Interaction between genetic regions responsible for the starch properties in non-glutinous rice varieties in Hokkaido, Japan.

Starch properties are the major determinants of grain quality and food characteristics in rice (Oryza sativa L.). Understanding the interactions between genetic regions responsible for starch properties will lead to the development of rice cultivars with desirable characteristics. This study investigated the genetic effect and interaction between qAC9.3, a low-amylose quantitative trait locus (QTL), and the genetic region around Starch branching enzyme IIb (SbeIIb). Both these factors are responsible for the starch properties of the Hokkaido breeding population. The amylose content, pasting temperature, and amylopectin chain-length distribution were compared using F5 lines derived from the cross between the lower amylose content and lower pasting temperature strain 'Hokkai332 (qAC9.3, SbeIIb)' and the higher amylose content and higher pasting temperature variety 'Kitagenki (-, SbeIIbsr )'. The qAC9.3 genotype exhibited low amylose content and reduced the hardness of boiled rice but increased the ratio of amylopectin long chains and did not alter the pasting temperature. In contrast, the SbeIIb genotype was associated with pasting temperature but did not affect the amylose content and hardness of boiled rice. It was suggested that appropriately selecting genotypes of these genetic regions and QTL would allow the fine-tuning of starch properties of cooked rice suitable for future demand.

Moderate Salinity Stress Affects Rice Quality by Influencing Expression of Amylose- and Protein-Content-Associated Genes.

Salinity is an environmental stress that severely impacts rice grain yield and quality. However, limited information is available on the molecular mechanism by which salinity reduces grain quality. In this study, we investigated the milling, appearance, eating and cooking, and nutritional quality among three japonica rice cultivars grown either under moderate salinity with an electrical conductivity of 4 dS/m or under non-saline conditions in a paddy field in Dongying, Shandong, China. Moderate salinity affected rice appearance quality predominantly by increasing chalkiness rate and chalkiness degree and affected rice eating and cooking and nutritional quality predominantly by decreasing amylose content and increasing protein content. We compared the expression levels of genes determining grain chalkiness, amylose content, and protein content in developing seeds (0, 5, 10, 15, and 20 days after flowering) of plants grown under saline or non-saline conditions. The chalkiness-related gene Chalk5 was up-regulated and WHITE-CORE RATE 1 was repressed. The genes Nuclear factor Y and Wx, which determine amylose content, were downregulated, while protein-content-associated genes OsAAP6 and OsGluA2 were upregulated by salinity in the developing seeds. These findings suggest some target genes that may be utilized to improve the grain quality under salinity stress conditions via gene-pyramiding breeding approaches.

The Waxy Gene Has Pleiotropic Effects on Hot Water-Soluble and -Insoluble Amylose Contents in Rice (Oryza sativa) Grains.

Rice (Oryza sativa) is a cereal crop with a starchy endosperm. Starch is composed of amylose and amylopectin. Amylose content (AC) is the principal determinant of rice quality, but varieties with similar ACs can still vary substantially in their quality. In this study, we analyzed the total AC (TAC) and its constituent fractions, the hot water-soluble amylose content (SAC) and hot water-insoluble amylose content (IAC), in two sets of related chromosome segment substitution lines of rice with a common genetic background grown in two years. We searched for quantitative trait loci (QTLs) associated with SAC, IAC, and TAC and identified one common QTL (qSAC-6, qIAC-6, and qTAC-6) on chromosome 6. Map-based cloning revealed that the gene underlying the trait associated with this common QTL is Waxy (Wx). An analysis of the colors of soluble and insoluble starch-iodine complexes and their λmax values (wavelengths at the positions of their peak absorbance values) as well as gel permeation chromatography revealed that Wx is responsible for the biosynthesis of amylose, comprising a large proportion of the soluble fractions of the SAC. Wx is also involved in the biosynthesis of long chains of amylopectin, comprising the hot water-insoluble fractions of the IAC. These findings highlight the pleiotropic effects of Wx on the SAC and IAC. This pleiotropy indicates that these traits have a positive genetic correlation. Therefore, further studies of rice quality should use rice varieties with the same Wx genotype to eliminate the pleiotropic effects of this gene, allowing the independent relationship between the SAC or IAC and rice quality to be elucidated through a multiple correlation analysis. These findings are applicable to other valuable cereal crops as well.

Effect of nitrogen fertilizer on the quality traits of Indica rice with different amylose contents.

BACKGROUND: Nitrogen is a key factor affecting the quality of rice. Studying the impact of nitrogen fertilizer on the taste, physicochemical properties, and starch structure of Indica rice with different amylose contents is of great significance for scientifically fertilizing and cultivating high-quality rice varieties for consumption. RESULTS: The results indicate that increasing nitrogen fertilizer application reduces the amylose content and increases the protein content, resulting in a decrease in taste quality. Simultaneously, it reduces the intergranular porosity of starch particles, improving the appearance and milling quality of rice. Compared to the N1 treatment (nitrogen fertilizer application rate of 90 kg ha-1), the taste of low-amylose rice (Yixiangyou 2115) and high-amylose rice (Byou 268) decreased by 14.24% and 19.79%, respectively, under N4 treatment (nitrogen fertilizer application rate of 270 kg ha-1). The effect of nitrogen fertilizer on low-amylose rice is mainly reflected in increased rice hardness, enthalpy value, and setback viscosity, resulting in a decline in taste. The effect of nitrogen fertilizer on high-amylose rice is mainly reflected in a decrease in peak viscosity, an increase in gelatinization temperature, and crystallinity under high nitrogen levels. CONCLUSION: Increasing nitrogen fertilizer application can improve the appearance and milling quality of rice, but it also leads to an increase in protein content, hardness, gelatinization enthalpy, decrease in breakdown value, and a decline in palatability. In practical production, different production measures should be taken according to different production goals. © 2024 Society of Chemical Industry.

Tuber crops could be a potential food component for lowering starch digestibility and estimated glycemic index in rice.

BACKGROUND: Rice is considered a high estimated glycemic index (eGI) food because of its higher starch digestibility, which leads to type II diabetes and obesity as a result of a sedentary life style. Furthermore, the incresaing diabetes cases in rice-consuming populations worldwide need alternative methods to reduce the glycemic impact of rice, with dietary prescriptions based on the eGI value of food being an attractive and practical concept. Rice is often paired with vegetables, pulses, tubers and roots, a staple food group in Africa, Latin America and Asia, which are rich in fibre and health-promoting compounds. RESULTS: Rice from four categories (high protein, scented, general and pigmented) was analyzed for eGI and resistant starch (RS) content. Among the genotypes, Improved Lalat had the lowest eGI (53.12) with a relatively higher RS content (2.17%), whereas Hue showed the lowest RS (0.19%) with the highest eGI (76.3) value. The addition of tuber crops to rice caused a significant lowering of eGI where the maximum beneficial effect was shown by elephant foot yam (49.37) followed by yam bean (53.07) and taro (54.43). CONCLUSION: The present study suggests that combining rice with suitable tuber crops can significantly reduce its eGI value, potentially reducing the burden of diet-associated lifestyle diseases particularly diabetics. © 2024 Society of Chemical Industry.

A novel isolation technique for sweetpotato starch and its application in thermal property characterization.

BACKGROUND: The utilization of sweetpotato starch in the food industry is significantly influenced by the granule size of the starch. To isolate sweetpotato starch fractions with different sizes, an efficient isolation method is in demand. The differences in thermal properties of starch fractions with different sizes from various sweetpotato varieties were revealed insufficiently. RESULTS: In this study, we devised a time-saving isolation technique to effectively isolate sweetpotato starch fractions based on granule sizes. The new technique was proved applicable for sweetpotato varieties with different flesh colors. The amylose contents of the isolated starch fractions were in the range 16.49-23.27%. A positive association was observed between amylose content, relative crystallinity of starch fractions and their granule size. Conversely, both the swelling power and water solubility at 95 °C displayed a consistent decline from more than 30 g g-1 to lower than 20 g g-1 as the granule size increased. Tp, To and Tc decreased gradually with an increase of starch granule size, while the medium- or small-sized starch fractions showed higher ΔH. In the first stage of thermogravimetric analysis curves, the weight of the small-sized starch fractions decreased the slowest, but no definite pattern was detected in the second or third stage. CONCLUSION: Therefore, the newly established technique and the results of this study will help better understand the properties of sweetpotato starch fractions with different sizes and certainly provide guidelines for the utilization of sweetpotato starch in food processing and product development. © 2024 Society of Chemical Industry.

Development and validation of near-infrared spectroscopy procedures for prediction of cassava root dry matter and amylose contents in Ugandan cassava germplasm.

BACKGROUND: Cassava utilization for food and/or industrial products depends on inherent properties of root dry matter content (DMC) and the starch fraction of amylose content (AC). Accordingly, in the present study, near-infrared reflectance spectroscopy (NIRS) models were developed to aid breeding and selection of DMC and AC as critical industrial traits taking care of root sample preparation and cassava germplasm diversity available in Uganda. RESULTS: Upon undertaking calibrations and cross-validations, best models were adopted for validation. DMC in calibration samples ranged from 20 to 45 g 100g-1 , whereas, for amylose content, it ranged from 14 to 33 g 100g-1 . In the validation set, average DMC was 29.5 g 100g-1 , whereas, for amylose content, it was 24.64 g 100g-1 . For DMC, a modified partial least square regression model had regression coefficients (R2 ) of 0.98 and 0.96, respectively, in the calibration and validation set. These were also associated with low bias (-0.018) and ratio of performance deviation that ranged from 4.7 to 5.0. In addition, standard error of prediction values ranged from 0.9 g 100g-1 to 1.06 g 100g-1 . For AC, the regression coefficient was 0.91 for the calibration set and 0.94 for the validation set. A bias equivalent to -0.03 and a ratio of performance deviation of 4.23 were observed. CONCLUSION: These findings confirm the robustness of NIRS in the estimation of dry matter content and amylose content in cassava roots and thus justify its use in routine cassava breeding operations. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Convolutional neural network allows amylose content prediction in yam (Dioscorea alata L.) flour using near infrared spectroscopy.

BACKGROUND: Yam (Dioscorea alata L.) is the staple food of many populations in the intertropical zone, where it is grown. The lack of phenotyping methods for tuber quality has hindered the adoption of new genotypes from breeding programs. Recently, near-infrared spectroscopy (NIRS) has been used as a reliable tool to characterize the chemical composition of the yam tuber. However, it failed to predict the amylose content, although this trait is strongly involved in the quality of the product. RESULTS: This study used NIRS to predict the amylose content from 186 yam flour samples. Two calibration methods were developed and validated on an independent dataset: partial least squares (PLS) and convolutional neural networks (CNN). To evaluate final model performances, the coefficient of determination (R2 ), the root mean square error (RMSE), and the ratio of performance to deviation (RPD) were calculated using predictions on an independent validation dataset. The tested models showed contrasting performances (i.e., R2 of 0.72 and 0.89, RMSE of 1.33 and 0.81, RPD of 2.13 and 3.49 respectively, for the PLS and the CNN model). CONCLUSION: According to the quality standard for NIRS model prediction used in food science, the PLS method proved unsuccessful (RPD < 3 and R2 < 0.8) for predicting amylose content from yam flour but the CNN model proved to be reliable and efficient method. With the application of deep learning methods, this study established the proof of concept that amylose content, a key driver of yam textural quality and acceptance, can be predicted accurately using NIRS as a high throughput phenotyping method. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The kinase OsSK41/OsGSK5 negatively regulates amylose content in rice endosperm by affecting the interaction between OsEBP89 and OsBP5.

Amylose content (AC) is the main factor determining the palatability, viscosity, transparency, and digestibility of rice (Oryza sativa) grains. AC in rice grains is mainly controlled by different alleles of the Waxy (Wx) gene. The AP2/EREBP transcription factor OsEBP89 interacts with the MYC-like protein OsBP5 to synergistically regulate the expression of Wx. Here, we determined that the GLYCOGEN SYNTHASE KINASE 5 (OsGSK5, also named SHAGGY-like kinase 41 [OsSK41]) inhibits the transcriptional activation activity of OsEBP89 in rice grains during amylose biosynthesis. The loss of OsSK41 function enhanced Wx expression and increased AC in rice grains. By contrast, the loss of function of OsEBP89 reduced Wx expression and decreased AC in rice grains. OsSK41 interacts with OsEBP89 and phosphorylates four of its sites (Thr-28, Thr-30, Ser-238, and Thr-257), which makes OsEBP89 unstable and attenuates its interaction with OsBP5. Wx promoter activity was relatively weak when regulated by the phosphomimic variant OsEBP89E -OsBP5 but relatively strong when regulated by the nonphosphorylatable variant OsEBP89A -OsBP5. Therefore, OsSK41-mediated phosphorylation of OsEBP89 represents an additional layer of complexity in the regulation of amylose biosynthesis during rice grain development. In addition, our findings provide four possible sites for regulating rice grain AC via precise gene editing.

Association mapping for protein, total soluble sugars, starch, amylose and chlorophyll content in rice.

BACKGROUND: Protein, starch, amylose and total soluble sugars are basic metabolites of seed that influence the eating, cooking and nutritional qualities of rice. Chlorophyll is responsible for the absorption and utilization of the light energy influencing photosynthetic efficiency in rice plant. Mapping of these traits are very important for detection of more number of robust markers for improvement of these traits through molecular breeding approaches. RESULTS: A representative panel population was developed by including 120 germplasm lines from the initial shortlisted 274 lines for mapping of the six biochemical traits using 136 microsatellite markers through association mapping. A wide genetic variation was detected for the traits, total protein, starch, amylose, total soluble sugars, chlorophyll a, and chlorophyll b content in the population. Specific allele frequency, gene diversity, informative markers and other diversity parameters obtained from the population indicated the effectiveness of utilization of the population and markers for mapping of these traits. The fixation indices values estimated from the population indicated the existence of linkage disequilibrium for the six traits. The population genetic structure at K = 3 showed correspondence with majority of the members in each group for the six traits. The reported QTL, qProt1, qPC6.2, and qPC8.2 for protein content; qTSS8.1 for total soluble sugar; qAC1.2 for amylose content; qCH2 and qSLCHH for chlorophyll a (Chl. a) while qChl5D for chlorophyll b (Chl. b) were validated in this population. The QTL controlling total protein content qPC1.2; qTSS7.1, qTSS8.2 and qTSS12.1 for total soluble sugars; qSC2.1, qSC2.2, qSC6.1 and qSC11.1 for starch content; qAC11.1, qAC11.2 and qAC11.3 for amylose content; qChla8.1 for Chl. a content and qChlb7.1 and qChlb8.1 for Chl. b identified by both Generalized Linear Model and Mixed Linear Model were detected as novel QTL. The chromosomal regions on chromosome 8 at 234 cM for grain protein content and total soluble sugars and at 363 cM for Chl. a and Chl. b along with the position at 48 cM on chromosome 11 for starch and amylose content are genetic hot spots for these traits. CONCLUSION: The validated, co-localized and the novel QTL detected in this study will be useful for improvement of protein, starch, amylose, total soluble sugars and chlorophyll content in rice.