Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities.
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ABSTRACT:
SUBMITTER: Tian Z
PROVIDER: S-EPMC2793318 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. Results A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes (SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and could be selected for further fine mapping. Conclusion This study illustrated the potential for dissecting genetic factors of complex traits in domesticated rice subspecies and provided highly associated markers to facilitate marker-assisted selection for breeding high-quality indica or japonica rice varieties.
| S-EPMC7556922 | biostudies-literature
Project description:The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy (Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII-3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection.
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Project description:The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.
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Project description:The effect of nitrogen fertilizer application on the quality of rice post-storage is not well understood. The eating and cooking quality (ECQ) of rice treated with 0 (CK, control), 160 (IN, insufficient nitrogen), 260 (AN, adequate nitrogen), and 420 (EN, excessive nitrogen) kg N/ha was analyzed over 12 months of storage. Results showed that the rate of nitrogen fertilizer application had no significant impact on the changes in taste value during storage. However, EN application significantly increased the hardness (p < 0.05), reduced the gumminess (p < 0.05), and delayed the decline in the viscosity of rice paste by two months after one-year storage, compared with other treatments. In conclusion, although EN application resulted in an inferior texture of rice, it delayed the quality change by two months during storage. It was demonstrated that a rational nitrogen application rate (0-260 kg N/ha) for rice cultivation is particularly important to obtain high ECQ; however, EN may be beneficial for the stability of the ECQ during storage.
| S-EPMC8213157 | biostudies-literature
Project description:A process of removing thinner kernels of rough rice, i.e., thickness fraction process, has been suggested as a method for increasing milling yields in the rice industry. This study aimed at determining whether physicochemical properties, cooking qualities, and sensory characteristics of rice samples could be changed by the addition of a thickness fraction into the rice process stream. Each of four long-grain rice cultivar lots was assigned into two groups: unfractionated and thickness-fractionated. For the thickness-fractionated group, thin rice kernels (<1.9 mm) of rough rice were discarded from unfractionated rice samples. Unfractionated and thickness-fractionated rice samples were compared with respect to physicochemical properties, cooking qualities, and sensory characteristics. The results showed that the removal of such thin kernels decreased the breakage and chalkiness rates and increased head rice yields. Fractionated rice samples exhibited lower amylose contents and crude protein contents but higher gelatinization temperatures than unfractionated rice samples. While the optimum cooking duration and width-expansion ratios of thickness-fractionated rice samples were higher than those of unfractionated ones, there was a negligible impact of the thickness fraction process on sensory characteristics of long-grain rice samples. In conclusion, the thickness fraction process affects physicochemical properties and cooking qualities more than the sensory characteristics of rice samples.
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Project description:Phospholipids belong to a significant class of lipids and comprise ~10% of total lipids in rice grains. Lysophospholipid (LPL) is derived from the hydrolysis of phospholipids and plays an important role in rice grain quality. Our previous study demonstrated that mutations in a phospholipase D gene (OsPLD?1) significantly altered lipid metabolites and reduced phytic acid content. In the present study, the effect of two ospld?1 mutations on LPL and other physicochemical prosperities of brown rice was further investigated, with the aim of assessing the overall importance of ospld?1 mutations in rice grain quality. Metabolite profiling revealed a ~15% increase in LPL level in both ospld?1 mutants as compared with their wild-type (WT) parent. Both ospld?1 mutations significantly lowered the apparent amylose content in brown rice flour (~1.9%) and altered viscosity profiles with significantly increased breakdown (+12.4%) and significantly reduced setback viscosity (-6.2%). Moreover, both ospld?1 mutations significantly lowered the gelatinization onset, peak temperature and retrogradation percentage of brown rice flour. This study demonstrated that OsPLD?1 plays a crucial role in rice grain quality and its mutation could, in general, improve the cooking and eating quality and nourishment of brown rice.
| S-EPMC7154823 | biostudies-literature
Project description:In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw , which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb . We validated the effects of Wxmw on rice grain quality using both transgenic lines and near-isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.
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Project description:Waste cooking oil (WCO), in many cases, can rejuvenate aged asphalt and restore its properties. However, the influence of WCO qualities on rejuvenation behaviors of aged asphalt has not been investigated in detail. The objective of this paper was to evaluate the effects of WCO viscosity and acid value on the basic, rheological, and chemical properties of a typical rejuvenated asphalt. Penetration, ring and ball (R and B) softening point, and ductility were tested to evaluate the influence of WCO qualities on basic properties of rejuvenated asphalts. Then, the rheological properties of rejuvenated asphalt were characterized based on rotational viscometer (RV), dynamic shear rheometer (DSR), and bending beam rheometer (BBR) test results. Further, SARA (saturates, aromatics, resins, and asphaltenes) fraction analysis and Fourier transform infrared spectroscopy (FTIR) tests were performed to investigate the effects of WCO qualities on asphalt chemical composition. Finally, grey correlation coefficients were calculated and the relationships between WCO qualities and rejuvenated asphalt properties were quantitatively evaluated. The experimental results indicated that WCO qualities influence the rejuvenation behaviors of aged asphalt significantly, and the WCO with higher qualities (low acid value and viscosity, as defined in this research) tends to achieve better rejuvenation effects. Based on the results of grey correlation analyses, the acid value is, relatively, a better indicator than viscosity in predicting the rejuvenation efficiency of WCO. The rejuvenation thresholds of WCO are varied with the categories of properties of rejuvenated asphalts, and WCO with an acid value of 0.4-0.7 mg KOH/g, or a viscosity of 140-540 mm²/s, can meet all of the performance requirements for asphalt rejuvenation used in this research.
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Project description:Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC.
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Project description:Improving rice eating and cooking quality (ECQ) is one of the primary tasks in rice production to meet the rising demands of consumers. However, improving grain ECQ without compromising yield faces a great challenge under varied nitrogen (N) supplies. Here, we report the approach to upgrade rice ECQ by native promoter-controlled high expression of a key N-dependent floral and circadian clock regulator Nhd1. The amplification of endogenous Nhd1 abundance alters rice heading date but does not affect the entire length of growth duration, N use efficiency and grain yield under both low and sufficient N conditions. Enhanced expression of Nhd1 reduces amylose content, pasting temperature and protein content while increasing gel consistence in grains. Metabolome and transcriptome analyses revealed that increased expression of Nhd1 mainly regulates the metabolism of carbohydrates and amino acids in the grain filling stage. Moreover, expression level of Nhd1 shows a positive relationship with grain ECQ in some local main cultivars. Thus, intensifying endogenous abundance of Nhd1 is a promising strategy to upgrade grain ECQ in rice production.
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