Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice

Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.

Cooking, morphological, mechanical and digestion properties of cooked rice with suppression of starch branching enzymes

Kernel components and some physicochemical properties of cooked rice were investigated and compared between a popular japonica rice Wu-xiang 9915 (WX) and its transgenic line (WX-SBEI/IIb^-) with suppression of starch branching enzyme I/IIb. The starch content, especially amylopectin content, was significantly lower in WX-SBEI/IIb^- than in WX. Brown rice flour had markedly higher gelatinization temperature in WX-SBEI/IIb^- than in WX. The cooked kernels of WX-SBEI/IIb^- had significantly lower volume swelling, leached material amount and wet weight than those of WX during cooking. Starch granules in WX kernel could be gelatinized completely and gradually from the exterior to the interior of endosperm, leading to breakage of cooked kernels. However, aggregate, elongated and small starch granules in the exterior of WX-SBEI/IIb^- endosperm could not be gelatinized completely and remained their morphologies during cooking, leading to a high resistance of kernels to cooking. Brown rice flour of WX-SBEI/IIb^- had significantly lower pasting viscosities, storage modulus and loss modulus but higher loss angle tangent than that of WX. The cooked kernels of WX-SBEI/IIb^- had considerably higher hardness, springiness and cohesiveness but lower adhesiveness than those of WX. The starch in cooked kernels was more resistant to digestion in WX-SBEI/IIb^- than in WX.

The draft genomes of five agriculturally important African orphan crops

BACKGROUND

The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution.

RESULTS

Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes.

CONCLUSIONS

These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species

BACKGROUND

Amaranth is a plant naturally resistant to various types of stresses that produces seeds of excellent nutritional quality, so amaranth is a promising system for food production. Amaranth wild relatives have survived climate changes and grow under harsh conditions, however no studies about morphological and molecular characteristics of their seeds are known. Therefore, we carried out a detailed morphological and molecular characterization of wild species A. powellii and A. hybridus, and compared them with the cultivated amaranth species A. hypochondriacus (waxy and non-waxy seeds) and A. cruentus.

RESULTS

Seed proteins were fractionated according to their polarity properties and were analysed in one-dimensional gel electrophoresis (1-DE) followed by nano-liquid chromatography coupled to tandem mass spectrometry (nLC-MS/MS). A total of 34 differentially accumulated protein bands were detected and 105 proteins were successfully identified. Late embryogenesis abundant proteins were detected as species-specific. Oleosins and oil bodies associated proteins were observed preferentially in A. cruentus. Different isoforms of the granule-bound starch synthase I, and several paralogs of 7S and 11S globulins were also identified. The in silico structural analysis from different isoforms of 11S globulins was carried out, including new types of 11S globulin not reported so far.

CONCLUSIONS

The results provide novel information about 11S globulins and proteins related in seed protection, which could play important roles in the nutritional value and adaptive tolerance to stress in amaranth species.

Crop resistant starch and genetic improvement: a review of recent advances

Resistant starch (RS), as a healthy dietary fiber, meets with great human favor along with the rapid development and improvement of global living standards. RS shows direct effects in reducing postprandial blood glucose levels, serum cholesterol levels and glycemic index. Therefore, RS plays an important role in preventing and improving non-communicable diseases, such as obesity, diabetes, colon cancer, cardiovascular diseases and chronic kidney disease. In addition, RS leads to its potential applied value in the development of high-quality foodstuffs, such as bread, noodles and dumplings. This paper reviews the recent advances in RS research, focusing mainly on RS classification and measurement, formation, quantitative trait locus mapping, genome-wide association studies, molecular marker development and genetic improvement through induced mutations, plant breeding combined with marker-assisted selection and genetic transformation. Challenges and perspectives on further RS research are also discussed.

Inhibition of starch branching enzymes in waxy rice increases the proportion of long branch-chains of amylopectin resulting in the comb-like profiles of starch granules

Starches with comb-like profiles have been detected in some cereal endosperms with inhibiting expression of starch branching enzyme (SBE). Although amylose is considered to be an important factor in the formation of the comb-like profile, the details remain unclear. In this study, a transgenic rice line (GLXN-SBEI/IIb^-) was derived from japonica waxy rice cultivar Guang-ling-xiang-nuo (GLXN) through antisense RNA inhibition of both SBEI and SBEIIb. The expression and activity of SBEI, SBEIIb and SBEIIa were declined. The GLXN-SBEI/IIb^- endosperm contained large and small starch granules, and these starch granules had the comb-like profiles. The comb-like profiles of starches were detected in GLXN-SBEI/IIb^- endosperm after 10 days after flowering with gradually increasing proportion of long branch-chains of amylopectin. The long branch-chains of amylopectin were responsible for forming the comb-like profiles at the outer region of starch granules. The gradually decreasing expression of SBEs influenced the synthesis of amylopectin during endosperm development, resulting in different structure between the inner and outer regions of starch granules from GLXN-SBEI/IIb^- endosperm. The above results indicated that the long branch-chains of amylopectin, not amylose, led to the formation of comb-like profiles of starch granules in cereal crops with inhibiting expression of SBEs.

Retrospective and perspective of rice breeding in China

Breeding is the art and science of selecting and changing crop traits for the benefit of human beings. For several decades, tremendous efforts have been made by Chinese scientists in rice breeding in improving grain yield, nutrition quality, and environmental performance, achieving substantial progress for global food security. Several generations of crop breeding technologies have been developed, for example, selection of better performance in the field among variants (conventional breeding), application of molecular markers for precise selection (molecular marker assisted breeding), and development of molecular design (molecular breeding by rational design). In this review, we briefly summarize the advances in conventional breeding, functional genomics for genes and networks in rice that regulate important agronomic traits, and molecular breeding in China with focuses on high yield, good quality, stress tolerance, and high nutrient-use efficiency. These findings have paved a new avenue for rational design of crops to develop ideal varieties with super performance and productivity.

Extraction and characterization of starch granule-associated proteins from rice that affect in vitro starch digestibility

Starch granule-associated proteins (SGAPs) including granule-surface proteins and granule-channel proteins in waxy, low- and high-amylose rice starch were extracted and identified. The in vitro digestibility of starch was investigated before and after the extraction of granule-channel proteins or total SGAPs. The results showed that 10 types of major differentially expressed proteins (DEPs) including 14-3-3-like protein and ribosomal protein were found among starches. In addition, the lack of only granule-channel proteins or total SGAPs led to significant and different changes in the levels of rapidly digestible starch, slowly digestible starch and resistant starch. Possible mechanisms are related to the accessibility of amylase into starch granules and structural properties of SGAPs. This study provides more information about DEPs in rice starch with different amylose content and supports further study on the relationship between SGAPs and in vitro starch digestibility.

Down-Regulation of SSSII-2 Gene Expression Results in Novel Low-Amylose Rice with Soft, Transparent Grains

Although soft rice, with low amylose content (AC), has high eating and cooking quality (ECQ), its appearance is poor due to the opaque endosperm. Here, a novel soft rice with low AC but a transparent appearance was generated by knocking-down the expression of SSSII-2, a gene encoding one isoform of soluble starch synthase (SSS). The physicochemical properties of the SSSII-2 RNAi rice are quite different from the control but more like the popular soft rice "Nanjing 46". The taste value assay further demonstrated that the ECQ of SSSII-2 RNAi rice was as high as "Nanjing 46", but only SSSII-2 RNAi rice retained the transparent endosperm under low moisture conditions. Further examination showed that the different morphologies and fine structures of the starch granules may contribute to the specific properties of SSSII-2 RNAi rice. Therefore, SSSII-2 has potential application in future high quality rice breeding programs.

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.

A Novel Mutation of OsPPDKB, Encoding Pyruvate Orthophosphate Dikinase, Affects Metabolism and Structure of Starch in the Rice Endosperm

Starch, as a main energy storage substance, plays an important role in plant growth and human life. Despite the fact that several enzymes and regulators involved in starch biosynthesis have been identified, the regulating mechanism of starch synthesis is still unclear. In this study, we isolated a rice floury endosperm mutant M14 from a mutant pool induced by ⁶⁰Co. Both total starch content and amylose content in M14 seeds significantly decreased, and starch thermal and pasting properties changed. Compound starch granules were defected in the floury endosperm of M14 seeds. Map-based cloning and a complementation test showed that the floury endosperm phenotype was determined by a gene of OsPPDKB, which encodes pyruvate orthophosphate dikinase (PPDK, EC 2.7.9.1). Subcellular localization analysis demonstrated that PPDK was localized in chloroplast and cytoplasm, the chOsPPDKB highly expressed in leaf and leaf sheath, and the cyOsPPDKB constitutively expressed with a high expression in developing endosperm. Moreover, the expression of starch synthesis-related genes was also obviously altered in M14 developing endosperm. The above results indicated that PPDK played an important role in starch metabolism and structure in rice endosperm.

Rice Functional Genomics Research: Past Decade and Future

Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

Gradually Decreasing Starch Branching Enzyme Expression Is Responsible for the Formation of Heterogeneous Starch Granules

Rice (Oryza sativa) endosperm is mainly occupied by homogeneous polygonal starch from inside to outside. However, morphologically different (heterogeneous) starches have been identified in some rice mutants. How these heterogeneous starches form remains unknown. A high-amylose rice line (TRS) generated through the antisense inhibition of starch branching synthase I (SBEI) and SBEIIb contains four heterogeneous starches: polygonal, aggregate, elongated, and hollow starch; these starches are regionally distributed in the endosperm from inside to outside. Here, we investigated the relationship between SBE dosage and the morphological architecture of heterogeneous starches in TRS endosperm from the view of the molecular structure of starch. The results indicated that their molecular structures underwent regular changes, including gradually increasing true amylose content but decreasing amylopectin content and gradually increasing the ratio of amylopectin long chain but decreasing the ratio of amylopectin short chain. Granule-bound starch synthase I (GBSSI) amounts in the four heterogeneous starches were not significantly different from each other, but SBEI, SBEIIa, and SBEIIb showed a gradually decreasing trend. Further immunostaining analysis revealed that the gradually decreasing SBEs acting on the formation of the four heterogeneous granules were mainly due to the spatial distribution of the three SBEs in the endosperm. It was suggested that the decreased amylopectin in starch might remove steric hindrance and provide extra space for abundant amylose accumulation when the GBSSI amount was not elevated. Furthermore, extra amylose coupled with altered amylopectin structure possibly led to morphological changes in heterogeneous granules.

Investigating glycemic potential of rice by unraveling compositional variations in mature grain and starch mobilization patterns during seed germination

Rice lines with slower starch digestibility provide opportunities in mitigating the global rise in type II diabetes and related non-communicable diseases. However, screening for low glycemic index (GI) in rice breeding programs is not possible due to time and cost constraints. This study evaluated the feasibility of using in vitro cooked grain amylolysis, starch mobilization patterns during seed germination, and variation in starch structure and composition in the mature seed to differentiate patterns of starch digestibility. Mobilization patterns of total starch, resistant starch, amylose and amylopectin chains, and free sugars during seed germination revealed that the process is analogous to digestion in the human gastrointestinal tract. The combination of these biochemical markers can be used as an alternative measure to predict GI. Additionally, transcriptome analysis of stored mRNA transcripts in high and low GI lines detected differences in starch metabolism and confirmed the importance of seed storage pathways in influencing digestibility. Pathway analyses supported by metabolomics data revealed that resistant starch, cell wall non-starch polysaccharides and flavonoids potentially contribute to slower digestibility. These new insights can guide precision breeding programs to produce low GI rice with acceptable cooking quality to help mitigate the burden of diet-associated lifestyle diseases.

Differences in specificity and compensatory functions among three major starch synthases determine the structure of amylopectin in rice endosperm

The lengths of amylopectin-branched chains are precise and influence the physicochemical properties of starch, which determine starch functionality. Three major isozymes of starch synthases (SSs), SSI, SSII(a), and SSIII(a), are primarily responsible for amylopectin chain elongation in the storage tissues of plants. To date, the majority of reported rice mutants were generated using japonica cultivars, which have almost inactive SSIIa. Although three SSs share some overlapping chain length preferences, whether they complement each other remains unknown due to the absence of suitable genetic combinations of materials. In this study, rice ss1/SS2a/SS3a and SS1/SS2a/ss3a were newly generated, and the chain length distribution patterns of all the possible combinations of presence and absence of SSI, SSIIa, and SSIIIa activities were compared. This study demonstrated that SSIIa can complement most SSI functions that use glucan chains with DP 6-7 to generate DP 8-12 chains but cannot fully compensate for the elongation of DP 16-19 chains. This suggests that SSIIa preferentially elongates outer but not inner chains of amylopectin. In addition, the results revealed that neither SSI nor SSIIIa compensate for SSIIa. Neither SSI nor SSIIa compensate for elongation of DP >30 by SSIIIa. SSIIa could not resolve the pleiotropic increase of SSI caused by the absence of SSIIIa; instead, SSIIa further elongated those branches elongated by SSI. These results revealed compensatory differences among three major SS isozymes responsible for lengths of amylopectin branches.

Progress in High-Amylose Cereal Crops through Inactivation of Starch Branching Enzymes

High-amylose cereal starches provide many health benefits for humans. The inhibition or mutation of starch branching enzyme (SBE) genes is an effective method to develop high-amylose cereal crops. This review summarizes the development of high-amylose cereal crops through the inactivation of one or more SBE isoforms or combination with other genes. This review also reveals the causes of increase in amylose content in high-amylose crops. A series of changes, including amylopectin structure, crystalline structure, thermal properties, and hydrolysis properties, occurs as amylose content increases. The different morphological starch granules nominated as heterogeneous starch granules or differently stained starch granules are detected in high-amylose cereal crops. Detailed studies on four heterogeneous starch granules in high-amylose rice, which is developed by antisense RNA inhibition of SBEI/IIb, indicate that granules with different morphologies possess various molecular structures and physicochemical and functional properties. This variation diversifies their applications in food and non-food industries. However, current knowledge regarding how these heterogeneous starch granules form and why they exhibit regional distribution in endosperm remain largely unknown.

Development of a High-Efficient Mutation Resource with Phenotypic Variation in Hexaploid Winter Wheat and Identification of Novel Alleles in the TaAGP.L-B1 Gene

Mutated genetic resources play an important role in gene/allele characterization. Currently, there are few hexaploid winter wheat mutated resources available. Here, we developed a hexaploid winter wheat resource by inducing mutations via EMS treatment by the single seed descent method. A broad mutation spectrum with high mutation frequency (∼19%) on phenotypic variations was identified. These mutations included spike, leaf and seed morphology, plant architecture, and heading date variations. To evaluate the efficiency of the resource for reverse genetic analysis, allelic variations in the TaAGP.L-B1 gene, encoding the AGPase large subunit, were screened by the TILLING approach. Four missense mutations were identified and one allele in line E3-1-3, resulted in an amino acid change predicated to have severe effects on gene function. The other three mutations were predicted to have no effect. Results of gene expression patterns and grain starch content demonstrated that the novel allele in E3-1-3 altered the function of TaAGP.L-B1. Our results indicated that this mutated genetic wheat resource contained broad spectrum phenotypic and genotypic variations, that may be useful for wheat improvement, gene discovery, and functional genomics.