Search Results (32)

Rice (Oryza sativa L.) is essential for global food security and sustains billions worldwide, emphasizing the need to improve production and quality. One key challenge in rice breeding is the inheritance and environmental sensitivity of amylose content, a starch component that influences the texture, water absorption, and firmness after cooking, which are crucial for market acceptance. While international markets prefer low-amylose varieties for their softness, intermediate- and high-amylose varieties are favored in Latin America for their firmness. The objective of this study was to develop a molecular quality assessment methodology that, combined with morphological and culinary evaluations, helps in the selection of rice varieties during the breeding process. First, ten Ecuadorian rice materials were evaluated for milling and culinary quality characteristics, revealing significant grain size, sterility, milling yield, cooking time, and texture variations. Amylose content (AC) is genetically regulated by the waxy gene and its allelic variants, affecting granule-bound starch synthase (GBSS) enzyme expression. Secondly, to classify rice varieties molecularly based on AC, the testing ten genotypes plus nine control varieties were analyzed using microsatellite (SSR) markers. The waxy molecular marker, combined with metaphor agarose gel electrophoresis (MAGE), proved effective for early-stage AC analysis, reducing variety selection costs and improving breeding efficiency. Additionally, a restriction enzyme protocol assay facilitated variety differentiation by selectively cleaving the waxy gene sequence at a specific single-nucleotide polymorphism (SNP) site, allowing for precise AC genetic classification. By integrating molecular techniques with traditional assessments, this study reveals that using marker-assisted selection in breeding programs, as well as supporting the identification and development of high-quality local rice varieties to meet market demands, improves production efficiency and optimizes the assessment of developing varieties under diverse environmental conditions. Full article

Starch biosynthesis is crucial in determining rice quality during rice endosperm development. This study obtained a stable inheritable white-core endosperm mutant, h5, by treating the japonica rice variety Nipponbare with MNU (N-methyl-N-nitro-sourea). The mutated gene is an allele of OsAGPL2, which encodes the large subunit of ADP-glucose pyrophosphorylase (AGPase), a key and rate-limiting enzyme in the rice starch biosynthesis pathway. A G-C mutation in the third exon of OsAGPL2 led to impaired starch synthesis, significantly reduced amylose content (AC) and gel consistency (GC), and a marked decrease in AGPase activity. The haplotype analysis revealed that an SNP in the 3′UTR and two SNPs in the 5′UTR of OsAGPL2 were associated with significant differences in AC and GC among rice resources. These SNPs can be utilized to design molecular markers for breeding programs to improve rice quality. This study elucidates the impact of OsAGPL2 on the eating and cooking quality of rice. It identifies superior haplotypes, providing a theoretical foundation and molecular markers for accumulating minor-effect genes to enhance rice quality. Full article

High quality stands as a pivotal competitive edge in the rice industry. Optimizing amylose content (AC) and the physicochemical properties of endosperm starch by regulating the Wx gene is crucial for enhancing rice grain quality. In this study, we created a novel Wx^b-d25 allele by deleting a 25 bp segment (−26 to −2) within the Wx core promoter using CRISPR/Cas9. Compared with the wild type and the previously reported Wx^b-i1, Wx^b-d25 exhibited no significant changes in agronomic traits. However, its grains displayed temperature-dependent variations in AC and altered transparency and viscosity characteristics, holding the potential to synergistically improve both the eating and cooking quality (ECQ) and appearance quality (AQ) of rice. Further studies demonstrated that this promoter modification, by partially disrupting the transcription initiator, significantly downregulated the original Wx-01 transcript and generated a novel Wx transcript (ONT.7395.1) in Wx^b-d25 grains. Despite its low expression abundance, the ONT.7395.1 transcript could be completely processed into mature Wx mRNA. The combined effects of the dual transcripts resulted in significantly increased Wx gene expression and AC in Wx^b-d25 grains under conventional cultivation conditions. These findings provide a genetic resource and a theoretical foundation for utilizing the Wx^b-d25 allele to improve rice grain quality. Full article

The demand for rice varieties with lower amylose content (AC) is increasing in Southeast Asia, primarily due to their desirable texture and cooking qualities. This study presents the development of whole-grain rice lines with low to intermediate glycemic index (GI) and reduced AC. We selected six rice lines for in vivo GI assessment based on their starch properties. We successfully identified two lines with low AC that exhibited low and intermediate GI values, respectively. Our findings indicate that dietary fiber (DF) content may significantly influence rice GI. The selected whole-grain low-GI line showed a higher ratio of soluble dietary fiber (SDF) to insoluble dietary fiber (IDF) compared to control varieties, highlighting SDF’s potential positive role in lowering whole-grain rice’s GI. This study underscores the feasibility of developing rice varieties with desirable agronomic traits, nutritional traits, and culinary attributes, particularly for individuals managing their blood sugar levels. Additionally, we proposed the positive role of starch composition, especially DF content, in modulating the GI of rice. This study reinforces the importance of incorporating starch properties and DF content into rice breeding programs to produce more health-oriented and marketable rice varieties. Full article

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 λ_max 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. Full article

Barley with high grain β-glucan content is valuable for functional foods. The identification of loci for high β-glucan content is, thus, of great importance for barley breeding. Segregation mapping for the content in β-glucan and other barley grain components (starch, protein, lipid, ash, phosphorous, calcium, sodium) was performed using the progeny of the cross between Glacier AC38, a mutant with high amylose, and CDC Fibar, a high β-glucan waxy cultivar. The offspring of this cross showed transgressive segregation for β-glucan content. Linkage analysis based on single-nucleotide polymorphism (SNP) molecular markers was used for the genotyping of the parents and recombinant inbred lines (RILs). Two Quantitative Trait Loci (QTL) for β-glucan content and several QTL for other grain components were found. The former ones, located on chromosomes 1H and 7H, explained 27.9% and 27.4% of the phenotypic variance, respectively. Glacier AC38 provided the allele for high β-glucan content at the QTL on chromosome 1H, whereas CDC Fibar contributed the allele at the QTL on chromosome 7H. Their recombination resulted in a novel haplotype with higher β-glucan content, up to 18.4%. Candidate genes are proposed for these two QTL: HvCslF9, involved in β-glucan biosynthesis, for the QTL on chromosome 1H; Horvu_PLANET_7H01G069300, a gene encoding an ATP-Binding Cassette (ABC) transporter, for the QTL on chromosome 7H. Full article

Fresh meat and fish are widely consumed foods with short and very short shelf lives, respectively. Efficient supply chains and the judicious use of food packaging are the most effective means of extending shelf life and thus reducing food waste and improving food safety. Food packaging that allows for the use of a modified atmosphere (MAP) is effective in extending the period where the food is both palatable and safe. However, monitoring the state of aging and the onset of spoilage of the product poses challenges. Microbial counts, pH measurements, and sensory evaluations are all informative but destructive and are therefore only useful for monitoring quality via sampling. More attractive would be a technology that can follow the progress of ageing in an individual product while leaving the food packaging intact. Here, we present a pH indicator to be placed inside each package that may be read by the naked eye. It is a colorimetric indicator with a matrix made of pure amylose (AM; 99% linear α-glucans) and cellulose nanofibers (CNFs). Suitable mechanical properties of films cast of the two polysaccharides were achieved via the optimization of the blending ratio. The films were loaded with either of two pH indicators: anthocyanin extracts from red cabbage (RCA) and the synthetic dye neutral red (NR). Mechanical, thermal, permeability, microstructural, and physical properties were tested for all composite films. Films with 35% CNF (35AC-RCA) and (35AC-NR) were selected for further study. Minced meat was packaged under MAP conditions (70% O₂ + 30% CO₂), while minced fish was packaged under MAP (70% N₂ + 30% CO₂) and stored at 5 °C for 20 days. Microbial growth, pH, and sensory scores of the minced meat systems differentiated between fresh (0–6 days) and medium-fresh (7–10 days), and minced fish between fresh (0–10 days) and medium-fresh (11–20 days). The total color difference showed that the RCA indicator was able to differentiate between fresh (red) and medium-fresh (pink-red) minced meat, while for minced fish, this indicator discriminated between three stages: fresh (red), medium-fresh (pink-red), and spoiled (pink-blue). The NR indicator failed to discriminate the freshness of either meat or fish under the effect of MAP. Pearson correlation statistical models showed a correlation between color change of the indicator, pH, content of gases, and gas content. In summary, RCA immobilized in an AM + 35% CNF nanocomposite film can monitor the freshness of packaged minced meat/fish under the effect of MAP via color change that may be evaluated with the naked eye. Full article

Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wx^mp allele derived from the ancestral Wx^mq allele, significantly influences AC and is prevalent among soft japonica rice varieties in southern China. Although both alleles are associated with lower AC, there remains a paucity of detailed understanding regarding the interplay between specific functional single nucleotide polymorphisms (SNPs) within these alleles and the overarching rice grain quality. To investigate this, we engineered three distinct transgenic rice lines, each harboring the Wx^mp, Wx^mq, or Wx^b−5c alleles in the background of the glutinous rice cultivar Nip(wx). This suite of transgenic rice lines showcased varying degrees of grain transparency inversely correlated to AC, which in turn influenced other physicochemical properties of the rice grains, such as taste value of cooked rice, gel consistency, and starch pasting properties. Additionally, analyses of gene expression and enzyme activity revealed that the functional SNPs, Ex4-53G to A and Ex5-53T to C, lead to a decline in the activity of granule-bound starch synthase I (GBSSI) without altering expression levels. Full article

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two japonica rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BC₃F₂ and BC₃F_2:3, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BC₃F₂ population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, qWCR3, was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, LOC_0s03g45210 and LOC_0s03g45320, exhibited sequence variations between the parents. Furthermore, the variation of LOC_Os03g45210 leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the qWCR3 gene, thus offering new genetic resources for rice quality improvement. Full article

Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wx^b is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wx^b and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wx^b) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs. Full article

The eating and cooking quality (ECQ) directly affects the taste of rice, being closely related to factors such as gelatinization temperature (GT), gel consistency (GC) and amylose content (AC). Mining the quantitative trait loci (QTLs), and gene loci controlling ECQ-related traits is vital. A genome-wide association study on ECQ-related traits was conducted, combining 1.2 million single nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Two QTLs for GT, one for GC and five for AC were identified, of which two were found in previously reported genes, and six were newly found. There were 28 positional candidate genes in the region of qAC11. Based on a linkage disequilibrium (LD) analysis, three candidate genes were screened within the LD region associated with AC. There were significant differences between the haplotypes of LOC_Os11g10170, but no significant differences were found for the other two genes. The qRT-PCR results showed that the gene expression levels in the accessions with high ACs were significantly larger than those in the accessions with low ACs at 35d and 42d after flowering. Hap 2 and Hap 3 of LOC_Os11g10170 reduced the AC by 13.09% and 10.77%, respectively. These results provide a theoretical and material basis for improving the ECQ of rice. Full article

Rice provides 70% of dietary carbohydrates and other essential nutrients. Breeding for consumer preferences and health benefits are the main considerations. Rice with a low amylose content offers a good cooking quality with its soft and sticky texture but fast starch digestibility with a high sugar release. Therefore, to provide health benefits, it is important to identify rice varieties with slow starch digestibility and a low amylose content. A total of 167 indigenous upland rice germplasms were analysed for amylose content (AC) and in vitro starch digestibility. The results showed that 167 upland rice genotypes were mostly low in AC, which was related to a soft and sticky texture during cooking. Based on the glutinous and non-glutinous types, thirteen and nine indigenous upland rice germplasms were selected with a lower AC than RD6 and KDML105 (check varieties). The in vitro starch digestibility and the hydrolysis were different at each time point and different in each variety. In the glutinous group, ULR155, ULR138, ULR308, and ULR241 released less sugar and had slower starch digestibility than RD6. In the non-glutinous group, ULR219 and ULR264 showed lower AC, slower digestion, and lower sugar release than KDML105. The results suggest that six indigenous upland rice varieties will provide a rice source to accommodate consumer preferences while also offering health benefits. Full article

It is important to clarify the effects of starch fine structure and protein components on the eating quality of indica rice. In this study, seven indica rice varieties with similar apparent amylose content (AAC) and protein content (PC) but different sensory taste values were selected and compared systematically. It was found that except for AAC and PC, these varieties showed significant differences in starch molecular structure and protein components. Compared with rice varieties with a low sensory taste value, varieties with a higher sensory taste value showed significantly lower amylose and higher amylopectin short chains (degree of polymerization 6–12) content; the protein component showed that the varieties with good taste value had higher albumin and lower globulin and glutelin content (p < 0.05). Rice varieties with lower AC, globulin, and glutelin content, as well as a higher content of albumin and amylopectin short chains, resulted in a higher swelling factor, peak viscosity, breakdown value, and ratio of hardness to stickiness, in which condition cooked rice showed a higher sensory taste value. Moreover, this study indicated that rice varieties with a higher content of albumin and amylopectin short chains were conducive to the good appearance of cooked rice. This study lays the foundation for the taste evaluation of good-tasting indica rice. Full article

Understanding the effects of genotype, environment and their interactions on rice quality is of great importance for rice breeding and cultivation. In this study, six rice varieties with two indica, two japonica and two indica–japonica types of rice were selected and planted at ten locations in Zhejiang Province to investigate the genotype (G) × environment (E) on physicochemical and sensory properties and the differences of volatile organic compounds (VOCs) among the three types of rice. Analysis of variances showed that apparent amylose content (AC), total protein content (PC), alkali spreading value (ASV), RVA profiles, and appearance (ACR), palatability (PCR), and sensory evaluation value (SEV) of cooked rice and texture of cooled cooked rice (TCCR) were mainly affected by genotypic variation, whereas the smell of cooked rice (SCR) was mainly affected by environment (p < 0.05). The G × E effect was significant for most parameters. The weather in the middle and late periods of filling had important effects on the formation of rice quality, especially on setback (SB) and pasting temperature (PT) (p < 0.01). They were negatively correlated with the texture of cooked rice (TCR) and SEV (p < 0.05). Peak viscosity (PV) and breakdown (BD) were positively related to the sensory evaluation parameters (p < 0.01) and could be used to predict cooked rice quality. A total of 59 VOCs were detected, and indica, japonica and indica–japonica had 9, 6 and 19 characteristic compounds, respectively. The principal component analysis showed that the physicochemical and sensory properties and VOCs of indica–japonica rice were more stable than those of indica and japonica rice at ten locations in Zhejiang Province. It is helpful for rice breeders to understand how the environment affects the physicochemical, sensory properties and VOCs of the three rice types, and it is also important for food enterprises to provide rice products with stable quality. Full article

We investigated the variations in metabolites associated with the quality of rice consumption when exposed to varying nitrogen fertilizer levels, as well as the regulatory role of pivotal metabolites within metabolic pathways. This research employed Hongyang 5 as the subject of experimentation, examining the metabolites of Hongyang 5 at three different nitrogen levels using non-targeted metabonomic analysis. The findings indicated that the overall assessment of the eating quality/palatability (CEQ) and amylose contents (AC) of Low nitrogen (D1: 180 kg·ha⁻¹) was notably greater than that of Medium nitrogen (D2: 270 kg·ha⁻¹) and High nitrogen (D3: 315 kg·ha⁻¹). Conversely, the amylopectin (APC), total starch (SC), and protein contents (AP) of D1 were remarkably lower than those observed in D2 and D3. The starch debranching enzyme (DBE) and granule-bound starch synthetase (GBSS) of D1 were remarkably higher than those of D2 and D3. The soluble starch synthase (SSS) of D1 was the lowest. The ADP-glucose pyro-phosphorylase (AGP) and starch branching enzyme (SBE) of D3 were remarkably higher than that of D1 and D2. We identified 76 differential metabolites (DMs) between D1 and D2 (20 up-regulated and 56 down-regulated). A total of 88 DMs were identified between D3 and D1 (42 up-regulated and 46 down-regulated). A total of 57 DMs were identified between D3 and D2. Most of the DMs related to rice-eating quality were involved in the lipid metabolic pathway and amino acid metabolic pathway. The essential metabolites within the metabolic pathway are classified as lipid metabolites and are (13(S)-hydroperoxylinolenic acid, PGB2, 3-phosphocholine, 7-epijasmonic acid, 20-carboxyleukotriene B4 and 11-dehydro-thromboxane B2), amino acid metabolites (4-guanidinobutanoic acid, (3R, 5S)-1-pyrroline-3-hydroxy-5-carboxylic acid, citric acid, (S)-2-Acetolactate, L-glutamine, L-2, 4-aminobutyric acid and putrescine). These key metabolites may be affected by nitrogen fertilizer conditions and play critical regulatory roles in the metabolic pathway, resulting in differences in rice eating quality. Full article