As a fundamental component of nucleic acids, phospholipids, and adenosine triphosphate, phosphorus (P) is critical to all life forms, however, the molecular mechanism of P translocation and distribution in rice grains are still not understood. Here, with the use of five different low phytic acid (lpa) rice mutants, the redistribution in the main P-containing compounds in rice grain, phytic acid (PA), lysophospholipid (LPL), and inorganic P (Pi), was investigated. The lpa mutants showed a significant decrease in PA and phytate-phosphorus (PA-P) concentration with a concomitant increase in Pi concentration. Moreover, defects in the OsST and OsMIK genes result in a great reduction of specific LPL components and LPL-phosphorus (LPL-P) contents in rice grain. In contrast, defective OsMRP5 and Os2-PGK genes led to a significant increase in individual LPL components. The effect of the Os2-PGK gene on the LPL accumulation was validated using breeding lines derived from a cross between KBNT-lpa (Os2-PGK mutation) and Jiahe218. This study demonstrates that these rice lpa mutants lead to the redistribution of Pi in endosperm and modify LPL biosynthesis. Increase LPLs in the endosperm in the lpa mutants may have practical applications in rice breeding to produce “healthier” rice.Keywords: lysophospholipids; phosphorus; phytic acid; rice;

Flower opening time (FT) is a critical factor for seed production in hybrid rice. To unravel the genetic basis of FT, a recombinant inbred (RI) line population including 184 lines was developed from the cross between a japonica variety Nipponbare and an early FT mutant (eft). A genetic linkage map was constructed using 70 SSR and 123 InDel markers, covering a total length of 1753.3 cM of the genome. The FT of both parents and RI lines was measured by the traditional grading scale method and a new time-interval method in two environments, i.e., Hainan (HN) and Hangzhou (HZ). A total of seven FT-related quantitative trait loci (QTLs) distributing on 4 chromosomes were detected in HN and HZ. qFT1b and qFT12 could be detected in both environments. The time-interval FT in Hangzhou allowed us to detect one more QTL (qFT-9) than the grading scale method. qFT1a is a major QTL explaining more than 60% of the total phenotypic variations in FT. Although FT had a positive correlation with heading date in Hangzhou (r = 0.16), no common QTL was detected for them, suggesting that FT and heading date are under different genetic controls. These discoveries may help to understand the genetics of flower opening time in rice and be useful for breeding early FT rice to facilitate hybrid seed production in the near future.

•Polyphenols in different fraction of buckwheat seeds were studied.•The hull had highest total phenolic contents.•More than 40 phenolics were identified by HPLC/MS.•Vitexin/isovitexin, hyperin and rutin were major phenolics in hulls.•Epicatechin-gallate was the predominant phenolic in bran and endosperm.The distribution of polyphenol profiles in different fractions of buckwheat seeds is less understood. In this study, polyphenols in the hull, bran and endosperm of eight common buckwheat cultivars were studied. The results showed that the hull had highest total phenolic content, followed by bran. Total proanthocyanidin contents in the hull were similar to those in the bran. Over 40 phenolics were identified by HPLC/MS. Prominent phenolics such as 1-O-Caffeoyl-6-O-rhamnopyranosyl-glycopyranoside, epicatechin-gallate, orientin/isorientin, vitexin/isovitexin, hyperin and rutin in different seed fractions were identified and quantified. The polyphenol profile in the hull was quite different from that of bran and endosperm. Vitexin/isovitexin, hyperin and rutin were major phenolics in hulls with content ranges of 101.65–188.78 mg/100 g, 53.55–274.10 mg/100 g and 62.43–173.57 mg/100 g, respectively. Epicatechin-gallate was the predominant phenol in bran and endosperm with content ranging from 150.44 to 354.67 mg/100 g and from 19.65 to 73.92 mg/100 g, respectively.Download high-res image (171KB)Download full-size image

•Variation in mineral elements in whole grain of 20 rices was investigated.•Ca, Na and K were mainly affected by the genotypic variance.•Fe, Zn and Cu were mainly affected by the environment variance.•17 genetic loci were identified to control the mineral contents.Twenty rice accessions were planted in Hainan province, China, for 2 years to investigate the effects of genotype, environment, and their interactions on the Ca, Mg, Na, K, Fe, Zn, and Cu contents in brown rice. Analysis of variance showed that the Ca, Na and K were mainly affected by the genotypic variance, whereas the Fe, Zn and Cu were mainly affected by the environment variance. The genotype × environment interaction effects for Mg, Na, Zn, and Cu were highly significant (P < 0.001), though it only accounted for a small proportion of the total variation (0.5–16.3%). The correlation analyses showed that Mg was significantly positively correlated with K, Fe, and Zn. A total of 9 and 8 single nucleotide polymorphism (SNP) loci were identified in 2011 and 2012, respectively, which were strongly associated with for Ca, Cu, K, Na, and Zn.

•Genetic diversity in some phytochemicals in brown rice was studied.•The predominant tocopherols (T) and tocotrienols (T3) were α-T and γ-T3.•The unsaturated fatty acids accounted for 74–81% of the total FAs.•Red rice had higher phenolics and VE content than white rice.•White rice had higher fatty acids than red rice.The genetic diversity of phenolic content (PC), individual phenolic acids, vitamin E isomers (VE) and fatty acids (FA) in the whole grain rice were investigated. The most abundant phenolic acid was ferulic acid ranging from 155.6 to 271.1 μg/g and comprising approximately 40–57% of total phenolic acid (TPA). The predominant tocopherols (T) and tocotrienols (T3) were α-T (6.43–12.67 μg/g) and γ-T3 (12.88–32.75 μg/g). The unsaturated fractions of FAs accounted for 74–81% of the total FAs in rice. Most of the phytochemicals among phenolics and VEs showed significant differences between white and red rice, with red rice demonstrating significantly higher levels. However, white rice had higher content of oleic, linolenic, eicosenoic and total fatty acids than red rice. The wide genetic diversity in whole grain rice allows food processors to have a good selection for producing rice products, and breeders to have new rice lines that can be bred for high nutrient levels.

Amylopectin is synthesized by the coordinated actions of many (iso)enzymes, including ADP-glucose pyrophosphorylase (AGPase), starch synthases (SSs), branching enzymes (BEs), and debranching enzymes (DBEs). Here, two polymorphic forms of starch synthase I (SSI) and pullulanase (PUL) in rice-developing seeds, designated as SSI-1/SSI-2 and PUL-1/PUL-2, were discovered for the first time by zymographic analysis. The SSI and PUL polymorphisms were strongly associated with the SSI microsatellite marker (p = 3.6 × 10–37) and PUL insertion/deletion (InDel) markers (p < 3.6 × 10–51). Western blotting and mass spectrometric analysis confirmed that the polymorphic bands were truly the SSI and PUL enzymes. Only one non-synonymous variation in SSI DNA sequence (the SNP A/G) causing the change of the amino acid K438 to E438 was observed, which coincided well with the polymorphic forms of SSI. Nine non-synonymous variations were found between PUL-1 and PUL-2. Two non-synonymous variations of PUL (F316L and D770E) were identified by mass spectrometric analysis, but all of the variations did not change the structure of PUL. The co-immunoprecipitation results revealed the differences in protein–protein interaction patterns, i.e., strong or weaker signals of SSI–BEI and SSI–BEIIb, between the two forms of SSI. The results will enhance our understanding of SSI and PUL properties and provide helpful information to understand their functions in starch biosynthesis in rice endosperm.

•This study is the first to report on the effects of anaerobic treatment on the antioxidant properties of GBR.•Anaerobic treatment improved the TPC, TFC and antioxidant activity.•The most pronounced increase in phenolic acids was the ferulic, coumaric, and sinapic acids.•γ-Aminobutyric acid (GABA) and some amino acids were increased significantly.•Anaerobic treatment had no effect on the content of the tocols.The effects of anaerobic treatment on the content of polyphenols, antioxidant capability, tocols, and free amino acids (FAAs) in the germinated brown rice (GBR) were investigated. The values of polyphenols and antioxidant capability significantly increased in treated groups, in which the three phenolic acids, i.e. ferulic, p-coumaric, and sinapic acids, showed the most pronounced increase. No significant change was observed in tocols. Among the evaluated FAAs, only the content of aspartic and glutamic acids in the white, red and black GBRs decreased by 75, 65 and 69%, and by 30, 18 and 39% after anaerobic treatment, respectively. While the contents of serine and threonine remained unchanged, all others significantly increased. In particular, the contents of γ-aminobutyric acid (GABA) increased 4.2-, 9.7- and 4.8-folds in the white, red and black GBRs, respectively. The results indicated that additional anaerobic treatment could be used in the production of GBR as a functional food.

•Starch properties from 14 rice varying in AAC were investigated.•The combination of AAC and GT for rice starch was not random.•AAC was the major factor affecting the physicochemical properties of rice starch.•Retrogradation property was determined by degree of crystallinity and GT, but not by AAC.The physicochemical properties of starches isolated from 14 rice cultivars produced in China were investigated. These rice starches showed a non-random combination of AAC and GT. Rice starches showed a typical A-type diffraction pattern with the degree of crystallinity ranging from 32.3% (a high AAC rice) to 45.5% (a waxy rice). AAC was significantly correlated with the pasting, thermal and textural properties. The positive correlations were found with PV, HPV, CPV, SB and HD (p < 0.05), while the negative corrections were found with SP, ADH, COH, To, Tp, Tc and ΔH (p < 0.05). However, AAC had no correlations with BD, PTime and percentage of retrogradation (R%). The degree of crystallinity and GT had a positive correlation with the retrogradation properties. It could be concluded that although AAC was the major factor affecting the physicochemical properties of rice starch, the retrogradation property of rice starch was mainly determined by the degree of crystallinity and GT.

•Rice flour physicochemical properties and their relations with LPLs were studied.•LPLs related with pasting viscosities, but had no relation with gelatinisation temperature.•Gelatinization enthalpy of rice flour was negative correlated with rice LPLs.•Role of native LPLs in rice flour properties could be independent of amylose.It is known that lysophospholipids (LPLs) may affect rice starch pasting and thermal properties possibly through the formation of an amylose–lipid complex. However, whether these effects of rice LPLs are independent of amylose are still not understood. Here, the diversity of rice flour pasting and thermal properties and their relationship with individual LPL components in native rice endosperm were studied. Several significant correlations between LPLs and pasting properties, such as cool paste viscosity (CPV), breakdown (BD) and consistency (CS) were clearly evident. Thermal properties generally had no relationship with LPLs except for gelatinization enthalpy. Using partial correlation analysis we found that, irrespective of apparent amylose content, CPV and individual LPLs were positively correlated, while BD, CS and other individual LPLs were negatively correlated. This study suggests naturally occurring individual LPLs can contribute to rice flour pasting and thermal properties, either independently or in combination with amylose.

•Phenolics and antioxidant activity of rice breeding lines have been characterised.•The dominant phenolic acids in rice grain is ferulic acid, p-coumaric acid, isoferulic acid and vanillic acid.•Phenolic dehydrodimers are only present in the insoluble bound fractions.•The breeding line YF53 has the highest TPC, TAC and antioxidant activity.Advanced breeding lines made from the cross between the black and white rice as parents were collected to evaluate phenolic levels and antioxidant properties. No free phenolic acid was found in the soluble fraction, while p-coumaric acid, ferulic acid, isoferulic acid and vanillic acid were identified in insoluble bound fractions. Of noteworthy, is isoferulic acid which has rarely been reported to occur in cereal grains. Phenolic dehydrodimers were only observed in the insoluble bound fractions, which mainly consisted of 8-5′-coupled diferulic acids and 5-5′-coupled diferulic acids. Cyanidin 3-glucoside, peonidin 3-glucoside and cyanidin occurred in black and some light-purple rice samples. The breeding line YF53 has the highest total phenolic content (23.3 mg ferulic acid equiv./g), total anthocyanin content (2.07 mg cyanidin-3-glu equiv./g), and antioxidant activities. The results indicate that it is possible to develop advanced breeding lines for improvement of the phenolic profiles and antioxidant capacity with high yield.

We determined the relationships among the structural properties, in vitro digestibility, and genetic factors in starches of 14 rice cultivars. Weight-based chain-length distributions in amylopectin ranged from 18.07% to 24.71% (fa, DP 6–12), 45.01% to 55.67% (fb1, DP 13–24), 12.72% to 14.05% (fb2, DP 25–36), and 10.80 to 20.72% (fb3, DP > 36), respectively. The contents of rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS) ranged from 78.5% to 87.5%, 1.2% to 6.0%, and 10.1% to 18.0%, respectively. AAC was negatively correlated with RDS content but positively correlated with RS content in rice starch. The proportion of short chains in amylopectin, i.e. the amount of fraction IIa (FrIIa) fractionated by gel permeation chromatography (GPC), was positively correlated with RDS. Starch synthase IIa (SSIIa) gene controlled the degree of crystallinity, the amount of fa chains of amylopectin. SSIIIa gene controlled the amount of fb1 chains. Wx gene controlled the FrI, FrIIa, RDS, and RS. Starch debranching enzyme isoamylase II (ISA2) gene also controlled the RDS, which may suggest that RDS was also affected by amylopectin structure, although no correlation between them was found. This study indicated that genetics (i.e., starch biosynthesis related genes) controlled the structural properties of starch, and both amylose content and amylopectin fine structure determined functional properties of rice starch (i.e., the digestion), each in a different way. Understanding the “genetics–structure–function” relationships in rice starches will assist plant breeders and food processors in developing new rice varieties and functional foods.

Mineral elements in brown rice grain play an important role in human health. In this study, variations in the content of iron (Fe), zinc (Zn), selenium (Se), cadmium (Cd), and lead (Pb) in 378 accessions of brown rice were investigated, and association mapping was used to detect the quantitative trait loci (QTLs) responsible for the variation. Among seven subpopulations, the mean values of Zn and Cd in the japonica group were significantly higher than in the indica groups. The population structure accounted for from 5.7% (Se) to 22.1% (Pb) of the total variation. Correlation analyses showed that Pb was positively correlated with the other minerals (P < 0.001) except for Se. For the five mineral elements investigated, 20 QTLs, including some previously reported and new candidate loci, were identified. Particularly, three cases of QTL colocalization, i.e. Cd and Pb on chromosome 5, Zn and Pb on chromosome 7, and Se and Pb on chromosome 11, were observed. This study suggested that the identified markers could feasibly be used to enhance desired micronutrients while reducing the heavy metal content in whole rice grain by marker-assisted selection (MAS).

Increasing grain weight and breeding for ideal plant architecture are two means to improve the productivity of rice. Quantitative trait locus (QTL) mapping was conducted on ten yield component traits using a recombinant inbred line population derived from an indica × indica cross (M201 × JY293). Correlation analysis revealed that plant height, panicle length and flag leaf length, classified as plant morphology traits, were positively correlated with grain shape traits such as thousand-grain weight, grain length and grain width. Two tillering traits, total and effective tiller numbers, showed negative correlations with nearly all the other traits tested. A total of 37 QTLs were detected over the 2-year study period, and 14 of them were identified in both years. Four clustered QTLs corresponding to known genes/QTLs (GW2, GS3, qGL3 and qTGW3.3) were revealed on chromosomes 2 and 3, which had pleiotropic effects on grain weight and plant architecture traits. QTL mapping demonstrated that qGL3 was a major QTL controlling grain length and weight, as well as plant height, panicle length and flag leaf length in rice. Three new QTLs, qTGW3.0, qGL2.2 and qETN4, were detected in both years and worth attention in breeding for high-yield rice varieties.

Wx is considered to be the most important gene controlling eating and cooking qualities and pasting properties in rice (Oryza sativa L.). In this study, a recombinant inbred line population derived from indica rice parents differing in apparent amylose content (AAC) was used to detect quantitative trait loci (QTLs) for ten grain quality parameters for rice quality improvement. QTL mapping was performed on the whole population and on two sub-populations based on Wx genotypes. A total of 29 QTLs were found in the whole population. Ten QTLs for 7 traits were detected in the two sub-populations, four of which (qPRO3.1, qPV9, qHPV9, and qCS7) were also detected in the whole population, whereas the other six were QTLs with minor effects that might be covered by the Wx locus. Besides the Wx locus with the largest effect on AAC and most pasting properties, there were another six QTL clusters contributing to grain quality located on chromosomes 2, 3, 5, 6 and 9. It was also found that some QTLs for peak viscosity, breakdown and consistency were closely linked to rice grain shape related QTLs on chromosome 3. A QTL cluster on chromosome 9 for peak viscosity, hot paste viscosity and cold paste viscosity was detectable in the whole population, which was close to the isoamylase 3 (ISA3) locus. A QTL cluster for both peak time and pasting temperature on chromosome 6 was near to the starch synthase I locus, and was potentially a new QTL with minor effect for peak time and pasting temperature. These findings will promote better understanding of the genetic regulation of rice eating and cooking qualities.

•Free and conjugated phenolics declined by about 50% 3 weeks post-flowering in red rice.•White rice had low phenolic levels that were similar after 2 weeks post-flowering.•Anthocyanin levels in black rice were highest at 2- and 3-weeks post-flowering.•Black rice had higher total bound phenolic acids than white & red rice at all stages.This study investigated differences in total phenolic content (TPC), antioxidant capacity, and phenolic acids in free, conjugated and bound fractions of white (unpolished), red and black rice at 1-, 2-, and 3-weeks of grain development after flowering and at maturity. Unlike the TPC (mg/100 g) of white rice (14.6–33.4) and red rice (66.8–422.2) which was significantly higher at 1-week than at later stages, the TPC of black rice (56.5–82.0) was highest at maturity. The antioxidant capacity measured by DPPH radical scavenging and ORAC methods generally followed a similar trend as TPC. Only black rice had detectable anthocyanins (26.5–174.7 mg/100 g). Cyanidin-3-glucoside (C3G) and peonidin-3-glucoside (P3G) were the main anthocyanins in black rice showing significantly higher levels at 2- and 3-weeks than at 1-week development and at maturity. At all stages, the phenolic acids existed mainly in the bound form as detected by HPLC and confirmed by LC–MS/MS. Black rice (20.1–31.7 mg/100 g) had higher total bound phenolic acids than white rice and red rice (7.0–11.8 mg/100 g). Protocatechuic acid was detected in red rice and black rice with relatively high levels at 1-week development (1.41 mg/100 g) and at maturity (4.48 mg/100 g), respectively. Vanillic acid (2.4–5.4 mg/100 g) was detected only in black rice where it peaked at maturity. p-Coumaric acid (<3.5 mg/100 g) did not differ significantly at most stages with somewhat high levels at 1-week for red and black rice. Ferulic acid (4.0–17.9 mg/100 g), the most abundant bound phenolic acid, had an inconsistent trend with higher levels being observed in black rice where it peaked at maturity. Isoferulic acid levels (0.8–1.6 mg/100 g) were generally low with slightly elevated values being observed at maturity. Overall black rice had higher total bound phenolic acids than white and red rice while white rice at all stages of development after flowering.

•Genetic diversity in starch physicochemical properties of 20 rice was analysed.•The amylose content and pasting viscosity parameter were mainly affected by genotypes.•The genotype × environment interaction effect for AAC and PT was not significant.•Association mapping identified 22 QTLs for all the traits except for CPV.Starch physicochemical properties determine the eating and cooking quality of rice. The genetic diversity in the apparent amylose content (AAC) and pasting viscosity parameters of 20 geographically diverse rice accessions were investigated. It was found that AAC and pasting viscosities differed widely among different accessions, but each accession performed relatively stably across two environments. Analysis of variance (ANOVA) indicated that all traits were predominantly controlled by genotypic variance, but the genotype × environment interaction effects were also significant except for AAC and PT. Significant correlations were found for each parameter between 2 years (P < 0.001). Association mapping identified a total of 22 main-effect quantitative trait loci (QTLs) responsible for all traits except for CPV. This study showed that starch physicochemical properties of rice were highly stable and mainly controlled by genetic factors, and gave insight into the molecular improvement of eating quality using marker assisted breeding with the identified QTLs/genes.

Uncovering the genetic basis of polyphenol content and antioxidant activity traits in rice accessions is important to improve the nutritional quality of whole grain rice and to ameliorate the increasing nutrition problem of the rice-eating population. In this study, 20 diverse rice accessions were planted in Hainan province, China, for 2 years to investigate the effects of genotype, environment, and their interactions on total phenolic (TPC), flavonoid (TFC), proanthocyanidins content (TPAC), ABTS, and DPPH radical scavenging activity by association mapping. Analyses of variance (ANOVA) showed that TPC, TFC, TPAC, ABTS, and DPPH were mainly affected by genetic variance, accounting for >94% of the total variance. The interaction between genotype × environment (G × E) was also highly significant (P < 0.001). Red-pericarp rice accumulates proanthocyanidins, which had significantly higher TPC, TFC, ABTS, and DPPH than white-pericarp rice. The correlation coefficient among these parameters were highly significant (r > 0.96; P < 0.001). Twenty-three putative unique loci were identified by association mapping. Five loci were close to previously identified genes or quantitative trait loci (QTLs). Among them, qPAC7-3 identified for TPAC in 2011 was near to the brown pericarp and seed coat (Rc) gene, and the locus at the qPC4/qFC4/qPAC4/qACA4/qACD4 cluster on chromosome 4 detected in two environments was near to a transcriptional activator A (Ra) gene. Some loci were identified in only one environment, indicating that these QTLs were sensitive to environment. This study provides a primary SNP-resource for further identification of genes responsible for polyhenol contents and antioxidant activity in rice whole grains.

Acquiring a complete understanding of rice starch lysophospholipids (LPLs), their biosynthetic pathways and genetic diversity, and the influence of genotype by environment interactions has been hampered by the lack of efficient high-throughput extraction and analysis methods. It was hypothesized a single-step aqueous n-propanol extraction combined with liquid chromatography–mass spectrometry (LC-MS) could be employed to analyze starch LPLs in white rice. The investigation found different grinding methods showed little effect on the final LPL detected, and a simple single-step extraction with 75% n-propanol (8 mL/0.15 g) heated at 100 °C for 2 h was as effective as an onerous multistep extraction method. A LC-MS method was optimized to simultaneously quantify 10 major LPLs in rice starch within 15 min. This method enables total and individual starch LPL analysis of a large number of rice samples at little cost. This approach could be applied to starch LPLs in other cereals.

Phospholipids (PLs) play a prominent role in both grain cellular structure and nutritional function of cereal crops. Their lyso forms (lysophospholipids, LPLs) often combine with cereal starch to form an amylose–lipid complex (ALC), which may influence starch properties. In this study, 20 rice accessions were grown over two seasons at the same location to explore diversity in LPLs of milled rice. Levels of specific LPLs differed significantly among rice genotypes, demonstrating there is a wide diversity in LPLs in rice grain. The main LPL components were lysophosphatidylcholine (LPC) 16:0 (ranging from 3009.7 to 4697.8 μg/g), LPC18:2 (836.6–2182.3 μg/g), lysophosphatidylethanolamine (LPE) 16:0 (625.7–1139.8 μg/g), and LPE18:2 (170.6–481.6 μg/g). Total LPC, total LPE, and total LPL ranged from 4727.1 to 7685.2 μg/g, from 882.8 to 1809.5 μg/g, and from 5609.8 to 9401.1 μg/g, respectively. Although significant (P < 0.001) environment and genotype × environment (G × E) interactions were detected by analysis of variance (ANOVA), these effects accounted for only 0.7–38.9 and 1.8–6.6% of the total variance, respectively. Correlation analysis between LPL components provided insight into the possible LPL biosynthesis pathway in plants. Hierarchical cluster analysis suggested that the 20 rice accessions could be classified into three groups, whereas principal component analysis also identified three groups, with the first two components explaining 57.7 and 16.2% of the total variance. Further genetic studies are needed to identify genes or quantitative trait loci (QTLs) underlying the genetic control of LPLs in rice grain.

Starch physicochemical properties strongly influence eating and cooking quality of rice. The cleaved amplified polymorphic sequences, derived CAPS, and InDel markers for 13 starch synthesis-related genes (SSRGs) were developed, and together with markers developed before, there are 35 markers tagged for 23 SSRGs, with each gene tagged with at least one marker. These and 108 other markers were used for association mapping for 20 starch physicochemical property parameters. A total of 64 main-effect loci or quantitative trait locus (QTLs) was detected. In addition, 56 and 62 loci were identified under the Wx and SSIIa background, respectively. Wx was a major main-effect QTL for apparent amylose content (AAC), pasting viscosity, gel texture, and retrogradation property (P < 0.0001). SSIIa was a major main-effect QTL for pasting temperature, thermal, and retrogradation properties (P < 0.0001), but it was a minor main-effect QTL for some pasting viscosity parameters, such as BD, CS, Stab, and SBratio. Four other SSRGs, SSIIa, BE1, SSIIc, and GBSSII were detected for AAC under Wx background. Wx was detected for Tc and ΔHg under the SSIIa background. PUL was detected for HD as main-effect QTL and under SSIIa background. AGPL2 and ISA1 were detected, respectively, for ΔHg and retrogradation as main-effect QTL, as well as under both Wx and SSIIa backgrounds. This study suggested that retrogradation properties were mainly controlled by Wx, SSIIa, and ISA1 with the relative effects in the order of SSIIa > Wx > ISA1. These results have direct applications to quality breeding programs.

Phospholipids (PLs) are a major class of lipid in rice grain. Although PLs are only a minor nutrient compared to starch and protein, they may have both nutritional and functional significance. We have systemically reviewed the literature on the class, distribution and variation of PLs in rice, their relation to rice end-use quality and human health, as well as available methods for analytical profiling. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI) and their lyso forms are the major PLs in rice. The deterioration of PC in rice bran during storage was considered as a trigger for the degradation of rice lipids with associated rancid flavour in paddy and brown rice. The lyso forms in rice endosperm represent the major starch lipid, and may form inclusion complexes with amylose, affecting the physicochemical properties and digestibility of starch, and hence its cooking and eating quality. Dietary PLs have a positive impact on several human diseases and reduce the side-effects of some drugs. As rice has long been consumed as a staple food in many Asian countries, rice PLs may have significant health benefits for those populations. Rice PLs may be influenced both by genetic (G) and environmental (E) factors, and resolving G × E interactions may allow future exploitation of PL composition and content, thus boosting rice eating quality and health benefits for consumers. We have identified and summarised the different methods used for rice PL analysis, and discussed the consequences of variation in reported PL values due to inconsistencies between methods. This review enhances the understanding of the nature and importance of PLs in rice and outlines potential approaches for manipulating PLs to improve the quality of rice grain and other cereals.Highlights► Rice phospholipids (PLs) have both nutritional and functional significance. ► PLs represent ∼10% and 50% of total lipids in rice bran and non-waxy white rice. ► PLs affect rice storage, starch physicochemical properties and digestibility. ► Rice starch lysophospholipids may help to control Type 2 diabetes. ► Rice PLs research can be significantly advanced using modern instruments.

Waxy (glutinous) rice is widely used in traditional foods, and understanding the genetic bases of its diverse physicochemical properties will contribute to breeding of new waxy rice with unique qualities. The objective of this study was to investigate the genetic relationship between the starch biosynthesis related genes and the physicochemical properties of waxy rice using association mapping. A total of 36 molecular markers representing 18 genes were used to genotype 50 waxy rice accessions for which starch properties were previously available. Most of the starch properties differed between high and low gelatinization temperature (GT) groups, whereas most traits were similar between the low-GT indica rice and low-GT japonica rice, suggesting GT was the main determinant of the starch quality of waxy rice. Association mapping indicated that the starch properties of waxy rice were mainly controlled by starch synthase IIa (SSIIa or SSII-3, a major gene responsible for the gelatinization temperature) and SSI. It was found that gene–gene interactions were also important for the genetic control of starch properties of waxy rice. This study suggests that application of the functional SNPs of SSIIa in molecular breeding may facilitate quality improvement of waxy rice.

Rice straw is always regarded as a by-product of rice production, but it could be a significant energy source for ruminant animals. Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering. The common wild rice, Oryza rufipogon Griff., which is considered to be the progenitor of Oryza sativa, has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement. In the present study, the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF), neutral detergent fiber (NDF), acid detergent lignin (ADL), and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR). The results indicated that all four traits tested were continuously distributed among the BILs, but many BILs showed transgressive segregation. A total of 16 QTLs were identified for the four traits, but no QTLs were in common in two environments, suggesting that environment has dramatic effects on fiber and lignin syntheses. Compared to the QTL positions for grain yield-related traits, there were no unfavorable correlations between grain yield components and cell wall traits in this population. The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.

Phytochemicals such as phenolics and flavonoids in rice grain are antioxidants that are associated with reduced risk of developing chronic diseases including cardiovascular disease, type-2 diabetes and some cancers. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. Association mapping based on linkage disequilibrium has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, genome-wide association mapping using models controlling both population structure (Q) and relative kinship (K) were performed to identify the marker loci/QTLs underlying the naturally occurring variations of grain color and nutritional quality traits in 416 rice germplasm accessions including red and black rice. A total of 41 marker loci were identified for all the traits, and it was confirmed that Ra (i.e., Prp-b for purple pericarp) and Rc (brown pericarp and seed coat) genes were main-effect loci for rice grain color and nutritional quality traits. RM228, RM339, fgr (fragrance gene) and RM316 were important markers associated with most of the traits. Association mapping for the traits of the 361 white or non-pigmented rice accessions (i.e., excluding the red and black rice) revealed a total of 11 markers for four color parameters, and one marker (RM346) for phenolic content. Among them, Wx gene locus was identified for the color parameters of lightness (L*), redness (a*) and hue angle (Ho). Our study suggested that the markers identified in this study can feasibly be used to improve nutritional quality or health benefit properties of rice by marker-assisted selection if the co-segregations of the marker–trait associations are validated in segregating populations.

Whole grain rice is rich in phenolic compounds. The effect of γ-irradiation on the main phenolic compounds in the rice grains of three genotypes (black, red, and white) was investigated. Three phenolic acids (p-coumaric acid, ferulic acid, and sinapinic acid) were identified as major phenolic compounds in all rice samples, while two anthocyanins (cyanidin-3-glucoside and peonidin-3-glucoside) were identified in pigmented grain samples. In general, γ-irradiation at most of doses could significantly (p < 0.05) decrease total phenolic acid contents in all samples and total anthocyanins contents in the black rice, but their decreases were not completely in a dose-dependent manner. Unexpectedly, 6 and 8 kGy significantly (p < 0.05) increased total contents of anthocyanins and phenolic acids in black rice. This study suggested that suitable doses of irradiation might be carefully selected and used to minimise the loss of antioxidant phenolic compounds in whole grain rice during storage.

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker–trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.

Physicochemical and functional properties of starches isolated from fifteen grain amaranth cultivars (Amaranthus spp.) produced in China were analysed in this study. Amaranth starches had low but diverse amylose contents, ranging from 4.7% to 12.5%. Wide variation was also found in physicochemical properties, such as swelling power, water solubility index, pasting, thermal and textural properties. Amylose content was significantly correlated with functional properties, including pasting, thermal and textural properties and appeared to be the important determinant for these properties. Correlations among pasting, thermal and textural parameters were also significant. Principal component analysis using 17 variables extracted four principal components that explained 88% of the total variance. The first component represented amylose content, pasting and gel textural properties and explained 59% of the total variance, while the second component represented the thermal properties and accounted for an additional 14.5% of the total variance.

The physicochemical properties of starch, such as apparent amylose content, gelatinization temperature, and pasting viscosities, determine the eating, cooking, and processing qualities of various products of rice. A recombinant inbred line (RIL) population derived from the reciprocal cross of Lemont (a premium high-quality tropical japonica rice) and Jiayu 293 (a high-yield but low-quality indica rice) was used to test the association of microsatellite markers of starch-synthesizing genes with starch quality parameters. The results confirmed the association of Wx and starch synthase I (SSI) alleles with various starch properties measured in rice flour. However, the starch properties were not associated with the starch branching enzyme 1 (SBE 1) gene alleles.Keywords: Microsatellite; paste viscosity; rice; simple sequence repeat; starch;

Phytochemicals such as phenolics and flavonoids, which are present in rice grains, are associated with reduced risk of developing chronic diseases such as cardiovascular disease, type 2 diabetes, and some cancers. The phenolic and flavonoid compounds in rice grain also contribute to the antioxidant activity. Biofortification of rice grain by conventional breeding is a way to improve nutritional quality so as to combat nutritional deficiency. Since wet chemistry measurement of phenolic and flavonoid contents and antioxidant activity are time-consuming and expensive, a rapid and nondestructive predictive method based on near-infrared spectroscopy (NIRS) would be valuable to measure these nutritional quality parameters. In the present study, calibration models for measurement of phenolic and flavonoid contents and antioxidant capacity were developed using principal component analysis (PCA), partial least-squares regression (PLS), and modified partial least-squares regression (mPLS) methods with the spectra of the dehulled grain (brown rice). The results showed that NIRS could effectively predict the total phenolic contents and antioxidant capacity by PLS and mPLS methods. The standard errors of prediction (SEP) were 47.1 and 45.9 mg gallic acid equivalent (GAE) for phenolic content, and the coefficients of determination (r2) were 0.849 and 0.864 by PLS and mPLS methods, respectively. Both PLS and mPLS methods gave similarly accurate performance for prediction of antioxidant capacity with SEP of 0.28 mM Trolox equivalent antioxidant capacity (TEAC) and r2 of 0.82. However, the NIRS models were not successful for flavonoid content with the three methods (r2 < 0.4). The models reported here are usable for routine screening of a large number of samples in early generation screening in breeding programs.

A total of 236 nonwaxy rice including 56 landraces (landrace set) obtained from the germplasm center and 180 cultivars and breeding lines (breeding line set) obtained from various breeding programs were studied for the genetic diversity of flour thermal and retrogradation properties, focusing on comparison of the differences between the landrace set and breeding line set. Wide diversity was found in all flour physicochemical properties, e.g. peak temperature (Tp) ranged from 63.2 to 79.8 °C, width at half peak height (ΔT1/2) of gelatinization ranged from 4.7 to 10.5 °C; enthalpy of gelatinization (ΔHg) ranged from 5.6 to 11.4 J/g, and retrogradation percentage (R%) ranged from 0.2% to 54.2%. The breeding line set had a larger range of thermal properties and R% than in the landrace set, whereas the range of retrogradation enthalpy was similar between two sets. The mean for all parameters differed between the two sets; mean ΔT1/2 of the landrace set was smaller than in the breeding line set, whereas other parameters were larger in the landrace set than the breeding line set. Correlation analysis showed that apparent amylose content was positively correlated with ΔHg (r = 0.65, P < 0.001) and R% (r = 0.68, P < 0.001), and negatively correlated with ΔT1/2 (r = −0.28, P < 0.001). All thermal and retrogradation properties themselves were correlated; the correlation between ΔT1/2 and all other parameters was negative, whereas all other pairs were positive.

High yield in rice mainly depends on large grain weight, ideal plant architecture and proper flowering time adapting to various geographic regions. To help achieve higher yield, phenotype variations of heading date (HD), plant architecture and grain shape in a panel of 416 rice accessions were investigated in this study. A total of 143 markers including 100 simple sequence repeat (SSR) markers and 43 gene-tagged markers were employed in association mapping to detect quantitative trait loci (QTL) responsible for these variations. Among the 7 subpopulations, POP5 in japonica group showed the largest values of HD and grain width (GW), but the smallest values of grain length (GL) and grain length to width ratio (GLW). Among the six indica groups, POP7 had the largest values of HD, GL, GLW, and 1 000-grain weight (TGW). A total of 27 QTLs were detected underlying these phenotypic variations in single year, while 12 of them could be detected in 2006 and 2007. GS3 marker was closely associated with GL, GW and GLW, and widely distributed in different groups. The starch synthesis related gene markers, SSI, SSIIa, SBE1, AGPL4, and ISA1, were linked to plant height (PH), panicle length (PL), flag leaf length (FLL), GW, and GLW. The SSR markers, RM267, RM340 and RM346, were linked to at least two traits. Therefore, these new markers will probably be used to improve rice grain yield or plant architecture when performing marker-assisted selection of proper alleles.

Gelatinization temperature (GT) is an important quality predictor that determines the cooking quality of rice. GT is genetically controlled by the starch synthase IIa (SSIIa) gene. Two functional single nucleotide polymorphisms (SNPs) inside the SSIIa have already been found to be responsible for the variation of GT. One of these, GC/TT SNP at 4329/4330 bp, could be genotyped by four primers in a single PCR (Bao et al., 2006a), but another one, G/A SNP at 4198 bp, has not been detected by a PCR-based marker. Here, we developed cleaved amplified polymorphic sequence (CAPS) and derived cleaved amplified polymorphic sequence (dCAPS) markers to detect these SNPs. A dCAPS marker that the PCR products were cleaved by the BseR I restriction endonuclease was designed to detect GC/TT SNP. Both CAPS and dCAPS markers were designed to detect G/A SNP using the restriction endonuclease Nla III and Tsp45 I, respectively. All the markers developed were co-dominant. It was known that the A allele of G/A SNP was rare among rice germplasm, but it was still in use by rice breeders. 11 rice accessions including landrace and breeding lines with A allele of G/A SNP were detected. The F2 individuals from two crosses were used to analyze the co-segregation between the SNP alleles and the GT. The segregation ratio of two SNPs did not conform to the expected Mendelian ratio of 1:2:1, but the SNPs were co-segregated with GT. The markers developed in the present study would be useful in molecular breeding for the improvement of the quality of rice grain.

Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment (G × E) interaction effects. The G × E effects for agronomic traits of rice have been dissected with various approaches, but not with the current available approach, the association studies. In this study, a total of 32 655 single nucleotide polymorphisms were used to carry out associations with 14 agronomic traits among 20 rice accessions in two environments. The G × E interaction effects for all the agronomic traits were at highly significant levels (P < 0.01), accounting for 3.4%–22.3% of the total sum of squares except for the length of brown rice. Twenty three putative quantitative trait loci (QTLs), including five previously known and several new promising associations, were identified for 10 of 14 traits. Analysis of the relationships between the traits for which QTLs and the genotype effects could be identified suggested that the higher the genotypic effect, the higher the possibility to identify QTLs for the given trait. The new QTLs detected in this study will facilitate dissection of the complex agronomic traits and may give insight into the G × E effects with association mapping.

Simultaneous heading of plants within the same rice variety, also refer to heading synchrony, is an important factor that affects simultaneous ripening of the variety. Understanding of the genetic basis of heading synchrony may contribute to molecular breeding of rice with simultaneous heading and ripening. In the present study, a doubled haploid (DH) population, derived from a cross between Chunjiang 06 and TN1 was used to analyze quantitative trait locus (QTL) for heading synchrony related traits, i.e., early heading date (EHD), late heading date (LHD), heading asynchrony (HAS), and tiller number (PN). A total of 19 QTLs for four traits distributed on nine chromosomes were detected in two environments. One QTL, qHAS-8 for HAS, explained 27.7% of the phenotypic variation, co-located with the QTLs for EHD and LHD, but it was only significant under long-day conditions in Hangzhou, China. The other three QTLs, qHAS-6, qHAS-9, and qHAS-10, were identified under short-day conditions in Hainan, China, each of which explained about 11% of the phenotypic variation. Two of them, qHAS-6 and qHAS-9, were co-located with the QTLs for EHD and LHD. Two QTLs, qPN-4 and qPN-5 for PN, were detected in Hangzhou, and qPN-5 was also detected in Hainan. However, none of them was co-located with QTLs for EHD, LHD, and HAS, suggesting that PN and HAS were controlled by different genetic factors. The results of this study can be useful in marker assisted breeding for improvement of heading synchrony.

•White, red and black rice grain fractions differ in phenolic distribution.•Free/conjugated phenolic acids mainly exist in rice embryo.•Bound phenolic acids are high in white rice bran.•p-Coumaric acid is predominantly in bound form in rice embryo and bran.•Cyanidin-3-O-rutinoside is identified in black rice bran.Whole rice grain comprising endosperm, embryo (or germ), and bran has potential beneficial health effects in addition to provision of nutrients. The distribution of phenolic acids and anthocyanins in endosperm, embryo, and bran of white, red, and black rice grains was investigated in this study. The total phenolic content (TPC) was highest in the bran, averaging 7.35 mg GAE/g and contributing 60%, 86% and 84% of phenolics in white, red and black rice. The average TPC of the embryo and endosperm were 2.79 and 0.11 mg GAE/g accounting for 17% and 23%, 4% and 10% and 7% and 9% in white, red and black rice, respectively. The antioxidant capacity determined using DPPH and ORAC displayed a trend similar to TPC. Free/conjugated phenolic acids in white, red and black rice bran accounted for 41%, 65% and 85% of total acids. Bound phenolic acids in rice bran accounted for 90% of total acids in whole grain. Cis-p-coumaric was detected in bound form in bran while cis-sinapic acid was detected in the free/conjugated form in embryo and bran. Cyanidin-3-O-glucoside and peonidin-3-O-glucoside were identified mainly in black rice bran as the total anthocyanins. Cyanindin-3-O-rutinoside was also detected in black rice bran.

Pasting properties are among the most important characteristics of starch, determining its applications in food processing and other industries. Pasting temperature derived from the Rapid Visco-analyser (RVA) (Newport Scientific), in most cases, is overestimated by the Thermocline for Windows software program. Here, two methods facilitating accurate measurement of pasting temperature by RVA were described. One is to change parameter setting to ‘screen’ the true point where the pasting viscosity begins to increase, the other is to manually record the time (T1) when the pasting viscosity begins to increase and calculate the pasting temperature with the formula of (45/3.8)×(T1–1)+50 for rice flour. The latter method gave a manually determined pasting temperature which was significantly correlated with the gelatinization temperature measured by differential scanning calorimetry.

II-32B is a key maintainer line used for hybrid rice breeding in China. However, it is of poor quality for most Chinese consumers because of its high apparent amylose content (AAC), high gelatinization temperature (GT) and non-fragrance. It is well known that the AAC, GT and fragrance traits are largely controlled by the Wx, starch synthase IIa (SSIIa), and fragrance (fgr) genes, respectively. With the aid of functional markers, we improved the quality of II-32B by introgressing the Wx, SSIIa, and fgr genes from Yixiang B, a fragrant maintainer line that has low AAC and low GT. The microsatellite allele (CT)17 of Wx, the contiguous single nucleotide polymorphism TT allele of SSIIa and the 8-bp deletion allele of fgr were transferred to II-32B by two backcrosses and three selfings. Molecular marker assisted selection was applied in the series to select for individuals carrying Wx-(CT)17, SSIIa-TT, and fgr-deletion alleles. According to the marker genotypes, seventeen homozygous lines for Wx-(CT)17, SSIIa-TT, and fgr gene markers were finally selected. The improved II-32B lines were fragrant with reduced AAC and GT.

Total phenolics, flavonoid contents and antioxidant capacity from a wide collection of rice germplasm were measured, and their relations to grain color, grain size and 100-grain weight were investigated. Highly significant genotypic differences were observed in total phenolics, flavonoid contents and 2,2-azino-bis-(3-ehylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) radical cation antioxidant capacity. They displayed an increasing order in the white rice, red rice and black rice, yet several white rice had higher phenolics and flavonoids contents than the red rice. Significant positive pair-wise correlations were found among the phenolics, flavonoid contents and antioxidant capacity, and the coefficient between the phenolic contents and antioxidant capacity was extremely high (r = 0.96). Among all rice accessions, the grain color parameters had negative correlations with the phenolics, flavonoid contents and antioxidant capacity (p < 0.001). The negative correlation between a* and antioxidant capacity, and the positive correlation between H° and antioxidant capacity were consistent within the respective white rice and red rice groups. Flavonoid contents had positive correlation with grain length and length to width ratio, and had negative correlation with the 100-grain weight among all rice accessions. It was also found that 100-grain weight still had negative correlations with phenolics, flavonoid contents and antioxidant capacity within the white rice genotypes. These relationships may serve as indexes to indirectly select breeding lines high in the phenolics, flavonoids and antioxidant capacity. Principal component analysis including the information for phenolics, flavonoids, antioxidant capacity, grain color parameters, grain size and 100-grain weight extracted five principal components that explained 83.7% of the total variances. The results of this study may provide new opportunities for rice breeders and eventually commercial rice growers to promote the production of rice with enhanced nutritional quality.

Three rice genotypes with different color were gamma irradiated at a dose of 2, 4, 6, 8and 10 kGy. The aim of this study was to investigate the effect of gamma irradiation on the phenolics content and the antioxidant activity, as well as physicochemical properties of whole grain rice. The bound phenolics content in all the genotypes were significantly increased with the increase of dose of irradiation. Gamma irradiation at high dose significantly increased the free, bound and total antioxidant activities of three rice genotypes except for the free antioxidant activities of red rice. Though the color parameters were slightly changed, these changes could not be visibly identified. Rapid visco-analyzer (RVA) viscosities and gel hardness decreased continuously with the increase of the irradiation doses. It is suggested that gamma irradiation enhanced the antioxidant potential and eating quality of whole grainrice.Highlights► Effects of irradiation on physicochemical properties of three rice were investigated. ► The bound phenolics and its antioxidant capacity were increased with the dosage increase. ► The color parameters of flour were slightly affected by irradiation. ► The viscosity and gel hardness were decreased continuously with the dosage increase.