Rice最新文献

The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.

Background: The growth and development of rice (Oryza sativa L.) are affected by multiple factors, such as ROS homeostasis and utilization of iron. Here, we demonstrate that OsUGE2, a gene encoding a UDP-glucose 4-epimerase, controls growth and development by regulating reactive oxygen species (ROS) and iron (Fe) level in rice. Knockout of this gene resulted in impaired growth, such as dwarf phenotype, weakened root growth and pale yellow leaves. Biochemical analysis showed that loss of function of OsUGE2 significantly altered the proportion and content of UDP-Glucose (UDP-Glc) and UDP-Galactose (UDP-Gal). Cellular observation indicates that the impaired growth may result from decreased cell length. More importantly, RNA-sequencing analysis showed that knockout of OsUGE2 significantly influenced the expression of genes related to oxidoreductase process and iron ion homeostasis. Consistently, the content of ROS and Fe are significantly decreased in OsUGE2 knockout mutant. Furthermore, knockout mutants of OsUGE2 are insensitive to both Fe deficiency and hydrogen peroxide (H₂O₂) treatment, which further confirmed that OsUGE2 control rice growth possibly through Fe and H₂O₂ signal. Collectively, these results reveal a new pathway that OsUGE2 could affect growth and development via influencing ROS homeostasis and Fe level in rice.

Chilling is a major abiotic stress affecting rice growth, development and geographical distribution. Plant vacuolar processing enzymes (VPEs) contribute to the seed storage protein processing and mediate the programmed cell death by abiotic and biotic stresses. However, little is known about the roles of plant VPEs in cold stress responses and tolerance regulation. Here, we found that OsVPE2 was a chilling-responsive gene. The early-indica rice variety Xiangzaoxian31 overexpressing OsVPE2 was more sensitive to chilling stress, whereas the OsVPE2-knockout mutants generated by the CRISPR-Cas9 technology exhibited significantly enhanced chilling tolerance at the seedling stage without causing yield loss. Deficiency of OsVPE2 reduces relative electrolyte leakage, accumulation of toxic compounds such as reactive oxygen species and malondialdehyde, and promotes antioxidant enzyme activities under chilling stress conditions. It was indicated that OsVPE2 mediated the disintegration of vacuoles under chilling stress, accompanied by the entry of swollen mitochondria into vacuoles. OsVPE2 suppressed the expression of genes that have a positive regulatory role in antioxidant process. Moreover, haplotype analysis suggested that the natural variation in the OsVPE2 non-coding region may endow OsVPE2 with different expression levels, thereby probably conferring differences in cold tolerance between japonica and indica sub-population. Our results thus reveal a new biological function of the VPE family in regulating cold resistance, and suggest that the gene editing or natural variations of OsVPE2 can be used to create cold tolerant rice varieties with stable yield.

Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2-4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.

HEI10 is a conserved E3 ubiquitin ligase involved in crossover formation during meiosis, and is thus essential for both male and female gamete development. Here, we have discovered a novel allele of HEI10 in rice that produces a truncated HEI10 protein missing its N-terminal RING domain, namely sh1 (shorter hei10 1). Unlike previously reported hei10 null alleles that are completely sterile, sh1 exhibits complete male sterility but retains partial female fertility. The causative sh1 mutation is a 76 kb inversion between OsFYVE4 and HEI10, which breaks the integrity of both genes. Allelic tests and complementation assays revealed that the gamete developmental defects of sh1 were caused by disruption of HEI10. Further studies demonstrated that short HEI10 can correctly localise to the nucleus, where it could interact with other proteins that direct meiosis; expressing short HEI10 in hei10 null lines partially restores female fertility. Our data reveal an intriguing mutant allele of HEI10 with differential effects on male and female fertility, providing a new tool to explore similarities and differences between male and female meiosis.

Background

With the increasing frequency of climatic anomalies, high temperatures and long-term rain often occur during the rice-harvesting period, especially for early rice crops in tropical and subtropical regions. Seed dormancy directly affects the resistance to pre-harvest sprouting (PHS). Therefore, in order to increase rice production, it is critical to enhance seed dormancy and avoid yield losses to PHS. The elucidation and utilization of the seed dormancy regulation mechanism is of great significance to rice production. Preliminary results indicated that the OsMKKK62-OsMKK3-OsMPK7/14 module might regulate ABA sensitivity and then control seed dormancy. The detailed mechanism is still unclear.

Results

The overexpression of OsMKK3 resulted in serious PHS. The expression levels of OsMKK3 and OsMPK7 were upregulated by ABA and GA at germination stage. OsMKK3 and OsMPK7 are both located in the nucleus and cytoplasm. The dormancy level of double knockout mutant mkk3/mft2 was lower than that of mkk3, indicating that OsMFT2 functions in the downstream of MKK3 cascade in regulating rice seeds germination. Biochemical results showed that OsMPK7 interacted with multiple core ABA signaling components according to yeast two-hybrid screening and luciferase complementation experiments, suggesting that MKK3 cascade regulates ABA signaling by modulating the core ABA signaling components. Moreover, the ABA response and ABA responsive genes of mpk7/14 were significantly higher than those of wild-type ZH11 when subjected to ABA treatment.

Conclusion

MKK3 cascade mediates the negative feedback loop of ABA signal through the interaction between OsMPK7 and core ABA signaling components in rice.

Abstract

Reactive oxygen species (ROS) act as a group of signaling molecules in rice functioning in regulation of development and stress responses. Respiratory burst oxidase homologues (Rbohs) are key enzymes in generation of ROS. However, the role of the nine Rboh family members was not fully understood in rice multiple disease resistance and yield traits. In this study, we constructed mutants of each Rboh genes and detected their requirement in rice multiple disease resistance and yield traits. Our results revealed that mutations of five Rboh genes (RbohA, RbohB, RbohE, RbohH, and RbohI) lead to compromised rice blast disease resistance in a disease nursery and lab conditions; mutations of five Rbohs (RbohA, RbohB, RbohC, RbohE, and RbohH) result in suppressed rice sheath blight resistance in a disease nursery and lab conditions; mutations of six Rbohs (RbohA, RbohB, RbohC, RbohE, RbohH and RbohI) lead to decreased rice leaf blight resistance in a paddy yard and ROS production induced by PAMPs and pathogen. Moreover, all Rboh genes participate in the regulation of rice yield traits, for all rboh mutants display one or more compromised yield traits, such as panicle number, grain number per panicle, seed setting rate, and grain weight, resulting in reduced yield per plant except rbohb and rbohf. Our results identified the Rboh family members involved in the regulation of rice resistance against multiple pathogens that caused the most serious diseases worldwide and provide theoretical supporting for breeding application of these Rbohs to coordinate rice disease resistance and yield traits.

Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.

Background

The leaf epidermis plays an important role in the transmission of light and the regulation of water and gas exchange, which influences the photosynthesis of mesophyll cells. Small papillae (SP) are one of the important structural elements of the leaf epidermis. The mechanism of the effect that small papillae have on rice leaf photosynthetic performance remains unclear.

Results

In this study, a small papilla deficient 25 (spd25) mutant was isolated from japonica rice Longjin1. Small papillae were absent on the adaxial and abaxial leaf surfaces of the spd25 mutant and the silicon and cuticular wax content in the spd25 mutant leaves decreased. Map-based cloning and functional analysis revealed that SPD25, encoding a guanine nucleotide exchange factor for Rop, is a novel allele of OsRopGEF10. The spd25 mutant showed an increased water loss rate and reduced relative water content. The lower stomatal conductance in the spd25 mutant prevented water loss but decreased the intercellular CO₂ concentration and net assimilation rate. The fluorescence parameters showed that the inhibited CO₂ assimilation reaction feedback regulated the photochemical electron-transfer reaction, but the performance of Photosystem II was stable. Further analysis indicated that the excess light energy absorbed by the spd25 mutant was dissipated in the form of non-photochemical quenching to avoid photodamage through the optical properties of small papillae.

Conclusions

SPD25 regulates the development of small papillae on the surface of rice leaves, which play an important role in balancing photosynthetic gas exchange and water loss. This study deepens our understanding of the physiological mechanisms by which small papillae affect photosynthetic performance.

Plastid ribosomal proteins play a crucial role in the growth and development of plants, mainly in the gene expression and translation of key genes in chloroplasts. While some information is known about the regulatory processes of plastid ribosomal proteins in various plant species, there is limited knowledge about the underlying mechanisms in rice. In this study, ethyl methanesulfonate (EMS) mutagenesis was used to generate a new mutant called wlp3 (white leaf and panicle3), characterized by white or albino leaves and panicles, which exhibited this phenotype from the second leaf stage until tillering. Furthermore, after a certain period, the newly emerging leaves developed the same phenotype as the rice variety ZH11, while the albino leaves of wlp3 showed an incomplete chloroplast structure and significantly low chlorophyll content. A transition mutation (T to C) at position 380 was identified in the coding region of the LOC_Os03g61260 gene, resulting in the substitution of isoleucine by threonine during translation. WLP3 encodes the ribosomal L18 subunit, which is localized in the chloroplast. Complementation experiments confirmed that LOC_Os03g61260 was responsible for the albino phenotype in rice. WLP3 has high expression in the coleoptile, leaves at the three-leaf stage, and panicles at the heading stage. Compared to the wild-type (WT), wlp3 exhibited reduced chlorophyll synthesis and significantly decreased expression levels of genes associated with plastid development. Yeast two-hybrid (Y2H) analysis revealed that WLP3 interacts with other ribosomal subunits, to influence chloroplast development. These results contribute to a better understanding of the underlying molecular mechanisms of chloroplast development and plastid gene translation.