Rice Genes Research Articles

OsbHLH6, a basic helix-loop-helix transcription factor, confers arsenic tolerance and root-to-shoot translocation in rice.

Arsenic (As) is extremely toxic to plants, posing a serious concern for food safety. Identification of genes responsive to As is significative for figuring out this issue. Here, we identified a bHLH transcription factor OsbHLH6 that was involved in mediating the processes of As tolerance, uptake, and root-to-shoot translocation in rice. The expression of OsbHLH6 gene was strongly induced after 3 and 48 h of arsenite [As(III)] treatment. The OsbHLH6-overexpressed transgenic rice (OE-OsbHLH6) was sensitive to, while the knockout mutant of OsbHLH6 gene (Osbhlh6) was tolerant to As(III) stress by affecting the contents of reactive oxygen species (ROS) and non-protein thiols (NPT), etc. Knockout of OsbHLH6 gene increased significantly the As concentration in roots, but decreased extensively As accumulation in shoots, compared to that in OE-OsbHLH6 and WT plants. The transcripts of phytochelatins (PCs) synthetase encoding genes OsPCS1 and OsPCS2, as well as As(III) transporter encoding genes OsLsi1 and OsABCC1 were greatly abundant in Osbhlh6 mutants than in OE-OsbHLH6 and WT plants under As(III) stress. In contrast, the expression of OsLsi2 gene was extensively suppressed by As(III) in Osbhlh6 mutants. OsbHLH6 acted as a transcriptional activator to bind directly to the promoter and regulate the expression of OsPrx2 gene that encodes a peroxidase precursor. Moreover, overexpression of OsbHLH6 gene resulted in significant change of expression ofamounts of abiotic stress-related genes, which might partially contribute to the As sensitivity of OE-OsbHLH6 plants. These findings may broaden our understanding of the molecular mechanism of OsbHLH6-mediated As response in rice and provide novel useful genes for rice As stress-resistant breeding.

Downregulation of the rice HRS1 HOMOLOG3 transcriptional repressor gene due to N deficiency directly co-activates ammonium and phosphate transporter genes.

Rice HRS1 HOMOLOG3 (OsHHO3) acts as a transcriptional repressor of AMMONIUM TRANSPORTER1 (OsAMT1) genes in rice; thus, reduced OsHHO3 expression in nitrogen (N)-deficient environments promotes ammonium uptake. In this study, we show that OsHHO3 also functions as a repressor of a specific subset of phosphate (Pi) transporter (PT) genes involved in the uptake and root-to-shoot translocation of Pi, including OsPT2, OsPT4, and OsPHO1;1. Consistently, disruption of OsHHO3 increased Pi uptake and Pi contents in shoots and roots, while overexpression of OsHHO3 generated the opposite effects. Furthermore, phosphorus (P) deficiency slightly decreased OsHHO3 expression, upregulating a specific subset of PT genes. However, N deficiency was more effective than P deficiency in suppressing OsHHO3 expression in roots, and unlike N deficiency-dependent activation of PT genes under the control of OsHHO3, the P deficiency-dependent activation of OsAMT1 genes was minimal. Interestingly, the simultaneous deficiency of both N and P promoted the OsHHO3-regulated expression of PT genes more significantly than the deficiency of either N or P, but diminished the expression of genes regulated by OsPHR2, a master regulator of Pi starvation-responsive transcriptional activation. Phenotypic analysis revealed that the inactivation and overexpression of OsHHO3 improved and reduced plant growth, respectively, under N-deficient and P-deficient conditions. These results suggest that OsHHO3 regulates a specific subset of PT genes independently of OsPHR2-mediated regulation and plays a critical role in the adaptation to diverse N and P environments.

Further enhancement of cold tolerance in rice seedlings by Piriformospora indica collaborating with plant growth-promoting bacteria: Evidence from the antioxidant defense, osmoregulation, photosynthesis, and related genes

As the global population continues to grow, so does the demand for food. However, cold stress due to global climate change greatly threatens the safe production of rice. Piriformospora indica plays a pivotal role as a functional microbiota in improving cold tolerance in rice. However, the addition of P. indica alone has a limited effect. In this study, an attempt was made to select plant growth-promoting bacteria (Agrobacterium rhizogenes and Bacillus subtilis) as helper bacteria to help P. indica function better and further enhance rice cold tolerance. Under cold stress, the co-addition of the three beneficial microorganisms significantly increased the biomass, photosynthetic performance indicators, osmoregulatory substance contents, and antioxidant enzyme activities of rice. P. indica and helper bacteria significantly reduced the cold stress-induced increases in malondialdehyde content and electrolyte leakage rate in rice leaves and triggered a substantial upregulation of cold-tolerant genes in rice. This suggests that P. indica and helper bacteria can synergistically improve the cold resistance of rice. The findings of the research offer a conceptual foundation and practical assistance for enhancing rice's resilience to cold temperatures.

Exploring the molecular mechanisms of rice blast resistance and advances in breeding for disease tolerance.

Rice blast, caused by the fungus Magnaporthe oryzae (syn. Pyricularia oryzae), is a major problem in rice cultivation and ranks among the most severe fungal diseases. Cloning and identifying resistance genes in rice, coupled with a comprehensive examination of the interaction between M. oryzae and rice, may provide insights into the mechanisms of rice disease resistance and facilitate the creation of new rice varieties with improved germplasm. These efforts are essential for protecting food security. This review examines the discovery of genes that confer resistance or susceptiblity to M. oryzae in rice over the last decade. It also discusses how knowledge of molecular mechanisms has been used in rice breeding and outlines key strategies for creating rice varieties resistant to this disease. The strategies discussed include gene pyramiding, molecular design breeding, editing susceptibility genes, and increasing expression of resistance genes through pathogen challenge. We address the prospects and challenges in breeding for rice blast resistance, emphasizing the need to fully exploit germplasm resources, employ cutting-edge methods to identify new resistance genes, and develop innovative breeding cultivars. Additionally, we underscore the importance of understanding the molecular basis of rice blast resistance and developing novel cultivars with broad-spectrum disease resistance.

Genome-wide association study reveals effect of nsSNPs on candidate genes in rice during iron deficiency.

Resource-poor areas with moisture deficit lands following aerobic and direct seeded rice (DSR) methods of cultivation face severe problems of iron deficiency. In this study, Bengal and Assam Aus rice panel was phenotyped at the seedling stage using an iron-deprived hydroponic medium for various shoot and root traits. A novel iron deficiency scoring scale was used to classify the tolerance reaction and could range anywhere between 0 and 9, indicating the most tolerant and susceptible, respectively. The GWAS results identified four putative candidate genes; OsFLA for number of leaves and shoot length, OsBIDK1 for root traits; average diameter, volume, biomass, projected area, and surface area, OsHPL3 for chlorophyll index of the third leaf and AKR2B (XBOS252) was for Fe score, (which was earlier reported in relation to Xa21). The nsSNP (nsSNPs) variations in these gene sequences were used to group the panel and identify superior haplotypes and donors. BR16 was identified as a superior donor, with higher chlorophyll index and shoot length than RA23, also higher values for root traits like root average diameter, root volume, root projected area and root surface area followed by Shete Bhado. The impact of identified nsSNPs on protein structure and stability was investigated. The conserved domains detected in the mutated proteins of the superior haplotypes are very informative, highlighting that natural selection favors abiotic stress tolerant variants in resource poor areas. Thus, justifying our choice of Aus landraces for association mapping of Fe deficiency tolerant genes in rice.

Comprehensive analysis of transcription factor binding sites and expression profiling of rice pathogenesis related genes (OsPR1)

Pathogenesis-related (PR) proteins, found in plants, play a crucial role in responding to both biotic and abiotic stresses and are categorized into 17 distinct families based on their properties and functions. We have conducted a phylogenetic analysis of OsPR1 genes (rice PR1 genes) in conjunction with 58 putative PR1 genes identified in Brachypodium distachyon, Hordeum vulgare, Brassica rapa, and Zea mays through BLASTP predictions. We extensively investigated the responses of the remaining 11 rice PR1 genes, using OsPR1a as a reference, under various stress conditions, including phytohormone treatments (salicylic acid and brassinosteroid [BR]), wounding, and heat stress (HS). In rice, of the 32 predicted OsPR1 genes, 12 have been well-characterized for their roles in disease resistance, while the functions of the remaining genes have not been studied extensively. In our study, we selected an additional 11 OsPR1 genes for further analysis and constructed a phylogenetic tree based on the presence of a 10-amino-acid-long conserved motif within these proteins. The phylogenetic analysis revealed that both OsPR1a from earlier studies and OsPR1-74 from our current study belong to the same clade. These genes consistently exhibit upregulation in response to diverse stress treatments such as biotic stress and abiotic stresses such as heat, drought, and salinity, indicating their potential roles in enhancing stress tolerance in rice. Significantly, this study delves into the previously unexplored role of OsPR1 genes in responding to Brassinosteroid (BR) and heat stress (HS) treatments, confirming their involvement in stress responses through qRT-PCR analysis. We found that seven genes were upregulated by EBR treatment. During heat stress (HS), six and seven genes were upregulated at 1hand 4h HS, respectively. The remaining genes OsPR1-22 and OsPR1-75 were upregulated at 1h but downregulated at 4h HS and under EBR treatment. In contrast, OsPR1-76 was upregulated at both 1h and 4h HS, but downregulated under EBR treatment. Promoters of PR1 genes in rice and other crops are rich in transcription factor binding sites (TFBSs) and feature a conserved Cysteine-rich secretory protein (SCP or CAP) motif. This study advances our understanding of PR1 gene regulation and its potential to enhance stress tolerance in rice.

Unleashing the Potential of CRISPR/Cas9 Genome Editing for Yield-Related Traits in Rice

Strategies to enhance rice productivity in response to global demand have been the paramount focus of breeders worldwide. Multiple factors, including agronomical traits such as plant architecture and grain formation and physiological traits such as photosynthetic efficiency and NUE (nitrogen use efficiency), as well as factors such as phytohormone perception and homeostasis and transcriptional regulation, indirectly influence rice grain yield. Advances in genetic analysis methodologies and functional genomics, numerous genes, QTLs (Quantitative Trait Loci), and SNPs (Single-Nucleotide Polymorphisms), linked to yield traits, have been identified and analyzed in rice. Genome editing allows for the targeted modification of identified genes to create novel mutations in rice, avoiding the unintended mutations often caused by random mutagenesis. Genome editing technologies, notably the CRISPR/Cas9 system, present a promising tool to generate precise and rapid modifications in the plant genome. Advancements in CRISPR have further enabled researchers to modify a larger number of genes with higher efficiency. This paper reviews recent research on genome editing of yield-related genes in rice, discusses available gene editing tools, and highlights their potential to expedite rice breeding programs.

Insights into Genes Encoding LEA_1 Domain-Containing Proteins in Cyperus esculentus, a Desiccation-Tolerant Tuber Plant

LEA_1 domain-containing proteins constitute a class of late-embryogenesis-abundant proteins that are highly hydrophilic and predominantly accumulate in mature seeds. Though LEA_1 proteins have been proven to be essential for seed desiccation tolerance and longevity, little information is available on their roles in non-seed storage organs. In this study, a first genome-wide characterization of the LEA_1 gene family was conducted in tigernut (Cyperus esculentus L., Cyperaceae), whose underground tubers are desiccation tolerant with a moisture content of less than 6%. Five family members identified in tigernut are comparative to four to six found in seven other Cyperaceae plants, but relatively more than three reported in Arabidopsis. Further comparison of 125 members from 29 plant species supports early divergence of the LEA_1 family into two phylogenetic groups before angiosperm radiation, and gene expansion in tigernut was contributed by whole-genome duplications occurring after the split with the eudicot clade. These two phylogenetic groups could be further divided into six orthogroups in the momocot clade, five of which are present in tigernut and the remaining one is Poaceae specific. Frequent structural variation and expression divergence of paralogs were also observed. Significantly, in contrast to seed-preferential expression of LEA_1 genes in Arabidopsis, rice, and maize, transcriptional profiling and qRT-PCR analysis revealed that CeLEA1 genes have evolved to predominantly express in tubers, exhibiting a seed desiccation-like accumulation during tuber development. Moreover, CeLEA1 transcripts in tubers were shown to be considerably more than that of their orthologs in purple nutsedge, another Cyperaceae plant producing desiccation-sensitive tubers. These results imply species-specific activation and key roles of CeLEA1 genes in the acquisition of desiccation tolerance of tigernut tubers as observed in orthodox seeds. Our findings not only improve the understanding of lineage-specific evolution of the LEA_1 family, but also provide valuable information for further functional analysis and genetic improvement in tigernut.

Genome‐Wide Association Study Revealed the Genetics of Seed Vigour Traits in Rice (Oryza sativa L.)

ABSTRACTA crucial phenotypic attribute for breeding rice for direct seeded condition is rapid uniform germination and build‐up of biomass during the initial period of seedling establishment. Seed vigour constitutes such traits that have gained potential to meet the requirements of breeding for direct seeded rice. In the present study, a set of 295 markers, including 215 candidate gene‐derived markers covering all chromosome, was used to discover the casual alleles for eight rice seed vigour‐related traits. Using a mixed linear model, the study identified 99 significant associations for seed vigour traits. Many associated markers originated from diverse candidate genes in rice. Notably, alleles from genes like RSR1, OsSRS3 and OsSWEET15 exhibited pleiotropic effects, influencing multiple seed vigour traits. This discovery underscores the potential of certain genes to impact various facets of seed vigour simultaneously. The new candidate gene markers associated with seed vigour traits may be utilized to incorporate variable alleles for seed vigour traits through marker‐assisted breeding programmes. Markers identified to be closely associated with more than one trait have significant application in the simultaneous improvement of multiple traits.

OsPDIL1-5: dual role in promoting growth and development while modulating drought stress tolerance in rice (Oryza sativa L.).

Drought tolerance and plant growth are critical factors affecting rice yield, and identifying genes that can enhance these traits is essential for improving crop resilience and productivity. Using a growth-depressed and drought-tolerant (gddt) mutant of the indica rice variety Huanghuazhan (HHZ) generated by radiation mutagenesis, we discovered a novel gene, GDDT, which plays a dual role in plant biology: it acts as a positive regulator of growth and development, but as a negative regulator of drought resistance. The gddt mutant displayed a marked reduction in plant growth and seed setting rate, yet exhibited an unexpected advantage in terms of drought tolerance. Our research revealed that the enhanced drought tolerance of the gddt mutant is primarily due to a decrease in stomatal size, density, and aperture, which reduces water loss, and an activation of the reactive oxygen species (ROS) scavenging system, which helps protect the plant from oxidative stress. These physiological changes are observed both under drought conditions and in normal growth conditions. This discovery highlights the importance of GDDT as a pleiotropic gene with significant implications for both plant growth and drought resistance. Through map-based cloning, we determined that the protein disulfide isomerase-like (PDIL) gene OsPDIL1-5 is the GDDT gene. The protein encoded by this gene was localized to the endoplasmic reticulum, consistent with its predicted function. Our findings provide new insights into the role of PDIL genes in rice and suggest that further study of GDDT could lead to a better understanding of how these genes contribute to the complex interplay between plant growth, development, and stress responses. This knowledge could pave the way for the development of rice varieties that are more resilient to drought, thereby increasing crop yields and ensuring food security in water-limited environments.

An efficient CRISPR-Cas12a-mediated MicroRNA knockout strategy in plants.

In recent years, the CRISPR-Cas9 nuclease has been used to knock out MicroRNA (miRNA) genes in plants, greatly promoting the study of miRNA function. However, due to its propensity for generating small insertions and deletions, Cas9 is not well-suited for achieving a complete knockout of miRNA genes. By contrast, CRISPR-Cas12a nuclease generates larger deletions, which could significantly disrupt the secondary structure of pre-miRNA and prevent the production of mature miRNAs. Through the case study of OsMIR390 in rice, we confirmed that Cas12a is a more efficient tool than Cas9 in generating knockout mutants of a miRNA gene. To further demonstrate CRISPR-Cas12a-mediated knockout of miRNA genes in rice, we targeted nine OsMIRNA genes that have different spaciotemporal expression and have not been previously investigated via genetic knockout approaches. With CRISPR-Cas12a, up to 100% genome editing efficiency was observed at these miRNA loci. The resulting larger deletions suggest Cas12a robustly generated null alleles of miRNA genes. Transcriptome profiling of the miRNA mutants, as well as phenotypic analysis of the rice grains revealed the function of these miRNAs in controlling gene expression and regulating grain quality and seed development. This study established CRISPR-Cas12a as an efficient tool for genetic knockout of miRNA genes in plants.

OsCNGC7 modulates calcium dynamics and accelerates leaf senescence in rice

Calcium plays a crucial role in regulating plant senescence. However, the specific effects of increased intranuclear calcium versus cytoplasmic calcium on aging remain unclear. Cyclic nucleotide-gated channels (CNGCs), which manage Ca2⁺ levels in plant cells, are particularly significant in this context. These channels are known to relocate between the nuclear envelope and the plasma membrane in response to stress and developmental signals. Through this movement, CNGCs help regulate the balance of cytosolic and intranuclear Ca2⁺. In this study, we categorized the 16 CNGC genes in rice into five subgroups. OsCNGCs are notably expressed in leaves, especially during the reproductive stage. Both OsCNGC6 and OsCNGC7 exhibit dual localization to the plasma membrane and the nuclear envelope. Knockdown of OsCNGC7 led to reduced levels of Ca2⁺ and K⁺ in plants. Conversely, yeast expressing the OsCNGC7 gene showed increased sensitivity to Ca2⁺. Additionally, while the [Ca2⁺]cyt was maintained at relatively low levels in both wild-type and OsCNGC7-RNAi lines, the fluorescence intensity was significantly higher in OsCNGC7-overexpressing lines, particularly in the nucleus of root tips. Overexpression of OsCNGC7 resulted in enhanced stomatal opening and accelerated leaf senescence from the tillering stage to grain filling in rice. Treatment with MeJA rapidly induced OsCNGC7 expression, while knockdown of OsCNGC7 delayed both MeJA-induced and dark-induced leaf senescence. Further analysis revealed that OsCNGC7 interacts with OsKAT2 and OsALMT2. In conclusion, our findings highlight the distinct roles of OsCNGCs in regulating senescence. This knowledge could provide new strategies for manipulating plant senescence and enhancing crop productivity.

Heading Date 3a Stimulates Tiller Bud Outgrowth in Oryza sativa L. through Strigolactone Signaling Pathway.

Heading date 3a (Hd3a, a FLOWERING LOCUS T (FT) ortholog from rice) is well known for its important role in rice (Oryza sativa L.), controlling floral transition under short-day (SD) conditions. Although the effect of Hd3a on promoting branching has been found, the underlying mechanism remains largely unknown. In this report, we overexpressed an Hd3a and BirAG (encoding a biotin ligase) fusion gene in rice, and found that early flowering and tiller bud outgrowth was promoted in BHd3aOE transgenic plants. On the contrary, knockout of Hd3a delayed flowering and tiller bud outgrowth. By using the BioID method, we identified multiple Hd3a proximal proteins. Among them, D14, D53, TPR1, TPR2, and TPRs are central components of the strigolactone signaling pathway, which has an inhibitory effect on rice tillering. The interaction between Hd3a, on the one hand, and D14 and D53 was further confirmed by the bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H), and co-immunoprecipitation (Co-IP) methods. We also found that Hd3a prevented the degradation of D53 induced by rac-GR24 (a strigolactone analog) in rice protoplasts. RT-qPCR assay showed that the expression levels of genes involved in strigolactone biosynthesis and signal transduction were altered significantly between WT and Hd3a overexpression (Hd3aOE) or mutant (hd3a) plants. OsFC1, a downstream target of the strigolactone signaling transduction pathway in controlling rice tillering, was downregulated significantly in Hd3aOE plants, whereas it was upregulated in hd3a lines. Collectively, these results indicate that Hd3a promotes tiller bud outgrowth in rice by attenuating the negative effect of strigolactone signaling on tillering and highlight a novel molecular network regulating rice tiller outgrowth by Hd3a.

Elevated proline and melatonin alter the methylation pattern in the promoter of their biosynthesis genes in rice

Salt stress upregulates osmoprotectants proline and melatonin in plants, and their exogenous application under salt stress can protect them from stress. While melatonin-induced plant epigenetic reprogramming is known in plants, such a mechanism is yet to be identified in the case of proline. The studies conducted so far used proline and melatonin along with one or more stress factors to look into their stress-alleviating effects. We investigated the impact of externally applied proline and melatonin on the methylation of promoter sequences of proline and melatonin biosynthesis genes in 14-day-old rice plants using a combination of biochemical, bioinformatics, and molecular techniques. Our findings demonstrate that exogenously applied proline and melatonin elevate endogenous levels of these compounds in rice, mimicking stress conditions in plants, as the biochemical assays corroborated the activation of antioxidant systems, particularly ascorbate peroxidase (APX) and catalase (CAT). Bioinformatics analysis unveiled multiple stress-responsive transcription factor binding sites on gene promoters associated with proline and melatonin biosynthesis pathways. Restriction analysis using the isoschizomer pair MspI/HpaII revealed distinct cytosine methylations at the restriction sites on the promoters analyzed in plants treated with proline and melatonin compared to the control. Differential methylation identified in the promoter sequences were matching with the biosynthesis of proline and melatonin and also the antioxidant enzyme levels. These observations are consistent with previous transcriptome data of proline and melatonin biosynthesis genes, providing insights into underlying regulatory mechanisms of proline and melatonin biosynthesis, their role in epigenome control during abiotic stress, and the evolution of various stress-tolerant varieties.

Sequence-based analysis of the rice CAMTA family: haplotype and network analyses

The calmodulin-binding transcription activator (CAMTA) family contributes to stress responses in many plant species. The Oryza sativa ssp. japonica genome harbors seven CAMTA genes; however, intraspecific variation and functional roles of this gene family have not been determined. Here, we comprehensively evaluated the structure and characteristics of the CAMTA genes in japonica rice using bioinformatics approaches and RT-qPCR. Within the CAMTA gene and promoter sequences, 527 single nucleotide polymorphisms were retrieved from 3,024 rice accessions. The CAMTA genes could be subdivided into 5–14 haplotypes. Association analyses between haplotypes and phenotypic traits, such as grain weight and salt stress parameters, identified phenotypic differences between rice subpopulations harboring different CAMTA haplotypes. Co-expression analyses and the identification of CAMTA-specific binding motifs revealed candidate genes regulated by CAMTA. A Gene Ontology functional enrichment analysis of 690 co-expressed genes revealed that CAMTA genes have key roles in defense responses. An interaction analysis identified 30 putative CAMTA interactors. Three genes were identified in co-expression and interaction network analyses, suggesting that they are potentially regulated by CAMTAs. Based on all information obtained together with the phenotypes of the CRISPR-Cas9 knockout mutant lines of three OskCAMTA genes generated, CAMTA1 likely plays important roles in the response to salt stress in rice. Overall, our findings suggest that the CAMTA gene family is involved in development and the salt stress response and reveal candidate target genes, providing a basis for further functional characterization.

Assessment of antioxidant properties in selected pigmented and non-pigmented rice (Oryza sativa L.) germplasm and determination of its association with Rc gene haplotypes

BackgroundAntioxidant properties of rice provide various health benefits due to its ability to inhibit cellular oxidation. Antioxidant content of rice is known to be linked with the pericarp pigmentation. The Rc gene of rice (Os07g0211500) codes for a basic helix-loop-helix (bHLH) protein, acting as a transcriptional factor in regulating proanthocyanidin biosynthesis. The current study was carried out to evaluate the variation of antioxidant properties in a selected panel of rice accessions and assess the possibility of using haplotypes defined based on the Rc gene to predict pericarp pigmentation and antioxidant content in rice.ResultsThirty-two rice accessions were evaluated for grain pericarp colour and antioxidant properties; total phenolic content (TPC), total flavonoids (TFC), proanthocyanidins (PAC) and radical scavenging activity (RSA). The parameters TPC, TFC and PAC showed significant positive correlation with RSA (r > 0.69; P < 0.01). The study panel showed a wide variation for antioxidant properties and rice accessions such as Sudu Heenati, Deweraddiri, Madathawalu, Masuran, Ld 368, At 311, Kalu Heenati, Bw 272-6B, Pokkali, At 362 and Wanni Dahanala exhibited profound potential with respect to antioxidant properties. Based on three-target sites previously reported as critical for the function of the coded bHLH protein (an A/C SNP at 1,353-bp, a 1-bp insertion/deletion at 1,388-bp, and a 14-bp insertion/deletion at 1,408-1,421-bp positioned in the mRNA corresponding to the exon 6 of rice Rc gene), three haplotypes were defined (H1-H3). Pigmentation of the rice pericarp could be successfully explained based on the defined haplotypes (H1 (C/G/+): red, and H2 (A/G/+) and H3 (C/G/-): white), and the H1 haplotype corresponded to a significantly (P < 0.05) higher TPC, TFC, PAC and RSA compared to the other haplotypes.ConclusionsThe studied rice accessions showed a significant variation with respect to antioxidant properties. Haplotype H1 defined based on the three-target sites in the exon 6 of Rc gene can detect rice accessions with red pigmented pericarp and high antioxidant properties effectively. Hence, its use can be recommended as an alternative to biochemical assays for screening during rice breeding programs.

Integration Linkage Mapping and Comparative Transcriptome Analysis to Dissect the Genetic Basis of Rice Salt Tolerance Associated with the Germination Stage.

Soil salinity poses a serious threat to rice production. The salt tolerance of rice at the germination stage is one of the major determinants of stable stand establishment, which is very important for direct seeding in saline soil. The complexity and polygenic nature of salt tolerance have limited the efficiency of discovering and cloning key genes in rice. In this study, an RIL population with an ultra-high-density genetic map was employed to investigate the salt-tolerant genetic basis in rice, and a total of 20 QTLs were detected, including a major and stable QTL (qRCL3-1). Subsequently, salt-specific DEGs from a comparative transcriptome analysis were overlaid onto annotated genes located on a stable QTL interval, and eight putative candidate genes were further identified. Finally, from the sequence alignment and variant analysis, OsCam1-1 was confirmed to be the most promising candidate gene for regulating salinity tolerance in rice. This study provides important information for elucidating the genetic and molecular basis of rice salt tolerance at the germination stage, and the genes detected here will be useful for improvements in rice salt tolerance.

Molecular Characteristics and Expression Patterns of Carotenoid Cleavage Oxygenase Family Genes in Rice (Oryza sativa L.)

Carotenoid cleavage oxygenases (CCOs) cleave carotenoid molecules to produce bioactive products that influence the synthesis of hormones such as abscisic acid (ABA) and strigolactones (SL), which regulate plant growth, development, and stress adaptation. Here, to explore the molecular characteristics of all members of the OsCCO family in rice, fourteen OsCCO family genes were identified in the genome-wide study. The results revealed that the OsCCO family included one OsNCED and four OsCCD subfamilies. The OsCCO family was phylogenetically close to members of the maize ZmCCO family and the Sorghum SbCCO family. A collinearity relationship was observed between OsNCED3 and OsNCED5 in rice, as well as OsCCD7 and OsNCED5 between rice and Arabidopsis, Sorghum, and maize. OsCCD4a and OsCCD7 were the key members in the protein interaction network of the OsCCO family, which was involved in the catabolic processes of carotenoids and terpenoid compounds. miRNAs targeting OsCCO family members were mostly involved in the abiotic stress response, and RNA-seq data further confirmed the molecular properties of OsCCO family genes in response to abiotic stress and hormone induction. qRT-PCR analysis showed the differential expression patterns of OsCCO members across various rice organs. Notably, OsCCD1 showed relatively high expression levels in all organs except for ripening seeds and endosperm. OsNCED2a, OsNCED3, OsCCD1, OsCCD4a, OsCCD7, OsCCD8a, and OsCCD8e were potentially involved in plant growth and differentiation. Meanwhile, OsNCED2a, OsNCED2b, OsNCED5, OsCCD8b, and OsCCD8d were associated with reproductive organ development, flowering, and seed formation. OsNCED3, OsCCD4b, OsCCD4c, OsCCD8b, and OsCCD8c were related to assimilate transport and seed maturation. These findings provide a theoretical basis for further functional analysis of the OsCCO family.

Exploring Lignin Biosynthesis Genes in Rice: Evolution, Function, and Expression.

Lignin is nature's second most abundant vascular plant biopolymer, playing significant roles in mechanical support, water transport, and stress responses. This study identified 90 lignin biosynthesis genes in rice based on phylogeny and motif constitution, and they belong to PAL, C4H, 4CL, HCT, C3H, CCoAOMT, CCR, F5H, COMT, and CAD families. Duplication events contributed largely to the expansion of these gene families, such as PAL, CCoAOMT, CCR, and CAD families, mainly attributed to tandem and segmental duplication. Microarray data of 33 tissue samples covering the entire life cycle of rice suggested fairly high PAL, HCT, C3H, CCoAOMT, CCR, COMT, and CAD gene expressions and rather variable C4H, 4CL, and F5H expressions. Some members of lignin-related genes (OsCCRL11, OsHCT1/2/5, OsCCoAOMT1/3/5, OsCOMT, OsC3H, OsCAD2, and OsPAL1/6) were expressed in all tissues examined. The expression patterns of lignin-related genes can be divided into two major groups with eight subgroups, each showing a distinct co-expression in tissues representing typically primary and secondary cell wall constitutions. Some lignin-related genes were strongly co-expressed in tissues typical of secondary cell walls. Combined HPLC analysis showed increased lignin monomer (H, G, and S) contents from young to old growth stages in five genotypes. Based on 90 genes' microarray data, 27 genes were selected for qRT-PCR gene expression analysis. Four genes (OsPAL9, OsCAD8C, OsCCR8, and OsCOMTL4) were significantly negatively correlated with lignin monomers. Furthermore, eleven genes were co-expressed in certain genotypes during secondary growth stages. Among them, six genes (OsC3H, OsCAD2, OsCCR2, OsCOMT, OsPAL2, and OsPAL8) were overlapped with microarray gene expressions, highlighting their importance in lignin biosynthesis.

Research Progress on Photoperiod Gene Regulation of Heading Date in Rice.

Heading date is a critical physiological process in rice that is influenced by both genetic and environmental factors. The photoperiodic pathway is a primary regulatory mechanism for rice heading, with key florigen genes Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T1) playing central roles. Upstream regulatory pathways, including Hd1 and Ehd1, also significantly impact this process. This review aims to provide a comprehensive examination of the localization, cloning, and functional roles of photoperiodic pathway-related genes in rice, and to explore the interactions among these genes as well as their pleiotropic effects on heading date. We systematically review recent advancements in the identification and functional analysis of genes involved in the photoperiodic pathway. We also discuss the molecular mechanisms underlying rice heading date variation and highlight the intricate interactions between key regulatory genes. Significant progress has been made in understanding the molecular mechanisms of heading date regulation through the cloning and functional analysis of photoperiod-regulating genes. However, the regulation of heading date remains complex, and many underlying mechanisms are not yet fully elucidated. This review consolidates current knowledge on the photoperiodic regulation of heading date in rice, emphasizing novel findings and gaps in the research. It highlights the need for further exploration of the interactions among flowering-related genes and their response to environmental signals. Despite advances, the full regulatory network of heading date remains unclear. Further research is needed to elucidate the intricate gene interactions, transcriptional and post-transcriptional regulatory mechanisms, and the role of epigenetic factors such as histone methylation in flowering time regulation. This review provides a detailed overview of the current understanding of photoperiodic pathway genes in rice, setting the stage for future research to address existing gaps and improve our knowledge of rice flowering regulation.