Accumulation of phytate and starch lysophospholipids in rice grains and responses to alterations in P supply or source-sink relations

The removal of phosphorus (P) from fields in the harvested seeds of staple crops is a major driver of the global P cycle, and consequently, there is interest in breeding grain crops with lower seed P concentrations. While it is expected that a reduction in seed total P would result in lower concentrations of the P-rich anti-nutrient phytate, the potential consequences for starch lysophospholipids (LPLs), which affect rice grain quality and health outcomes in humans, are unknown. We examined the accumulation of phytate and starch LPLs in developing indica (cv. IR64) and japonica (cv. Nipponbare) rice grains as well as the stability of starch LPLs and phytate under varying P supply treatments in hydroponics. Source-sink relationships during grain filling (drought and floret abortion) were also investigated in a pot study. Accumulation of phytate and starch LPLs in seeds continued until 18 days after anthesis (DAA) in cv. Nipponbare and 21 DAA in cv. IR64, which mirrored the accumulation of biomass in seeds. In the hydroponic study, permanent withdrawal of P from the nutrient solution at anthesis (until maturity) led to significant reductions in both phytate and starch LPLs with a similar trend observed when P was withdrawn at 8 DAA. In the pot study using soil, alteration of source-sink systems through drought stress during grain filling or floret abortion (manual removal of the top half of each panicle) also led to significant reductions in grain phytate and starch LPLs compared to control plants. These results indicate that in addition to affecting phytate concentrations, reduced P supply to rice plants during grain filling and alteration of source-sink relationships also impacts starch LPL concentrations. Given these complexities, breeding and selection for reduced seed P concentration in rice and other cereals should be undertaken with caution.     

稻米淀粉理化特性相关的水稻淀粉分支酶基因标记开发

 基于籼稻93 11和粳稻日本晴基因组间的序列差异,成功发展了水稻淀粉分支酶基因(Sbe)9个分子标记。利用这些标记对102份非糯材料进行了基因型检测,并分析了Sbe1、Sbe3基因标记基因型多态性对稻米淀粉理化特性的影响。Sbe1、Sbe3基因标记多态性位点对揭示非糯材料间稻米淀粉理化特性的差异不显著,说明淀粉分支酶基因这些等位性变异位点对非糯稻米的蒸煮食味品质影响不显著;在鉴定籼稻品种时,有6个标记的鉴定准确率达80%以上。还对标记开发的意义和分子标记辅助选择育种进行了探讨。     

Allelic Effects on Eating and Cooking Quality of SSⅡa and PUL Genes Under Wxmp Background in Rice

【Objective】Our aim is to analyze the genetic effects of soluble starch synthase gene SSⅡa and debranching enzyme gene PUL on eating and cooking quality under the same main gene background of Wxmp, so as to lay a theoretical basis for rice quality improvement. 【Method】In this study, a semi-glutinous rice line Ning 0145 and japonica rice variety Wuyunjing 21 were crossed to obtain F2 population and F3 lines. There was polymorphism in soluble starch synthase gene SSⅡa and debranching enzyme gene PUL but no polymorphism in other starch synthase related genes between the two parents. With molecular markers, some F2 plants and F3 lines containing Wxmp gene were selected and divided into four genotypes, SSⅡanPULn, SSⅡanPULw, SSⅡawPULnand SSⅡawPULw(n and w indicated that the genes were contributed by Ning 0145 and Wuyunjing 21, respectively). The allelic effects of SSⅡa and PUL genes on eating and cooking quality under the same Wxmp gene background was investigated by analyzing the eating and cooking quality and its differences among different genotypes. 【Result】There were significant differences for eating and cooking quality among genotypes of different parental origins. The allelic gene SSⅡaw and PULw from Wuyunjing 21 increased amylose content by 0.29%–1.00% and 0.62%–1.18% respectively, and the effect of PUL was greater than that of SSⅡa. There was interaction between SSⅡa and PUL genes. The SSⅡaw and PULw genes also decreased gel consistency and breakdown viscosity, increased hot paste viscosity, cool paste viscosity, setback viscosity and consistency viscosity, but had little effect on gelatinization temperature, peak viscosity and peak time. 【Conclusion】The genetic effects of SSⅡa and PUL genes on cooking and eating quality of rice under the background of Wxmp gene were clarified. The results lay a theoretical basis for improving rice quality by molecular marker-assisted selection of SSⅡa and PUL genes.     

水稻功能基因标记遗传距离与杂种优势的相关性研究

 利用与产量性状相关的功能基因标记分析了29个杂交水稻组合亲本间（18个不育系和11个恢复系）的遗传差异,结合29个亲本所配组合（47个）的F1表现,研究了功能基因标记遗传距离与杂种优势的相关性。结果表明,功能基因标记遗传距离与产量杂种优势呈显著正相关（r=0.29*）,而与其他主要产量构成因素的杂种优势相关不显著。说明功能基因标记有可能应用于杂交水稻杂种优势预测,但得到的相关系数偏小,还不足以预测杂种优势。     

Formation,characterization, and glucose response in mice to rice starch with low digestibility produced by citric acid treatment

The optimum conditions for producing rice starch enriched in slowly digestible and resistant fractions by citric acid treatment determined by a response surface methodology (RSM) model equation, were: reaction temperature, 128.4 °C; reaction time, 13.8 h; and citric acid, 2.62 mmol/20 g starch. The slowly digestible and resistant starch fractions of the optimally acid-treated rice starch totalled 54.1%, which was 28.1% higher than the control. The slowly digestible and resistant fractions of the acid-treated rice starch did not differ significantly after heat treatment, whereas those of raw rice starch decreased by 49.6–63.8%, depending on the type of heat treatment (cooking at 100 °C or autoclaving). The slowly digestible fraction of the acid-treated starch increased by 8.9–14.2%. After autoclaving, the glucose response of the acid-treated starch was lower than untreated starch, but similar to that of Novelose 330. After heat treatment, the rate of blood glucose decrease was slower for the acid-treated starch than for Novelose 330. Compared to raw rice starch, the acid-treated starch exhibited increases in apparent amylose content, blue value, dextrose equivalent, cold-water solubility and transmittance, and decreases in wavelength of maximum absorbance, viscosity, and gel-forming ability.     

亚洲栽培稻遗传变异分析最少SSR引物数的研究

以69份类型明确的亚洲栽培稻品种为材料,选用120对SSR引物,通过评估遗传多样性和群体结构,研究分析其遗传变异对SSR引物数的要求。结果表明:1)120对引物在69份试验材料中共检测到1256个等位变异,每个位点的等位基因数差异较大,变化范围为2~27,平均为10.5;平均Nei基因多样性指数变化范围为0.4058~0.9452,平均为0.7616;2)分析亚洲栽培稻遗传多样性时,至少需要72对SSR引物;3)分析亚洲栽培稻群体结构时所需最少引物数可降低至60对。     

Development of new markers to genotype the functional SNPs of SSIIa, a gene responsible for gelatinization temperature of rice starch

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.     

Effect of high-pressure treatment on rheological,thermal and structural changes in Basmati rice flour slurry

Rheological, thermal and structural changes in high pressure (HP) treated Basmati rice flour dispersions were studied as function of pressure level (350–650 MPa), slurry concentration (with 1:5, 1:3 and 1:2 flour-to-water ratios) and holding time (7.5–15 min). Rice flour dispersions exhibited a gradual liquid–solid gel transformation as they gelatinized and/or denatured and behaved as viscoelastic fluid following HP treatment. Mechanical strength (G′) of pressurized gel increased with applied pressure and rice concentration. Differential scanning calorimeter (DSC) thermograms of rice slurry measured after pressure treatment indicated a reduction in peak enthalpy in proportion with the extent of gelatinization and/or denaturation of starch and proteins. Pressure-treated rice samples had a progressively lower gelatinization temperature. A 15 min pressure treatment at 550 MPa was found sufficient to complete gelatinization of protein free isolated rice starch while the slurry required 650 MPa. The presence of proteins might have been responsible for the slower starch gelatinization in the rice slurry during pressure treatment. The sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier-transform infrared (FTIR) spectroscopy results indicated some minor changes in protein subunits and secondary structure of rice protein. This study has provided complementary information on pressure-induced changes in physical (thermal stability, overall structure) and molecular level (secondary structure) of rice protein.     

利用SRAP分子标记分析47份杂草稻样品遗传多样性

 利用SRAP分子标记分析了采集于杂草稻多发地区的47份样本的遗传多样性,旨在从基因的开放式阅读框区域（ORFs）深入研究杂草稻的遗传背景,为进一步揭示其来源提供依据。结果表明,参试的我国杂草稻材料在110对引物组合中共扩增出845种类型的谱带,多态性谱带590种,多态率为6982%,平均每对引物可以检测到54条多态性谱带。说明SRAP分子标记对于杂草稻基因组开放式阅读框区域序列的多态性具有很高的检测效率,适用于遗传多样性研究。我国杂草稻材料Shannon Weaver多样性指数（I）为063,且南北方杂草稻多样性指数（I）相当,分别为063和062。聚类分析结果表明,南方收集的杂草稻与北方收集杂草稻群体间遗传分化较大,遗传差异明显。程氏指数判定结果也表明杂草稻呈南籼北粳的分布状态。     

Population Structure and Marker-Trait Association in Indigenous Aromatic Rice

Joha rice of Assam is a class of rice with aroma, good cooking qualities and excellent palatability, which are grown in different places of Assam with their adaptability to local situations. A total of 143 simple sequence repeat markers were used in this study to reveal sufficient genetic variations among the 40 Joha and 14 non-Joha rice genotypes. Polymorphism information content of these markers were from 0.17 to 0.88, where the average of 3.7 alleles were observed. The model-based population assignment and dendrogram analysis identified three distinct groups in the 54 rice accessions, which established a clear identity of Joha accessions from the Basmati accessions, indicating high diversity and strong population structure in Joha rice. Furthermore, a total of 29 significant marker-trait associations(P 0.05) for 10 characters were detected. The QTLs related with yield and grain quality can be used effectively in crop improvement programs and for further fine mapping and validation of specific genes to develop gene-based perfect markers in rice breeding and for mining of better alleles of these genes in Joha rice collections.     

水稻科学数据平台的创建及应用

国家水稻数据中心(http://www.ricedata.cn)是一个以水稻为研究对象,融贯多学科的综合性数据平台。它创建了中国水稻品种及其系谱数据库,构建大品种指纹数据集和优异种质数据集,开发“系谱树”和骨干亲本算法;创建了水稻功能基因数据库,以文献析出的方式整合国内外报道的水稻功能基因,开发基于浏览器的遗传图谱生成程序和基因结构图生成程序,构建重要功能基因的分子标记数据集和育种上有利基因的整合数据集;自主开发了用于知识管理的本体系统,开创性地将此系统应用于水稻功能基因数据库和参考文献数据库的管理。平台致力于在生物数据与育种需求之间架起一座桥梁,目前已得到广泛应用,在国内产生重要影响。     

Physico-chemical Characteristics as Indicators of Starch Availability from Milled Rice

The hypothesis was tested that certain physico-chemical characteristics might be used as indicators of total starch availability and rate of starch availability of milled rice. Milled unparboiled (uPB) and parboiled (PB) rice samples (n=93) were characterized using standardized methods of physical tests and chemical analyses and anin vitromethod was used for measuring the rate of starch digestion on a subsample of rice (n=26). The rice varieties were dominated by medium long, bold rice grain with high amylose rice and intermediate gelatinization temperature (GT), but a wide range in all characteristics was measured. Small amounts of resistant starch (RS) were measured in the cooked rice, indicating virtually complete starch availability. The RS of PB rice (0·4 g/100 g rice as eaten) was significantly (P<0·004) higher than the RS of uPB rice (0·1 g/100 g) however. The rate of starch digestion was significantly affected by both variety and parboiling. The starch digestion index (SDI) values of the PB samples (mean value 73·7) were significantly (P<0·001) lower than those of the uPB samples (mean value 79·0). The apparent amylose content (AC) was the strongest determinant for SDI in both uPB and PB rice. The widths and shapes of the raw grains and the elongation after cooking were correlated significantly with SDI values for the uPB rice, while the relatively mild parboiling procedure followed in this study eliminated this correlation. The minimum cooking times were correlated significantly with the SDI values in the uPB samples.     

稻米品质形成和调控机理概述

针对国内外稻米品质的研究现状,分析了稻米品质的形成机制,探讨了不同生育期稻米品质形成的影响因素。在全球气候变化的背景之下,如何适应CO2浓度和温度增高的影响将是今后提高稻米品质的研究方向之一。     

Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

A collection of 167 Thai and exotic rice accessions was subjected for evaluation of genetic diversity and assessment of relationship by simple sequence repeat(SSR) markers. Among a total of 49 SSR markers, 13 markers distributing over 12 rice chromosomes showed clear polymorphic band patterns, and they were selected for genetic assessment. A total of 110 alleles were detected with an average of 8.46 alleles per locus. The averages of gene diversity, heterozygosity and polymorphic information content were 0.59, 0.02 and 0.56, respectively. The unweighted-pair group method with arithmetic averages(UPGMA) clustering analysis was performed for genetic distance, and phylogenetic tree was constructed. The result showed that this rice collection was divided into two major groups, classified as japonica and indica subspecies. Within the japonica group, temperate japonica and tropical japonica subgroups can be clearly separated. Three-dimensional principal component analysis projection and model-based population structure analysis showed consistent clustering results with two major groups of UPGMA analysis, supporting the classification of japonica and indica subspecies. The indica allelic frequency was also investigated to provide an indicative guide for breeders to overcome the practical problems on sterility of inter-subspecies hybrid offspring. This rice collection and information obtained in this study will be useful for rice breeding programs.     

Effect of partial gelatinization and retrogradation on the enzymatic digestion of waxy rice starch

The effect of partial gelatinization and retrogradation on in vitro enzymatic digestibility of waxy rice starch was investigated, and the relationship between the residual crystallinity and digestibility measured. An aqueous dispersion of starch (5%, dry weight basis) was partially gelatinized by heating at different temperatures (60, 65, or 70 °C for 5 min). The relative melting enthalpy values of the starch samples, based on the melting enthalpy of native starch, were 69.0, 36.7, and 8.5%, respectively. Retrograded starch samples were also prepared by storing a fully gelatinized starch paste (5% starch) at 4 °C for 2, 4, or 7 d, and the relative melting enthalpy values for the starch samples were 36.7, 67.2, and 79.9%, respectively. The partial gelatinization and retrogradation changed the enzymatic digestion behavior of the waxy rice starch samples, and the changes were significant in the initial stage of digestion. The digestion rate was reduced as the melting enthalpy increased. The amounts of slowly digestible starch (SDS) and resistant starch (RS) correlated positively with the relative melting enthalpy of the partially gelatinized or retrograded starch samples. The glycemic index (GI) estimated using an in vitro digestion test correlated negatively with the relative melting enthalpy. At similar melting enthalpy levels, the partially gelatinized starch samples were more resistant to enzymatic digestion than the retrograded starch samples, indicating that the thermal history and the crystalline morphology affected the enzymatic digestion behavior of starch.     

Physical properties of cryomilled rice starch

Cryomilling of rice starch was evaluated as a non-chemical way to modify starch structure and properties. Cryomilling in a liquid nitrogen bath (63–77.2 K) was done to Quest (10.80% amylose) and Pelde (20.75% amylose) rice starch at five different time frames (0, 15, 30, 45, and 60 min). The viscosity of the cryomilled rice starch decreased significantly (p < 0.05) with increasing milling duration, including peak viscosity, hot-paste viscosity, cold-paste viscosity, breakdown, and consistency. Increasing milling time significantly increased (p < 0.05) water solubility index and water absorption index. Infra-red spectroscopy and X-ray diffraction crystallography both showed that the crystallinity of the cryomilled starch decreased with increasing milling time. Differential scanning calorimetry (DSC) analyses showed that after 60 min cryomilling there was partial loss of crystallinity (86% for Quest and 91% for Pelde) of both cryomilled starches. The cryomilling process modified the rice starch by causing a loss of crystallinity, that reduced its pasting temperature and increased water absorption, and by fragmentation of starch (probably the amylopectin fraction) that reduced the viscosity and increased solubility.     

Wx^mp基因背景下可溶性淀粉合成酶基因SSⅡa和去分支酶基因PUL对水稻蒸煮食味品质的影响

【目的】分析在同一主效基因(Wx^mp)背景下可溶性淀粉合成酶基因SSⅡa和去分支酶基因PUL对稻米蒸煮食味品质的影响,以期为水稻品质遗传改良提供依据。【方法】选择在SSⅡa和PUL存在多态性而其他淀粉合成酶相关基因没有多态性的半糯品系宁0145和粳稻品种武运粳21进行杂交,获得F2群体与F3株系。利用分子标记,选择含有Wx^mp基因的F2单株与F3株系,将这些F2单株与F3株系分成SSⅡa^nPUL^n、SSⅡa^nPUL^w、SSⅡa^wPUL^n和SSⅡa^wPUL^w4种基因型(n和w分别表示该基因来源于宁0145和武运粳21),分析不同基因型蒸煮食味品质性状的差异,探讨同一Wxmp基因背景下不同SSⅡa和PUL等位基因对蒸煮食味品质性状的影响。【结果】不同基因型间蒸煮食味品质性状均存在显著差异,来源于武运粳21的SSⅡa^w基因和PUL^w基因分别使直链淀粉含量增加0.29%~1.00%和0.62%~1.18%,且PUL的效应大于SSⅡa,两者间存在互作效应。SSⅡa^w基因和PUL^w基因降低胶稠度和崩解值,提高了热浆黏度、冷胶黏度、消减值和回复值,对糊化温度、峰值黏度和峰值时间的作用较小。【结论】明确了Wx^mp背景下SSⅡa和PUL基因对稻米蒸煮食味品质的遗传效应,该研究结果为SSⅡa和PUL基因的分子标记辅助选择改良稻米品质提供了理论依据。     

稻瘟病菌生理小种RAPD分析及其与马唐瘟的差异

氯化卞法微量提取稻瘟病菌７个生理小各和马唐瘟病菌基因组ＤＮＡ，用６０个随机引物进行ＰＣＲ扩增，其中２１个引物的特异性扩增条带，第一引物－菌系组合扩增到３－１９条，平均１０．３条；其中有多态性条速为１－１２条，平均６．１条，多态性为６１．１％。说明稻瘟病菌群体有丰富的ＲＡＰＤ多态性。引物ＯＰＨ１、ＯＰＨ２，ＯＰＨ４，ＯＰＨ１３，ＯＰＨ１４，ＯＰＫ１４等扩增的条带多，多态性丰富，而且可以有效地区分稻瘟     

Effect of germination time on physicochemical properties of brown rice flour and starch from different rice cultivars

The present work was designed to obtain information on the effect of germination time on the selected physicochemical properties of brown rice flour and starch prepared from three different rice cultivars. Changes in total starch, amylose and amylopectin contents of flour, amylopectin/amylose ratio and molecular weight of starch, gelatinization, pasting, rheological, and morphological properties of flour and starch during 5 days of germination were investigated. Significant changes of pasting and rheological properties of brown rice flour were found during germination, but only small changes of these properties could be found in isolated starch. Scanning electron micrographs of flour showed that the continuous matrix structure of flour was highly destroyed after germination and scanning electron micrographs of isolated starch showed that after three days of germination, pits and holes were discovered on the surface of some starch granules. Germination had little effect on the average molecular weight of starch, but the polydispersity value in germinated brown rice (2–5 days germination) was higher than that in non-germinated brown rice. The changes observed in physicochemical properties of brown rice flour and starch after germination provided a crucial basis for understanding flour and starch modification mechanisms with potential applications for an industrial scale.     

Variation in root system architecture and drought response in rice (Oryza sativa): Phenotyping of the OryzaSNP panel in rainfed lowland fields

Root growth at soil depths below 30 cm may provide access to critical soil water reserves during drought in rainfed lowland rice. In this study, the OryzaSNP panel, a set of 20 lines representing genetic diversity in rice used for the discovery of DNA sequence polymorphisms, was evaluated for root characteristics in the field over three seasons varying in drought severity. Root length density (RLD) at a depth of 30–45 cm varied up to 74–92% among genotypes under drought stress (2008–2009 dry seasons), ranging from 0.024 to 0.23 cm cm⁻³ in 2008 and from 0.19 to 0.81 cm cm⁻³ in 2009. Real-time monitoring of soil moisture profiles revealed significant differences among genotypes, and these differences were correlated with RLD at those soil depths. Among the lines evaluated, the Aus isozyme group, particularly the genotype Dular, showed greater drought resistance associated with deep root growth and the highest drought response index (less reduction in yield by drought stress). Since the set of genotypes used in this study has been completely sequenced for SNP markers, the phenotypic information on root growth and drought avoidance responses presented here could be used in initial analysis of the genetic basis of dehydration avoidance traits and in facilitating improvement in drought resistance in rice.