Rapid prediction of head rice yield and grain shape for genome-wide association study in indica rice

Rice milling and appearance qualities are the main determinants of market price of the milled rice, so great breeding efforts have been directed to improve the milling and appearance quality. The success of breeding efforts depends on the accurate and rapid phenotyping of the quality traits in early generations. This study was conducted to first validate the effectiveness of the PaddyCheck to measure head rice yield (HRY) and paddy grain length of 40 indica rice cultivars. The results indicated that the PaddyCheck data had positively correlated with the lab methods of HRY (r = 0.81**) and grain length (r = 0.97**). An association panel including 281 indica rice accessions was phenotyped with the PaddyCheck and the data were used for genome-wide association study (GWAS) to identify quantitative trait locus (QTL) for milling and appearance quality. A total of nine QTLs were identified, among which the major genes GS3 and qSW5 were identified for grain length and width, respectively. Furthermore, a novel QTL on short arm of chromosome 6 was identified for HRY. Our study indicated that PaddyCheck measurement was accurate and effective, and could be applied in rice breeding for improvement of grain shape and milling quality. The nine QTLs identified in indica rice could be used in marker assisted selection in rice breeding programs.     

Molecular Dissection of the Relationships among Tiller Number,Plant Height and Heading Date in Rice

Abstract

Appropriate plant height, tiller number and heading date are important traits for maximizing rice production. In order to understand the genetic basis of the relationships among these three plant traits, we mapped quantitative trait loci (QTLs) using a recombinant inbred population and detected two-locus interactions for plant height and tiller number at two growth stages and for heading date in two years. There were significant negative correlations between tiller number and plant height, and between tiller number at maturity and heading date. A significant positive correlation was observed between heading date and plant height at maturity. A total of 29 QTLs for the three traits were identified over the two years. Results show that QTLs and majority of two-locus interactions for plant height and tiller numbers at 35 days after transplanting were different from those at maturity, indicating that different genes and interactions control the traits at different developmental stages. A large proportion of QTLs and interactions could only be detected in one year, suggesting that QTLs and two-locus interactions for the traits were dependent on the environment. Results suggest that pleiotropy and/or close linkage of genomic regions and pleiotropy of common two-locus combinations may be the genetic basis for the close correlations among the three traits. A QTL with a large effect for heading date, which was located in RG424-RZ667 on chromosome 6, also showed large effects on tiller number and plant height at maturity.     

QTL analysis of cold tolerance at seedling stage in rice (Oryza sativa L.) using recombination inbred lines

Cold tolerance at seedling stage of rice (Oryza sativa L.) is a favorable trait for the stable establishment in temperate and high-elevation areas. In the present study, 71 recombinant inbred lines (RIL) derived from the cross of Asominori (Japonica) and IR24 (Indica) were used to identify quantitative trait loci (QTL) affecting cold tolerance at seedling stage. The putative QTL was further confirmed using some chromosome segment substitution lines (CSSLs), in which IR24 was used as the donor parent and Asominori as the recurrent parent. The average seedling mortality was used as cold tolerance after cold treatment with 6 °C for 7 days and recovery culture with 25 °C for 4 days at three-leaf seedling stage. Three QTL affecting cold tolerance at seedling stage were detected on chromosomes 1, 5 and 6 with LOD scores ranging from 2.2 to 4.1 using composite interval mapping (CIM). Among them, qSCT-1 located in the region of XNpb87-2-C955 on chromosome 1 was a major QTL which explained 24.51% of total phenotypic variance and favorable allele came from japonica parent, Asominori. In addition, IR24 alleles at the other two loci (qSCT-5 and qSCT-6) increased cold tolerance. And these three QTL were confirmed by four lines from the IR24 CSSLs. Transferring favorable allele from japonica variety to indica background or pyramiding different QTL identified from indica is an effective way to improve cold tolerance of rice.     

联合QTL定位和转录组分析揭示玉米开花期的遗传基础

开花期对玉米适应不同环境具有决定性作用,是重要的育种目标,对玉米开花期进行QTL定位是进行花期性状改良的基础工作。以玉米自交系黄早四和1462为亲本构建的F_2:3群体为材料,结合高密度SNP标记对玉米抽雄期和散粉期进行QTL定位。结果表明,F_2:3群体的抽雄期和散粉期呈正态分布,且两性状之间呈极显著相关。利用WinQTLcart 2.5软件的复合区间作图法共检测5个控制抽雄期的QTL,分别位于3、5、6、7、9号染色体上,贡献率在6.19%～26.39%;同时检测到4个控制散粉期的QTL,位于3、5、6、7号染色体上,贡献率7.48%～28.28%,这些QTL的基因作用方式以部分显性和超显性为主。共计发现3个主效QTL(贡献率超过10%),分别位于3号和6号染色体上。利用两个亲本的V6时期的茎尖进行转录分析,在主效QTL置信区间内共发现21个差异表达基因,其中包含可能控制玉米花期的候选基因。     

利用分池分析获得南大2419中一个抗赤霉病位点的分子标记

赤霉病是小麦的一种灾难性病害。为了发掘抗赤霉病基因,对小麦品种望水白×南大2419的F2群体及其重组自交系群体进行了赤霉病表型鉴定,并根据F2抗性表型分别配制抗病池和感病池,用RAPD方法筛选与抗赤霉病基因连锁的候选标记。通过F2代选择基因型分析,发现S1021与抗赤霉病性有关。利用重组自交系群体证实了上述结果。这一标记在重组自交系中解释了8 %以上的表型变异。为了便于该基因在育种中的应用,将该RAPD标记转化成了SCAR标记并定位于染色体2B。区间作图表明南大2419是这一QTL的供体亲本。本研究表明,将分池法与选择基因型分析相结合,可以利用F2代群体定位效应较小的QTL位点。     

Quantitative trait loci for seedling vigor in rice under field conditions

Previous QTL studies on seedling vigor in rice (Oryza sativa L.) were conducted all based on laboratory germination tests. In the current study, a set of recombinant inbred lines derived from a rice cross were assessed for seedling vigor related traits in natural field environments including two treatments (drained soil and flooded soil). Composite interval mapping identified nine QTL for seedling vigor traits that correlated positively with each other. Individual QTL explained 4–14% of the total trait variation. Among the QTL, three and four were specific to the drained and flooded treatments, respectively, while two others were common between the two treatments. Four QTL (qFV-1-1, qFV-3-2, qFV-5-1 and qFV-10) each simultaneously showed effect on two or more traits with additive effects always in the same direction. The QTL qFV-5-1 could be further resolved into at least two linked loci, qFV-5-1a controlling seedling height and qFV-5-1b controlling seedling dry weight while the QTL qFV-10 could be a single locus with a pleiotropic effect on both seedling height and dry weight. The QTL qFV-1-1 and qFV-3-2 expressed specially under the flooded conditions, each pleiotropically controlling both coleoptile and seedling emergence. These two QTL were completely different from that affecting seedling emergence in the drained conditions. Comparison of the QTL indicated that the QTL mapping results based on field assessments could to some extent coincide with those based on lab tests but the discrepancy between the two kinds of experiments could not be overlooked.     

Investigating early vigour in upland rice (Oryza sativa L.): Part II. Identification of QTLs controlling early vigour under greenhouse and field conditions

Early vigour is an important characteristic for direct-seeded rice systems. The genetic control of early vigour was studied using a population of 129 backcross lines derived from a cross between Vandana, an improved indica, and Moroberekan, a traditional japonica. Screening was conducted under controlled conditions in greenhouse and field conditions, and indicators of early vigour, including shoot length, shoot biomass, leaf area, number of roots, root biomass, partitioning coefficients, and growth rates, were measured. Phenotypic correlations suggested that traits that were related and combined could be used to define early vigour. Broad-sense heritability ranged from moderate to high. Many regions were identified containing more than one QTL, suggesting that these traits were controlled by pleiotropic and/or closely linked QTLs. Many QTLs were specific to one environment but G × E interaction analysis showed that the main effects of the environment were large. Differences in temperature between experiments resulted in large differences in seedling age when expressed in thermal time. Different genes (QTLs) may be expected to control growth at different time intervals and thus may partly explain the limited agreement between experiments. However, several regions showed co-location of QTLs from more than one experiment. Comparisons with published studies revealed that these regions were previously identified in different genetic backgrounds and could potentially be used as introgression targets in a marker-assisted breeding program to improve germplasm for direct-seeded environments.     

Genetic and physiological analysis of tolerance to acute iron toxicity in rice

Background

Fe toxicity occurs in lowland rice production due to excess ferrous iron (Fe²⁺) formation in reduced soils. To contribute to the breeding for tolerance to Fe toxicity in rice, we determined quantitative trait loci (QTL) by screening two different bi-parental mapping populations under iron pulse stresses (1,000 mg L⁻¹ = 17.9 mM Fe²⁺ for 5 days) in hydroponic solution, followed by experiments with selected lines to determine whether QTLs were associated with iron exclusion (i.e. root based mechanisms), or iron inclusion (i.e. shoot-based mechanisms).

Results

In an IR29/Pokkali F₈ recombinant inbred population, 7 QTLs were detected for leaf bronzing score on chromosome 1, 2, 4, 7 and 12, respectively, individually explaining 9.2-18.7% of the phenotypic variation. Two tolerant recombinant inbred lines carrying putative QTLs were selected for further experiments. Based on Fe uptake into the shoot, the dominant tolerance mechanism of the tolerant line FL510 was determined to be exclusion with its root architecture being conducive to air transport and thus the ability to oxidize Fe²⁺ in rhizosphere. In line FL483, the iron tolerance was related mainly to shoot-based mechanisms (tolerant inclusion mechanism). In a Nipponbare/Kasalath/Nipponbare backcross inbred population, 3 QTLs were mapped on chromosomes 1, 3 and 8, respectively. These QTLs explained 11.6-18.6% of the total phenotypic variation. The effect of QTLs on chromosome 1 and 3 were confirmed by using chromosome segment substitution lines (SL), carrying Kasalath introgressions in the genetic background on Nipponbare. The Fe uptake in shoots of substitution lines suggests that the effect of the QTL on chromosome 1 was associated with shoot tolerance while the QTL on chromosome 3 was associated with iron exclusion.

Conclusion

Tolerance of certain genotypes were classified into shoot- and root- based mechanisms. Comparing our findings with previously reported QTLs for iron toxicity tolerance, we identified co-localization for some QTLs in both pluse and chronic stresses, especially on chromosome 1.     

多个环境下小麦千粒重QTL定位的稳定性分析

为尽可能多的探寻千粒重的重要遗传位点并验证其在不同生态条件下的稳定性,以142个和尚麦/豫8679的F9:10重组自交系(RIL)及其亲本为试验材料,分析了千粒重在北京(2006、2007)、安徽合肥(2007、2008)、四川成都(2007、2008)和山东泰安(2009、2010)8个环境下的性状表现,并利用已构建的含有170个SSR标记和2个EST标记的遗传图谱对该性状进行了QTL定位分析。结果共检测到35个QTLs,可解释表型变异的4.36%～16.80%;涉及小麦1A、1B、2A、2D、3A、3B、4A、4D、5A、5B、6D和7D染色体,特别是1B、2A、3B染色体上(Xwmc269、Xgwm33、Xwmc419、Xbarc124、Xgwm636、Xgwm359、Xgwm533、Xwmc307、Xwmc418)的QTL可在多个环境下稳定的表达,为千粒重的QTL精细定位和分子标记辅助选择奠定了基础。     

波兰小麦×普通小麦品系“中13”RIL群体籽粒特性的QTL定位

小麦籽粒特性与籽粒产量和品质密切相关。本研究以波兰小麦(Tiriticum polonicum L.)×普通小麦(Triticum aestivum L.)品系"中13"杂交组合衍生的99个F8重组自交系(Recombinant inbred lines,RIL)群体为材料,利用SSR分子标记构建连锁遗传图谱。根据两年实验数据,利用复合区间作图法对粒重、粒长和粒宽3个籽粒特性相关性状进行了QTL定位分析,共检测到12个与籽粒特性相关的加性QTL位点。其中,3个粒重QTL,1个位于1A染色体上,另外2个都在2A染色体上,单个QTL可解释表型变异的13.35%～20.04%;5个粒长QTL,其中2个位于2A染色体上,其余3个分别位于3A、5A和2B染色体上,单个QTL可解释表型变异的8.53%～21.03%;4个粒宽QTL,分别位于1A、2A、3B和5B染色体上,单个QTL可解释表型变异的9.76%～40.79%。在2A染色体上共检测到5个籽粒特性相关性状的QTL,表明2A染色体与籽粒特性关系密切。     

六棱大麦抗赤霉病QTL的定位(英文)

赤霉病是最严重的大麦病害之一。由于赤霉病抗性是受多基因控制的数量性状(QTL),并且一些表型性状也影响大麦赤霉病的抗病,如棱数、株高和抽穗期等,所以抗赤霉病大麦品种的选育十分困难。为了明确加拿大六棱大麦中赤霉病抗性以及相关性状的QTLs,本研究在4年中对93个家系的DH作图群体中赤霉病抗性、呕吐毒素(DON)含量、株高、抽穗期和成熟期等相关性状进行调查,并利用分子标记(444个DArT和26个SSR标记)构建的连锁图谱对QTL开展复合区间作图。结果表明,本研究共检测到4个影响赤霉病的QTLs,其中,2个主要的QTLs定位在3H和7H染色体上,它们的加性效应为-3.44和-3.69,分别解释14.1%和17.5%的表型差异,总共解释31.6%的赤霉病抗性差异;另外2个QTLs定位于7H染色体上,但二者同时也与DON含量显著相关。此外,在3H、5H和7H染色体上确定了5个影响株高的QTLs,在2H、4H、5H和7H上确定了4个影响抽穗期的QTLs。同时发现2个赤霉病抗性QTLs和1个DON累积QTL与控制株高的QTLs聚集重叠,1个赤霉病抗性QTL和抽穗期QTLs重叠。这些与赤霉病抗性、株高及抽穗期等农艺性状紧密连锁的分子标记可进一步用于有效提高抗赤霉病大麦品种的选育效率。     

Analysis of quantitative trait loci for some starch properties of rice (Oryza sativa L.): thermal properties, gel texture and swelling volume

To understand the genetic basis of gelatinization temperature (GT), gel textural traits and flour swelling volume, quantitative trait loci (QTL) were mapped for these traits using a doubled haploid (DH) population derived from a cross between indica variety Zai-Ye-Qing 8 (ZYQ8) and japonica variety Jing-Xi 17 (JX17). The results indicated that the starch property parameters were continuously distributed among the DH lines, and some DH lines showed transgressive segregation for all the parameters. A total of 16 QTLs were identified for seven traits. A major QTL, the alk gene on chromosome 6 was significant for the three GT traits, onset temperature (T_o), peak temperature (T_p), and completion temperature (T_c). This locus could explain 49.4, 38.9, and 28.3% of the total variance, respectively, indicating that GT parameters were substantially controlled by the alk gene which has previously been identified for alkali spreading value (ASV). The additive effects of alk on T_o,T_p and T_c were from ZYQ8. Another two QTLs on chromosomes 1 and 7 were also identified for the three GT parameters, whose positive effects were contributed from JX17. Another QTL on chromosome 10 with the positive effects coming from ZYQ8 was significant only for T_c. However, the enthalpy (ΔH) of gelatinization was controlled by two minor QTLs on chromosomes 1 and 7. A major QTL, the Wx gene on chromosome 6 was identified for gel hardness and flour swelling volume which explained 58.8 and 36.6% of the total variances, respectively. Another two QTLs were also detected for flour swelling volume, one of which (qSV-7) could explain 21.4% of the total variance. However, gel cohesiveness was controlled by a major QTL located between alk and Wx on chromosome 6.     

Effects of genes increasing the number of spikelets per panicle,TAW1 and APO1, on yield and yield-related traits in rice

The genes TAWAWA1 (TAW1) and ABERRANT PANICLE ORGANIZATION1 (APO1) increase the number of spikelets per panicle (SN). In the present study, we examined the effects of these genes on morphological traits, yield, and yield-related traits including yield components using the near-isogenic lines (NILs) in the genetic background of a japonica rice variety, Koshihikari – NIL-taw1, NIL-apo1-D3, and NIL-apo1-D4 – in a field experiment. The SN and total number of spikelets per area of the three NILs were larger than those of Koshihikari. However, the yield of the three NILs did not exceed that of Koshihikari due to their low filling ability. Interestingly, our field experiments indicated that TAW1 did not affect the diameter of internodes and the PN, whereas APO1 decreased the PN and increased the diameter of internodes. These results suggest that TAW1 and APO1 differently affect yield-related traits.     

Identification and validation of QTLs for cold tolerance at the booting stage and other agronomic traits in a rice cross of a Japanese tolerant variety,Hananomai, and a NERICA parent,WAB56-104

In Africa, cold temperatures occur in the highlands of East and Southern Africa and in some areas of the Sahel region of West Africa leading to substantial rice yield losses. Cold tolerance (CT) at booting stage on basis of spikelet fertility after cold water irrigation was evaluated using F₂ population derived from a cross between temperate japonica, Hananomai, and tropical japonica, WAB56-104. Two Quantitative trait loci (QTLs) for CT were detected on chromosome 8 and 10 with enhanced effects on the trait coming from Hananomai and WAB56-104 allele, respectively. The QTLs explained 30% and 33% of phenotypic variation in spikelet fertility, respectively. CT was negatively correlated with panicle number (r = ?0.35, p < 0.01) and positively correlated with panicle weight (r = 0.61, p < 0.001). Selected BC₁F₄ and BC₁F₅ genotypes having homozygous alleles for both CT QTLs exhibited higher spikelet fertility under cold stress. The identified QTLs will be useful in the development of cold-tolerant varieties for production in high altitude areas through marker-assisted selection.     

Dissection of gene loci underlying pasting temperature in cassava

In this study, a fine genetic map within the quantitative trait loci (QTL) underlying pasting temperature (PT) of cassava (Manihot esculenta Crantz) was constructed using newly developed simple sequence repeat (SSR) markers. The SSRs were designed on the basis of two scaffolds (S11341 and S4043) of the cassava genome, which covered previously identified QTL regions of the PT trait. A total of 55 and 61 SSR markers derived from S11341 and S4043, respectively, representing 0.29% of the cassava genome, were generated; of which 23 and 19 showed informative polymorphic patterns. Consequently, all identified informative polymorphic markers were used to genotype 200 F₁ progeny plants. The genotypic data were then analyzed, and the results showed that 480 markers were distributed across 23 linkage groups (LGs) with total length of 1,334 centimorgans (cM). An analysis of QTL underlying the PT trait revealed that marker EME81 on LG 1 had significant associations (P < 0.0001) in all environments evaluated. Four candidate genes were identified and selected for gene expression analysis in the parents, and among F₁ lines with high and low PT values. Significant differences were observed in relative expression of carbohydrate phosphorylase (CP) and starch synthase II (SSII) between high and low PT in 6-month-old cassava. We found CP and SSII genes to potentially control the PT trait. In addition, the marker EME81 was found to be a promising marker for specific PT trait selection in cassava populations, which should facilitate marker-assisted selection for desired PT traits.     

两个水稻抗褐飞虱隐性基因的遗传分析与初步定位

选用抗褐飞虱的海南普通野生稻渗入系WB01与感虫品种9311杂交,构建F2群体。采用141个具有多态性的SSR标记对303个F2:3株系进行分析,并应用MapMaker/EXP3.0和Windows QTL Cartographer2.0对水稻抗褐飞虱的数量性状基因座进行检测和遗传效应分析。共检测到2个抗性QTL,分别位于第4和第8染色体上,LOD值分别为2.92和3.15,贡献率分别为11.3%和14.9%。     

QTL mapping rolling,stomatal conductance and dimension traits of excised leaves in the Bala × Azucena recombinant inbred population of rice

The identification of markers linked to genes contributing to drought resistance promises opportunities to breed high yielding rice varieties for drought prone areas. Several studies using different mapping populations have previously identified quantitative trait loci (QTLs) for traits theoretically related to drought resistance. A mapping population of 176 F₆ recombinant inbred lines (RILs) derived from two upland rice varieties with contrasting aboveground drought avoidance traits (Bala and Azucena) with a linkage map of 157 markers was used to map QTLs for aboveground leaf morphological and physiological traits related to drought avoidance. Plants were grown for 6 weeks under controlled environmental conditions with three replications. Leaves were excised and placed on a balance. The rate of leaf rolling and water loss was recorded, after which leaf area, dry weight and specific leaf area were characterized. A simple method of estimating time to stomatal closure was employed. A total of 13 QTLs were detected for leaf morphological traits, three for initial transpiration and four for the proportion of water loss required to reach a specific advanced state of leaf rolling. No QTLs were detected for time of stomatal closure or speed of leaf rolling, nor for either water loss or transpiration at stomatal closure despite clear parental differences and moderate heritabilities in most of these traits. The co-location of QTLs for traits measured here and for drought avoidance previously reported from field experiments on chromosome 1, 3 and 5 link the genetics of drought resistance to leaf dimensions and physiology. However, a physiological explanation for a QTL for drought avoidance on chromosome 7 remains elusive.     

Analysis of yield attributes and crop physiological traits of Liangyoupeijiu,a hybrid rice recently bred in China

Crop physiological traits of Liangyoupeijiu, a “super” hybrid rice variety recently bred in China, were compared with those of Takanari and Nipponbare in 2003 and 2004 in Kyoto, Japan. Liangyoupeijiu showed a significantly higher grain yield than Nipponbare in both years, and achieved a grain yield of 11.8 t ha⁻¹ in 2004, which is the highest yield observed under environmental conditions in Kyoto. Liangyoupeijiu had longer growth duration and larger leaf area duration (LAD) before heading, causing larger biomass accumulation before heading than the other two varieties. Liangyoupeijiu had a large number of grains and translocated a large amount of carbohydrates from the vegetative organ to the panicle during the grain filling period. The three yield components measured were panicle weight at heading (P₀), the amount of carbohydrates translocated from the leaf and stem to the panicle during the grain filling period (ΔT), and the newly assimilated carbohydrates during grain filling (ΔW). It was found that the sum of P₀ and ΔT were strongly correlated with grain yield when all the data (n = 8) were combined (r = 0.876**). However, there was no significant difference in the radiation use efficiency (RUE) of the whole growth period between Liangyoupeijiu and Nipponbare for both years. Even though the growth duration was shorter, Takanari, an indica/japonica cross-bred variety, showed a similar yield to Liangyoupeijiu in both years. The mean RUE of the whole growth period was significantly higher in Takanari, 1.60 and 1.64 g MJ⁻¹ in 2003 and 2004, respectively, than in Liangyoupeijiu, which had a RUE of 1.46 and 1.52 g MJ⁻¹ in 2003 and 2004, respectively. The high grain yield of Takanari was mainly due to its high RUE compared with Liangyoupeijiu and its large P₀ and ΔT. Our result showed that the high grain yield of Liangyoupeijiu was due to its large biomass accumulation before heading, which resulted from its large LAD rather than its RUE.     

Screening,Inheritance and Linkage Marker Analyses of Salt Tolerance in Mutated Scented Japonica Rice (Oryza sativa L.)

Abstract

We grew 1005 mutated scented japonica rice lines to the seventh steady genetic generation, and treated the seedlings with six true leaves with 300 mM NaCl for three days. Only the salt-tolerant line, SM61, survived. We obtained F₁, F₂ and F₃ populations from the cross between SM61 and a salt-susceptible indica variety, TCS17. After culture with 200 mM NaCl for five days, SM61 and F₁ (SM61×TCS17; TCS17×SM61) plants survived (R) while TCS17 plants did not (S). The R to S ratio in 513 F₂ plants showed a good fit to the Mendelian 3 : 1 segregation ratio by a Chi-square test indicating that the salt-tolerance of SM61 was governed by a single dominant gene. The mutated salt-tolerance gene explained close to 100% of the total phenotypic variation, and was tightly linked to RM223 (marker) located on chromosome 8, which was different from the results of previous studies investigating the relationship of QTLs with salt tolerance. This is the first report of mapping tightly linked markers of a single dominant mutated salt-tolerance gene.     

Genetic relationship between grain yield and the contents of protein and fat in a recombinant inbred population of rice

To study the genetic relationship between grain yield and the nutrient contents in rice, 209 recombinant inbred lines derived from a cross between indica rice Xieqingzao B and Milyang 46 were used to determine quantitative trait loci (QTLs) affecting the yields and contents of the two major nutritional components in brown rice. Seven traits were analyzed, including brown rice recovery (BRR), protein content (PC), fat content (FC), grain yield (GYD), brown rice yield (BRYD), protein yield (PYD) and fat yield (FYD). The nutrient contents were significantly negatively correlated with BRR, GYD and BRYD, and the variations on nutrient yield were mainly ascribed to GYD. A total of 22 QTLs distributed on 10 regions of eight chromosomes were detected. Two QTL clusters were found on the short arm of chromosome 6 and the long arm of chromosome 10, respectively. The former was responsible for all the seven traits, and the latter for all the traits except BRR and FC. In both regions, the maternal alleles decreased nutrient contents, but they increased the yields of grain, brown rice, protein and fat. Implication of these results for the breeding of rice varieties with enhancing nutritional capacity is discussed.