GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development

Biological Roles of Lipids in Rice

Lipids are organic nonpolar molecules with essential biological and economic importance. While the genetic pathways and regulatory networks of lipid biosynthesis and metabolism have been extensively studied and thoroughly reviewed in oil crops such as soybeans, less attention has been paid to the biological roles of lipids in rice, a staple food for the global population and a model species for plant molecular biology research, leaving a considerable knowledge gap in the biological roles of lipids. In this review, we endeavor to furnish a current overview of the advancements in understanding the genetic foundations and physiological functions of lipids, including triacylglycerol, fatty acids, and very-long-chain fatty acids. We aim to summarize the key genes in lipid biosynthesis, metabolism, and transcriptional regulation underpinning rice's developmental and growth processes, biotic stress responses, abiotic stress responses, fertility, seed longevity, and recent efforts in rice oil genetic improvement.

Chalkiness and premature controlled by energy homeostasis in OsNAC02 Ko-mutant during vegetative endosperm development

BACKGROUND

Chalkiness is a common phenotype induced by various reasons, such as abiotic stress or the imbalance of starch synthesis and metabolism during the development period. However, the reason mainly for one gene losing its function such as NAC (TFs has a large family in rice) which may cause premature is rarely known to us.

RESULTS

The Ko-Osnac02 mutant demonstrated an obviously early maturation stage compared to the wild type (WT) with 15 days earlier. The result showed that the mature endosperm of Ko-Osnac02 mutant exhibited chalkiness, characterized by white-core and white-belly in mature endosperm. As grain filling rate is a crucial factor in determining the yield and quality of rice (Oryza sativa, ssp. japonica), it's significant that mutant has a lower amylose content (AC) and higher soluble sugar content in the mature endosperm. Interestingly among the top DEGs in the RNA sequencing of N2 (3DAP) and WT seeds revealed that the OsBAM2 (LOC_Os10g32810) expressed significantly high in N2 mutant, which involved in Maltose up-regulated by the starch degradation. As Prediction of Protein interaction showed in the chalky endosperm formation in N2 seeds (3 DAP), seven genes were expressed at a lower-level which should be verified by a heatmap diagrams based on DEGs of N2 versus WT. The Tubulin genes controlling cell cycle are downregulated together with the MCM family genes MCM4 ( ↓), MCM7 ( ↑), which may cause white-core in the early endosperm development. In conclusion, the developing period drastically decreased in the Ko-Osnac02 mutants, which might cause the chalkiness in seeds during the early endosperm development.

CONCLUSIONS

The gene OsNAC02 which controls a great genetic co-network for cell cycle regulation in early development, and KO-Osnac02 mutant shows prematurity and white-core in endosperm.

Insertion of a miniature inverted-repeat transposable element into the promoter of OsTCP4 results in more tillers and a lower grain size in rice

A class I PCF type protein, TCP4, was identified as a transcription factor associated with both grain size and tillering through a DNA pull-down-MS assay combined with a genome-wide association study. This transcription factor was found to have a significant role in the variations among the 533 rice accessions, dividing them into two main subspecies. A Tourist-like miniature inverted-repeat transposable element (MITE) was discovered in the promoter of TCP4 in japonica/geng accessions (TCP4M+), which was found to suppress the expression of TCP4 at the transcriptional level. The MITE-deleted haplotype (TCP4M-) was mainly found in indica/xian accessions. ChIP-qPCR and EMSA demonstrated the binding of TCP4 to promoters of grain reservoir genes such as SSIIa and Amy3D in vivo and in vitro, respectively. The introduction of the genomic sequence of TCP4M+ into different TCP4M- cultivars was found to affect the expression of TCP4 in the transgenic rice, resulting in decreased expression of its downstream target gene SSIIa, increased tiller number, and decreased seed length. This study revealed that a Tourist-like MITE contributes to subspecies divergence by regulating the expression of TCP4 in response to environmental pressure, thus influencing source-sink balance by regulating starch biosynthesis in rice.

Sucrose phosphate synthase 8 is required for the remobilization of carbon reserves in rice stems during grain filling

Carbon reserve remobilization in stems is closely related to rice grain filling. Sucrose phosphate synthase (SPS) is highly associated with carbon reserve remobilization. In this study, we investigated the expression pattern of SPS genes in various rice tissues, and found that SPS8 is the major SPS isoform in rice stems during the grain-filling stage. We then constructed sps8 mutants using the CRISPR/Cas9 system. The SPS activity of the sps8 mutants was markedly reduced in the stems. In addition, the sps8 mutants exhibited significant starch accumulation in stems. 14C-labelling experiments revealed that the remobilization of non-structural carbohydrates from rice stems to grains was impaired in the sps8 mutants. In the sps8 mutants, grain filling was delayed and yield decreased by 15% due to a reduced percentage of ripened grains. RNA sequencing and quantitative PCR analyses indicated that the genes involved in starch synthesis and degradation were up-regulated in the sps8 mutant stems. In addition, the activity of the enzymes involved in starch synthesis and degradation was increased in the sps8 stems. These results demonstrate that SPS8 is required for carbon reserve remobilization from rice stems to grains, and that its absence may enhance 'futile cycles' of starch synthesis and degradation in rice stems.

GS6.1 controls kernel size and plant architecture in rice

MAIN CONCLUSION

A novel QTL GS6.1 increases yield per plant by controlling kernel size, plant architecture, and kernel filling in rice. Kernel size and plant architecture are critical agronomic traits that greatly influence kernel yield in rice. Using the single-segment substitution lines (SSSLs) with an indica cultivar Huajingxian74 as a recipient parent and American Jasmine as a donor parent, we identified a novel quantitative trait locus (QTL), named GS6.1. Near isogenic line-GS6.1 (NIL-GS6.1) produces long and narrow kernels by regulating cell length and width in the spikelet hulls, thus increasing the 1000-kernel weight. Compared with the control, the plant height, panicles per plant, panicle length, kernels per plant, secondary branches per panicle, and yield per plant of NIL-GS6.1 are increased. In addition, GS6.1 regulates the kernel filling rate. GS6.1 controls kernel size by modulating the transcription levels of part of EXPANSINs, kernel filling-related genes, and kernel size-related genes. These results indicate that GS6.1 might be beneficial for improving kernel yield and plant architecture in rice breeding by molecular design.

Genetic dissection of grain morphology and yield components in a wheat line with defective grain filling

KEY MESSAGE

We identified stable QTL for grain morphology and yield component traits in a wheat defective grain filling line and validated genetic effects in a panel of cultivars using breeding-relevant markers. Grain filling capacity is essential for grain yield and appearance quality in cereal crops. Identification of genetic loci for grain filling is important for wheat improvement. However, there are few genetic studies on grain filling in wheat. Here, a defective grain filling (DGF) line wdgf1 characterized by shrunken grains was identified in a population derived from multi-round crosses involving nine parents and a recombinant inbreed line (RIL) population was generated from the cross between wdgf1 and a sister line with normal grains. We constructed a genetic map of the RIL population using the wheat 15K single nucleotide polymorphism chip and detected 25 stable quantitative trait loci (QTL) for grain morphology and yield components, including three for DGF, eleven for grain size, six for thousand grain weight, three for grain number per spike and two for spike number per m². Among them, QDGF.caas-7A is co-located with QTGW.caas-7A and can explain 39.4-64.6% of the phenotypic variances, indicating that this QTL is a major locus controlling DGF. Sequencing and linkage mapping showed that TaSus2-2B and Rht-B1 were candidate genes for QTGW.caas-2B and the QTL cluster (QTGW.caas-4B, QGNS.caas-4B, and QSN.caas-4B), respectively. We developed kompetitive allele-specific PCR markers tightly linked to the stable QTL without corresponding to known yield-related genes, and validated their genetic effects in a diverse panel of wheat cultivars. These findings not only lay a solid foundation for genetic dissection underlying grain filling and yield formation, but also provide useful tools for marker-assisted breeding.

OsMADS1 Regulates Grain Quality, Gene Expressions, and Regulatory Networks of Starch and Storage Protein Metabolisms in Rice

OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the 'Oat-like rice' mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1^Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1^Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding.

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.

Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice

Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes, GBSSI and SSIIa, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.

MATE transporter GFD1 cooperates with sugar transporters, mediates carbohydrate partitioning and controls grain-filling duration, grain size and number in rice

More than half of the world's food is provided by cereals, as humans obtain >60% of daily calories from grains. Producing more carbohydrates is always the final target of crop cultivation. The carbohydrate partitioning pathway directly affects grain yield, but the molecular mechanisms and biological functions are poorly understood, including rice (Oryza sativa L.), one of the most important food sources. Here, we reported a prolonged grain filling duration mutant 1 (gfd1), exhibiting a long grain-filling duration, less grain number per panicle and bigger grain size without changing grain weight. Map-based cloning and molecular biological analyses revealed that GFD1 encoded a MATE transporter and expressed high in vascular tissues of the stem, spikelet hulls and rachilla, but low in the leaf, controlling carbohydrate partitioning in the stem and grain but not in the leaf. GFD1 protein was partially localized on the plasma membrane and in the Golgi apparatus, and was finally verified to interact with two sugar transporters, OsSWEET4 and OsSUT2. Genetic analyses showed that GFD1 might control grain-filling duration through OsSWEET4, adjust grain size with OsSUT2 and synergistically modulate grain number per panicle with both OsSUT2 and OsSWEET4. Together, our work proved that the three transporters, which are all initially classified in the major facilitator superfamily family, could control starch storage in both the primary sink (grain) and temporary sink (stem), and affect carbohydrate partitioning in the whole plant through physical interaction, giving a new vision of sugar transporter interactome and providing a tool for rice yield improvement.

Understanding the regulation of cereal grain filling: The way forward

During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.

Nitrogen and potassium interactions optimized asynchronous spikelet filling and increased grain yield of japonica rice

Poor grain filling severely reduces rice yield. Fertilizers play a vital role in regulating grain filling, especially nitrogen (N) and potassium (K). In this field study we aimed to investigate the interactive effects of N and K on the asynchronous filling properties of superior and inferior spikelets of japonica rice. We looked at grain filling under three N rates (0, 90, and 180 kg N ha^-1) and three K rates (0, 60, and 120 kg K₂O ha^-1) during 2020 and 2021. Across two years, the results showed that the combined use of N and K on superior and inferior spikelets significantly increased their weight by 1.29 mg and 2.31 mg, their maximum grain filling rate by 0.24 mg d^-1 and 0.07 mg d^-1, and their average grain filling rate by 0.21 mg d^-1 and 0.06 mg d^-1, respectively, in comparison with the control (N0K0) treatment. Likewise, K supply increased the average contribution rate of superior and inferior spikelets to yield by 9.1% and 10.0%, respectively. Correlation analysis showed that the grain filling rate of superior and inferior spikelets was an important factor in determining the spikelet weight, whereas the grain filling time was not. We also found that the 1,000-grain weight mainly increased after increasing the spikelets' maximum grain filling rate and average grain filling rate. Collectively, these results illustrate that the combined use of N and K can optimize the asynchronous filling of superior and inferior spikelets and, in particular, enhance inferior spikelet weight with higher rice yield.

Nudix hydrolase 14 influences plant development and grain chalkiness in rice

Nudix hydrolases (NUDX) can hydrolyze a wide range of organic pyrophosphates and are widely distributed in various organisms. Previous studies have shown that NUDXs are extensively involved in biotic and abiotic stress responses in different plant species; however, the role of NUDXs in plant growth and development remains largely unknown. In the present study, we identified and characterized OsNUDX14 localized in the mitochondria in rice. Results showed that OsNUDX14 is constitutively expressed in various tissues and most strongly expressed in mature leaves. We used CRISPR/Cas9 introducing mutations that editing OsNUDX14 and its encoding product. OsNUDX14-Cas9 (nudx14) lines presented early flowering and a larger flag leaf angle during the reproductive stage. In addition, OsNUDX14 affected grain chalkiness in rice. Furthermore, transcript profile analysis indicated that OsNUDX14 is associated with lignin biosynthesis in rice. Six major haplotypes were identified by six OsNUDX14 missense mutations, including Hap_1 to Hap_6. Accessions having the Hap_5 allele were geographically located mainly in South and Southeast Asia with a low frequency in the Xian/indica subspecies. This study revealed that OsNUDX14 is associated with plant development and grain chalkiness, providing a potential opportunity to optimize plant architecture and quality for crop breeding.

OPAQUE3, encoding a transmembrane bZIP transcription factor, regulates endosperm storage protein and starch biosynthesis in rice

Starch and storage proteins are the main components of rice (Oryza sativa L.) grains. Despite their importance, the molecular regulatory mechanisms of storage protein and starch biosynthesis remain largely elusive. Here, we identified a rice opaque endosperm mutant, opaque3 (o3), that overaccumulates 57-kDa proglutelins and has significantly lower protein and starch contents than the wild type. The o3 mutant also has abnormal protein body structures and compound starch grains in its endosperm cells. OPAQUE3 (O3) encodes a transmembrane basic leucine zipper (bZIP) transcription factor (OsbZIP60) and is localized in the endoplasmic reticulum (ER) and the nucleus, but it is localized mostly in the nucleus under ER stress. We demonstrated that O3 could activate the expression of several starch synthesis-related genes (GBSSI, AGPL2, SBEI, and ISA2) and storage protein synthesis-related genes (OsGluA2, Prol14, and Glb1). O3 also plays an important role in protein processing and export in the ER by directly binding to the promoters and activating the expression of OsBIP1 and PDIL1-1, two major chaperones that assist with folding of immature secretory proteins in the ER of rice endosperm cells. High-temperature conditions aggravate ER stress and result in more abnormal grain development in o3 mutants. We also revealed that OsbZIP50 can assist O3 in response to ER stress, especially under high-temperature conditions. We thus demonstrate that O3 plays a central role in rice grain development by participating simultaneously in the regulation of storage protein and starch biosynthesis and the maintenance of ER homeostasis in endosperm cells.

Low Light Stress Increases Chalkiness by Disturbing Starch Synthesis and Grain Filling of Rice

Low light stress increases the chalkiness of rice; however, this effect has not been fully characterized. In this study, we demonstrated that low light resulted in markedly decreased activity of ADP-glucose pyrophosphorylase in the grains and those of sucrose synthase and soluble starch synthase in the early period of grain filling. Furthermore, low light also resulted in decreased activities of granule-bound starch synthase and starch branching enzyme in the late period of grain filling. Therefore, the maximum and mean grain filling rates were reduced but the time to reach the maximum grain filling rates and effective grain filling period were increased by low light. Thus, it significantly decreased the grain weight at the maximum grain filling rate and grain weight and retarded the endosperm growth and development, leading to a loose arrangement of the amyloplasts and an increase in the chalkiness of the rice grains. Compared to the grains at the top panicle part, low light led to a greater decrease in the grain weight at the maximum grain filling rate and time to reach the grain weight at the maximum grain filling rate at the bottom panicle part, which contributed to an increase in chalkiness by increasing the rates of different chalky types at the bottom panicle part. In conclusion, low light disturbed starch synthesis in grains, thereby impeding the grain filling progress and increasing chalkiness, particularly for grains at the bottom panicle part.

Proteomic analysis of Euryale ferox Salisb seeds at different developmental stages

The development of plant seeds is accompanied by changes in their internal substances. The edible part of E. ferox is the seed, and starch and flavonoids are the storage substances and functional substances in E. ferox seeds respectively. Herein, four time points of seed development, including after flowering T10 (10 days), T20 (20 days), T30 (30 days) and T40 (40 days), were investigated by using iTRAQ technology. A total of 2809 differential proteins were identified. The enrichment analysis of differential proteins found that they were mainly enriched in starch synthesis pathways and flavonoid biosynthesis pathways. The key candidate enzymes for starch synthesis, APS (c54069), APL (c55730), SBE (c56416), SSS (c54912) and GBSS (c53181), were identified. At the same time,PAL (c50934), CHS (c49212), F3H (c35949) and ANS (c54610) may be key enzymes in flavonoid biosynthesis. In addition, the ABA signal transduction pathway was analyzed and it was identified that PYL3 (c54854) and ABI5 (c56122) are up-regulated from T10 to T40, and it is speculated that they play an important regulatory role in the development of E. ferox seeds. Together, these results reveals the dynamic changes during the development of E. ferox seeds, which will provide guidance for the study of the molecular mechanism of starch and flavonoids.

Five Rice Seed-Specific NF-YC Genes Redundantly Regulate Grain Quality and Seed Germination via Interfering Gibberellin Pathway

NF-YCs are important transcription factors with diverse functions in the plant kingdoms including seed development. NF-YC8, 9, 10, 11 and 12 are close homologs with similar seed-specific expression patterns. Despite the fact that some of the NF-YCs are functionally known; their biological roles have not been systematically explored yet, given the potential functional redundancy. In this study, we generated pentuple mutant pnfyc of NF-YC8-12 and revealed their functions in the regulation of grain quality and seed germination. pnfyc grains displayed significantly more chalkiness with abnormal starch granule packaging. pnfyc seed germination and post-germination growth are much slower than the wild-type NIP, largely owing to the GA-deficiency as exogenous GA was able to fully recover the germination phenotype. The RNA-seq experiment identified a total of 469 differentially expressed genes, and several GA-, ABA- and grain quality control-related genes might be transcriptionally regulated by the five NF-YCs, as revealed by qRT-PCR analysis. The results demonstrated the redundant functions of NF-YC8-12 in regulating GA pathways that underpin rice grain quality and seed germination, and shed a novel light on the functions of the seed-specific NF-YCs.

The phosphoinositide-specific phospholipase C1 modulates flowering time and grain size in rice

Preferential expression of OsPLC1 is detected at the heading stage of rice, OsPLC1 overexpression results in early flowering, increased-grain size and yield; however, opposing phenotypes produced in the osplc1 mutants. Abstract: The importance of phospholipase C (PLC) in plant development has been demonstrated in several studies. OsPLC1, a member of PI-PLC in rice, although its role in the response to salt stress of rice seedlings has been reported, its functions in the growth and development of rice is elusive. Here, we report that OsPLC1 expression could be detectable in various tissues throughout the developmental stages of rice, and the highest expression level of OsPLC1 was detected at the heading stage. OsPLC1 overexpression (OE) produced rice plants with early flowering, whereas OsPLC1 loss-of-function led to delay in flowering. The expression levels of subset genes, which are involved in the control of flowering time in rice, were altered in the plants of OE and osplc1. In addition, the enlargement of grain size was observed in OE plants, however, the reduction of grain size was noticed in osplc1 mutants. The increase in the grain size and the grain yield of OE lines were associated with the improvement of cell length and expression levels of a set of genes related to cell expansion, contrarily, the decrease in osplc1 mutant grain size and yield were linked to declined cell length and expression levels of related genes. No significant differences, in terms of the grain quality of mature seeds, were found in OE and osplc1 mutants, with compared to those in Nipponbare (Nip). In summary, our study suggests that OsPLC1 could modulate rice flowering time and grain size.

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.

Effect of Panicle Morphology on Grain Filling and Rice Yield: Genetic Control and Molecular Regulation

The demand for rice is likely to increase approximately 1.5 times by the year 2050. In contrast, the rice production is stagnant since the past decade as the ongoing rice breeding program is unable to increase the production further, primarily because of the problem in grain filling. Investigations have revealed several reasons for poor filling of the grains in the inferior spikelets of the compact panicle, which are otherwise genetically competent to develop into well-filled grains. Among these, the important reasons are 1) poor activities of the starch biosynthesizing enzymes, 2) high ethylene production leading to inhibition in expressions of the starch biosynthesizing enzymes, 3) insufficient division of the endosperm cells and endoreduplication of their nuclei, 4) low accumulation of cytokinins and indole-3-acetic acid (IAA) that promote grain filling, and 5) altered expressions of the miRNAs unfavorable for grain filling. At the genetic level, several genes/QTLs linked to the yield traits have been identified, but the information so far has not been put into perspective toward increasing the rice production. Keeping in view the genetic competency of the inferior spikelets to develop into well-filled grains and based on the findings from the recent research studies, improving grain filling in these spikelets seems plausible through the following biotechnological interventions: 1) spikelet-specific knockdown of the genes involved in ethylene synthesis and overexpression of β-CAS (β-cyanoalanine) for enhanced scavenging of CN⁻ formed as a byproduct of ethylene biosynthesis; 2) designing molecular means for increased accumulation of cytokinins, abscisic acid (ABA), and IAA in the caryopses; 3) manipulation of expression of the transcription factors like MYC and OsbZIP58 to drive the expression of the starch biosynthesizing enzymes; 4) spikelet-specific overexpression of the cyclins like CycB;1 and CycH;1 for promoting endosperm cell division; and 5) the targeted increase in accumulation of ABA in the straw during the grain filling stage for increased carbon resource remobilization to the grains. Identification of genes determining panicle compactness could also lead to an increase in rice yield through conversion of a compact-panicle into a lax/open one. These efforts have the ability to increase rice production by as much as 30%, which could be more than the set production target by the year 2050.

Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century

The eating and cooking quality (ECQ) of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance. It has therefore been of paramount importance in rice breeding programs. Here, we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice. Innovations in gene- and genome-editing techniques have enabled improvements in rice ECQ. Significant genes and quantitative trait loci (QTLs) have been shown to regulate starch composition, thereby affecting amylose content and thermal and pasting properties. A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma. Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties. The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

OsMADS14 and NF-YB1 cooperate in the direct activation of OsAGPL2 and Waxy during starch synthesis in rice endosperm

Starch synthesis makes a dramatic contribution to the yield and nutritional value of cereal crops. Although several starch synthesis enzymes and related regulators have been reported, the underlying regulatory mechanisms of starch synthesis remain largely unknown. OsMADS14 is a FRUITFULL (FUL)-like MADS-box gene in rice (Oryza sativa). Here we show that two null mutations of OsMADS14 result in a shrunken and chalky grain phenotype. It is caused by obviously defective compound starch granules and a significantly reduced content of both total starch and amylose in the endosperm. Transcriptomic profiling analyses revealed that the loss-of-function of OsMADS14 leads to significantly downregulated expression of many core starch synthesis genes, including OsAGPL2 and Waxy. Both in vitro and in vivo assays demonstrate that the OsMADS14 protein directly binds to stretches of DNA with a CArG-box consensus in the putative regulatory regions of OsAGPL2 and Waxy. Protein-protein interaction experiments also suggest that OsMADS14 interacts with nuclear factor NF-YB1 to promote the transcription of OsAGPL2 and Waxy. Our study thus demonstrates that OsMADS14 plays an essential role in the synthesis of storage starch and provides novel insights into the underlying molecular mechanism that may be used to improve rice cultivars by molecular breeding.

Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types

Grain filling affects grain weight and quality and is among the most critical factors in determining the yield and quality of cereal crops. Though hybrids have larger panicles and numerous spikelets with a larger sink capacity than conventional varieties, data on the grain filling commonalities and differences between foxtail millet varieties with different panicle types remain sparse. In this study, we found that "Zhang Gu 13" (ZG, large panicle) exhibits a significantly higher panicle weight than "Yu Gu 18" (YG, conventional panicle) at the early stage of grain filling, but the weight of YG increased rapidly and gradually overtook ZG during the middle stages. A temporal expression pattern analysis demonstrated that the genes involved in photosynthesis, metabolic pathways, and phenylpropanoid biosynthesis were downregulated, while those related to peroxisome function, purine metabolism, and zeatin biosynthesis were upregulated during grain filling in both varieties. A total of 6,832 differentially expressed genes (DEGs) were identified in both varieties, with the majority identified at the early and late stages. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that the upregulated DEGs in YG were associated with gibberellin (GA) biosynthesis, ATP-binding cassette (ABC) transporters, and plant hormone signal transduction. Photosynthesis-related DEGs, such as photosystem and antenna proteins, were significantly upregulated in ZG. This study provides preliminary insights into the differences in gene expression and molecular mechanisms of grain filling between ZG and YG in the North China summer-sowing region.

A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.)

Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.

NnABI4-Mediated ABA Regulation of Starch Biosynthesis in Lotus (Nelumbo nucifera Gaertn)

Starch is an important component in lotus. ABA is an important plant hormone, which plays a very crucial role in regulating plant starch synthesis. Using ‘MRH’ as experimental materials, the leaves were sprayed with exogenous ABA before the rhizome expansion. The results showed that stomatal conductance and transpiration rate decreased while net photosynthetic rate increased. The total starch content of the underground rhizome of lotus increased significantly. Meanwhile, qPCR results showed that the relative expression levels of NnSS1, NnSBE1 and NnABI4 were all upregulated after ABA treatment. Then, yeast one-hybrid and dual luciferase assay suggested that NnABI4 protein can promote the expression of NnSS1 by directly binding to its promoter. In addition, subcellular localization results showed that NnABI4 encodes a nuclear protein, and NnSS1 protein was located in the chloroplast. Finally, these results indicate that ABA induced the upregulated expression of NnABI4, and NnABI4 promoted the expression of NnSS1 and thus enhanced starch accumulation in lotus rhizomes. This will provide a theoretical basis for studying the molecular mechanism of ABA regulating starch synthesis in plant.

Starch biosynthesis in cereal endosperms: An updated review over the last decade

Starch is a vital energy source for living organisms and is a key raw material and additive in the food and non-food industries. Starch has received continuous attention in multiple research fields. The endosperm of cereals (e.g., rice, corn, wheat, and barley) is the most important site for the synthesis of storage starch. Around 2010, several excellent reviews summarized key progress in various fields of starch research, serving as important references for subsequent research. In the past 10 years, many achievements have been made in the study of starch synthesis and regulation in cereals. The present review provides an update on research progress in starch synthesis of cereal endosperms over the past decade, focusing on new enzymes and non-enzymatic proteins involved in starch synthesis, regulatory networks of starch synthesis, and the use of elite alleles of starch synthesis-related genes in cereal breeding programs. We also provide perspectives on future research directions that will further our understanding of cereal starch biosynthesis and regulation to support the rational design of ideal quality grain.

DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.

Construction of a weight-based seed sorting system for the third-generation hybrid rice

BACKGROUND

The third-generation hybrid rice technology can be constructed by transforming a recessive nuclear male sterile (NMS) mutant with a transgenic cassette containing three functional modules: the wild type male fertility gene to restore the fertility of the mutant, the pollen killer gene that specifically kills the pollen grains carrying the transgene, and the red fluorescence protein (RFP) gene to mark the transgenic seed (maintainer). The transgenic plant produces 1:1 NMS seeds and maintainer seeds that can be distinguished by the RFP signal. However, the RFP signals in the partially filled or pathogen-infected maintainer seeds are often too weak to be detected by RFP-based seed sorting machine, resulting in intermingling of the maintainer seeds with NMS seeds.

RESULTS

Here we constructed a weight-based seed sorting system for the third-generation hybrid rice technology by silencing the genes encoding ADP-glucose pyrophosphorylase (AGP) essential for endosperm starch biosynthesis via endosperm-specific expression of artificial microRNAs (amiRNAs). In this system, the NMS seeds have normal endosperm and are heavy, but the maintainer seeds have shrunken endosperms and are light-weighted. The maintainer seeds can be easily and accurately sorted out from the NMS seeds by weight-sorting machines, so pure and fully filled NMS seeds are available.

CONCLUSIONS

The weight-based seed sorting system shows obvious advantages over the RFP-based seed sorting system in accuracy, efficiency, and cost for propagation of pure male sterile seeds. These characteristics will significantly increase the value and transgenic safety of the third-generation hybrid rice technology.

Era-like GTP protein gene expression in rice

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Identification of novel QTLs for grain fertility and associated traits to decipher poor grain filling of basal spikelets in dense panicle rice

High grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility and associated traits like panicle compactness, and ethylene production that significantly influences the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1, and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1, and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in a dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.

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.

Exploiting Genic Male Sterility in Rice: From Molecular Dissection to Breeding Applications

Rice (Oryza sativa L.) occupies a very salient and indispensable status among cereal crops, as its vast production is used to feed nearly half of the world's population. Male sterile plants are the fundamental breeding materials needed for specific propagation in order to meet the elevated current food demands. The development of the rice varieties with desired traits has become the ultimate need of the time. Genic male sterility is a predominant system that is vastly deployed and exploited for crop improvement. Hence, the identification of new genetic elements and the cognizance of the underlying regulatory networks affecting male sterility in rice are crucial to harness heterosis and ensure global food security. Over the years, a variety of genomics studies have uncovered numerous mechanisms regulating male sterility in rice, which provided a deeper and wider understanding on the complex molecular basis of anther and pollen development. The recent advances in genomics and the emergence of multiple biotechnological methods have revolutionized the field of rice breeding. In this review, we have briefly documented the recent evolution, exploration, and exploitation of genic male sterility to the improvement of rice crop production. Furthermore, this review describes future perspectives with focus on state-of-the-art developments in the engineering of male sterility to overcome issues associated with male sterility-mediated rice breeding to address the current challenges. Finally, we provide our perspectives on diversified studies regarding the identification and characterization of genic male sterility genes, the development of new biotechnology-based male sterility systems, and their integrated applications for hybrid rice breeding.

Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice

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4-way Multiparental population covered the limitations of the biparental structure.

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The combination of SNP and bin-GWAS showed a powerful tool for QTL mapping.

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qPGWC8.2 harbored a novel predicted gene for rice chalkiness quality.

Introduction

The multiparental population provides us the chance to identify superior alleles controlling a trait for genetic improvement. Genome wide association studies at bin level (bin-GWAS) are expected to be more power in QTL mapping than GWAS at SNP level (SNP-GWAS).

Objectives

This study is to estimate genetic effects of QTL conferring grain appearance quality in rice by SNP-GWAS and bin-GWAS, compare their power in QTL mapping and identify the superior alleles of all detected QTL from 4 parents for genetic improvement.

Methods

A 4-way MAGIC population and its four founders were cultivated in two environments to dissect the genetic basis of rice grain appearance quality. Both SNP-GWAS and bin-GWAS were conducted for QTL mapping. Multiple comparison among 4 parental bin/alleles was used to identify the superior alleles.

Results

A total of 16 and 20 QTL associated with grain appearance quality were identified by SNP- and bin-GWAS, respectively. A minor chalkiness QTL qPGWC8.2/qDEC8 was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior parental alleles for GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were almost carried by the high-quality parents Cypress and Yuejingsimiao (YJSM), while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles.

Conclusions

Both SNP- and bin-GWAS methods are encouraged for joint QTL mapping with MAGIC population. qPGWC8.2/qDEC8 is a novel candidate gene strongly associated with chalkiness. The superior alleles of GS3, GW5, GL3.1, GW7, Chalk5 and qPGWC8.2 were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.

The NAC transcription factor NAC019-A1 is a negative regulator of starch synthesis in wheat developing endosperm

Starch is a major component of wheat (Triticum aestivum L.) endosperm and is an important part of the human diet. The functions of many starch synthesis genes have been elucidated. However, little is known about their regulatory mechanisms in wheat. Here, we identified a novel NAC transcription factor, TaNAC019-A1 (TraesCS3A02G077900), that negatively regulates starch synthesis in wheat and rice (Oryza sativa L.) endosperms. TaNAC019-A1 was highly expressed in the endosperm of developing grains and encoded a nucleus-localized transcriptional repressor. Overexpression of TaNAC019-A1 in rice and wheat led to significantly reduced starch content, kernel weight, and kernel width. The TaNAC019-A1-overexpression wheat lines had smaller A-type starch granules and fewer B-type starch granules than wild-type. Moreover, TaNAC019-A1 could directly bind to the 'ACGCAG' motif in the promoter regions of ADP-glucose pyrophosphorylase small subunit 1 (TaAGPS1-A1, TraesCS7A02G287400) and TaAGPS1-B1 (TraesCS7B02G183300) and repress their expression, thereby inhibiting starch synthesis in wheat endosperm. One haplotype of TaNAC019-B1 (TaNAC019-B1-Hap2, TraesCS3B02G092800) was positively associated with thousand-kernel weight and underwent positive selection during the Chinese wheat breeding process. Our data demonstrate that TaNAC019-A1 is a negative regulator of starch synthesis in wheat endosperm and provide novel insight into wheat yield improvement.

iTRAQ-based quantitative proteomic analysis reveals the metabolic pathways of grain chalkiness in response to nitrogen topdressing in rice

Grain chalkiness is a highly undesirable trait that adversely affects rice quality. This chalkiness is easily influenced by the application of chemical nitrogen (N) fertilizer at the late growth stage. However, on the molecular mechanism underlying grain chalkiness caused by late N fertilization is not fully clear. In this study, proteomic differences in expression were determined in developing grains exposed to N topdressing (108 kg N ha^-1, N+) and a control (0 kg N ha^-1, N0), using the rice variety OM052, which has a high level of chalkiness. A total of 198 differentially expressed proteins (DEPs) were detected between the N+ and N0 treatments, including 9 up-regulated proteins and 189 down-regulated proteins. Of these DEPs, approximately half were associated with carbohydrate metabolism (glycolysis, tricarboxylic acid cycle, pentose phosphate pathway, fermentation and starch metabolism) and N metabolism (protein synthesis, folding, degradation and storage, amino acid synthesis and catabolism). A detailed pathway dissection revealed that multiple metabolic pathways during the grain filling stage were involved in the N-induced grain chalkiness. Reduced abundances of proteins associated with respiratory metabolism and energy metabolism drastically impaired the biosynthesis and deposition of starch in the developmental endosperms, which might be a crucial trigger for the increase in grain chalkiness. The disturbed N metabolism and differential expression of storage proteins up-regulated during the grain filling stage are able to partially explain the occurrence of grain chalkiness in rice.

Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice (Oryza rufipogon Griff.) under Rice (Oryza sativa L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance

Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.

GBSS-BINDING PROTEIN, encoding a CBM48 domain-containing protein, affects rice quality and yield

The percentage of amylose in the endosperm of rice (Oryza sativa) largely determines grain cooking and eating qualities. Granule-bound starch synthase I (GBSSI) and GBSSII are responsible for amylose biosynthesis in the endosperm and leaf, respectively. Here, we identified OsGBP, a rice GBSS-binding protein that interacted with GBSSI and GBSSII in vitro and in vivo. The total starch and amylose contents in osgbp mutants were significantly lower than those of wild type in leaves and grains, resulting in reduced grain weight and quality. The carbohydrate-binding module 48 (CBM48) domain present in the C-terminus of OsGBP is crucial for OsGBP binding to starch. In the osgbp mutant, the extent of GBSSI and GBSSII binding to starch in the leaf and endosperm was significantly lower than wild type. Our data suggest that OsGBP plays an important role in leaf and endosperm starch biosynthesis by mediating the binding of GBSS proteins to developing starch granules. This elucidation of the function of OsGBP enhances our understanding of the molecular basis of starch biosynthesis in rice and contributes information that can be potentially used for the genetic improvement of yield and grain quality.

Generation of High Yielding and Fragrant Rice (Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations

The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.

Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes

High amylose starch can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava (Manihot esculenta Crantz) with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. All BE1-RNAi plant lines (BE1i) and BE2-RNAi plant lines (BE2i) were grown up in the field, but with reduced total biomass production. Considerably high amylose content in the storage roots of BE2i plant lines was achieved. Storage starch granules of BE1i and BE2i plants had similar morphology as wild type (WT), however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis.

Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice

Background

Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development.

Results

A comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits.

Conclusion

This comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.

Characterization of AtWRI1 in fatty acids and starch synthesis in rice

WRINKLED1 (WRI1) belongs to AP2/EREBP transcription factor. Its function in dicots for fatty acids synthesis has been deeply studied, but its role in monocot, especially in rice, is still poorly understood. Here, with the overexpression of AtWRI1 in rice, we found its overexpression increased fatty acids content in vegetative organs and seed coat including aleurone layer (SCAL) but decreased fatty acids content in endosperm. Meanwhile, the overexpression of AtWRI1 increased starch content in endosperm. These results provide a new insight into the function of AtWRI1in monocot and make a previous basement for the study of the connection of fatty acids and starch synthesis in rice.

NF-YC12 is a key multi-functional regulator of accumulation of seed storage substances in rice

Starch and storage proteins, the primary storage substances of cereal endosperm, are a major source of food for humans. However, the transcriptional regulatory networks of the synthesis and accumulation of storage substances remain largely unknown. Here, we identified a rice endosperm-specific gene, NF-YC12, that encodes a putative nuclear factor-Y transcription factor subunit C. NF-YC12 is expressed in the aleurone layer and starchy endosperm during grain development. Knockout of NF-YC12 significantly decreased grain weight as well as altering starch and protein accumulation and starch granule formation. RNA-sequencing analysis revealed that in the nf-yc12 mutant genes related to starch biosynthesis and the metabolism of energy reserves were enriched in the down-regulated category. In addition, starch and protein contents in seeds differed between NF-YC12-overexpression lines and the wild-type. NF-YC12 was found to interact with NF-YB1. ChIP-qPCR and yeast one-hybrid assays showed that NF-YC12 regulated the rice sucrose transporter OsSUT1 in coordination with NF-YB1 in the aleurone layer. In addition, NF-YC12 was directly bound to the promoters of FLO6 (FLOURY ENDOSPERM6) and OsGS1;3 (glutamine synthetase1) in developing endosperm. This study demonstrates a transcriptional regulatory network involving NF-YC12, which coordinates multiple pathways to regulate endosperm development and the accumulation of storage substances in rice seeds.

Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat

Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.

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

FLO15encodes a plastidic glyoxalase I protein, OsGLYI7, which affects compound starch granule formation and starch synthesis in rice endosperm. Starch synthesis in rice (Oryza sativa) endosperm is a sophisticated process, and its underlying molecular machinery still remains to be elucidated. Here, we identified and characterized two allelic rice floury endosperm 15 (flo15) mutants, both with a white-core endosperm. The flo15 grains were characterized by defects in compound starch granule development, along with decreased starch content. Map-based cloning of the flo15 mutants identified mutations in OsGLYI7, which encodes a glyoxalase I (GLYI) involved in methylglyoxal (MG) detoxification. The mutations of FLO15/OsGLYI7 resulted in increased MG content in flo15 developing endosperms. FLO15/OsGLYI7 localizes to the plastids, and the in vitro GLYI activity derived from flo15 was significantly decreased relative to the wild type. Moreover, the expression of starch synthesis-related genes was obviously altered in the flo15 mutants. These findings suggest that FLO15 plays an important role in compound starch granule formation and starch synthesis in rice endosperm.

OsPK2 encodes a plastidic pyruvate kinase involved in rice endosperm starch synthesis, compound granule formation and grain filling

Starch is the main form of energy storage in higher plants. Although several enzymes and regulators of starch biosynthesis have been defined, the complete molecular machinery remains largely unknown. Screening for irregularities in endosperm formation in rice represents valuable prospect for studying starch synthesis pathway. Here, we identified a novel rice white-core endosperm and defective grain filling mutant, ospk2, which displays significantly lower grain weight, decreased starch content and alteration of starch physicochemical properties when compared to wild-type grains. The normal starch compound granules were drastically reduced and more single granules filled the endosperm cells of ospk2. Meanwhile, the germination rate of ospk2 seeds after 1-year storage was observably reduced compared with wild-type. Map-based cloning of OsPK2 indicated that it encodes a pyruvate kinase (PK, ATP: pyruvate 2-O-phosphotransferase, EC 2.7.1.40), which catalyses an irreversible step of glycolysis. OsPK2 has a constitutive expression in rice and its protein localizes in chloroplasts. Enzyme assay showed that the protein product from expressed OsPK2 and the crude protein extracted from tissues of wild-type exhibits strong PK activity; however, the mutant presented reduced protein activity. OsPK2 (PKpα1) and three other putative rice plastidic isozymes, PKpα2, PKpβ1 and PKpβ2, can interact to form heteromer. Moreover, the mutation leads to multiple metabolic disorders. Altogether, these results denote new insights into the role of OsPK2 in plant seed development, especially in starch synthesis, compound granules formation and grain filling, which would be useful for genetic improvement of high yield and rice grain quality.

Carbohydrate reserves and seed development: an overview

Seeds are one of the most important food sources, providing humans and animals with essential nutrients. These nutrients include carbohydrates, lipids, proteins, vitamins and minerals. Carbohydrates are one of the main energy sources for both plant and animal cells and play a fundamental role in seed development, human nutrition and the food industry. Many studies have focused on the molecular pathways that control carbohydrate flow during seed development in monocot and dicot species. For this reason, an overview of seed biodiversity focused on the multiple metabolic and physiological mechanisms that govern seed carbohydrate storage function in the plant kingdom is required. A large number of mutants affecting carbohydrate metabolism, which display defective seed development, are currently available for many plant species. The physiological, biochemical and biomolecular study of such mutants has led researchers to understand better how metabolism of carbohydrates works in plants and the critical role that these carbohydrates, and especially starch, play during seed development. In this review, we summarize and analyze the newest findings related to carbohydrate metabolism's effects on seed development, pointing out key regulatory genes and enzymes that influence seed sugar import and metabolism. Our review also aims to provide guidelines for future research in the field and in this way to assist seed quality optimization by targeted genetic engineering and classical breeding programs.

WB1, a Regulator of Endosperm Development in Rice, Is Identified by a Modified MutMap Method

Abnormally developed endosperm strongly affects rice (Oryza sativa) appearance quality and grain weight. Endosperm formation is a complex process, and although many enzymes and related regulators have been identified, many other related factors remain largely unknown. Here, we report the isolation and characterization of a recessive mutation of White Belly 1 (WB1), which regulates rice endosperm development, using a modified MutMap method in the rice mutant wb1. The wb1 mutant develops a white-belly endosperm and abnormal starch granules in the inner portion of white grains. Representative of the white-belly phenotype, grains of wb1 showed a higher grain chalkiness rate and degree and a lower 1000-grain weight (decreased by ~34%), in comparison with that of Wild Type (WT). The contents of amylose and amylopectin in wb1 significantly decreased, and its physical properties were also altered. We adopted the modified MutMap method to identify 2.52 Mb candidate regions with a high specificity, where we detected 275 SNPs in chromosome 4. Finally, we identified 19 SNPs at 12 candidate genes. Transcript levels analysis of all candidate genes showed that WB1 (Os04t0413500), encoding a cell-wall invertase, was the most probable cause of white-belly endosperm phenotype. Switching off WB1 with the CRISPR/cas9 system in Japonica cv. Nipponbare demonstrates that WB1 regulates endosperm development and that different mutations of WB1 disrupt its biological function. All of these results taken together suggest that the wb1 mutant is controlled by the mutation of WB1, and that the modified MutMap method is feasible to identify mutant genes, and could promote genetic improvement in rice.

Rice Interploidy Crosses Disrupt Epigenetic Regulation, Gene Expression, and Seed Development

Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5' and 3' flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylation-related genes including OsMET1b and OsCMT3a were upregulated in the 2×4 cross (pollinating a diploid "mother" with a tetraploid "father") but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4×2 crosses. WUSCHEL homeobox2 (WOX2)-like (WOX2L), an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.