FLOURY ENDOSPERM15 encodes a glyoxalase I involved in compound granule formation and starch synthesis in rice endosperm

Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza

The genus Oryza is of utmost importance to human civilization as two of its species became agronomically productive and widely cultivated, and also because wild rice is a treasure trove of beneficial alleles that can be used for crop improvement. Most of the wild rice genotypes are known for their stress tolerance several times more than the domesticated rice varieties. In this study, we aimed to carry out an exhaustive genomic survey to identify glyoxalase I (GLYI) and glyoxalase II (GLYII) genes across the 11 rice genomes sequenced so far. Notably, we found the putatively functional metal-dependent GLYI and GLYII enzymes to be conserved throughout domestication and a few homologous pairs to have undergone beneficial mutations to drive positive selection, and thus, acquire newer functions. Interestingly, we also report four newly identified GLYII members in O. sativa subsp. japonica in addition to the three previously reported GLYII genes. The presence of different types of cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under various developmental processes besides stress adaptation. Publicly available data suggests the role of glyoxalase genes particularly in salinity stress in both wild and cultivated rice as is also confirmed through qRT-PCR. Interestingly, we found less accumulation of MG and concurrently higher enzymatic activity of GLYI and GLYII proteins in stressed seedlings of selected wild rice genotypes indicating that glyoxalases indeed contribute to the intrinsic stress tolerance of wild rice.

Natural variation of WBR7 confers rice high yield and quality by modulating sucrose supply in sink organs

Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7A (allele in cultivar Jin23B) compared with WBR7G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130)KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B)COM, resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality.

Genome-Wide Analysis and Expression Profiling of Glyoxalase Gene Families Under Abiotic Stresses in Cucumber (Cucumis sativus L.)

The glyoxalase pathway, consisting of glyoxalase I (GLYI) and glyoxalase II (GLYII), is an enzymatic system that converts cytotoxic methylglyoxal to non-toxic S-D-lactoylglutathione. Although the GLY gene family has been analyzed in Arabidopsis, rice, grape, cabbage, and soybean, cucumber studies are lacking. Here, we analyzed the cucumber GLY gene family, identifying 13 CsGLYI and 2 CsGLYII genes. Furthermore, we investigated the physicochemical properties, phylogenetic relationships, chromosomal localization and colinearity, gene structure, conserved motifs, cis-regulatory elements, and protein-protein interaction networks of the CsGLY family. They were primarily localized in the cytoplasm, chloroplasts, and mitochondria, with a minor presence in the nucleus. The classification of CsGLYI and CsGLYII genes into five classes closely resembled the homologous genes in Arabidopsis and soybean. Additionally, hormone-responsive elements dominated the promoter region of GLY genes, alongside light- and stress-responsive elements. The predicted interaction proteins of CsGLYIs and CsGLYIIs exerted a significant role in cellular respiration, amino acid synthesis, and metabolism, as well as methylglyoxal catabolism. In addition, the expression profiles of GLY genes were distinct in different tissues of cucumber as well as under diverse abiotic stresses. This study is conducive to the further exploration of the functional diversity among glyoxalase genes and the mechanisms of stress responses in cucumber.

Phenotypic Analysis and Gene Cloning of Rice Floury Endosperm Mutant wcr (White-Core Rice)

The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting in reduced grain weight. The total starch and amylose content remained unchanged, but the levels of the four component proteins in the mutant brown rice significantly decreased. Additionally, the milled rice (inner endosperm) showed a significant decrease in total starch and amylose content, accompanied by a nearly threefold increase in albumin content. The swelling capacity of mutant starch was reduced, and its chain length distribution was altered. The target gene was mapped on chromosome 5 within a 65 kb region. A frameshift mutation occurred due to an insertion of an extra C base in the second exon of the cyOsPPDKB gene, which encodes pyruvate phosphate dikinase. Expression analysis revealed that wcr not only affected genes involved in starch metabolism but also downregulated expression levels of genes associated with storage protein synthesis. Overall, wcr plays a crucial role as a regulator factor influencing protein synthesis and starch metabolism in rice grains.

Genome-wide association mapping of quantitative trait loci for chalkiness-related traits in rice (Oryza sativa L.)

Grain chalkiness directly affects the commercial value of rice. Genes related to chalkiness reported thus far have been discovered in mutants, but it has not been identified whether these genes can be used to improve rice quality by breeding. Therefore, discovering more quantitative trait loci (QTLs) or genes related to chalkiness in the rice germplasm is necessary. This study entails a genome-wide association study on the degree of endosperm chalkiness (DEC) and percentage of grains with chalkiness (PGWC) by combining 1.2 million single-nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Thirteen QTLs for DEC and nine for PGWC were identified, of which four were detected simultaneously for both DEC and PGWC; further, qDEC11/qPGWC11 was identified as the major QTL. By combining linkage disequilibrium analysis and SNP information, LOC_Os11g10170 was identified as the candidate gene for DEC. There were significant differences among the haplotypes of LOC_Os11g10170, and the Hap 1 of LOC_Os11g10170 was observed to reduce the DEC by 6.19%. The qRT-PCR results showed that the gene expression levels in accessions with high DEC values were significantly higher than those in accessions with low DEC values during days 21-42 after flowering, with a maximum at 28 days. These results provide molecular markers and germplasm resources for genetic improvement of the chalkiness-related traits in rice.

Rice LIKE EARLY STARVATION1 cooperates with FLOURY ENDOSPERM6 to modulate starch biosynthesis and endosperm development

In cereal grains, starch is synthesized by the concerted actions of multiple enzymes on the surface of starch granules within the amyloplast. However, little is known about how starch-synthesizing enzymes access starch granules, especially for amylopectin biosynthesis. Here, we show that the rice (Oryza sativa) floury endosperm9 (flo9) mutant is defective in amylopectin biosynthesis, leading to grains exhibiting a floury endosperm with a hollow core. Molecular cloning revealed that FLO9 encodes a plant-specific protein homologous to Arabidopsis (Arabidopsis thaliana) LIKE EARLY STARVATION1 (LESV). Unlike Arabidopsis LESV, which is involved in starch metabolism in leaves, OsLESV is required for starch granule initiation in the endosperm. OsLESV can directly bind to starch by its C-terminal tryptophan (Trp)-rich region. Cellular and biochemical evidence suggests that OsLESV interacts with the starch-binding protein FLO6, and loss-of-function mutations of either gene impair ISOAMYLASE1 (ISA1) targeting to starch granules. Genetically, OsLESV acts synergistically with FLO6 to regulate starch biosynthesis and endosperm development. Together, our results identify OsLESV-FLO6 as a non-enzymatic molecular module responsible for ISA1 localization on starch granules, and present a target gene for use in biotechnology to control starch content and composition in rice endosperm.

Role of methylglyoxal and glyoxalase in the regulation of plant response to heavy metal stress

KEY MESSAGE

Methylglyoxal and glyoxalase function a significant role in plant response to heavy metal stress. We update and discuss the most recent developments of methylglyoxal and glyoxalase in regulating plant response to heavy metal stress. Methylglyoxal (MG), a by-product of several metabolic processes, is created by both enzymatic and non-enzymatic mechanisms. It plays an important role in plant growth and development, signal transduction, and response to heavy metal stress (HMS). Changes in MG content and glyoxalase (GLY) activity under HMS imply that they may be potential biomarkers of plant stress resistance. In this review, we summarize recent advances in research on the mechanisms of MG and GLY in the regulation of plant responses to HMS. It has been discovered that appropriate concentrations of MG assist plants in maintaining a balance between growth and development and survival defense, therefore shielding them from heavy metal harm. MG and GLY regulate plant physiological processes by remodeling cellular redox homeostasis, regulating stomatal movement, and crosstalking with other signaling molecules (including abscisic acid, gibberellic acid, jasmonic acid, cytokinin, salicylic acid, melatonin, ethylene, hydrogen sulfide, and nitric oxide). We also discuss the involvement of MG and GLY in the regulation of plant responses to HMS at the transcriptional, translational, and metabolic levels. Lastly, considering the current state of research, we present a perspective on the future direction of MG research to elucidate the MG anti-stress mechanism and offer a theoretical foundation and useful advice for the remediation of heavy metal-contaminated environments in the future.

Starch Properties and Morphology of Eight Floury Endosperm Mutants in Rice

Besides increasing grain yield, improving rice (Oryza sativa L.) quality has been paid more and more attention recently. Cooking and eating quality (CEQ) is an important indicator of rice quality. Since CEQs are quantitative traits and challenging for measurement, efforts have mainly focused on two major genes, Wx and SSIIa. Chalkiness and floury endosperm significantly affect the eating quality of rice, leading to noticeable changes in CEQ. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and evaluating changes in CEQs indirectly facilitate the exploration of the minor genes controlling CEQ. In this study, eight mutants with different degrees of floury endosperm, generated through ethylmethane sulfonate (EMS) mutagenesis, were analyzed. These mutants exhibited wide variation in starch morphology and CEQs. Particularly, the z2 mutant showed spherical starch granules significantly increased rapid visco analyzer (RVA) indexes and urea swelling, while the z4 mutant displayed extremely sharp starch granules and significantly decreased RVA indexes and urea swelling compared to the wild type. Additionally, these mutants still maintained correlations with certain RVA profiles, suggesting that the genes PUL, which affect these indexes, may not undergo mutation. Cloning these mutated genes in the future, especially in z2 and z4, will enhance the genetic network of rice eating quality and hold significant importance for molecular marker-assisted breeding to improve rice quality.

Genome-wide analysis and expression profiling of glyoxalase gene families in oat (Avena sativa) indicate their responses to abiotic stress during seed germination

Abiotic stresses have deleterious effects on seed germination and seedling establishment, leading to significant crop yield losses. Adverse environmental conditions can cause the accumulation of methylglyoxal (MG) within plant cells, which can negatively impact plant growth and development. The glyoxalase system, which consists of the glutathione (GSH)-dependent enzymes glyoxalase I (GLX1) and glyoxalase II (GLX2), as well as the GSH-independent glyoxalase III (GLX3 or DJ-1), plays a crucial role in detoxifying MG. However, genome-wide analysis of glyoxalase genes has not been performed for one of the agricultural important species, oat (Avena sativa). This study identified a total of 26 AsGLX1 genes, including 8 genes encoding Ni²⁺-dependent GLX1s and 2 genes encoding Zn²⁺-dependent GLX1s. Additionally, 14 AsGLX2 genes were identified, of which 3 genes encoded proteins with both lactamase B and hydroxyacylglutathione hydrolase C-terminal domains and potential catalytic activity, and 15 AsGLX3 genes encoding proteins containing double DJ-1 domains. The domain architecture of the three gene families strongly correlates with the clades observed in the phylogenetic trees. The AsGLX1, AsGLX2, and AsGLX3 genes were evenly distributed in the A, C, and D subgenomes, and gene duplication of AsGLX1 and AsGLX3 genes resulted from tandem duplications. Besides the core cis-elements, hormone responsive elements dominated the promoter regions of the glyoxalase genes, and stress responsive elements were also frequently observed. The subcellular localization of glyoxalases was predicted to be primarily in the cytoplasm, chloroplasts, and mitochondria, with a few presents in the nucleus, which is consistent with their tissue-specific expression. The highest expression levels were observed in leaves and seeds, indicating that these genes may play important roles in maintaining leaf function and ensuring seed vigor. Moreover, based on in silico predication and expression pattern analysis, AsGLX1-7A, AsGLX2-5D, AsDJ-1-5D, AsGLX1-3D2, and AsGLX1-2A were suggested as promising candidate genes for improving stress resistance or seed vigor in oat. Overall, the identification and analysis of the glyoxalase gene families in this study can provide new strategies for improving oat stress resistance and seed vigor.

A mitochondrion-associated PPR protein, WBG1, regulates grain chalkiness in rice

Rice kernel quality has vital commercial value. Grain chalkiness deteriorates rice's appearance and palatability. However, the molecular mechanisms that govern grain chalkiness remain unclear and may be regulated by many factors. In this study, we identified a stable hereditary mutant, white belly grain 1 (wbg1), which has a white belly in its mature grains. The grain filling rate of wbg1 was lower than that of the wild type across the whole filling period, and the starch granules in the chalky part were oval or round and loosely arranged. Map-based cloning showed that wbg1 was an allelic mutant of FLO10, which encodes a mitochondrion-targeted P-type pentatricopeptide repeat protein. Amino acid sequence analysis found that two PPR motifs present in the C-terminal of WBG1 were lost in wbg1. This deletion reduced the splicing efficiency of nad1 intron 1 to approximately 50% in wbg1, thereby partially reducing the activity of complex I and affecting ATP production in wbg1 grains. Furthermore, haplotype analysis showed that WBG1 was associated with grain width between indica and japonica rice varieties. These results suggested that WBG1 influences rice grain chalkiness and grain width by regulating the splicing efficiency of nad1 intron 1. This deepens understanding of the molecular mechanisms governing rice grain quality and provides theoretical support for molecular breeding to improve rice quality.

New Fructokinase, OsFRK3, Regulates Starch Accumulation and Grain Filling in Rice

Plant fructokinase (FRK) guarantees the growth and development of higher plants by participating in carbohydrate metabolism. In this study, a new fructokinase, OsFRK3, was identified using bioinformatics analysis, enzyme assay, bacterial growth assay, and yeast complementation test. Then, we created OsFRK3 knockout transgenic lines (osfrk3-1 and osfrk3-2) by the CRISPR/Cas9 technology. We found that the 1000-grain weight decreased notably (approximately -3.6% and -6.1%, respectively) in osfrk3-1 and osfrk3-2. Evidently decreased grain width, grain thickness, and endosperm filling rate were detected in the osfrk3 mutants (osfrk3-1 and osfrk3-2) compared with those of the WT. In addition, the content of seed total starch was significantly decreased by 3.42 and 4.80% in osfrk3 lines, compared with that in the WT. The level of maltose was significantly reduced in the mutants, while that of sucrose and fructose was obviously increased in the mutants. The transcript levels of OsGBSS1, OsBEIIb, OsPFP1β, and OsAGPL1 were significantly decreased in the osfrk3 mutants. These results suggest that OsFRK3 may positively regulate the accumulation of starch through influencing the sugar metabolism.

Fructose-6-phosphate-2-kinase/fructose-2,6-bisphosphatase regulates energy metabolism and synthesis of storage products in developing rice endosperm

Starch accounts for about 80-85 % of the dry weight of grains and determines yield by impact on grain weight. And, the content and composition of starch also determine appearance, eating, cooking and nutritional quality of rice. By coordinating crucial reactions of the primary carbohydrate metabolism in all eukaryotes, fructose-2,6-bisphosphate (Fru-2,6-P₂) is a traffic signal in metabolism. However, the metabolic regulation of starch in plant sink tissues by Fru-2,6-P₂ remains unclear. Here we isolated rice mutant floury endosperm23 (flo23) which has opaque endosperm and anomalous compound starch grains (SGs). flo23 mutant grains had reduced contents of starch, lipids and proteins. Map-based cloning and genetic complementation experiments showed that FLO23 encodes a cytoplasmic Fructose-6-phosphate-2-kinase/Fructose-2,6-bisphosphatase (F2KP). Mutation of OsF2KP2 decreased Fru-2,6-P₂ content in endosperm cells, leading to drastically reduced phosphoenolpyruvate (PEP) and pyruvate contents and disordered glycolysis and energy metabolism. The results imply that OsF2KP2 participates in the glycolytic pathway by providing precursors and energy for synthesis of grain storage compounds.

Combined Effects of Different Alleles of FLO2, Wx and SSIIa on the Cooking and Eating Quality of Rice

The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in molecular breeding. However, their interactive effects on CEQ have not been fully understood. In this study, a recombinant inbred line (RIL) population was constructed by crossing the white-core mutant GM645 with the transparent phenotype of the japonica rice variety Tainung 67 (TN67). GM645 and TN67 contain different alleles of FLOURY ENDOSPERM2 (FLO2), Wx, and SSIIa. The effects of different allele combinations of FLO2, Wx, and SSIIa on the CEQ of rice were investigated. The inbred lines with the mutation allele flo2 had a significantly lower apparent amylose content (AAC), viscosity characteristics except for setback (SB), and gel texture properties compared to those lines with the FLO2 allele. The allelic combination of FLO2 and Wx significantly affected the AAC, breakdown (BD), and gel textural properties, which could explain most of the variations in those rice quality traits that were correlated with AAC. The allelic combination of FLO2 and SSIIa significantly affected the hot paste viscosity (HPV) and pasting temperature (PT). The Wx × SSIIa interaction had a significant effect on the PT. The interaction of FLO2, Wx and SSIIa significantly affected the AAC, cold paste viscosity (CPV), PT, and consistency viscosity (CS). These results highlight the important roles of these quality-related genes in regulating the CEQ of rice and provide new clues for rice-quality improvement by marker-assisted selection.

OsGLYI3, a glyoxalase gene expressed in rice seed, contributes to seed longevity and salt stress tolerance

The glyoxalase pathway plays a vital role in the chemical detoxification of methylglyoxal (MG) in biological systems. Our previous study suggested that OsGLYI3 may be effective in seed natural aging. In this study, the rice OsGLYI3 gene was cloned and characterized as specifically expressed in the seed. The accelerated aging (AA) treatment results indicated significant roles of OsGLYI3 in seed longevity and vigor, as the seeds of the transgenic lines with overexpressed and knocked-out OsGLYI3 exhibited higher and lower germination, respectively. The AA treatment also increased the superoxide dismutase (SOD) activity in the overexpressed transgenic seeds compared to the wild-type seeds yet lowered the SOD activity in the CRISPR/Cas9-derived transgenic rice lines. Rice OsGLYI3 was markedly upregulated in response to NaCl induced stress conditions. Compared to wild-type plants, overexpressed transgenic rice lines exhibited increased GLYI activity, decreased MG levels and improved salt stress tolerance, while CRISPR/Cas9 knockout transgenic rice lines showed decreased glyoxalase I activity, increased MG levels, and greater sensitivity to stress treatments with NaCl. Collectively, our results confirmed for the first time that OsGLYI3 is specifically expressed in rice seeds and contributes to seed longevity and salt stress tolerance.

Genetic control of grain appearance quality in rice

Grain appearance, one of the key determinants of rice quality, reflects the ability to attract consumers, and is characterized by four major properties: grain shape, chalkiness, transparency, and color. Mining of valuable genes, genetic mechanisms, and breeding cultivars with improved grain appearance are essential research areas in rice biology. However, grain appearance is a complex and comprehensive trait, making it challenging to understand the molecular details, and therefore, achieve precise improvement. This review highlights the current findings of grain appearance control, including a detailed description of the key genes involved in the formation of grain appearance, and the major environmental factors affecting chalkiness. We also discuss the integration of current knowledge on valuable genes to enable accurate breeding strategies for generation of rice grains with superior appearance quality.

The CBM48 domain-containing protein FLO6 regulates starch synthesis by interacting with SSIVb and GBSS in rice

FLO6 is involved in starch synthesis by interacting with SSIVb and GBSS in rice. Starch synthesized and stored in plastids including chloroplasts and amyloplasts plays a vital role in plant growth and provides the major energy for human diet. However, the molecular mechanisms by which regulate starch synthesis remain largely unknown. In this study, we identified and characterized a rice floury endosperm mutant M39, which exhibited defective starch granule formation in pericarp and endosperm, accompanied by the decreased starch content and amylose content. The abnormal starch accumulation in M39 pollen grains caused a significant decrease in plant fertility. Chloroplasts in M39 leaves contained no or only one large starch granule. Positional cloning combined with complementary experiment demonstrated that the mutant phenotypes were restored by the FLOURY ENDOSPERM6 (FLO6). FLO6 was generally expressed in various tissues, including leaf, anther and developing endosperm. FLO6 is a chloroplast and amyloplast-localized protein that is able to bind to starch by its carbohydrate-binding module 48 (CBM48) domain. Interestingly, we found that FLO6 interacted with starch synthase IVb (SSIVb) and granule-bound starch synthase (GBSSI and GBSSII). Together, our results suggested that FLO6 plays a critical role in starch synthesis through cooperating with several starch synthesis enzymes throughout plant growth and development.

Substandard starch grain4 may function in amyloplast development by influencing starch and lipid metabolism in rice endosperm

The amyloplast is a specialized plastid in rice endosperm cells where starch is synthesized and stored as starch granules (SGs). However, little is known about the molecular mechanism underlying amyloplast and SG development. In this study, a novel mutant (c134) demonstrating a floury endosperm with enlarged SGs and amyloplasts was identified. The floury endosperm was caused by rounder, loosely packed SG. Grain-quality profile and expression analysis showed reduced contents of total starch and amylose in the c134 mutant, as well as reduced expression of a number of genes involved in starch biosynthesis. Galactosyldiacylglycerol (GDG) content and fatty acid synthesis play important roles in plastid development, and in the c134 endosperm, an obvious decrease in GDG and various fatty acids was observed, with down-regulated expression of various genes involved in lipid biosynthesis. Furthermore, map-based cloning revealed an amino acid substitution (glycine to aspartic acid) in the substandard starch grain4 (SSG4) protein. The results of this study suggest that SSG4 influences the regulation of starch and lipid metabolism as well as amyloplast development, a finding that is useful for potential genetic improvement of rice grain quality in future starch and lipid breeding and biotechnology.

Genetic Control and High Temperature Effects on Starch Biosynthesis and Grain Quality in Rice

Grain quality is one of the key targets to be improved for rice breeders and covers cooking, eating, nutritional, appearance, milling, and sensory properties. Cooking and eating quality are mostly of concern to consumers and mainly determined by starch structure and composition. Although many starch synthesis enzymes have been identified and starch synthesis system has been established for a long time, novel functions of some starch synthesis genes have continually been found, and many important regulatory factors for seed development and grain quality control have recently been identified. Here, we summarize the progress in this field as comprehensively as possible and hopefully reveal some underlying molecular mechanisms controlling eating quality in rice. The regulatory network of amylose content (AC) determination is emphasized, as AC is the most important index for rice eating quality (REQ). Moreover, the regulatory mechanism of REQ, especially AC influenced by high temperature which is concerned as a most harmful environmental factor during grain filling is highlighted in this review.

FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice

As a staple food for more than half of the world's population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to their unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on floury endosperm in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential floury genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performances of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01226-z.

Rice FLOURY SHRUNKEN ENDOSPERM 5 Encodes a Putative Plant Organelle RNA Recognition Protein that Is Required for cis-Splicing of Mitochondrial nad4 Intron 1

BACKGROUND

The sequences of several important mitochondrion-encoded genes involved in respiration in higher plants are interrupted by introns. Many nuclear-encoded factors are involved in splicing these introns, but the mechanisms underlying this splicing remain unknown.

RESULTS

We isolated and characterized a rice mutant named floury shrunken endosperm 5 (fse5). In addition to having floury shrunken endosperm, the fse5 seeds either failed to germinate or produced seedlings which grew slowly and died ultimately. Fse5 encodes a putative plant organelle RNA recognition (PORR) protein targeted to mitochondria. Mutation of Fse5 hindered the splicing of the first intron of nad4, which encodes an essential subunit of mitochondrial NADH dehydrogenase complex I. The assembly and NADH dehydrogenase activity of complex I were subsequently disrupted by this mutation, and the structure of the mitochondria was abnormal in the fse5 mutant. The FSE5 protein was shown to interact with mitochondrial intron splicing factor 68 (MISF68), which is also a splicing factor for nad4 intron 1 identified previously via yeast two-hybrid (Y2H) assays.

CONCLUSION

Fse5 which encodes a PORR domain-containing protein, is essential for the splicing of nad4 intron 1, and loss of Fse5 function affects seed development and seedling growth.

From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor

Background

The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), to convert MG into D-lactate, which is further metabolized to pyruvate by D-lactate dehydrogenases (D-LDH). Since D-lactate formation occurs solely by the action of glyoxalase enzymes, its metabolism may be considered as the ultimate step of MG detoxification. By maintaining steady state levels of MG and other reactive dicarbonyl compounds, the glyoxalase pathway serves as an important line of defence against glycation and oxidative stress in living organisms. Therefore, considering the general role of glyoxalases in stress adaptation and the ability of Sorghum bicolor to withstand prolonged drought, the sorghum glyoxalase pathway warrants an in-depth investigation with regard to the presence, regulation and distribution of glyoxalase and D-LDH genes.

Result

Through this study, we have identified 15 GLYI and 6 GLYII genes in sorghum. In addition, 4 D-LDH genes were also identified, forming the first ever report on genome-wide identification of any plant D-LDH family. Our in silico analysis indicates homology of putatively active SbGLYI, SbGLYII and SbDLDH proteins to several functionally characterised glyoxalases and D-LDHs from Arabidopsis and rice. Further, these three gene families exhibit development and tissue-specific variations in their expression patterns. Importantly, we could predict the distribution of putatively active SbGLYI, SbGLYII and SbDLDH proteins in at least four different sub-cellular compartments namely, cytoplasm, chloroplast, nucleus and mitochondria. Most of the members of the sorghum glyoxalase and D-LDH gene families are indeed found to be highly stress responsive.

Conclusion

This study emphasizes the role of glyoxalases as well as that of D-LDH in the complete detoxification of MG in sorghum. In particular, we propose that D-LDH which metabolizes the specific end product of glyoxalases pathway is essential for complete MG detoxification. By proposing a cellular model for detoxification of MG via glyoxalase pathway in sorghum, we suggest that different sub-cellular organelles are actively involved in MG metabolism in plants.

Lose-of-Function of a Rice Nucleolus-Localized Pentatricopeptide Repeat Protein Is Responsible for the floury endosperm14 Mutant Phenotypes

BACKGROUND

The endosperm of rice (Oryza sativa) has been usually used for the study of starch synthesis. Although several related factors have been revealed, other unknown members remain to be identified, given that starch synthesis is a complicated and sophisticated process.

RESULTS

Here, we identified and characterized a new rice seed mutant, floury endosperm14 (flo14), which showed chalked endosperm and seed-lethal phenotypes. Map-based cloning indicated FLO14 encodes a novel P-family PPR protein which contains ten PPR motifs. Afterwards the gene was named OsNPPR3. Subcellular localization showed OsNPPR3 was targeted to nucleolus. Quantitative RT-PCR analysis demonstrated that OsNPPR3 was universally expressed in various tissues, with pronounced levels during rice endosperm development. Molecular analysis further suggested that OsNPPR3 was involved in the regulation of expression levels and splicing of a few genes in mitochondria.

CONCLUSION

The study demonstrates that the nucleolus-localized PPR protein is responsible for the flo14 mutant phenotypes through affecting nuclear and mitochondrial gene expression and splicing.

Methylglyoxal triggers the heat tolerance in maize seedlings by driving AsA-GSH cycle and reactive oxygen species-/methylglyoxal-scavenging system

Traditionally, methylglyoxal (MG) was looked upon as a toxic byproduct of cellular metabolism. Nowadays, MG has been found to be a novel signaling molecule. However, whether MG can trigger the heat tolerance in maize seedlings and the underlying mechanisms is still elusive. In this study, the maize seedlings irrigated with MG increased the survival percentage of seedlings under heat stress (HS), remitted a decrease in tissue vitality and an increase in electrolyte leakage, and reduced membrane lipid peroxidation, implying MG could trigger the heat tolerance of maize seedlings. The further experiments showed that MG drove the ascorbic acid (AsA)-glutathione (GSH) cycle by activating enzymes (glutathione reductase, monodehydroascorbate reductase, dehydroascorbate reductase, and ascorbate peroxidase) and increasing the contents of antioxidants (AsA and GSH) and the ratio of GSH/(GSH + oxidized glutathione) and AsA/(AsA + dehydroascorbate) under both non-HS and HS. Also, the reactive oxygen species (ROS)-scavenger system (catalase, guaiacol peroxidase, carotenoid, total phenols, and flavonoids) and MG-scavenger system (glyoxalase I and glyoxalas II) also were up-regulated in maize seedlings pretreated with MG under non-HS and HS. This work for the first time reported that MG could trigger the heat tolerance of maize seedlings by driving the AsA-GSH cycle and ROS-/MG-scavenging system.