8, Mu-AS-19, Mu-AS-20 and Mu-AS-35 exhibited moderate resistant response while Hy-AS-92, Hy-AS-98, Hy-AS-99, Hy-AS-101, Hy-AS-102 and Hy-AS-107 showed resistant response to brown spot disease. Brown spot resistant rice genotypes had lesser values of malondialdehyde and total oxidant status and higher antioxidant activities i.e. superoxide dismutase, peroxidase, total phenolic content and lycopene. The selected resistant rice genotypes had resistance capacity against Bipolaris oryzae stress. In conclusion, identified resistant mutants i.e. Mu-AS-8, Mu-AS-19, Mu-AS-20 and Mu-AS-35 and hybrids i.e. Hy-AS-92, Hy-AS-98, Hy-AS-99, Hy-AS-101, Hy-AS-102 and Hy-AS-107 could be used in rice breeding program to achieve sustainable rice production by coping the emerging challenge of brown spot disease under variable climate conditions.

PDL1-dependent trans-acting siRNAs regulate lateral organ polarity development in rice

Leaves and glumes act as lateral organs and have essential effects on photosynthesis and seed morphology, thus affecting yield. However, the molecular mechanisms controlling their polarity development in rice is still worth further analysis. Here, we isolated a polarity defect of lateral organs 1 (pdl1) mutant in rice, which exhibits twisted/filamentous-shaped leaves and cracked/filamentous-shaped lemmas caused by defects in polarity development. PDL1 encodes a SUPPRESSOR OF GENE SILENCING 3 protein localized in the cytoplasm granules. PDL1 is expressed in the shoot apical meristem, inflorescence meristem, floral meristem, and lateral organs including leaf and floral organs. PDL1 is involved in the synthesis of tasiR-ARF, which may subsequently modulate the expression of OsARFs. Meanwhile, the expression of abaxial miR165/166 and the adaxial identity genes OSHBs was increased and decreased significantly, respectively. The results of this study clarified the molecular mechanism that the PDL1-mediated tasiR-ARF synthesis regulates the lateral organ polarity development in rice.

The Importance of Positive Influences for Gamma Rays in Creating of Novel Drought Stress-Tolerant Rice Mutants across ISSR Markers

The Importance of Positive Influences for Gamma Rays in Creating of Novel Drought Stress-Tolerant Rice Mutants across ISSR Markers

Assessing Deepwater Rice Mutant Populations for Some Morpho-Physiological and Agronomic Traits

Unlike most current rice cultivars, rice produced in the deepwater habitat may live for at least a month in water depths exceeding 50 cm. In this experiment, 30 M6 populations developed by irradiation of Laksmidigha rice seeds utilizing 200 Gy dose of gamma rays were assessed based on morpho-physiological and agronomic traits. Six mutant populations exhibited noticeably longer leaves, with LD-200-1-1-2-6 being the only mutant population to have noticeably more grain weight/hill than the parent. But none of the mutant populations had significantly wider leaf breadth at any of the three points of the flag leaf and average as well. Six mutant populations LD-200-1-3-3-3, LD-200-1-3-3-4, LD-200-1-3-3-5, LD-200-1-3-2-1, LD-200-1-1-2-1 and LD-200-1-1-2-6 produced significantly higher grain yield/hill which also had significantly longer panicle lengths, internode lengths and heavier 1000-grain weight than the parent. It was discovered through a correlation analysis that grain weight/hill was positively and significantly connected with panicle length and 1000-grain weight, whereas its association with internode distance was positively but not significantly correlated. But the correlation of internode distance with 1000-grain weight was significantly positive. The six mutant populations that significantly increased grain yield/hill compared to the parent also had higher levels of total chlorophyll and chlorophyll "a" in their flag leaves. In anatomical studies of roots, it was found that all the 21 cross sections showed damaged cortex with different degrees except LD-200-1-3-3-7 and LD-200-1-1-2-5. Even the parent grown in Chamber-1 showed minimum cortex damage. Also, the grain yield of these two mutant populations did not differ significantly from the parent although chlorophyll “a” and total chlorophyll contents were much higher.

Identificação de famílias mutantes de arroz com tolerância ao frio

Abstract The objective of this work was to characterize chilling tolerance in rice mutant families of the M4 generation, at the seedling stage. Two experiments were carried out: chilling tolerance was evaluated in 43 mutant families, in the 'BRS Querência' original genotype, and in 19 commercial genotypes. In Experiment II, 8 mutant families from Experiment I, 'BRS Querência', and a mutant of the M5 generation were tested. In both experiments, seedlings were evaluated under two conditions: 10°C for seven days and 25°C for seven days. In Experiment I, the induced mutations in rice led to varied responses in chilling tolerance traits, with some M4 mutant families outperforming the original genotype. Experiment II highlighted the impact of mutations on chilling-tolerance, particularly in terms of leaf discoloration and plant recovery. Mutant families of the M4 generation differ from the original genotype 'BRS Querência' in chilling tolerance at the seedling stage. The mutant families M36, M54, and M56 and 'BRS Querência' show genetic similarity, indicating a lack of chilling tolerance during the seedling stage. The mutant families M17, M21, M22, and M26 are promising for rice breeding programs because they present chilling tolerance. The M30 mutant family exhibits the best performance for all analyzed traits, indicating chilling tolerance at the seedling stage.

Field screening for blast resistance gene donors, among rice mutant lines of Mira-1

Rice blast disease, caused by Pyricularia grisea was one of the most destructive fungal diseases in rice worldwide. Therefore, resistance breeding requires continuous efforts to enrich the reservoir of resistance rice lines to effectively tackle the disease. Mutation induction of the Mira-1 rice variety by gamma rays has been conducted, and M6 generation of rice mutant lines was used for this experiment. The rice mutant lines were selected from a total 112 number of rice mutant lines and it had been planted at Cikembar, Sukabumi Village. Cikembar is a hot spot area of blast disease which was used by researchers for the identification of rice lines resistant to blast, and plants were naturally infected. Disease progress was recorded as leaf and neck blast from 0 to 9 ( highly resistant to highly susceptible ). The results showed that disease severity was significantly different in the rice mutant lines studied and it was consistent and not affected by the plant arrangement in the field. Five rice mutant lines showed high resistance to blast disease, and it found 25 numbers of rice mutant lines scored 1 or resistant to blast disease, meanwhile, their wild type of Mira-1 rice variety showed susceptibility to leaf blast and neck blast diseases respectively. The agronomic traits of rice mutant lines were better than their wild type of Mira-1 rice variety. It was found that Mi-37, Mi-77, the Mi-82 rice mutant lines were the best lines for the gene donors of rice-resistant mutant line.

Development of Rice Mutants with Enhanced Resilience to Drought Stress and Their Evaluation by Lab Assay, Field, and Multivariate Analysis.

Drought is one of the foremost devastating abiotic stresses reported for rice crops. To improve the productivity of rice, diversity is being enlarged by induced mutation using a source of gamma rays. But this type of mutation rarely results in fruitful products because the chances of getting the desired mutant are very low. The present study aimed to evaluate the rice mutants against drought or osmotic stress. In this study, three experiments were conducted that comprised of seventy-one mutants originating from different doses of gamma rays (Cs137) along with parent RICF-160 and commercial variety (Kainat) were tested. In the first experiment, germination and seedling attributes were calculated under control and osmotic stress conditions created by using 16% (0.6 MPa) polyethylene glycol (PEG-6000). Results revealed that all the mutants exhibited significant (p < 0.01) responses to PEG-induced osmotic stress. Principal component biplot analysis (PCBA) revealed the first seventeen cumulative PCs with eigenvalues >1 contributed 88%. It was noted that the germination percentage (GP), germination rate (GR), coefficient velocity of germination (CVG), and seed vigor (SV) contributed maximum and positively in PC1. Results showed the highest germination percentage (GP) at 48 hrs in mutant NMSF-11 (88.9%) followed by NMSf-38 (73.3%). Similarly, the germination rate (GR) and coefficient velocity of germination (CVG) were measured highest in NMSF-11 (9.7 and 118.1%), respectively. In stress conditions, the mutants NMSF-35 and NMSF-36 depicted the highest GP, GR, and CVG. The maximum seed vigor (SV), shoot length (SL), root length (RL), and fresh weight (FW) were observed in mutants NMSF-50 and NMSF-51 under both conditions, whereas the mutants NMSF-59, NMSF-60, NMSF-64, and NMSF-67 showed lower values for SV, SL, RL, and FW. In the second experiment, a field trial was conducted at the Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, in two control and stress sets. A bit different trend was observed among all mutants for agronomic parameters under both conditions. In the third experiment, biochemical profiling was done in Marker Assisted Breeding (MAB) Lab-1, Plant Breeding and Genetics Division. A significant variation was seen in enzymatic antioxidants and chlorophyll content in both control and stress conditions. Under control conditions, the ascorbate peroxidase (APX) content was observed higher in mutant NMSF-49 (106.07 Units/g. f. wt.). In comparison with the stress, the ascorbate peroxidase activity was higher in NMSF-41 (82.34 Units/g. f. wt.). Catalase (CAT) activity was observed maximum in NMSF-29 (17.54 Units/g. f. wt.) and NMSF-40 (14.17 Units/g. f. wt.) under control and stress conditions, respectively. Peroxidase (POD) activity was observed maximum in NMSF-51 (22.55 Units/g. f. wt. and 10.84 Units/g. f. wt.) under control and stress conditions, respectively. In conclusion, to fit in the changing climate conditions for resilient rice crop production, the promising mutant lines may be used to transfer the desirable drought-tolerant/drought-resistant genes in rice germplasm.

Assessment of mutant rice genotypes on growth cycle length and response to reduced water availability

Assessment of mutant rice genotypes on growth cycle length and response to reduced water availability

Multi-omics analysis identifies EcCS4 is negatively regulated in response to phytotoxin isovaleric acid stress in Echinochloa crus-galli.

Knowledge of herbicidal targets is critical for weed management and food safety. The phytotoxin isovaleric acid (ISA) is effective against weeds with a broad spectrum, carries low environmental risks, and is thus an excellent herbicide lead. However, the biochemical and molecular mechanisms underlying the action of ISA remain unclear. Multi-omics data showed that acetyl coenzyme A (acetyl-CoA) was the key affected metabolite, and that citrate synthase (CS) 4 was substantially down-regulated under ISA treatment in Echinochloa crus-galli leaves. In particular, the transcript level of EcCS4 was the most significantly regulated among the six genes involved in the top 10 different pathways. The EcCS4 encodes a protein of 472 amino acids and is localized to the cell membrane and mitochondria, similar to the CS4s of other plants. The protein content of EcCS4 was down-regulated after ISA treatment at 0.5 h. ISA markedly inhibited the CS4 activity in vitro in a concentration-dependent manner (IC50 = 41.35 μM). In addition, the transgenic rice plants overexpressing EcCS4 (IC50 = 111.8 mM for OECS4-8 line) were more sensitive, whereas loss-of-function rice mutant lines (IC50 = 746.5 mM for oscs4-19) were more resistant to ISA, compared to wild type (WT) plants (IC50 = 355.6 mM). CS4 was first reported as a negative regulator of plant responses to ISA. These results highlight that CS4 is a candidate target gene for the development of novel herbicides and for breeding herbicide-resistant crops. © 2023 Society of Chemical Industry.

Plasma membrane-localized H+-ATPase OsAHA3 functions in saline-alkaline stress tolerance in rice.

A novel function of plasma membrane-localized H+-ATPase, OsAHA3, was identified in rice, which is involved in saline-alkaline tolerance and specifically responds to high pH during saline-alkaline stress. Saline-alkaline stress causes serious damage to crop production on irrigated land. Plants suffer more severe damage under saline-alkaline stress than under salinity stress alone. Plasma membrane-localized proton (H+) pump (H+-ATPase) is an important enzyme that controls plant growth and development by catalyzing H+ efflux and enabling effective charge balance. Many studies about the role of plasma membrane H+-ATPases in saline-alkaline stress tolerance have been reported in Arabidopsis, especially on the AtAHA2 (Arabidopsis thaliana H+-ATPase 2) gene; however, whether and how plasma membrane H+-ATPases play a role in saline-alkaline stress tolerance in rice remain unknown. Here, using the activation-tagged rice mutant pool, we found that the plasma membrane-localized H+-ATPase OsAHA3 (Oryza sativa autoinhibited H+-ATPase 3) is involved in saline-alkaline stress tolerance. Activation-tagged line 29 (AC29) was identified as a loss-of-function mutant of OsAHA3 and showed more severe growth retardation under saline-alkaline stress with high pH than under salinity stress. Moreover, osaha3 loss-of-function mutants generated by CRISPR/Cas9 system exhibited saline-alkaline stress sensitive phenotypes; staining of leaves with nitrotetrazolium blue chloride (NBT) and diaminobenzidine (DAB) revealed more reactive oxygen species (ROS) accumulation in osaha3 mutants. OsAHA3-overexpressing plants showed increased saline-alkaline stress tolerance than wild-type plants. Tissue-specific expression analysis revealed high expression level of OsAHA3 in leaf, sheath, glume, and panicle. Overall, our results revealed a novel function of plasma membrane-localized H+-ATPase, OsAHA3, which is involved in saline-alkaline stress tolerance and specifically responds to high pH.

Comparative characterisation of structural, physicochemical and digestive properties of rice starches isolated from novel high‐amylose mutants

SummaryNovel high‐amylose rice mutants with unique starch properties were developed from a low‐amylose rice variety. The objective of this study was to explore the impacts of apparent amylose content and amylopectin structure on the physical and nutritional properties of rice starch by comparing novel mutants with conventional rice varieties. The rice mutants demonstrated a specific amylopectin characteristic, indicating an extremely lower portion of short chains (15.2%–16.5%) than the other rice varieties (27.3%–31.1%). The starch gel prepared from the rice mutant exhibited significantly higher compressive and breaking stress than the other high‐amylose rice variety with a higher apparent amylose content, indicating that amylopectin characteristics markedly influenced the starch gel structure. The rice mutant demonstrated the highest content of undigested starch after 120 min of digestion in raw starch (50.5%) and starch gel (53.0%). The starch from newly developed rice mutants were found to have markedly high resistance to digestion due to its amylopectin structure and formation of harder gel.

Rice OsANN9 Enhances Drought Tolerance through Modulating ROS Scavenging Systems.

Drought is a critical abiotic stress which leads to crop yield and a decrease in quality. Annexins belong to a multi-gene family of calcium- and lipid-binding proteins and play diverse roles in plant growth and development. Herein, we report a rice annexin protein, OsANN9, which in addition to regular annexin repeats and type-II Ca2+ binding sites, also consists of a C2H2-type zinc-finger domain. We found that the expression of OsANN9 was upregulated by polyethylene glycol (PEG) or water-deficient treatment. Moreover, plants that overexpressed OsANN9 had increased survival rates under drought stress, while both OsANN9-RNAi and osann9 mutants showed sensitivity to drought. In addition, the overexpression of OsANN9 increased superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities, which regulate reactive oxygen species homeostasis. Collectively, these findings indicate that OsANN9 may function as a positive regulator in response to drought stress by modulating antioxidant accumulation. Interestingly, the setting rates of osann9 mutant rice plants significantly decreased in comparison to wild-type plants, suggesting that OsANN9 might be involved in other molecular mechanisms in the rice seed development stage.

Advanced Mutant Line Developed from Fatemadhan Shows Salinity Tolerance at both Seedling and Reproductive Stages

The generation of high-yielding rice mutants and their assessment under salt stress offers a great possibility to isolate salt tolerant line(s) with desired trait of interest. Two separate experiments were conducted at the seedling and reproductive stages of rice to assess the level of salinity tolerance of few advanced high-yielding rice mutants. In the first experiment, rice seedlings were grown under hydroponic conditions and 14-day-old seedlings were subjected to salt stress (EC=10 dS/m; 7 days). Salt stress caused significant reduction in root and shoot length and biomass and leaf chlorophyll content; however, a little reduction was found in the mutant Line-1. In contrast, a sharp increase in shoot Na+/K+ ratio was found in all the genotypes except, Binadhan-10, FL-478 and the mutant Line-1, which exhibited little increased ratio. The second experiment involved exposure of plant to salt stress (EC=10 dS/m) for three weeks at the late booting stage in a sizable plastic tub filled with field soil. Salt stress resulted in a significant decrease in yield and yield attributing traits in all the genotypes except Binadhan-10. Grain yield per panicle was found significantly positive correlation with panicle length, the number of filled grains per panicle, and 100-seed weight under both control and salt stress conditions. Based on the studied traits and stress tolerance indices, Binadhan-10 and mutant Line-1 categorized as salt tolerant and rest of the genotypes were categorized as susceptible, which is also evident from the biplot of principal component analysis. Considering the results from both of the experiments, mutant Line-1 was found tolerant genotype at both seedling and reproductive stage. However, further studies are required to determine the genetic issues controlling the salinity tolerance in mutant Line-1 and the high-yield potential of mutant Line-65 under control condition in a way to develop salt tolerant and high-yielding rice varieties, respectively.

SMALL PLANT AND ORGAN 1 (SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice

Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.

OsALB3 Is Required for Chloroplast Development by Promoting the Accumulation of Light-Harvesting Chlorophyll-Binding Proteins in Rice

ALBINO3 (ALB3) protein functions in the insertion and assembly of thylakoid membrane protein complexes and plays a critical role for chloroplast development in Arabidopsis. However, the biological function of ALB3 homologs in rice, OsALB3, remains elusive. Here, we identified a rice mutant, yellow leaf and lethal1 (yll1), that displayed yellow leaves and died at the seedling stage. The content of chlorophyll in yll1, compared with wild type, was significantly decreased. Transmission electron microscopy observation shows that the chloroplast of yll1 lacks thylakoid membranes. The causal mutation, which is located in OsALB3, was isolated by Mutmap+ combined with a simple mutation filtering process. Knockout of OsALB3 leads to yellow leaves and seedling lethality, mimicking the phenotype of yll1. OsALB3 is widely expressed and OsALB3 is chloroplast-localized. Moreover, the content of light-harvesting chlorophyll-binding proteins in yll1 is reduced. Together, our study demonstrated the essential role of OsALB3 in chloroplast development and provided clues to the possible conserved molecular function of ALB3 in rice.

Disruption of the rice ALS1 localized in chloroplast causes seedling-lethal albino phenotype

Chloroplasts are the organelles responsible for photosynthesis and regulate normal plant growth. Although translation elongation factors play important roles in chloroplast development, functional studies of chloroplast translation elongation factors in higher plants remain very sparse. Here, we obtained a rice mutant exhibiting seedling-lethal albino phenotype and named it albino and lethal seedling 1 (als1). Consistently, low content of photosynthetic pigments, malformed chloroplasts and defective photosynthesis were observed in als1 mutant leaves. Map-based cloning experiment showed that als1 mutant had a T base insertion in Os02g0595700, causing a frame shift and premature stop codon. ALS1 encoded a GTP-binding protein EF-Tu, which acts as a translation elongation factor in chloroplast protein translation. ALS1 was found to be expressed throughout plant with highest expression level in young leaves. Moreover, ALS1 was located in chloroplast, whereas the truncated als1 could not normally be located in chloroplast. Additionally, the ALS1 mutation significantly influenced the expression of downstream genes, such as genes relevant to chlorophyll biosynthesis, photosynthesis as well as chloroplast development. These results show that ALS1 acts as a key regulator of chloroplast development and plant growth.

GW9 determines grain size and floral organ identity in rice.

Grain weight is an important determinant of grain yield. However, the underlying regulatory mechanisms for grain size remain to be fully elucidated. Here, we identify a rice mutant grain weight 9 (gw9), which exhibits larger and heavier grains due to excessive cell proliferation and expansion in spikelet hull. GW9 encodes a nucleus-localized protein containing both C2H2 zincfinger (C2H2-ZnF) and VRN2-EMF2-FIS2-SUZ12 (VEFS) domains, serving as a negative regulator of grain size and weight. Interestingly, the non-frameshift mutations in C2H2-ZnF domain result in increased plant height and larger grain size, whereas frameshift mutations in both C2H2-ZnF and VEFS domains lead to dwarf and malformed spikelet. These observations indicated the dual functions of GW9 in regulating grain size and floral organ identity through the C2H2-ZnF and VEFS domains, respectively. Further investigation revealed the interaction between GW9 and the E3 ubiquitin ligase protein GW2, with GW9 being the target of ubiquitination by GW2. Genetic analyses suggest that GW9 and GW2 function in a coordinated pathway controlling grain size and weight. Our findings provide a novel insight into the functional role of GW9 in the regulation of grain size and weight, offering potential molecular strategies for improving rice yield.

Discrepancies in resistant starch and starch physicochemical properties between rice mutants similar in high amylose content.

The content of resistant starch (RS) was considered positively correlated with the apparent amylose content (AAC). Here, we analyzed two Indica rice mutants, RS111 and Zhedagaozhi 1B, similar in high AAC and found that their RS content differed remarkably. RS111 had higher RS3 content but lower RS2 content than Zhedagaozhi 1B; correspondingly, cooked RS111 showed slower digestibility. RS111 had smaller irregular and oval starch granules when compared with Zhedagaozhi 1B and the wild type. Zhedagaozhi 1B showed a B-type starch pattern, different from RS111 and the wild type, which showed A-type starch. Meantime, RS111 had more fa and fb1 but less fb3 than Zhedagaozhi 1B. Both mutants showed decreased viscosity and swelling power when compared with the parents. RS111 had the lowest viscosity, and Zhedagaozhi 1B had the smallest swelling power. The different fine structures of amylopectin between RS111 and Zhedagaozhi 1B led to different starch types, gelatinization properties, paste viscosity, and digestibility. In addition to enhancing amylose content, modifications on amylopectin structure showed great potent in breeding rice with different RS2 and RS3 content, which could meet the increasing needs for various rice germplasms.

MiRiQ Database: A Platform forIn Silico Rice Mutant Screening.

Genetic studies using mutant resources have significantly contributed to elucidating plant gene function. Massive mutant libraries sequenced by next-generation sequencing technology facilitate mutant identification and functional analysis of genes of interest. Here, we report the creation and release of an open-access database (https://miriq.agr.kyushu-u.ac.jp/index.php), called Mutation-induced Rice in Kyushu University (MiRiQ), designed for in silico mutant screening based on a whole-genome-sequenced mutant library. This database allows any user to easily find mutants of interest without laborious efforts such as large-scale screening by PCR. The initial version of the MiRiQ database (version 1.0) harbors a total of 1.6 million single-nucleotide variants (SNVs) and InDels of 721 M1 plants that were mutagenized by N-methyl-N-nitrosourea treatment of the rice cultivar Nipponbare (Oryza sativa ssp. japonica). The SNVs were distributed among 87% of all 35,630 annotated protein-coding genes of the Nipponbare genome and were predicted to induce missense and nonsense mutations. The MiRiQ database provides built-in tools, such as a search tool by keywords and JBrowse for mutation searches. Users can request mutant seeds in the M2 or M3 generations from a request form linked to this database. We believe that the availability of a wide range of gene mutations in this database will benefit the plant science community and breeders worldwide by accelerating functional genomic research and crop improvement.