Starch Synthesis-related Genes Research Articles

SlNAP1 promotes tomato fruit ripening by regulating carbohydrate metabolism

Many studies showed NAC transcription factors play an important role in fruit ripening. Moreover, sucrose and starch metabolism is also closely related to fruit ripening. However, there are a few studies focus on whether NAC regulates sucrose and starch metabolism to influence fruit ripening. In this study, virus-induced gene silencing (VIGS) of SlNAP1 suppressed fruit ripening and delayed color transformation. The chlorophyll (including Chla, Chlb, and Chla + b) degradation and carotenoid synthesis in SlNAP1-silenced fruits were dramatically suppressed. Silencing SlNAP1 decreased soluble sugar and reducing sugar accumulation in fruits, and increased starch content. The activity of starch degrading enzymes, including α amylase (AMY) and β amylase (BAM) was significantly lower in SlNAP1-silenced fruits than in the control fruits, whereas denosine diphosphoglucose pyrophosphorylase (AGP) activity was significantly higher. In addition, the expression of starch degradation-related genes (SlAMY1, SlAMY2, SlBAM1, SlBAM7, SlGWD, SlPWD) in SlNAP1-silenced fruits was significantly suppressed, while starch synthesis-related genes (SlAGPase1, SlAGPase2) was significantly increased. Compared with the control fruits, SlNAP1-silenced fruits showed significantly lower sucrose and glucose content. The expression level of sucrose and glucose metabolism-related genes such as Slsus1, Slsus3, SlSPS, SlHxk1, SlHxk2, SlPK1, and SlPK2 was significantly lower in SlNAP1-silenced fruits than in the control fruits. Overall, this study revealed that SlNAP1 gene might positively regulate fruit ripening by influencing carbohydrate metabolism.

Single-cell RNA-sequencing provides new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass leaf blades

As an important warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) flourishes in warm areas around the world due to the existence of the C4 photosynthetic pathway. However, how C4 photosynthesis operates in bermudagrass leaves is still poorly understood. In this study, we performed single-cell RNA-sequencing on 5296 cells from bermudagrass leaf blades. Eight cell clusters corresponding to mesophyll, bundle sheath, epidermis and vascular bundle cells were successfully identified using known cell marker genes. Expression profiling indicated that genes encoding NADP-dependent malic enzymes (NADP-MEs) were highly expressed in bundle sheath cells, whereas NAD-ME genes were weakly expressed in all cell types, suggesting C4 photosynthesis of bermudagrass leaf blades might be NADP-ME type rather than NAD-ME type. The results also indicated that starch synthesis-related genes showed preferential expression in bundle sheath cells, whereas starch degradation-related genes were highly expressed in mesophyll cells, which agrees with the observed accumulation of starch-filled chloroplasts in bundle sheath cells. Gene co-expression analysis further revealed that different families of transcription factors were co-expressed with multiple C4 photosynthesis-related genes, suggesting a complex transcription regulatory network of C4 photosynthesis might exist in bermudagrass leaf blades. These findings collectively provided new insights into the cell-specific expression patterns and transcriptional regulation of photosynthetic genes in bermudagrass.

Difference in responsiveness of expressions of starch synthesis-related genes to CRCT among rice cultivars

ABSTRACT CO2-Responsive CCT Protein (CRCT) is a transcription factor regulating the expression of starch synthesis-related genes in the vegetative organs of rice. Among six rice cultivars (Nipponbare, Koshihikari, Habataki, Takanari, Momiroman, Leafstar), the expression of CRCT was highly correlated with the starch content of leaf sheath in Nipponbare, but not in Koshihikari, Takanari and Momiroman during plant development. Meanwhile, the expressions of starch synthesis-related genes such as ADP-glucose pyrophosphorylase large subunit 1 was correlated with CRCT expression in Nipponbare, Momiroman, and Leafstar, but the correlations were ambiguous in Koshihikari, Habataki, and Takanari. In addition, the slopes of its regression lines in Nipponbare were larger than those cultivars. These results suggest that the influence of CRCT on starch synthesis varies among these cultivars. Additionally, the similar cultivar differences were observed when these gene expressions were analyzed after sucrose treatment in leaf blade. Some mutations in the promoter regions of the starch synthesis-related genes were identified among these cultivars. There were cultivars in which the presence of mutations correlated with decreased expression of starch synthesis genes in response to CRCT. Thus, these mutations can partially explain the responsiveness of the starch synthesis-related genes to CRCT, and difference in starch content of vegetative organs among rice cultivars.

Regulatory loops between rice transcription factors OsNAC25 and OsNAC20/26 balance starch synthesis.

Several starch synthesis regulators have been identified, but these regulators are situated in the terminus of the regulatory network. Their upstream regulators and the complex regulatory network formed between these regulators remain largely unknown. A previous study demonstrated that NAM, ATAF, and CUC (NAC) transcription factors, OsNAC20 and OsNAC26 (OsNAC20/26), redundantly and positively regulate the accumulation of storage material in rice (Oryza sativa) endosperm. In this study, we detected OsNAC25 as an upstream regulator and interacting protein of OsNAC20/26. Both OsNAC25 mutation and OE resulted in a chalky seed phenotype, decreased starch content, and reduced expression of starch synthesis-related genes, but the mechanisms were different. In the osnac25 mutant, decreased expression of OsNAC20/26 resulted in reduced starch synthesis; however, in OsNAC25-overexpressing plants, the OsNAC25-OsNAC20/26 complex inhibited OsNAC20/26 binding to the promoter of starch synthesis-related genes. In addition, OsNAC20/26 positively regulated OsNAC25. Therefore, the mutual regulation between OsNAC25 and OsNAC20/26 forms a positive regulatory loop to stimulate the expression of starch synthesis-related genes and meet the great demand for starch accumulation in the grain filling stage. Simultaneously, a negative regulatory loop forms among the 3 proteins to avoid the excessive expression of starch synthesis-related genes. Collectively, our findings demonstrate that both promotion and inhibition mechanisms between OsNAC25 and OsNAC20/26 are essential for maintaining stable expression of starch synthesis-related genes and normal starch accumulation.

AGPS and BAM genes dramatically improve ‘Ganlv 1′ (Actinidia eriantha) fruit quality through starch metabolism during fruit development

In previous field investigations, we found that Actinidia eriantha has sweeter flavor than other kiwifruit, which provided an opportunity to explore the formation mechanism of sweet flavor. In this study, we selected three cultivars of kiwifruit with different accumulation characters of starch and sugar, i.e., ‘Ganlv 1′ (A. eriantha), ‘Jinkui’ (A. chinensis var. deliciosa), and ‘Jinyan’ (A. eriantha × A. chinensis var. chinensis), as materials to identify the key regulatory enzymes and genes. Our results showed that the maximum starch content in A. eriantha was the highest. Importantly, the A. eriantha also had the highest degradation rate, because of the highest amylase activity in A. eriantha among the cultivars tested. Fifty-nine differentially expressed genes involved in starch metabolism were identified by the transcriptome data, the accuracy of transcriptome data was verified by qRT-PCR analysis. Among these genes, starch synthesis related genes were significantly up-regulated at 120 DAFB in A. eriantha, including AGPS1.1, AGPS1.2 and WAXY1. And key degradation related genes were also identified, such as BAM3.2, BAM3.3, PHO1, PHO2.2, SUS2.1 and SUS2.2. Moreover, transient transformations provided overexpressing AcBAM3.3 in kiwifruit could up-regulate the expression of AcBAM3.3 gene and degrade starch content by 15.1∼22.3 %. In conclusion, the stronger biosynthesis capacity and the faster inversion rate of starch in the fruit of A. eriantha were the reasons for its higher sweet flavor in which benefit to fruit quality.

Loss of RSR1 function increases the abscisic acid content and improves rice quality performance at high temperature

Rice starch regulator1 (RSR1) participates in the regulation of starch synthesis in rice, but it's function on starch synthesis and quality formation in response to high temperature is unknown. RSR1 mutation resulted in a significant increase in the abscisic acid (ABA) content in rice grains under both normal and high temperature, and the effect of high temperature on grain filling and quality formation of the rsr1 mutants was significantly reduced. The grain size, 1000-kernels weight, amylose content, gelatinization temperature, and starch viscosity of the rsr1 mutants were less sensitive to high temperature. Loss of RSR1 function increased the expression levels of starch synthesis-related genes and reduced their responses to high temperature to some extent. Besides, the percentage of germinated seeds from rsr1 mutants was significantly lower than that of the wild-type, and the difference was more significant under ABA treatment. The shoot lengths of the rsr1 mutants were remarkably shorter than those of the wild-type, which was further exacerbated by ABA treatment. These results indicated that loss function of RSR1 can improve rice quality performance at high temperature by moderately increasing the ABA content of rice grains, which provides theoretical significance for the cultivation of better-quality rice with high-temperature resistance.

Transcriptomics and physiology reveal the mechanism of potassium indole-3-butyrate (IBAK) mediating rice resistance to salt stress

BackgroundIBAK, as a plant growth regulator, has broad application prospects in improving crop resistance to abiotic stress.ResultsIn this study, the regulation mechanism of IBAK on rice was revealed by physiology and transcriptomics by spraying 80 mg·L−1 IBAK solution on rice leaves at the early jointing stage under salt stress. The results showed that spraying IBAK solution on leaves under salt stress could significantly increase K+ content, decrease Na+ content, increase net photosynthetic rate (Pn), and increase the activity of catalase (CAT) and the contents of glutathione (GSH) and soluble protein in rice leaves. Using IBAK under salt stress increased the expression of plant hormone signal transduction pathway-related genes LOC4332548 and LOC4330957, which may help rice to more effectively sense and respond to plant hormone signals and enhance resistance to salt stress. In addition, the photosynthesis pathway-related genes LOC4339270, LOC4327150, and LOC4346326 were upregulated after using IBAK under salt stress, and the upregulation of these genes may be beneficial to improve the efficiency of photosynthesis and increase the photosynthetic capacity of rice. Regarding starch and sucrose metabolism pathway, spraying IBAK on leaves could promote the expression of sucrose synthesis-related gene LOC4347800 and increase the expression of starch synthesis-related genes LOC4330709 and LOC4343010 under salt stress. Finally, IBAK spraying resulted in the upregulation of multiple 50 S and 30 S ribosomal protein genes in the ribosome pathway, which may increase protein synthesis, help maintain cell function, and promote rice growth and development.ConclusionThe results of this study revealed the mechanism of IBAK mediating resistance to salt stress in rice.

Physicochemical properties, eating and cooking quality and genetic variability: a comparative analysis in selected rice varieties of South India

The physicochemical characteristics and digestibility properties of rice are greatly influenced by its genetic variability. In this study, we attempt to understand the overall quality of five traditional and popularly consumed rice varieties of Kerala. The major traits affecting the eating and cooking quality of rice such as amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) were determined and correlated with the expression of the starch-synthesis-related genes (SSRGs). The Wx is a major SSRG, which modulates the amylose content and the eating as well as cooking qualities of rice. The rice varieties including, Jaya, Matta and Rakthashali were found to have intermediate amylose content (Wxa allele) while Kuruva and Pokkali were found to have high Amylose Content (Wxa allele). The glycemic index (GI) of all varieties was found to be in the range of 51.0–58.6. Among the screened rice varieties, Pokkali was found to have the lowest glycemic index and digestibility with appreciable eating and cooking qualities. Pokkali rice, with its low GI (51.0), could be a recommended variety for diabetes management. Furthermore, the rice eating and cooking qualities, and plant breeding techniques coordinated by the expression of the starch synthesis-related gene (Wx), could be a novel approach to improve the valuable germplasm.Graphical

JAZ1 gene regulates starch biosynthesis and changes physicochemical properties in wheat grains

Starch is the main component of crop grains. Jasmonate-ZIM domain (JAZ1), is a transcriptional repressor in the jasmonate signaling pathway, has been widely studied in plant development, and stresses responses. However, its function in crop starch biosynthesis remains unclear. In this study, the intrinsic relationship between TaJAZ1 and starch biosynthesis was studied using barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. The results showed that, compared with the control, grain length, thousand kernel weight, contents of total starch and amylopectin were significantly increased in grains of BSMV-TaJAZ1-silenced plants. And its starch ultrastructures, such as volume, surface area, relative crystallinity, and some viscosity parameters were also significantly changed in above grains. Moreover, the molecular mechanisms of TaJAZ1 involving starch biosynthesis were further explored by measuring the expression levels of starch synthesis-related genes. Results showed that TaJAZ1 gene silencing increased the expression of TaAGPS1, TaAGPL1, TaBEIIb and TaSSI and decreased TaGBSSI or TaSSIIIa, while their expressions were separately decreased or increased in TaJAZ1 transiently overexpression wheat plants. To conclude, these findings showed that TaJAZ1 involved starch synthesis by affecting the expression levels of six starch synthesis enzyme-related genes further changing the components, ultrastructures, and physicochemical properties of starch in wheat grain.

Effects of knockout of CO2-responsive CCT protein, a regulator of starch synthesis on physiological characteristics of rice

ABSTRACT CO2-Responsive CCT Protein (CRCT) is suggested to be a positive regulator of starch synthesis-related genes in the vegetative organs of rice. To investigate the physiological function of CRCT, we produced CRCT knockout lines by CRISPR/Cas9 system. CRCT knockout tended to slightly reduce photosynthetic performance and had some adverse effects on growth parameters such as tiller number and straw dry weight. The starch content in the leaf sheath of CRCT knockout lines was significantly lower than that of wild-type. qRT-PCR and RNA-seq analysis showed that sucrose treatment induced the expression of CRCT, which, in turn, induced many starch synthesis-related genes in wild-type, whereas this induction did not occur in CRCT knockout lines. In conclusion, our results suggest that sugar induction of starch synthesis-related genes is almost fully dependent on CRCT, making it a necessary factor for normal photosynthesis and growth of rice.

Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.)

Chalkiness is one of the most important agronomic traits in rice breeding, which directly affects the quality of rice seed. In this study, we identified a chalkiness endosperm mutant, chalk-h, from N-methyl-N-nitrosourea (MNU)-induced japonica rice cultivar Hwacheong (HC). Compared with wild type (WT)-HC, chalk-h showed severe chalkiness in the endosperm, yellowish green leaves, as well as reduced plant height. Scanning electron microscopy (SEM) analysis showed that starch grains in the chalk-h mutant were irregular in size and loosely arranged, with large gaps between granules, forming ovoid or orbicular shapes. MutMap analysis revealed that the phenotype of chalk-h is controlled by a single recessive gene LOC_Os11g39670 encoding seryl-tRNA synthetase, which is renamed as CHALK-H. A point mutation occurs in chalk-h on the sixth exon (at nucleotide 791) of CHALK-H, in which adenine (A) is replaced by thymidine (T), resulting in an amino acid codon change from glutamine (Glu) to valine (Val). The chalk-h mutant exhibited a heat-sensitive phenotype from the 3-leaf stage, including yellow-green leaves and reduced pigment content. The transcriptional expression of starch synthesis-related genes was down-regulated in the chalk-h mutants compared to WT-HC at different grain-filling stages. With an increase in temperature, the expression of photosynthesis-related genes was down-regulated in the chalk-h mutant compared to WT-HC. Overexpression of CHALK-H rescued the phenotype of chalk-h, with endosperm and leaf color similar to those of WT-HC. Our findings reveal that CHALK-H is a causative gene controlling chalkiness and leaf color of the chalk-h mutant. CHALK-H is the same gene locus as TSCD11, which was reported to be involved in chloroplast development under high temperature. We suggest that CHALK-H/TSCD11 plays important roles not only in chloroplast development, but also in photosynthesis and starch synthesis during rice growth and development, so it has great application potential in rice breeding for high quality and yield.

Disentangling the resistant mechanism of Fusarium wilt TR4 interactions with different cultivars and its elicitor application.

Fusarium wilt of banana, especially Tropical Race 4 (TR4) is a major factor restricting banana production. Developing a resistant cultivar and inducing plant defenses by elicitor application are currently two of the best options to control this disease. Isotianil is a monocarboxylic acid amide that has been used as a fungicide to control rice blast and could potentially induce systemic acquired resistance in plants. To determine the control effect of elicitor isotianil on TR4 in different resistant cultivars, a greenhouse pot experiment was conducted and its results showed that isotianil could significantly alleviate the symptoms of TR4, provide enhanced disease control on the cultivars 'Baxi' and 'Yunjiao No.1' with control effect 50.14% and 56.14%, respectively. We compared the infection processes in 'Baxi' (susceptible cultivars) and 'Yunjiao No.1' (resistant cultivars) two cultivars inoculated with pathogen TR4. The results showed that TR4 hyphae could rapidly penetrate the cortex into the root vascular bundle for colonization, and the colonization capacity in 'Baxi' was significantly higher than that in 'Yunjiao No.1'. The accumulation of a large number of starch grains was observed in corms cells, and further analysis showed that the starch content in 'Yunjiao No. 1' as resistant cultivar was significantly higher than that in 'Baxi' as susceptible cultivar, and isotianil application could significantly increase the starch content in 'Baxi'. Besides, a mass of tyloses were observed in the roots and corms and these tyloses increased after application with isotianil. Furthermore, the total starch and tyloses contents and the control effect in the corms of 'Yunjiao No.1' was higher than that in the 'Baxi'. Moreover, the expression levels of key genes for plant resistance induction and starch synthesis were analyzed, and the results suggested that these genes were significantly upregulated at different time points after the application of isotianil. These results suggest that there are significant differences between cultivars in response to TR4 invasion and plant reactions with respect to starch accumulation, tyloses formation and the expression of plant resistance induction and starch synthesis related genes. Results also indicate that isotianil application may contribute to disease control by inducing host plant defense against TR4 infection and could be potentially used together with resistant cultivar as integrated approach to manage this destructive disease. Further research under field conditions should be included in the next phases of study.

Identification of a new allele of soluble starch synthase IIIa involved in the elongation of amylopectin long chains in a chalky rice mutant

A chalky endosperm mutant (GM03) induced from an indica rice GLA4 was used to investigate the functional gene in starch biosynthesis. Bulked segregant analysis and sanger sequencing determined that a novel mutation in soluble starch synthase IIIa (SSIIIa) is responsible for the chalky phenotype in GM03. Complementary test by transforming the active SSIIIa gene driven by its native promoter to GM03 recovered the phenotype to its wildtype. The expression of SSIIIa was significantly decreased, while SSIIIa protein was not detected in GM03. The mutation of SSIIIa led to increased expression of most of starch synthesis related genes and elevated the levels of most of proteins in GM03. The CRISPR/Cas9 technology was used for targeted disruption of SSIIIa, and the mutant lines exhibited chalky endosperm which phenocopied the GM03. Additionally, the starch fine structure in the knockout mutant lines ss3a-1 and ss3a-2 was similar with the GM03, which showed increased amylose content, higher proportions of B1 and B2 chains, much lower proportions of B3 chains and decreased degree of crystallinity, leading to altered thermal properties with lower gelatinization temperature and enthalpy. Collectively, these results suggested that SSIIIa plays an important role in starch synthesis by elongating amylopectin long chains in rice.

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.

Mutation of TL1, encoding a novel C2H2 zinc finger protein, improves grains eating and cooking quality in rice.

The cloning and characterization of a novel C2H2 zinc finger protein that affects rice eating and cooking quality by regulating amylose content and amylopectin chain-length distribution in rice. One of the major objectives in rice breeding aims to increase simultaneously yield and grain quality especially eating and cooking quality (ECQ). Controlling amylose content (AC) and amylopectin chain-length distribution (ACLD) in rice is a major strategy for improving rice ECQ. Previous studies show that some starch synthesis-related genes (SSRGs) are required for normal AC and ACLD, but its underlying regulating network is still unclear. Here, we report the cloning and characterization of a novel C2H2 zinc finger protein TL1 (Translucent endosperm 1) that positively regulates amylose synthesis in rice grains. Loss of TL1 function reduced apparent amylose content (AAC), total starch, gel consistency, and gelatinisation temperature, whereas increased viscosity, total lipid, and ratio of amylopectin A chains with degree of polymerization (DP) 6-12 to B1 chains with DP 13-24, resulting in an enhanced grain ECQ. The improved ECQ was accompanied by altered expression patterns of several tested SSRGs in tl1 mutant grains. Furthermore, knockout of TL1 in the high-yielding rice variety JiaHua NO.1 reduced AAC without obvious side effects on major agronomic traits. These findings expand our understanding of the regulating networks of grain starch metabolism and provide new insights into how rice ECQ quality can be improved via genetic approach.

A Maize CBM Domain Containing the Protein ZmCBM48-1 Positively Regulates Starch Synthesis in the Rice Endosperm

Starch directly determines the grain yield and quality. The key enzymes participating in the process of starch synthesis have been cloned and characterized. Nevertheless, the regulatory mechanisms of starch synthesis remain unclear. In this study, we identified a novel starch regulatory gene, ZmCBM48-1, which contained a carbohydrate-binding module 48 (CBM48) domain. ZmCBM48-1 was highly expressed in the maize endosperm and was localized in the plastids. Compared with the wild type lines, the overexpression of ZmCBM48-1 in rice altered the grain size and 1000-grain weight, increased the starch content, and decreased the soluble sugar content. Additionally, the transgenic rice seeds exhibited an alterant endosperm cell shape and starch structure. Meanwhile, the physicochemical characteristics (gelatinization properties) of starch were influenced in the transgenic lines of the endosperm compared with the wild type seeds. Furthermore, ZmCBM48-1 played a positive regulatory role in the starch synthesis pathway by up-regulating several starch synthesis-related genes. Collectively, the results presented here suggest that ZmCBM48-1 acts as a key regulatory factor in starch synthesis, and could be helpful for devising strategies for modulating starch production for a high yield and good quality in maize endosperm.

The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts

BackgroundHigh-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome.ResultsA cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel.ConclusionThe data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.

Starch fine structure and functional properties during seed development in BEIIb active and deficient rice

Loss of starch branching enzyme IIb (BEIIb) leads to altered starch structure and increased amylose content. The changes in starch fine structure and function during seed development were investigated as a result from differentially expressed genes between wildtype (WT) and be2b rice. The expression patterns of all starch synthesis related genes except the AGPS1 were altered in be2b. From five to 15 days after flowering (DAF), the amylose content and proportion of A chains of amylopectin increased, while those of B2, B3 chains and average chain length declined in both WT and be2b. The mutant had a C-type crystalline pattern and a higher relative crystallinity (RC) at five and 10 DAF, which was transferred to a B-type and a lower RC at 15 DAF in be2b, while the WT had A-type starch at all developmental stages. A possible model for amylose and amylopectin structure in WT and be2b was proposed.

Genome wide association study on development and evolution of glutinous rice

BackgroundGlutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers’ preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous.ResultsHere, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then introgressed into indica in SER, SEA and EAR.ConclusionsThe cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.

Diurnal changes in starch molecular structures and expression profiles of starch biosynthesis enzymes in rice developing seeds

The diurnal changes in the expression profiles of starch synthesis related enzymes (SSREs) has been previously studied in transitory starches, while its influences on storage starch molecular structures in the rice endosperm during seed development have not been elucidated. In this study, the changes in the transcript levels of starch synthesis related genes (SSRGs), the protein abundances and enzyme activities of SSREs as well as starch molecular structures in rice endosperm at 10 days after flowering (DAF) over the diurnal cycle were analyzed. It was found that the expression profiles of SSRG and the protein contents of SSREs displayed different diurnal patterns between two indica rice varieties with medium- and high-amylose content (AC), respectively. The expression levels of SSRGs were higher in the light time, and most SSREs also accumulated during this period except debranching enzymes. Amylose synthesis displayed distinct diurnal patterns in two rice varieties, which is attributed to the diurnal changes in the protein content of granule-bound starch synthase I (GBSSI), but amylopectin chain-length distributions (CLDs) remained unaltered due to its vast numbers of branches. The results provide the first step to understand the roles of each enzyme isoform involved in starch synthesis in response to diurnal regulation in rice endosperm.