Glucan, Water-Dikinase 1 (GWD1), an ideal biotechnological target for potential improving yield and quality in rice

Rice Promoter Editing: An Efficient Genetic Improvement Strategy

Gene expression levels in rice (Oryza sativa L.) and other plant species are determined by the promoters, which directly control phenotypic characteristics. As essential components of genes, promoters regulate the intensity, location, and timing of gene expression. They contain numerous regulatory elements and serve as binding sites for proteins that modulate transcription, including transcription factors and RNA polymerases. Genome editing can alter promoter sequences, thereby precisely modifying the expression patterns of specific genes, and ultimately affecting the morphology, quality, and resistance of rice. This paper summarizes research on rice promoter editing conducted in recent years, focusing on improvements in yield, heading date, quality, and disease resistance. It is expected to inform the application of promoter editing and encourage further research and development in crop genetic improvement with promote.

Starch phosphorylation-A needle in a haystack

Phosphoesterification is the only naturally occurring covalent starch modification identified to date, and it has a major impact on overall starch metabolism. The incorporation of phosphate groups mediated by dikinases [α-glucan, water dikinase (GWD), EC 2.7.9.4; phosphoglucan, water dikinase (PWD), EC 2.7.9.5] massively alters the starch granule properties; however, previous studies did not determine whether the starch-related dikinases bind the phosphate to the glucosyl units within the amylopectin molecules in a specific pattern or randomly. In order to answer this challenging question, a number of approaches were initially pursued until a protocol could be established that enabled a massive step forward in the in vitro analysis of phosphorylated glucan chains obtained from starch. For this purpose, phosphorylation by GWD was investigated, including the final state of phosphorylation i.e., the state of substrate saturation when GWD lacks further free hydroxyl groups at OH-C6 for the catalysis of monophosphate esters. Since the separated phosphorylated glucan chains were required for the analysis, isoamylase digestion was performed to cleave the α-1,6-glycosidic bonds and to allow for the removal of the huge number of existing neutral chains by means of anion exchange chromatography. Via Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) MS and MALDI-MS/MS, the phosphorylated α-glucan chains were analysed, and the position of the phosphate group within the chain in relation to the reducing end was determined. Here, we demonstrate a protocol that enables the analysis of phosphorylated oligosaccharides, even in small quantities.

OsLESV and OsESV1 promote transitory and storage starch biosynthesis to determine rice grain quality and yield

Transitory starch is an important carbon source in leaves, and its biosynthesis and metabolism are closely related to grain quality and yield. The molecular mechanisms controlling leaf transitory starch biosynthesis and degradation and their effects on rice (Oryza sativa) quality and yield remain unclear. Here, we show that OsLESV and OsESV1, the rice orthologs of AtLESV and AtESV1, are associated with transitory starch biosynthesis in rice. The total starch and amylose contents in leaves and endosperms are significantly reduced, and the final grain quality and yield are compromised in oslesv and osesv1 single and oslesv esv1 double mutants. Furthermore, we found that OsLESV and OsESV1 bind to starch, and this binding depends on a highly conserved C-terminal tryptophan-rich region that acts as a starch-binding domain. Importantly, OsLESV and OsESV1 also interact with the key enzymes of starch biosynthesis, granule-bound starch synthase I (GBSSI), GBSSII, and pyruvate orthophosphote dikiase (PPDKB), to maintain their protein stability and activity. OsLESV and OsESV1 also facilitate the targeting of GBSSI and GBSSII from plastid stroma to starch granules. Overexpression of GBSSI, GBSSII, and PPDKB can partly rescue the phenotypic defects of the oslesv and osesv1 mutants. Thus, we demonstrate that OsLESV and OsESV1 play a key role in regulating the biosynthesis of both leaf transitory starch and endosperm storage starch in rice. These findings deepen our understanding of the molecular mechanisms underlying transitory starch biosynthesis in rice leaves and reveal how the transitory starch metabolism affects rice grain quality and yield, providing useful information for the genetic improvement of rice grain quality and yield.

Transcriptomics and starch biosynthesis analysis in leaves and developing seeds of mung bean provide a basis for genetic engineering of starch composition and seed quality

Mung bean starch is distinguished by its exceptional high amylose content and regulation of starch biosynthesis in leaves and storage tissues, such as seeds, share considerable similarities. Genetic engineering of starch composition and content, requires detailed knowledge of starch biosynthetic gene expression and enzymatic regulation. In this study we applied detailed transcriptomic analyses to unravel the global differential gene expression patterns in mung bean leaves and in seeds during various stages of development. The objective was to identify candidate genes and regulatory mechanisms that may enable generation of desirable seed qualities through the use of genetic engineering. Notable differences in gene expression, in particular low expression of the Protein Targeting to Starch (PTST), starch synthase (SS) 3, and starch branching enzyme1 (SBE1) encoding genes in developing seeds as compared to leaves were evident. These differences were related to starch molecular structures and granule morphologies. Specifically, the starch molecular size distribution at different stages of seed development correlated with the starch biosynthesis gene expression of the SBE1, SS1, granule-bound starch synthases (GBSS) and isoamylase 1 (ISA1) encoding genes. Furthermore, putative hormonal and redox controlled regulation were observed, which may be explained by abscisic acid (ABA) and indole-3-acetic acid (IAA) induced signal transduction, and redox regulation of ferredoxins and thioredoxins, respectively. The morphology of starch granules in leaves and developing seeds were clearly distinguishable and could be correlated to differential expression of SS1. Here, we present a first comprehensive transcriptomic dataset of developing mung bean seeds, and combined these findings may enable generation of genetic engineering strategies of for example starch biosynthetic genes for increasing starch levels in seeds and constitute a valuable toolkit for improving mung bean seed quality.

OsCRLK2, a Receptor-Like Kinase Identified by QTL Analysis, is Involved in the Regulation of Rice Quality

The quality of rice (Oryza sativa L) is determined by a combination of appearance, flavor, aroma, texture, storage characteristics, and nutritional composition. Rice quality directly influences acceptance by consumers and commercial value. The genetic mechanism underlying rice quality is highly complex, and is influenced by genotype, environment, and chemical factors such as starch type, protein content, and amino acid composition. Minor variations in these chemical components may lead to substantial differences in rice quality. Among these components, starch is the most crucial and influential factor in determining rice quality. In this study, quantitative trait loci (QTLs) associated with eight physicochemical properties related to the rapid viscosity analysis (RVA) profile were identified using a high-density sequence map constructed using recombinant inbred lines (RILs). Fifty-nine QTLs were identified across three environments, among which qGT6.4 was a novel locus co-located across all three environments. By integrating RNA-seq data, we identified the differentially expressed candidate gene OsCRLK2 within the qGT6.4 interval. osclrk2 mutants exhibited decreased gelatinization temperature (GT), apparent amylose content (AAC) and viscosity, and increased chalkiness. Furthermore, osclrk2 mutants exhibited downregulated expression of the majority of starch biosynthesis-related genes compared to wild type (WT) plants. In summary, OsCRLK2, which encodes a receptor-like protein kinase, appears to consistently influence rice quality across different environments. This discovery provides a new genetic resource for use in the molecular breeding of rice cultivars with improved quality.

RGA1 regulates grain size, rice quality and seed germination in the small and round grain mutant srg5

BACKGROUND

Generating elite rice varieties with high yield and superior quality is the main goal of rice breeding programs. Key agronomic traits, including grain size and seed germination characteristics, affect the final yield and quality of rice. The RGA1 gene, which encodes the α-subunit of rice G-protein, plays an important role in regulating rice architecture, seed size and abiotic stress responses. However, whether RGA1 is involved in the regulation of rice quality and seed germination traits is still unclear.

RESULTS

In this study, a rice mutant small and round grain 5 (srg5), was identified in an EMS-induced rice mutant library. Systematic analysis of its major agronomic traits revealed that the srg5 mutant exhibited a semi-dwarf plant height with small and round grain and reduced panicle length. Analysis of the physicochemical properties of rice showed that the difference in rice eating and cooking quality (ECQ) between the srg5 mutant and its wild-type control was small, but the appearance quality was significantly improved. Interestingly, a significant suppression of rice seed germination and shoot growth was observed in the srg5 mutant, which was mainly related to the regulation of ABA metabolism. RGA1 was identified as the candidate gene for the srg5 mutant by BSA analysis. A SNP at the splice site of the first intron disrupted the normal splicing of the RGA1 transcript precursor, resulting in a premature stop codon. Additional linkage analysis confirmed that the target gene causing the srg5 mutant phenotype was RGA1. Finally, the introduction of the RGA1 mutant allele into two indica rice varieties also resulted in small and round rice grains with less chalkiness.

CONCLUSIONS

These results indicate that RGA1 is not only involved in the control of rice architecture and grain size, but also in the regulation of rice quality and seed germination. This study sheds new light on the biological functions of RGA1, thereby providing valuable information for future systematic analysis of the G-protein pathway and its potential application in rice breeding programs.

Salinity inhibits seed germination and embryo growth by reducing starch mobilization efficiency in barley

Barley is one of the world's earliest domesticated crops, which is widely used for beer production, animal feeding, and health care. Barley seed germination, particularly in increasingly saline soils, is key to ensure the safety of crop production. However, the mechanism of salt-affected seed germination in barley remains elusive. Here, two different colored barley varieties were used to independently study the regulation mechanism of salt tolerance during barley seed germination. High salinity delays barley seed germination by slowing down starch mobilization efficiency in seeds. The starch plate test revealed that salinity had a significant inhibitory effect on α-amylase activity in barley seeds. Further, NaCl treatment down-regulated the expression of Amy1, Amy2 and Amy3 genes in germinated seeds, thereby inhibiting α-amylase activity. In addition, the result of embryogenic culture system in vitro showed that the shoot elongation of barley was significantly inhibited by salt stress. These findings indicate that it is a feasible idea to study the regulation mechanism of salinity on barley seed germination and embryo growth from the aspect of starch-related source-sink communication.

Gene editing of non-coding regulatory DNA and its application in crop improvement

The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.

Peculiar properties of tuber starch in a potato mutant lacking the α-glucan water dikinase 1 gene GWD1 created by targeted mutagenesis using the CRISPR/dMac3-Cas9 system

Glucose chains in starch are phosphorylated and contribute to structural stabilization. Phosphate groups contained in starch also play a role in retaining moisture. α-Glucan water dikinase 1 (GWD1) is involved in the phosphorylation of glucose chains in starch. In this study, we generated potato mutants of the GWD1 gene using the CRISPR/dMac3-Cas9 system. Observation of the phenotypes of the GWD1-deficient mutants revealed their physiological roles in tuber starch formation. The 4-allele mutants showed growth retardation and a delay in tuber formation. A significant decrease in phosphorus content was detected in the tuber starch of the gwd1 mutant. This mutant starch showed a higher amylose content than the wild-type starch, whereas its gelatinization temperature was slightly lower than that of the WT starch. The peak viscosity of the mutant starch was lower than that of the WT starch. These observations revealed that the starch of the gwd1 mutants had peculiar and unique properties compared to those of WT, sbe3 and gbss1 mutant starches. The amount of tissue-released water due to freeze-thawing treatment was determined on tubers of the gwd1 mutant and compared with those of WT and the other mutants. Significantly less water loss was found in the gwd1, sbe3 and gbss1 mutant tubers than in the WT tubers. Our results indicate that the GWD1 gene is not only important for potato growth, but also largely effective for the traits of tuber starch.

A syntelog-based pan-genome provides insights into rice domestication and de-domestication

BACKGROUND

Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate.

RESULTS

Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.

CONCLUSIONS

This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.

Transcriptome analysis of differential sugar accumulation in the developing embryo of contrasting two Castanea mollissima cultivars

Chinese chestnut (Castanea mollissima) is an important nut tree species, and its embryo is rich in sugar. We combined metabolomic and transcriptomic data to analyze metabolites and genes related to sugar in two Chinese chestnut cultivars at 60, 70, 80, 90 and 100 days after flowering (DAF). The soluble sugar content of high-sugar cultivar at maturity is 1.5 times that of low-sugar cultivar. Thirty sugar metabolites were identified in embryo, with the most dominant being sucrose. Analysis of the gene expression patterns revealed that the high-sugar cultivar promoted the conversion of starch to sucrose by up-regulating genes related to starch degradation and sucrose synthesis at 90-100 DAF. It also strongly increased the enzyme activity of SUS-synthetic, which may promote sucrose synthesis. Gene co-expression network analysis showed that ABA and peroxide were related to starch decomposition during Chinese chestnut ripening. Our study analyzed the composition and molecular synthesis mechanism of sugar in Chinese chestnut embryos, and provided a new insight into the regulation pattern of high sugar accumulation in Chinese chestnut nuts.

More than the main structural genes: Regulation of resistant starch formation in rice endosperm and its potential application

In the past decade, research on resistant starch has evoked interest due to the prevention and inhibition of chronic human diseases, such as diabetes, cancer, and obesity. Increasing the amylose content (AC) and resistant starch (RS) has been pivotal in improving the nutritional benefit of rice. However, the exact mechanism of RS formation is complex due to interconnected genetic factors regulating amylose-amylopectin variation. In this review, we discussed the regulatory factors influencing the RS formation centered on the transcription, post-transcriptional, and post-translational processes. Furthermore, we described the developments in RS and AC levels in rice compared with other high RS cereals. Briefly, we enumerated potential applications of high RS mutants in health, medical, and other industries. We contest that the information captured herein can be deployed for marker-assisted breeding and precision breeding techniques through genome editing to improve rice varieties with enhanced RS content.

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.

Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test

The release of new wheat varieties is based on two main characteristics, grain yield and quality, to meet the consumer's demand. Identifying the genetic architecture for yield and key quality traits has wide attention for genetic improvement to meet the global requirement. In this sense, the use of landraces represents an impressive source of natural allelic variation. In this study, a genome-wide association analysis (GWAS) with PCA and kinship matrix was performed to detect QTLs in bread wheat for fifteen quality and agronomic traits using 170 diverse landraces from 24 Mediterranean countries in two years of field trials. A total of 53 QTL hotspots containing 165 significant marker-trait associations (MTAs) were located across the genome for quality and agronomical traits except for chromosome 2D. The major specific QTL hotspots for quality traits were QTL_3B.3 (13 MTAs with a mean PVE of 8.2%) and QTL_4A.3 (15 MTAs, mean PVE of 11.0%), and for yield-related traits were QTL_2B.1 (8 MTAs, mean PVE of 7.4%) and QTL_4B.2 (5 MTAs, mean PVE of 10.0%). A search for candidate genes (CG) identified 807 gene models within the QTL hotspots. Ten of these CGs were expressed specifically in grain supporting the role of identified QTLs in Landraces, associated to bread wheat quality traits and grain formation. A cross-validation approach within the collection was performed to calculate the accuracies of genomic prediction for quality and agronomical traits, ranging from -0.03 to 0.64 for quality and 0.46 to 0.65 for agronomic traits. In addition, five prediction equations using the phenotypic data were developed to predict bread loaf volume in landraces. The prediction ability varied from 0.67 to 0.82 depending on the complexity of the traits considered to predict loaf volume.

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

Co-Overexpression of Two Key Source Genes, OsBMY4 and OsISA3, Improves Multiple Key Traits of Rice Seeds

Optimized source-sink interactions are determinants of both rice yield and quality. However, most source genes have not been well studied in rice, a major grain crop. In this study, OsBMY4 and OsISA3, the key β-amylase and debranching enzymes that control transient starch degradation in rice leaves, were co-overexpressed in rice in order to accelerate starch degradation efficiency and increase the sugar supply for sink organs. Systematic analyses of the transgenic rice indicated that co-overexpression of OsBMY4 and OsISA3 not only promoted rice yield and quality, but also improved seed germination and stress tolerance. Moreover, since the OsBMY4 gene has not been characterized, we generated osbmy4 mutants using CRIPSR/Cas9 gene editing, which helped to reveal the roles of β-amylase in rice yield and quality. This study demonstrated that specific modulation of the expression of some key source genes improves the source-sink balance and leads to improvements in multiple key traits of rice seeds.

Pyruvate transporter BnaBASS2 impacts seed oil accumulation in Brassica napus

Bile acid: sodium symporter family protein 2 (BASS2) is a sodium-dependent pyruvate transporter, which transports pyruvate from cytosol into plastid in plants. In this study, we investigated the function of chloroplast envelope membrane-localized BnaBASS2 in seed metabolism and seed oil accumulation of Brassica napus (B. napus). Four BASS2 genes were identified in the genome of B. napus. BnaA05.BASS2 was overexpressed while BnaA05.BASS2 and BnaC04.BASS2-1 were mutated by CRISPR in B. napus. Metabolite analysis revealed that the manipulation of BnaBASS2 caused significant changes in glycolysis-, fatty acid synthesis-, and energy-related metabolites in the chloroplasts of 31 day-after-flowering (DAF) seeds. The analysis of fatty acids and lipids in developing seeds showed that BnaBASS2 could affect lipid metabolism and oil accumulation in developing seeds. Moreover, the overexpression (OE) of BnaA05.BASS2 could promote the expression level of multiple genes involved in the synthesis of oil and the formation of oil body during seed development. Disruption of BnaA05.BASS2 and BnaC04.BASS2-1 resulted in decreasing the seed oil content (SOC) by 2.8%-5.0%, while OE of BnaA05.BASS2 significantly promoted the SOC by 1.4%-3.4%. Together, our results suggest that BnaBASS2 is a potential target gene for breeding B. napus with high SOC.

Starch phosphorylase 2 is essential for cellular carbohydrate partitioning in maize

Carbohydrate partitioning is essential for plant growth and development, and its hindrance will result in excess accumulation of carbohydrates in source tissues. Most of the related mutants in maize (Zea mays L.) display impaired whole-plant sucrose transport, but other mechanisms affecting carbohydrate partitioning have seldom been reported. Here, we characterized chlorotic leaf3 (chl3), a recessive mutation causing leaf chlorosis with starch accumulation excessively in bundle sheath chloroplasts, suggesting that chl3 is defective in carbohydrate partitioning. Positional cloning revealed that the chl3 phenotype results from a frameshift mutation in ZmPHOH, which encodes starch phosphorylase 2. Two mutants in ZmPHOH exhibited the same phenotype as chl3, and both alleles failed to complement the chl3 mutant phenotype in an allelism test. Inactivation of ZmPHOH in chl3 leaves reduced the efficiency of transitory starch conversion, resulting in increased leaf starch contents and altered carbohydrate metabolism patterns. RNA-seq revealed the transcriptional downregulation of genes related to photosynthesis and carbohydrate metabolism in chl3 leaves compared to the wild type. Our results demonstrate that transitory starch remobilization is very important for cellular carbohydrate partitioning in maize, in which ZmPHOH plays an indispensable role.

Strategies for Efficient Gene Editing in Protoplasts of Solanum tuberosum Theme: Determining gRNA Efficiency Design by Utilizing Protoplast (Research)

Potato, Solanum tuberosum is a highly diverse tetraploid crop. Elite cultivars are extremely heterozygous with a high prevalence of small length polymorphisms (indels) and single nucleotide polymorphisms (SNPs) within and between cultivars, which must be considered in CRISPR/Cas gene editing strategies and designs to obtain successful gene editing. In the present study, in-depth sequencing of the gene encoding glucan water dikinase (GWD) 1 and the downy mildew resistant 6 (DMR6-1) genes in the potato cultivars Saturna and Wotan, respectively, revealed both indels and a 1.3–2.8 higher SNP prevalence when compared to the heterozygous diploid RH genome sequence as expected for a tetraploid compared to a diploid. This complicates guide RNA (gRNA) and diagnostic PCR designs. At the same time, high editing efficiencies at the cell pool (protoplast) level are pivotal for achieving full allelic knock-out in tetraploids. Furthermore, high editing efficiencies reduce the downstream cumbersome and delicate ex-plant regeneration. Here, CRISPR/Cas ribonucleoprotein particles (RNPs) were delivered transiently to protoplasts by polyethylene glycol (PEG) mediated transformation. For each of GWD1 and the DMR6-1, 6–10 gRNAs were designed to target regions comprising the 5′ and the 3′ end of the two genes. Similar to other studies including several organisms, editing efficiency of the individual RNPs varied significantly, and some generated specific indel patterns. RNP’s targeting the 5′ end of GWD1 yielded significantly higher editing efficiency as compared to targeting the 3′ end. For DMR6-1, such an effect was not seen. Simultaneously targeting each of the two target regions with two RNPs (multiplexing) yielded a clear positive synergistic effect on the total editing when targeting the 3′ end of the GWD1 gene only. Multiplexing of the two genes, residing on different chromosomes, yielded no or a slightly negative effect on editing from the single or combined gRNA/RNPs. These initial findings may instigate much larger studies needed for facilitating and optimizing precision breeding in plants.