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.     

An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R² = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R² = 11.25%) and trough viscosity (p < 0.01, R² = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.     

An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R² = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R² = 11.25%) and trough viscosity (p < 0.01, R² = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.     

Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in Upland Rice

Genome-wide association study (GWAS) was performed for 16 agronomic traits including nitrogen use efficiency (NUE) and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38 390 single nucleotide polymorphism (SNP) markers. This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels. Using another set of five grain traits, we identified previously known genes (GW5, GS3, Awn1 and Glabrous1), thus validating the pertinence and accuracy of our datasets for GWAS. A total of 369 significant associations were detected between SNPs and agronomic traits, gathered into 46 distinct haplotype groups and 28 isolated markers. Few association signals were identified for the complex quantitative trait NUE, however, larger number of quantitative trait loci (QTLs) were detected for its component traits, with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency, respectively. Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb. The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits. However, because of the quantitative and complex nature of NUE-related traits, GWAS might have not captured a large number of QTLs with limited effects.     

两个垩白突变体的鉴定及突变基因的图位克隆

【目的】研究两个水稻垩白突变体胚乳垩白的形成机制,为稻米品质改良提供理论基础。【方法】以从中花11的EMS突变体库中筛选出的两个稳定遗传的垩白突变体eb6、eb7为材料,对其进行农艺性状、稻米理化性质和遗传学分析,并利用eb6与南京11衍生的F2群体对控制垩白的基因进行图位克隆。同时对候选基因的表达模式及淀粉合成相关基因在突变体及野生型中表达情况进行了分析。【结果】与野生型相比,两个突变体胚乳中央部位呈现白色且不透明,淀粉复合颗粒形状不规则且排列疏松,而突变体胚乳边缘部位与野生型无异,都为半透明状,淀粉复合颗粒呈多面体且排列致密。相对于野生型,突变体eb6、eb7成熟种子中的直链淀粉含量和胶稠度显著降低,蛋白质含量显著升高。RVA谱分析显示突变体淀粉黏滞性明显低于野生型。同时,支链淀粉聚合度分析显示突变体eb6中聚合度(DP)小于16的短链显著增加,DP为16~23的中长链显著减少。遗传分析表明突变体eb6、eb7胚乳垩白表型由单隐性核基因控制,并且它们为一对等位突变体。利用突变体eb6与南京11杂交衍生的F2群体将突变体基因定位在第1染色体长臂上物理距离86.6 kb的区间内。该区间包含22个开放阅读框(ORF),其中ORF13编码腺苷二磷酸葡萄糖焦磷酸化酶大亚基2(Os AGPL2)。序列分析发现eb6与eb7分别在Os AGPL2第3、第7外显子上发生1个单碱基替换,并分别导致一个氨基酸替换。RT-PCR及原位杂交结果显示,Os AGPL2主要在水稻发育中的籽粒中表达。同时Os AGPL2的突变导致了多个淀粉合成相关基因在水稻籽粒灌浆过程中的表达模式发生改变。【结论】突变体eb6、eb7籽粒胚乳出现严重垩白表型为Os AGPL2突变所致。本研究进一步证明了Os AGPL2在调控水稻籽粒胚乳中淀粉的合成、淀粉复合颗粒的形成及稻米理化性质的平衡中起着重要的作用。     

Rice landrace diversity in Nepal: Variability of agro-morphological traits and SSR markers in landraces from a high-altitude site

Nepal has a wide diversity of rice landraces in all rice-growing areas from low to high altitude. A baseline survey in Jumla, a high-altitude site (2200–3000 m), identified rice landraces with different names that differed in phenotype and were adapted to the extreme high-altitude environment. Jumli Marshi was the most common traditional rice variety, accounting for 85% of samples collected. The genetic diversity of these landraces was assessed by agro-morphological variability and microsatellite marker polymorphism. Forty-two qualitative and quantitative traits and 39 microsatellite (simple sequence repeats, SSR) markers were assessed among accessions with 10 different names. The accessions showed low morphological diversity with an average Shannon Weaver diversity index of 0.23. Only 16 morphological traits showed significant variation among the accessions. Discriminant function analysis showed that only 36% of accessions could be clustered according to name by morphological traits. Only one SSR locus was polymorphic, distinguishing only one accession. The names used by farmers to describe the phenotypic characteristics of panicle and grains were inconsistent indicators of genetic identity. We conclude that the Jumla landrace population has a narrow genetic base. The diversity detected was sufficiently low for it to be possible that there was a single origin for all of the Jumla landraces.     

Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza Rufipogon

Grain size is one of the critical agronomic traits governing grain yield and quality in rice. However, the underlying genetic mechanisms that control grain size in rice are poorly understood. We used an introgression line derived from Zhonghui 8015 and Oryza rufipogon Griff. This introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain size. Genome-wide association study (GWAS) was performed using 28 193 SNPs through a general linear model, and 56 significant SNPs on different loci associated with the 4 grain size traits were detected. Cloned genes including GS3 and qGL3 showed substantial effects on grain length and size. Seven new stable loci were identified with pleiotropic effects on grain size. Haplotype, gene expression analyses, combined gene-based associations, and functional annotations permitted the shortlisting of important dominant genes including GS3 and qGL3.     

Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

Excavating single nucleotide polymorphisms(SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study(GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length(GL), grain width(GW), 1000-grain weight(TGW), and grain length/width(GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and q GL3 were found to regulate GL. On chromosome 6, TGW6 and GW6 a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3 K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.     

Association Mapping and Marker Development of Genes for Starch Lysophospholipid Synthesis in Rice

Phospholipids are a major kind of lipids in rice grains and have fundamental nutritional and functional benefits to the plant. Their lyso forms(lysophospholipids, LPLs) often form inclusion complexes with amylose or independently influence the physicochemical and functional properties of rice starch. However, the genetic basis for LPL synthesis in rice endosperm is largely unknown. Here, we performed a preliminary association test of 13 LPL compositions among 20 rice accessions, and identified 22 putative main-effect quantitative trait loci responsible for all LPLs except for LPC14:0 and LPE14:0. Five derived cleaved amplified polymorphic sequences and one insertion/deletion marker for three LPL-synthesis-related candidate genes were developed. Association analysis revealed two markers significantly associated with starch LPL traits. These results provide an insight into the genetic basis of phospholipid biosynthesis in rice and may contribute to the rice quality breeding programs using functional markers.     

Genetic bases of source-,sink-,and yield-related traits revealed by genome-wide association study in Xian rice

The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.     

Genetic Diversity Analysis of Rice Germplasm in Tripura State of Northeast India Using Drought and Blast Linked Markers

We genotyped 74 rice germplasms including Tripura's local landraces, improved varieties, cultivars and breeding lines and other rice varieties using molecular markers for genetic diversity, drought QTLs, and blast resistance genes. The number of alleles per locus ranged from 2 to 5 with an average of 2.9. The polymorphic information content value per locus ranged from 0.059 (RM537) to 0.755 (RM252) with an average of 0.475. Cluster analysis based on 30 simple sequence repeat markers revealed 5 clusters and also indicated the presence of variability within the rice accessions. The drought QTL qDTY2.1 was found in 56.0% of germplasms and qDTY1.1 was detected in only 6.8% of the germplasms. Out of seven rice blast resistance genes screened, only two rice varieties, RCPL-1-82 and Buh Vubuk (Lubuk), were positive for four blast resistance genes while only Releng possessed two blast resistance genes. Among 74 rice germplasms, only three accessions, Releng, RCPL1-82 and Buh Vubuk (Lubuk), possessed both drought-related QTLs and blast resistance genes. Overall, the 74 indigenous rice genotypes showed low level of genetic diversity, which is in contrast to high level of genetic diversity among rice varieties in northeast India, where highlights the good farming practice, conservation of germplasms and the limitation of molecular markers employed in this study. The presence of both drought related QTLs and blast resistance genes in some of the germplasms can be useful in future breeding programmes.     

Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our long-term goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.     

Transferring Translucent Endosperm Mutant Gene Wx-mq and Rice Stripe Disease Resistance Gene Stv-b by Marker-Assisted Selection in Rice (Oryza sativa)

A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-bⁱ and a translucent endosperm mutant gene Wx-mq. From F₂ generations, a sequence characterized amplified region (SCAR) marker tightly linked with Stv-bⁱ and a cleaved amplified polymorphic sequence (CAPS) marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.     

Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection

Apparent amylose content (AAC), the key determinant of rice end-use quality attributes, is primarily controlled by the Waxy gene which codes for granule bound starch synthase (GBSS). We examined the combination of sequence variation in the Waxy gene and environmental effects, and their associations with AAC using 171 rice accessions originating from 43 countries. The combination of two single-nucleotide-polymorphism (SNP) markers in the Waxy gene allows for the identification of three marker haplotypes in this gene. The first SNP is at the leader intron splice site (In1 SNP), and the second polymorphism is in exon 6. The haplotypes explained 86.7% of the variation in AAC and discriminated the three market classes of low, intermediate and high AAC rice from each other. The environment affected the AAC of all haplotypes. Higher air temperature during grain development associated with a decrease in AAC of low and intermediate AAC-types, but with an increase in AAC of high AAC-type. The association of AAC with several Waxy RM190 microsatellite-(CT_n) alleles in combination with the In1 SNP was also examined. In conclusion, the Waxy haplotypes studied appear to be useful markers for selecting the AAC of breeding lines developed from the world's rice germplasm.     

Functional Marker Development and Effect Analysis of Grain Size Gene GW2 in Extreme Grain Size Germplasm in Rice

GW2 is an important gene that regulates grain width and weight. We used c DNA clone to obtain the sequences of GW2 from large- and small-grained rice varieties,TD70 and Kasalath,respectively. Then,we developed a d CAPS(derived cleaved amplified polymorphic sequence) marker on the basis of the sequence difference between functional and nonfunctional GW2 genes to analyze the genotypes and phenotypes of recombinant inbred lines. Results showed that the sequence of GW2TD70 had a single nucleotide deletion at site 316 that generates a termination codon. This codon terminated the GW2 protein in advance. By contrast,the sequence of GW2 Kasalath encoded an intact protein. A novel d CAPS marker was designed in accordance with a base A deletion at site 316 of the sequence. After the PCR product was digested by Apo I,TD70 showed 21 and 30 bp fragments,and Kasalath showed a 51 bp fragment. Up to 82 lines contained GW2TD70,and 158 lines contained GW2 Kasalath. The lines that contained TD70 alleles displayed substantial increases in width and 1000-grain weight. This result suggested that GW2 played a critical role in rice breeding.     

Relationship Between Allelopathic Effects and Functional Traits of Different Allelopathic Potential Rice Accessions at Different Growth Stages

In this study,effects of temperature,light and their interactions on allelopathic effects and the functional traits specific leaf area(SLA)and stem mass fraction(SMF)of different allelopathic potential rice accessions at different growth stages were analyzed.The main results were as follows:Allelopathic responses to temperature and light varied with different allelopathic potential rice accessions at different growth stages.With the rise of temperature and the extension of photoperiod,allelopathic effect increased firstly and then decreased at 2–3 leaf stage,but increased constantly at the 4–5 and 7–8 leaf stages in strong allelopathic rice accessions[O.longistaminata,F1(O.longistaminata×RD23),F2(RL159 and RL169)].Temperature had significant impact on allelopathic effect without considering light factors,but light showed little effect on rice allelopathy at the same temperature conditions.The greatest allelopathic effect was attained with moderate temperature and long photoperiod at 2–3 leaf stage in strong allelopathic rice accessions,but all the rice accessions showed weak allelopathic effects at the low temperature condition(15oC/10oC),and the influence of different factors on allelopathy followed a general trend as temperatureleaf stagelight,indicating that among the multiple factors impacting rice allelopathy,temperature was the main factor.Allelopathic characteristics of F1 and F2 to various temperature and light were similar to O.longistaminata,showing that allelopathic genes from wild rice can be expressed in its descendants.Temperature and light also had significant effects on SLA and SMF,and rice allelopathy was closely correlative to SLA in strong allelopathic rice accessions at the 4–5 and 7–8 leaf stages,but there was no correlation between rice allelopathy and SMF at different growth stages.These results suggested that rice adjust the relationship between allelopathy and SLA and adapt to the varied environments,and that high temperature and long photoperiod can enhance rice allelopathic activity.     

甘蓝型油菜分枝角度QTL定位及候选基因分析

分枝角度是油菜重要株型性状.为筛选和发现适度紧凑的分枝角度调控基因,以提高产量利于机械化收获,以分枝角度差异显著的油菜品种Holly和APL01为亲本构建的重组自交系(RIL)群体为材料,在2个环境中对分枝角度进行QTL定位及候选基因分析.结果表明,RIL群体分枝角度表现出连续变异且呈正态分布.利用前期构建的高密度SN...     

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。     

Rice root morphological traits are related to isozyme group and adaptation

Rice accessions from the International Rice Research Institute (IRRI) germplasm bank were evaluated for root traits of 40-day-old plants grown in soil in the greenhouse. The 136 accessions represented six groups defined on the basis of isozyme classification, with isozyme group six further subdivided on the basis of origin and morphology. An additional 28 rice cultivars were evaluated for seminal root xylem vessel diameter when grown in pots in a growth chamber. Rice groups differed in root thickness, root xylem vessel diameter, root:shoot ratio, and patterns of root distribution. Isozyme group 1, which corresponds generally to the indica subspecies, had thin, superficial roots with narrow vessels and a low root:shoot ratio. The other major isozyme group, group 6, comprising japonica types, was characterized by thick roots with wider vessels, a greater proportion of the root weight below 15 cm, and a larger root:shoot ratio. On an average, the bulu and temperate group 6 accessions were similar to the non-bulu types except that their root:shoot ratios and proportion of root weight above 15 cm were more similar to group 1. Group 2, with aus types from South Asia, was characterized by intermediate root thickness, but vertical root distribution and root:shoot ratio were more similar to group 6. The minor isozyme groups 3–5 were represented by few accessions, and in general, they had root thickness and root distribution profiles more similar to group 1 than to group 6. While significant differences were observed among isozyme groups for all the traits under study, there was significant variation within groups and groups overlapped for all traits measured. This study highlights the wide range of variability for constitutive root traits in rice. For example, root thickness ranged from 0.68 to 1.04 mm, seminal root xylem vessel diameters from 30 to 58 μm, root:shoot ratios from 0.05 to 0.21, and accessions had from 44 to 73% of the total root weight concentrated in the surface 15 cm of soil. For the 28 cultivars evaluated, root xylem vessel diameter was highly correlated with reported values of leaf epicuticular wax content (r=0.89). These values indicate the range of genetic variation within the rice genome for root morphological traits.     

Molecular genetic mapping of quantitative trait loci for milling quality in rice (Oryza sativa L.)

Identification and mapping of genomic regions controlling quantitative trait loci (QTLs) was undertaken to determine the genomic regions associated with milling traits in rice to facilitate breeding of new rice varieties with high milling quality. The recombinant inbred (RI) population used was derived from cross of a japonica variety, ‘Asominori’, with an indica variety, ‘IR24’ through 289 RFLP markers. Three milling traits, namely, brown rice percentage (BRP), milled rice percentage (MRP), and milled head rice percentage (MHP), which are the main indicators of milling quality in rice, were estimated for each RI line and their parental varieties. Continuous distributions and transgressive segregations of three milling traits were observed in the RI population, showing that the three traits were quantitatively inherited. Two QTLs (qBRP-9 and qBRP-10) for BRP were identified and mapped to chromosomes 9 and 10, and explained 7.2 and 21.3% of the total phenotype variation, respectively. Two QTLs (qMRP-11 and qMRP-12) governing MRP were detected and mapped to chromosomes 11 and 12, accounted for 12.2 and 7.7% of total phenotype variation, respectively. In addition, three QTLs (qMHP-1, qMHP-3 and qMHP-5) controlling MHP were observed and mapped to chromosomes 1, 3 and 5, and explained 16.0, 22.1 and 8.7% of the total phenotype variation, respectively. Among them, five QTLs (qBRP-9, qBRP-10, qMRP-11, qMHP-3 and qMHP-5) from japonica parent, Asominori, and two QTLs (qMRP-12, qMHP-1) from indica IR24 can improve milling quality in rice. The results and the tightly linked molecular markers that flank the QTL will be useful in breeding for improvement of milling quality in rice.