Fine mapping and candidate gene analysis of the floury endosperm gene, FLO(a), in rice

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

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

Starch: A Flexible, Adaptable Carbon Store Coupled to Plant Growth

Research in the past decade has uncovered new and surprising information about the pathways of starch synthesis and degradation. This includes the discovery of previously unsuspected protein families required both for processes and for the long-sought mechanism of initiation of starch granules. There is also growing recognition of the central role of leaf starch turnover in making carbon available for growth across the day-night cycle. Sophisticated systems-level control mechanisms involving the circadian clock set rates of nighttime starch mobilization that maintain a steady supply of carbon until dawn and modulate partitioning of photosynthate into starch in the light, optimizing the fraction of assimilated carbon that can be used for growth. These discoveries also uncover complexities: Results from experiments with Arabidopsis leaves in conventional controlled environments are not necessarily applicable to other organs or species or to growth in natural, fluctuating environments.

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) regulates starch biosynthesis and seed development via heterotetramer formation in rice (Oryza sativa L.)

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) reversibly converts fructose 6-phosphate and pyrophosphate to fructose 1, 6-bisphosphate and orthophosphate during glycolysis, and has diverse functions in plants. However, mechanisms underlying the regulation of starch metabolism by PFP1 remain elusive. This study addressed the function of PFP1 in rice floury endosperm and defective grain filling. Compared with the wild type, pfp1-3 exhibited remarkably low grain weight and starch content, significantly increased protein and lipid content, and altered starch physicochemical properties and changes in embryo development. Map-based cloning revealed that pfp1-3 is a novel allele and encodes the regulatory β-subunit of PFP1 (PFP1β). Measurement of nicotinamide adenine dinucleotide (NAD+) showed that mutation of PFP1β markedly decreased its enzyme activity. PFP1β and three of four putative catalytic α-subunits of PFP1, PFP1α1, PFP1α2, and PFP1α4, interacted with each other to form a heterotetramer. Additionally, PFP1β, PFP1α1 and PFP1α2 also formed homodimers. Furthermore, transcriptome analysis revealed that mutation of PFP1β significantly altered expression of many essential enzymes in starch biosynthesis pathways. Concentrations of multiple lipid and glycolytic intermediates and trehalose metabolites were elevated in pfp1-3 endosperm, indicating that PFP1 modulates endosperm metabolism, potentially through reversible adjustments to metabolic fluxes. Taken together, these findings provide new insights into seed endosperm development and starch biosynthesis and will help in the breeding of rice cultivars with higher grain yield and quality.

FLOURY ENDOSPERM16 encoding a NAD-dependent cytosolic malate dehydrogenase plays an important role in starch synthesis and seed development in rice

Starch is the most important form of energy storage in cereal crops. Many key enzymes involved in starch biosynthesis have been identified. However, the molecular mechanisms underlying the regulation of starch biosynthesis are largely unknown. In this study, we isolated a novel floury endosperm rice (Oryza sativa) mutant flo16 with defective starch grain (SG) formation. The amylose content and amylopectin structure were both altered in the flo16 mutant. Map-based cloning and complementation tests demonstrated that FLO16 encodes a NAD-dependent cytosolic malate dehydrogenase (CMDH). The ATP contents were decreased in the mutant, resulting in significant reductions in the activity of starch synthesis-related enzymes. Our results indicated that FLO16 plays a critical role in redox homeostasis that is important for compound SG formation and subsequent starch biosynthesis in rice endosperm. Overexpression of FLO16 significantly improved grain weight, suggesting a possible application of FLO16 in rice breeding. These findings provide a novel insight into the regulation of starch synthesis and seed development in rice.

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.

A new SNP in cyOsPPDK gene is associated with floury endosperm in Suweon 542

Pyruvate orthophosphate dikinase (PPDK) is a component of glycolysis to mediate endosperm energy charge by adjusting the ratio of ATP to ADP and AMP that proposed to balance the flow of carbon into starch, protein, fatty acid and amino acid biosynthesis. However, these were inconsistent with the first report of a T-DNA insertional knockout mutant of the rice PPDK gene (flo4) showed that rice with inactivated PPDK gene failed to produce a opaque seeds. Therefore, the PPDK might have multifaceted functions in grain filling stage, which in some ways might depend on the direction of the reversible catalysis. Suweon 542 is a rice (Oryza sativa L.) mutant developed from Oryza sativa ssp. japonica cv. Namil. Suweon 542 has a milky-white floury endosperm suitable for dry filling, with low starch damage, low grain hardness, and fine flour particle size. The mutant locus on chromosome 5 controls the floury endosperm phenotype of Suweon 542. Fine mapping of this locus is required for efficient breeding of rice germplasm suitable for dry milling. In this study, whole genome of Suweon 542 and Milyang 23 were re-sequenced using Illumina HiSeq 2500. Co-segregation analysis of F_3:4 family populations derived from Suweon 542/Milyang 23 was performed using eight CAPS markers and phenotypic evaluation of the endosperm. The target region was mapped to a 33 kb region and identified to encode cytosolic pyruvate orthophosphate dikinase protein (cyOsPPDK). A G→A SNP in exon 8 of cyOsPPDK resulting in a missense mutation from Gly to Asp at amino acid position 404 was responsible for the floury endosperm of Suweon 542. qRT-PCR experiments revealed that FLO4-4 was expressed to a considerably higher level in Suweon 542 than in Namil during the grain filling stage. Overall, fine mapping of FLO4-4 and candidate gene analysis provided further insight into the floury endosperm of rice, and reveal a novel SNP in cyOsPPDK gene can affect the floury endosperm phenotype through active PPDK gene during grain filling stage.

Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits

BACKGROUND

Rice represents one the most important foods all over the world. In Europe, Italy is the first rice producer and Italian production is driven by tradition and quality. All main rice grain quality traits, like cooking properties, texture, gelatinization temperature, chalkiness and yield, are related to the content and composition of starch and seed-storage proteins in the endosperm and to grain shape. In addition, a number of nutraceutical compounds and allergens are known to have a significant effect on grain quality determination. To investigate the genetic bases underlying the qualitative differences that characterize traditional Italian rice cultivars, a comparative RNA-Seq-based transcriptomic analysis of developing caryopsis was conducted at 14 days after flowering on six popular Italian varieties (Carnaroli, Arborio, Balilla, Vialone Nano, Gigante Vercelli and Volano) phenotypically differing for qualitative grain-related traits.

RESULTS

Co-regulation analyses of differentially expressed genes showing the same expression patterns in the six genotypes highlighted clusters of loci up or down-regulated in specific varieties, with respect to the others. Among them, we detected loci involved in cell wall biosynthesis, protein metabolism and redox homeostasis, classes of genes affecting in chalkiness determination. Moreover, loci encoding for seed-storage proteins, allergens or involved in the biosynthesis of specific nutraceutical compounds were also present and specifically regulated in the different clusters. A wider investigation of all the DEGs detected in pair-wise comparisons revealed transcriptional variation, among the six genotypes, for quality-related loci involved in starch biosynthesis (e.g. GBSSI, starch synthases and AGPase), genes encoding for transcription factors, additional seed storage proteins, allergens or belonging to additional nutraceutical compounds biosynthetic pathways and loci affecting grain size. Putative functional SNPs associated to amylose content in starch, gelatinization temperature and grain size were also identified.

CONCLUSIONS

The present work represents a more extended phenotypic characterization of a set of rice accessions that present a wider genetic variability than described nowadays in literature. The results provide the first transcriptional picture for several of the grain quality differences observed among the Italian rice varieties analyzed and reveal that each variety is characterized by the over-expression of a peculiar set of loci affecting grain appearance and quality. A list of candidates and SNPs affecting specific grain properties has been identified offering a starting point for further works aimed to characterize genes and molecular markers for breeding programs.

Designing climate-resilient rice with ideal grain quality suited for high-temperature stress

To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality.

Three novel alleles of FLOURY ENDOSPERM2 (FLO2) confer dull grains with low amylose content in rice

Rice is a major food source for much of the world, and expanding our knowledge of genes conferring specific rice grain attributes will benefit both farmer and consumer. Here we present novel dull grain mutants with a low amylose content (AC) derived from mutagenesis of Oryza sativa, ssp. japonica cv. Taikeng 8 (TK8). Positional cloning of the gene conferring the dull grain phenotype revealed a point mutation located at the acceptor splice site of intron 11 of FLOURY ENDOSPERM2 (FLO2), encoding a tetratricopeptide repeat domain (TPR)-containing protein. Three novel flo2 alleles were identified herein, which surprisingly conferred dull rather than floury grains. The allelic diversity of flo2 perturbed the expression of starch synthesis-related genes including OsAGPL2, OsAGPS2b, OsGBSSI, OsBEI, OsBEIIb, OsISA1, and OsPUL. The effect of the flo2 mutations on the physicochemical properties of the grain included a low breakdown, setback, and consistency of rice, indicating a good elasticity and soft texture of cooked rice grains. The effects of FLO2, combined with the genetic background of the germplasm and environmental effects, resulted in a variety of different amylose content levels, grain appearance, and physicochemical properties of rice, providing a host of useful information to future grain-quality research and breeding.

Agronomic and genetic analysis of Suweon 542, a rice floury mutant line suitable for dry milling

BACKGROUND

Producing rice flour of good quality by dry milling is necessary to reduce milling costs and promote the processed rice food industry. This study was conducted to evaluate the dry milling properties of Suweon 542, a floury endosperm mutant, and identify the chromosomal region responsible for the floury endosperm characteristics.

RESULTS

Compared with the wild type, after dry milling process, the grain hardness of Suweon 542 was significantly lower because of its round and loosely packed starch granules. Also, the flour of Suweon 542 had significantly smaller particles and less damaged starch than Namil and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Considering that the yield loss of Suweon 542 due to its floury endosperm was largely compensated for by an increased number of spikelets per panicle, Suweon 542 has potential value as a raw material for rice flour production. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from Suweon 542/Milyang 23 showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of Suweon 542 was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population.

CONCLUSIONS

The floury endosperm of Suweon 542 is suitable for dry milling, with a small flour particle size and low damaged starch content. Further physical mapping of flo7(t), the floury endosperm locus of Suweon 542, would facilitate efficient breeding of rice cultivars with proper dry milling adaptability that can be used in the processed rice food industry.

Yield-related QTLs and their applications in rice genetic improvement

Grain yield is one of the most important indexes in rice breeding, which is governed by quantitative trait loci (QTLs). Different mapping populations have been used to explore the QTLs controlling yield related traits. Primary populations such as F(2) and recombinant inbred line populations have been widely used to discover QTLs in rice genome-wide, with hundreds of yield-related QTLs detected. Advanced populations such as near isogenic lines (NILs) are efficient to further fine-map and clone target QTLs. NILs for primarily identified QTLs have been proposed and confirmed to be the ideal population for map-based cloning. To date, 20 QTLs directly affecting rice grain yield and its components have been cloned with NIL-F(2) populations, and 14 new grain yield QTLs have been validated in the NILs. The molecular mechanisms of a continuously increasing number of genes are being unveiled, which aids in the understanding of the formation of grain yield. Favorable alleles for rice breeding have been 'mined' from natural cultivars and wild rice by association analysis of known functional genes with target trait performance. Reasonable combination of favorable alleles has the potential to increase grain yield via use of functional marker assisted selection.