Mapping Quantitative Trait Loci for Grain Appearance Traits of Rice Using a Recombinant Inbred Line Population

A linkage map consisting of 221 markers was constructed based on a recombinant inbred line (RIL) population from the cross between Zhenshan 97 and Minghui 63. Quantitative trait loci (QTL) mapping was carried out for grain appearance traits such as grain length, grain width and grain shape in rice in 1998 and 1999. Based on interval mapping method at the threshold LOD≥2.4, six, two and two QTLs were detected for grain length, grain width and grain shape, respectively, in 1998; In 1999, three, two and two QTLs were identified for the three traits, respectively. Of them, seven QTLs were simultaneously identified in both of the years. The QTL with large effects located in the interval RG393-C1087 on chromosome 3 not only controlled the grain length, but also influenced the grain shape. It explained 57.5%, 61.4% and 26.7%, 29.9% of phenotypic variation of the grain length and the grain shape in two years, respectively. The QTL with large effects located in the interval RG360-C734B on chromosome 5 affected the grain width and the grain shape. It explained 44.2%, 53.2% and 32.1%, 36.0% of phenotypic variation of the grain width and the shape in two years, respectively. Eight, five and five QTLs were identified for the grain length, width and shape, respectively, based on mixed linear-model composite interval mapping method at P =0.005. Their general contributions were 58.81%, 44.75%, and 57.47%. One QTL for the grain length was found to be significant interaction with environment.     

Mapping QTLs for improving grain yield using the USDA rice mini-core collection

Yield is the most important and complex trait for genetic improvement in crops, and marker-assisted selection enhances the improvement efficiency. The USDA rice mini-core collection derived from over 18,000 accessions of global origins is an ideal panel for association mapping. We phenotyped 203 O. sativa accessions for 14 agronomic traits and identified 5 that were highly and significantly correlated with grain yield per plant: plant height, plant weight, tillers, panicle length, and kernels/branch. Genotyping with 155 genome-wide molecular markers demonstrated 5 main cluster groups. Linkage disequilibrium (LD) decayed at least 20 cM and marker pairs with significant LD ranged from 4.64 to 6.06% in four main groups. Model comparisons revealed that different dimensions of principal component analysis affected yield and its correlated traits for mapping accuracy, and kinship did not improve the mapping in this collection. Thirty marker–trait associations were highly significant, 4 for yield, 3 for plant height, 6 for plant weight, 9 for tillers, 5 for panicle length and 3 for kernels/branch. Twenty-one markers contributed to the 30 associations, because 8 markers were co-associated with 2 or more traits. Allelic analysis of OSR13, RM471 and RM7003 for their co-associations with yield traits demonstrated that allele 126 bp of RM471 and 108 bp of RM7003 should receive greater attention, because they had the greatest positive effect on yield traits. Tagging the QTLs responsible for multiple yield traits may simultaneously help dissect the complex yield traits and elevate the efficiency to improve grain yield using marker-assisted selection in rice.     

Quantitative trait locus analysis for rice panicle and grain characteristics

 The development of molecular genetic maps has accelerated the identification and mapping of genomic regions controlling quantitative characters, referred to as quantitative trait loci or QTLs. A molecular map derived from an F₂ population of a tropical japonica×indica cross (Labelle/Black Gora) consisted of 116 restriction fragment length polymorphism (RFLP) markers. Composite interval mapping was used to identify the QTLs controlling six panicle and grain characteristics. Two QTLs were identified for panicle size at LOD>3.0, with one on chromosome 3 accounting for 16% of the phenotypic variation. Four loci controlling spikelet fertility accounted for 23% of the phenotypic variation. Seven, four, three and two QTLs were detected for grain length, breadth, shape and weight, respectively, with the most prominent QTLs being on chromosomes 3, 4, and 7. Grain shape, measured as the ratio of length to breadth, was mostly controlled by loci on chromosomes 3 and 7 that coincided with the most important QTLs identified for length and breadth, respectively. A model including three loci accounted for 45% of the phenotypic variation for this trait. The identification of economically important QTLs will be useful in breeding for improved grain characteristics. Received: 18 July 1997 / Accepted: 9 December 1997     

Large‐scale GWAS in sorghum reveals common genetic control of grain size among cereals

Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype’s genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome‐wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC‐NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype’s capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.     

水稻粒长QTL定位与主效基因的遗传分析

该研究利用短粒普通野生稻矮杆突变体和长粒栽培稻品种KJ01组配杂交组合F_1,构建分离群体F_2;并对该群体粒长进行性状遗传分析,利用平均分布于水稻的12条染色体上的132对多态分子标记对该群体进行QTL定位及主效QTLs遗传分析,为进一步克隆新的主效粒长基因奠定基础,并为水稻粒形育种提供理论依据。结果表明:(1)所构建的水稻杂交组合分离群体F_2的粒长性状为多基因控制的数量性状。(2)对543株F_2分离群体进行QTL连锁分析,构建了控制水稻粒长的连锁遗传图谱,总长为1 713.94 cM,共检测出24个QTLs,只有3个表现为加性遗传效应,其余位点均表现为遗传负效应。(3)检测到的3个主效QTLs分别位于3号染色体的分子标记PSM379～RID24455、RID24455～RM15689和RM571～RM16238之间,且三者对表型的贡献率分别为54.85%、31.02%和7.62%。(4)在标记PSM379～RID24455之间已克隆到的粒长基因为该研究新发现的主效QTL位点。     

Development of Chromosome Segment Substitution Lines Derived from Backcross between Two Sequenced Rice Cultivars, <Emphasis Type="Italic">Indica</Emphasis> Recipient 93-11 and <Emphasis Type="Italic">Japonica</Emphasis> Donor Nipponbare

Chromosome segment substitution lines (CSSLs) are powerful tools for detecting and precisely mapping quantitative trait loci (QTLs) and evaluating gene action as a single factor. In this study, 103 CSSLs were produced using two sequenced rice cultivars: 93-11, an elite restorer indica cultivar as recipient, and Nipponbare, a japonica cultivar, as donor. Each CSSL carried a single chromosome substituted segment. The total length of the substituted segments in the CSSLs was 2,590.6 cM, which was 1.7 times of the rice genome. To evaluate the potential application of these CSSLs for QTL detection, phenotypic variations of seed shattering, grain length and grain width in 10 CSSLs were observed. Two QTLs for seed shattering and three for grain length and grain width were identified and mapped on rice chromosomes. The results demonstrate that CSSLs are excellent genetic materials for dissecting complex traits into a set of monogenic loci. These CSSLs are of great potential value for QTL mapping and plant marker-assisted breeding (MAB).     

Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid

Milling properties, protein content, and flour color are important factors in rice. A marker-based genetic analysis of these traits was carried out in this study using recombinant inbred lines (RILs) derived from an elite hybrid cross ’Shanyou 63’, the most-widely grown rice hybrid in production in China. Correlation analysis shows that the traits were inter-correlated, though the coefficients were generally small. Quantitative trait locus (QTL) analysis with both interval mapping (IM) and composite interval mapping (CIM) revealed that the milling properties were controlled by the same few loci that are responsible for grain shape. The QTL located in the interval of RM42-C734b was the major locus for brown rice yield, and the QTL located in the interval of C1087-RZ403 was the major locus for head rice yield. These two QTLs are the loci for grain width and length, respectively. The Wx gene plays a major role in determining protein content and flour color, and is modified by several QTLs with minor effect. The implications of the results in rice breeding were discussed. Received: 15 September 2000 / Accepted: 31 March 2001     

水稻粒形性状的遗传及相关基因定位与克隆研究进展

作物育种的首要目标是提高产量。水稻粒形是与水稻产量性状直接相关,与品质性状存在着密切关系的数量性状,其评价指标主要是粒长、粒宽、粒厚、长/宽和长/厚。近年来,水稻粒形的数量遗传研究取得了重要进展,并成功定位克隆了一批控制水稻粒形的基因。文章综述了水稻粒形的经典遗传研究、QTL定位、粒形基因的克隆和功能分析以及在水稻超高产育种中的利用。     

Genetic Relationships Among Panicle Characteristics of Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) Using Unconditional and Conditional QTL Analyses

Using mixed-model-based composite interval mapping and conditional statistical methods, we studied quantitative trait loci (QTLs) with epistatic effects and QTLs by environment interaction effects for rice seed set percent (SSP), filled grain number per plant (FGP), and panicle length (PL). A population of 241 recombinant inbred lines was used which was derived from a cross between “Zhenshan 97” and “Minghui 63.” Its linkage map included 221 molecular markers. Our QTL analysis detected 28, 25, and 32 QTLs for SSP, FGP, and PL, respectively. Each QTL explained 1.37%∼13.19% of the mean phenotypic variation. A comparison of conventional and conditional mapping provided information about the genetic control system involved in the synthetic process of SSP, FGP, and PL at the level of individual QTLs. Conditional QTLs with reduced (or increased) effects were identified for SSP, which were significantly influenced by FGP or PL. Some QTLs could express independently for the given traits, thereby providing possibilities for simultaneous improvement of SSR and PL, and SSR and FGP. Epistasis was more sensitive to environmental conditions than were additive effects.     

水稻粒形遗传的研究进展

水稻（Oryza sativa）粒形性状包括粒长、粒宽、粒厚、粒重和长宽比等,是构成水稻产量的重要因素之一。因此,阐明水稻粒形遗传控制的机理,对提高水稻产量具有十分重要的意义。水稻粒形的遗传是多基因共同作用的数量性状遗传,相对于单一基因控制的性状,研究要相对复杂。该文综述了水稻粒形的遗传特点、QTL定位和基因克隆,并展望了粒形遗传的研究前景。     

稻米粒形的QTL定位及上位性和QE互作分析

利用'广陆矮4号'×'佳辐占'水稻重组自交系构建了SSR标记的遗传图谱.联合2007年和2008年获得的两组稻米粒长(GL)、粒宽(GW)、长宽比(L/W)数据应用混合线性模型方法进行QTL定位,并作加性效应、加性×加性上位互作效应以及加性QTL、上位性QTL与环境的互作效应分析.结果显示;(1)在加性效应分析中两个群体共检测到4个控制粒长的QTL,4个控制粒宽的QTL,5个控制长宽比的QTL,贡献率分别为13.81%、15.36%和 16.29%.(2)在上位互作效应分析中两个群体共检测到2对控制粒长的互作QTL,1对控制粒宽的互作QTL,3对控制长宽比的互作QTL,贡献率分别为5.77%、2.59%和7.42%.(3)环境互作检测中,发现共有13个加性QTL和4对QTL的加性×加性上位性与环境产生了互作效应.结果表明,上位性效应和加性效应都影响稻米粒形遗传,QE互作效应也对粒形有着显著的影响.     

Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the<Emphasis Type="Italic"> Oryza sativa</Emphasis> variety IR64 and the wild relative<Emphasis Type="Italic"> O. rufipogon</Emphasis>

The objective of this study was to identify quantitative trait loci (QTLs) associated with grain quality in rice. Two hundred eighty-five BC₂F₂ families developed from an interspecific cross between cv IR64 and Oryza rufipogon (IRGC 105491) were evaluated for 14 seed quality traits. A total of 165 markers consisting of 131 single sequence repeats and 34 restriction fragment length polymorphism markers were used to create a genetic linkage map spanning the 12 rice chromosomes. Twenty-three independent QTLs were identified using single point analysis, interval mapping, and composite interval mapping. These loci consisted of one QTL for filled rough/total rough rice ratio, two for grain density, one for percentage of de-husked rice grains, two for percentage of green rice grains, three for percentage of damaged-yellow rice grains, two for percentage of red rice grains, one for milled rice recovery, three for head rice recovery, four for broken rice grains, two for crushed rice grains, one for amylose content, and one for gel consistency. For most of the QTLs identified in this study, the O. rufipogon-derived allele contributed an undesirable effect. For amylose content and gel consistency, the O. rufipogon allele may be useful in an IR64 background, depending on the cultural preferences of the consumer. Careful selection against the regions associated with negative effects will be required to avoid unwanted grain quality characteristics during the development of improved varieties for yield and yield components using introgressions from O. rufipogon.Communicated by D. Mackill     

Validation of gene based marker-QTL association for grain dimension traits in rice

Validation of marker-QTL association for genes grain size 3 (GS3), grain weight 2 (GW2), seed width 5 (qSW5) and a QTL qgrl7.1 for grain length was undertaken in a set of 242 diverse rice germplasm. Further, the study was extended to an F₂ mapping population derived from cross of Sonasal, a short grain aromatic rice landrace with Pusa Basmati 1121, a variety with extra long slender grains. Seven gene specific markers, namely, SF28, SR17, RGS1and RGS2 based on GS3, W004 for GW2, MS40671 for qSW5 and RM505 for qgrl7.1, were used for validation. Single marker analysis revealed significant association of these markers to grain size and shape. The marker SF28 explained highest phenotypic variance (37 %) while the marker W004 explained lowest variance (2.6 %) for grain length in the germplasm set at the significance level P?<?0.05. Three markers namely, SF28, MS40671 and RM505 were polymorphic between the parents Sonasal and Pusa Basmati 1121. In the F₂ population, the marker SF28 linked to gene GS3 explained highest phenotypic variance (32.5 %), while RM505 linked to qgrl7.1 explained 5.4 % of phenotypic variance for grain length. The marker SF28 was found to be most robust in the validation studies both in germplasm and F₂ population. The validated gene specific markers can be utilised in marker assisted selection for improving grain size and shape as these traits have significant contribution towards grain quality and grain yield. This is the first study on validation of gene based markers for grain dimension traits in Indian rice germplasm.     

Unigene derived microsatellite markers for the cereal genomes

Unigene derived microsatellite (UGMS) markers have the advantage of assaying variation in the expressed component of the genome with unique identity and positions. We characterized the microsatellite motifs present in the unigenes of five cereal species namely, rice, wheat, maize, Sorghum and barley and compared with those in Arabidopsis. The overall UGMS frequency in the five cereal species was 1/7.6 kb. The maximum UGMS frequency was in rice (1/3.6 kb) and the lowest in wheat (1/10.6 kb). GC-rich trinucleotide repeat motifs coding for alanine followed by arginine and the dinucleotide repeat motif GA were found to be abundant UGMS classes across all the five cereal species. Primers could be designed for 95% (wheat and barley) to 97% (rice) of the identified microsatellites. The proportion and frequency of occurrence of long hypervariable class I (≥20 nucleotides) and potentially variable class II (12–20 nucleotides) UGMS across five cereal species were characterized. The class I UGMS markers were physically mapped in silico on to the finished rice genome and bin-mapped in wheat. Comparative mapping based on class I UGMS markers in rice and wheat revealed syntenic relationships between the two genomes. High degree of conservation and cross-transferability of the class I UGMS markers were evident among the five cereal species, which was validated experimentally. The class I UGMS-conserved orthologous set (COS) markers identified in this study would be useful for understanding the evolution of genes and genomes in cereals. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Multiple Alleles for Tuber Shape in Diploid Potato Detected by Qualitative and Quantitative Genetic Analysis Using Rflps

Tuber shape in potato is commonly regarded as displaying continuous variation, yet at the diploid level phenotypes can be discerned visually, having round or long tubers. Inheritance of qualitative tuber shape can be explained by a single locus Ro, round being dominant to long. With restriction fragment length polymorphisms (RFLPs) the Ro locus was mapped on chromosome 10. Tuber shape was also studied as a quantitative trait, using the length/width ratio as trait value. The estimated broad sense heritability was h(2) = 0.80. The morphologically mapped Ro locus explained 75% of the genetic variation, indicating the presence of a major quantitative trait locus (QTL) at the Ro locus and minor genetic factors. RFLP alleles linked with Ro alleles were used to divide the progeny into four genotypic classes: Ro( &) Ro( &) : Ro( &) ro : roRo( &) : roro = 1 : 1 : 1 : 1. The recessive ro allele is identical by descent in both parents. The significantly different effects (P = 0.0157) of the non-identical alleles Ro( &) and Ro( &) provided evidence for multiallelism at the Ro locus. Linkage mapping of the Ro locus was compared with QTL mapping. Only those markers which are polymorphic in both parents allow accurate QTL mapping when genetic factors segregate from both parents. This finding applies to QTL mapping in all outbreeders without homozygous inbred strains.     

Epistasis for Three Grain Yield Components in Rice (Oryza Sativa L.)

The genetic basis for three grain yield components of rice, 1000 kernel weight (KW), grain number per panicle (GN), and grain weight per panicle (GWP), was investigated using restriction fragment length polymorphism markers and F(4) progeny testing from a cross between rice subspecies japonica (cultivar Lemont from USA) and indica (cv. Tequing from China). Following identification of 19 QTL affecting these traits, we investigated the role of epistasis in genetic control of these phenotypes. Among 63 markers distributed throughout the genome that appeared to be involved in 79 highly significant (P < 0.001) interactions, most (46 or 73%) did not appear to have ``main'''' effects on the relevant traits, but influenced the trait(s) predominantly through interactions. These results indicate that epistasis is an important genetic basis for complex traits such as yield components, especially traits of low heritability such as GN and GWP. The identification of epistatic loci is an important step toward resolution of discrepancies between quantitative trait loci mapping and classical genetic dogma, contributes to better understanding of the persistence of quantitative genetic variation in populations, and impels reconsideration of optimal mapping methodology and marker-assisted breeding strategies for improvement of complex traits.     

籼型黑米粒形性状的遗传效应及其与矿质元素含量的遗传相关性

采用禾谷类作物种子数量性状的遗传模型,分析了灿型黑米稻品种双列杂交F1和F2种子的粒重,粒长,粒宽和粒长／粒宽等粒形性状的遗传效应及其与米粒中矿质元素Fe,Zn,Mn和P含量的遗传相关性,结果表明：4种粒形性状同时受制于种子直接遗传效应,母体效应和细胞质作用影响,其中种子直接遗传效应比母体效应和细胞质效应的作用更大,且种子直接遗传效应以加性效应占主导,粒重,粒宽和粒长／粒宽的种子直接遗传率较高,杂种早代单粒选择效果较好,粒长的种子直接遗传率和母体遗传率均属中等,较高世代的杂种进行单株选择和单粒选择均有一定效果,4种粒形性状与其米粒中矿质元素Fe,Zn,Mn和P含量表现较强的种子直接加性相关,直接显性相关,细胞质相关,母体加性相关和母体显性相关,在特种稻育种实践中,可以通过粒形性的间接选择,达到改良其矿质元素含量等营养品质性状的目标。     

Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid

Appearance quality of the rice grain represents a major problem of rice production in many rice-producing areas of the world, especially in hybrid rice production in China. In this study, we conducted a molecular marker-based genetic analysis of the traits that are determinants of the appearance quality of rice grains, including traits specifying grain shape and endosperm opacity. The materials used in the analysis included an F_2:3 population and an F₁₀ recombinant inbred line population from a cross between the parents of Shanyou 63, the most widely grown rice hybrid in China. Molecular marker-based QTL (quantitative trait locus) analyses revealed that grain length and grain width were each controlled by a major QTL accounting for a very large proportion of the genetic variation, plus one or two minor QTLs each explaining a small proportion of the genetic variation. The major QTLs can be detected in both the F_2:3 and recombinant inbred line population using both paddy rice and brown rice, whereas the minor QTLs were detected only occasionally. The QTL located in the interval of RG393-C1087 on chromosome 3 is the major locus for grain length, and the one in the interval RG360-C734a on chromosome 5 plays a major role in determining grain width. Similarly, white belly, which largely determines the opacity of the endosperm, is almost entirely controlled by a major locus on chromosome 5, located in the same genomic region as the major QTL for grain width. The implications of the results with respect to hybrid rice improvement were discussed. Received: 20 February 2000 / Accepted: 21 March 2000