Identification of quantitative trait loci underlying milling quality of rice (Oryza sativa) grains

Milling quality of rice grains is important to both producers and consumers. In this study, quantitative trait loci (QTLs) controlling brown rice rate (BR), milled rice recovery (MR) and head rice recovery (HR) were analysed by composite interval mapping over 2 years using 98 backcross inbred lines (BILs). A total of 12 QTLs for the three traits were detected, of which five were for BR, four for MR and three for HR. The proportion of phenotypic variation explained by individual QTLs ranged from 7.5 to 19.9%, and additive effects contributed by a single QTL accounted for 0.46 to 2.34% of the variation. QTL‐by‐environment interactions were observed by comparing QTL mapping of the same population grown in two consecutive years. Three of five QTLs for BR and two of four QTLs for MR were detected in 2 years, and all three QTLs for HR were detected in 1 year only. BR was significantly correlated with MR, and all four QTLs of MR were located in the same regions as those of BR. This indicated that QTLs for highly correlated traits could often be detected in the same interval.     

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

Panicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F₂ population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.     

Mapping of quantitative trait loci associated with rice black‐streaked dwarf virus disease and its insect vector in rice (Oryza sativa L.)

Rice black‐streaked dwarf virus disease (RBSDVD), transmitted by small brown planthopper (SBPH, Laodelphax striatellus), causes serious loss in rice production. Breeding resistant cultivars are one of the most effective strategies to control the virus disease and its vector. By both natural inoculations in the field and modified seedling‐box screening test in the glasshouse, an indica variety WR24 showed high resistance to RBSDVD and SBPH. An F_2:3 population consisting of 153 lines derived from a cross between WR24 and a susceptible japonica variety Suyunuo was used for quantitative trait loci (QTL) analysis of RBSDVD and SBPH resistance. The linkage map consisting of 130 SSR markers was constructed with an average marker interval of 13.90 cM, spanning a total of 1890.9 cM. Totally, five QTLs for RBSDV resistance, viz. qRBSDV3^WR24, qRBSDV6^WR24, qRBSDV7^WR24, qRBSDV9^WR24 and qRBSDV11^WR24, were detected on chromosomes 3, 6, 7, 9 and 11, with LOD scores of 2.7, 3.08, 3.13, 5.28 and 3.7, respectively. Meanwhile, three QTLs for SBPH resistance, including qSBPH5^WR24, qSBPH7^WR24 and qSBPH10^WR24, were mapped on chromosomes 5, 7 and 10, with LOD scores of 2.18, 3.5 and 3.57, respectively. All resistant alleles were from WR24. Among these QTLs, qRBSDV7^WR24, qSBPH5^WR24 and qSBPH10^WR24 were newly reported, and qSBPH10^WR24 showed major effect that explained 17.9% of total phenotypic variance. The RBSDVD and SBPH resistance QTLs and the tightly linked DNA markers can be utilized in RBSDV and SBPH resistance breeding in rice.     

Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage

Seed longevity varies considerably in cultivated rice (Oryza sativa L.), but the underlying genetic mechanism of longevity has not been well elucidated. Quantitative trait loci (QTL) that control seed longevity after various periods of seed storage were sought using recombinant inbred lines derived from a combination involving ‘Milyang23’(Indica‐type) and ‘Akihikari’ (Japonica‐type). In all, 12 QTLs for germination and normal seedling growth were detected as indices of seed longevity on chromosome 7 (one region) and chromosome 9 (two regions) in treated seeds that had been stored under laboratory conditions for 1, 2 or 3 years.‘Milyang23’ alleles of all QTLs promoted germination and normal seedling growth after all durations of storage. These QTL regions were detected repeatedly in more than one seed condition. Therefore, we infer that these regions control seed longevity.     

Mapping quantitative trait loci associated with starch paste viscosity in rice (Oryza sativa L.) under different environmental conditions

A recombinant inbred line (RIL) population consisting of 153 lines derived from a cross between indica ‘Zhongyouzao8’ and japonica ‘Toyonishiki’ rice was used to detect stable quantitative trait loci (QTL) for rapid visco analyser (RVA) characteristics under four environmental conditions. We identified 93 QTL for RVA profiles, and four pleiotropic regions harbouring stably expressed QTL were detected on chromosomes 2, 6, 7 and 11. These newly identified and stable QTL will facilitate further research into the genetic mechanism regulating RVA profiles. Amylose content (AC) was correlated with RVA traits. AC and RVA traits were unaffected by indica–japonica subspecies differentiation, suggesting that RVA profiles were mainly influenced by the Wx gene. The RIL population was divided into two subpopulations according to Wx genotypes. A total of 106 QTL associated with RVA profiles were detected in the subpopulations. These QTL differed from those detected in the whole population in terms of their genomic location, number, logarithm of odds values and amount of phenotypic variance explained. Using this strategy, we detected QTL with minor effects and eliminated false due to the Wx gene.     

Novel quantitative trait loci for yield and yield related traits identified in Basmati rice (Oryza sativa)

Increasing crop productivity is one of the prime goals of crop breeding research. Rice grain yield is a complex quantitative trait governed by polygenes. Although several QTLs governing grain yield traits have been reported and limited attempts have been made to map QTLs for grain yield parameters in Basmati rice. A population from the cross Sonasal and Pusa Basmati 1121 comprising 352 RILs was generated through the single seed descent method. A total of 12 QTLs governing yield and yield-related traits were mapped on six chromosomes, namely, 1, 2, 3, 7, 8 and 9, of which five QTLs were novel. We identified a novel and robust epistatic QTL (qPH1.1 and qPL1.1) governing plant height and panicle length, flanked by the markers RM5336-RM1 on chromosome 1. The gene encoding brassinosteroid insensitive 1-associated receptor kinase 1 precursor is the putative candidate gene underlying this epistatic QTL. Another novel QTL, qNT3.1, governing tiller number was bracketed to a region of .77 Mb between the markers RM15247 and RM15281 on chromosome 3. Of the 57 annotated gene models, Os03g0437600 encoding alpha/beta-fold hydrolase, a homologous to AtKai2 is a putative candidate gene underlying the novel QTL qNT3.1. The other QTLs such as qDFF1.1 governing days to 50% flowering co-localizes with the gene Ghd7, QTL for plant height qPH1.2 co-localizes with the gene sd1, the QTLs for panicle length co-localizes with FUWA and DEP2, the QTL for tiller number co-localizes with OsRLCK57 and QTLs for thousand-grain weight co-localize with the major gene GS3. The QTLs identified in the current study can be effectively used in marker-assisted selection for developing Basmati rice varieties with a higher yield.     

Mapping of quantitative trait loci (QTLs) for rice protein and fat content using doubled haploid lines

Rice protein content (RPC) and rice fatcontent (RFC) are two important componentsof rice nutritional quality. In order toexamine the genetic basis of these traits,a doubled haploid (DH) population and anRFLP linkage map consisting of 232 markerloci were used to search QTLs for thetraits with the computer programQTLMapper1.0. This program is based onmixed linear models and allows simultaneousmapping of both main-effect and digenicepistastic QTLs in a DH population. RPC andRFC were evaluated based on a dry weightbasis of head rice by the Kjeldahl andSoxhlet methods respectively. A total offive main-effect QTLs for RPC wereresolved. The five QTLs collectivelyexplained 74% of the phenotypic variationwith LOD=15.2. Among these QTLs, the majorQTL qRPC-5 with the largest effectwas mapped in the interval of RG435-RG172aon chromosome 5. It accounted for 35% ofthe phenotypic variation with a LOD of16.7. At this locus the allele from theparent `Gui 630' increased RPC by 1.32%.The second QTL qRPC-7 was mapped inthe interval ZG34B-G20 on chromosome 7. Itexplained 23% of the phenotypic variancewith a LOD of 6.1. Its positive alleles,also from the parent `Gui 630', increasedRPC by 1.05%. As for the remaining threeQTLs, their additive effects wererelatively small and their positive alleleswere all inherited from the parent `02428'.Three QTLs for RFC were mapped onchromosome 1, 2 and 5 respectively. Theycollectively explained 44% of thephenotypic variation. Among these loci,QTLs qRFC-2 and qRFC-5 withlarger effects individually accounted for24% and 26% of the phenotypic variancerespectively. At QTL qRFC-2 thepositive allele came from the parent `Gui630', while at QTL qRFC-5 thepositive allele from the parent `02428'.The fact that both parents possess thepositive alleles at the QTLs for the twotraits provides an appropriate explanationfor the large transgressive segregationobserved in the DH lines. Furthermore, onlyone pair of epistatic loci explaining only5.1% of the phenotypic variance wasdetected for RPC, whereas seven pairs ofepistatic loci were resolved for RFC. Thetotal absolute effects of these RFCinteractions amounted to 0.97% which ismuch larger than that (0.42%) of the threemain-effect QTLs for the trait. Alongwith the observation that RPC showed a highheritability (78%), these resultsdemonstrate that RPC in the DH populationcould be mainly controlled by relativelyfew QTLs with large main-effects. As forRFC, epistatic interactions might be aneven more important component of thegenetic basis and the segregation of the DHlines could be largely explained by a fewmain-effect QTLs and many epistatic loci.In addition, a highly negative correlation(r = –0.45) between RPC and RFC inthe DH population was observed. Thiscorrelation could be largely explained bythe linkage of qRPC-5 and qRFC-5 with the directions of effectsopposite and the co-locations of the twoepistatic loci for RFC respectively withtwo different main-effect QTLs for RPC. Theinformation reported in the present papermay be useful for improving ricenutritional quality by means ofmarker-assisted selection.     

Identification of quantitative trait loci (QTLs) for the characters of vascular bundles in peduncle related to indica-japonica differentiation in rice (Oryza sativa L.)

The number of vascular bundles in peduncle and the ratio of vascular bundles to primary rachis branches (V/R ratio)distinguishable between indica andjaponica, are the traits associated with the processes of differentiation between indica and japonica inrice (Oryza sativa L.). In this paper a doubled-haploid population derived from the F₁ hybrid of a cross between anindica cultivar and a japonicacultivar was used to map quantitative trait loci(QTLs) controlling numbers of vascular bundles in peduncle, primary rachis branches and the V/R ratio. For vascular bundles, three QTLs were detected and they collectively explained 58.8% of the total variation. Among them, the QTLqVB-8 with the largest effect,located on chromosome 8, individually accounted for 31.1% of the total variation. Two QTLs controlling primary rachis branches, located on chromosome 8and 10 respectively, were identified and they individually explained 10.5% and18.0% of the total variation respectively. Three QTLs for the V/R ratio, mapped on chromosome 1, 2 and 8, respectively,jointly explained 61.3% of the total variation. Of the three QTLs, the QTL qV/R-1 with the largest additive effect,explained 25.3% of the total variation,was located on chromosome 1 and found to be closely linked to the gene sh-2, a major gene underlying grain-shattering ability. In addition, four and two pairs of significant epistatic QTLs were detected for vascular bundles and the V/R ratio,respectively, but none for rachis branches. Our results suggested that the numbers of vascular bundles and primary rachis branches were independently controlled by different polygenic systems, but the two polygenic systems shared a fraction of quantitative trait loci. The present study also demonstrated that the chromosome region carrying the QTL qV/R-1 for the V/R ratio and the gene sh-2 might play an important role in the processes ofindica-japonica differentiation in rice (Oryza sativa L.). This revised version was published online in August 2006 with corrections to the Cover Date.     

Mapping quantitative trait loci influencing panicle‐related traits from Chinese common wild rice (Oryza rufipogon) using introgression lines

Panicle‐related traits are important agronomic traits which directly associated with grain yield. In this study, we investigated quantitative trait loci (QTLs) associated with panicle‐related traits using a set of 265 introgression lines (ILs) of common wild rice (Oryza rufipogon Griff.) in the background of Indica high‐yielding cultivar Guichao 2 (O. sativa L.). A total of 39 QTLs associated with panicle‐related traits including panicle length (PL), primary branch number (PBN), secondary branch number (SBN), spikelet number per panicle (SPP) and spikelet density (SD), were detected in the ILs with single‐point analysis. The alleles of 20 QTLs derived from wild rice showed positive effects, and some QTLs, such as, QPl1b for PL, QPbn8 for PBN, QSd4 and QSd11b for SD and QSpp4 for SPP showed larger positive effects, providing good candidates and useful information for marker‐aided improvement of yield potential of rice. Most of the QTLs controlling SPP, SBN and SD were located in cluster or closely linked on chromosomes, and the directions of their additive effects were consistent, which explained the genetic basis of significant correlations between their phenotypic characters.     

Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa×O. rufipogon BC1F7 population

Asian cultivated rice was domesticated from the wild rice, Oryza rufipogon and throughout the domestication process, a wide range of morphological and physiological changes altered the ancestral form. This study was conducted to identify the genetic basis of changes associated with the domestication process. An recombinant Inbred line (RIL) population consisting of 120 lines was developed from a cross between the Juponica cultivar.‘Hwayeongbyeo’and a presumed wild progenitor. O. rufipogon Griff. Acc.01944. The population was genotyped with 124 simple sequence length repeat (SSR) markers, providing an average interval size of 15 cM, and also evaluated for 20 traits related to domestication and agricultural performance. A total of 63 quantitative trait locus (QTLs) and one locus associated with qualitative variation for pericarp coloration were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to seven. Phenotypic variation associated with each QTL ranged from 3.7 to 40.4%. with an average of 15.3%. The results indicated that most domestication‐related traits clustered in chromosomal blocks, and the positions of many of these clusters were consistent with those reported in previous studies and with skewed segregation ratios in these BC₁,F₇ RILs. For 13 (20.6%) of the QTLs identified in this study. the O. rufipogan ‐derived allele contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favourable alleles from O. rufipogan were detected for panicle length, spikelets per panicle, days to heading and leaf discoloration associated with cold stress. When compared with previous studies involving interspecific crosses, it can be concluded that O. rufipogon is useful as a source of valuable alleles for rice improvement and that many of the introgressed regions contain genes that have a favourable impact on phenotype in different genetic backgrounds and different environments.     

QTL analysis for resistance to preharvest sprouting in rice (Oryza sativa)

Preharvest sprouting (PHS) is caused by early breaking of seed dormancy. In Sichuan, a major hybrid rice seed production area of China, PHS in hybrid seeds originated from ‘G46A’ parent may lead to severe yield loss, causing serious damage to agricultural production. To detect quantitative trait loci (QTLs) governing PHS, we developed an F₂ population of 164 plants derived from ‘G46B’ and ‘K81’, a near‐isogenic introgression line of G46B, with high level of resistance to PHS. PHS was evaluated under controlled field and laboratory conditions. Using simple sequence repeat markers, we constructed a linkage map from this population and identified three QTLs for PHS, namely qPSR2, qPSR5 and qPSR8, which were located on chromosomes 2, 5 and 8, respectively. Among these QTLs, qPSR8, residing in the interval between RM447 and RM3754 on chromosome 8, was the major QTL controlling PHS, for it had a relative high logarithm of the odds (LOD) score and explained 43.04% of the phenotypic variation. These results were correspondent to those identified in extreme low germination rate plants (ELGP) using linkage and linkage disequilibrium. At all loci, ‘K81’ was responsible for enhancing the resistance to PHS.     

Fine mapping of qSS‐9, a major and stable quantitative trait locus,for seed storability in rice (Oryza sativa L.)

Seed storability in rice (Oryza sativa L.) is an important agronomic trait. We previously showed a quantitative trait locus of seed storability, qSS‐9, on chromosome 9 in a backcross population of ‘Koshihikari’ (japonica) / ‘Kasalath’ (indica) // ‘Koshihikari’. In this study, fine mapping of the chromosomal location of qSS‐9 was performed. Effect of ‘Kasalath’ allele of qSS‐9 was validated using a chromosome segment substitution line, SL36, which harboured the target quantitative trait loci (QTL) from ‘Kasalath’ in the genetic background of ‘Nipponbare’ under different ageing treatments in different environments. Subsequently, an F₂ population from a cross between ‘Nipponbare’ and SL36 was used for fine mapping of qSS‐9. Simultaneously, four subnear isogenic lines (sub‐NILs) that represented different recombination breakpoints across the qSS‐9 region were developed from F₃ progeny. Finally, the qSS‐9 locus was located between the Indel markers Y10 and Y13, which delimit a region of 147 kb in the ‘Nipponbare’ genome. These results provide a springboard for map‐based cloning of qSS‐9 and possibilities for breeding rice varieties with strong seed storability.     

Quantitative trait loci mapping and stability for low temperature germination ability of rice

A high rate of germination at low temperatures is necessary for economic yields to be maintained. In this paper, the genetic control of low temperature germination ability (LTG) was assessed by the measurement of germination rate (GR), germination rate index (GI) and mean germination time (MGT), and genetically mapped using a set of recombinant inbred lines, derived from a cross between the japonica cultivar 'Asominori' and the indica cultivar 'IR24'. Putative quantitative trait loci (QTL) were validated by testing in two related sets of chromosome segment substitution lines (CSSL). In this genetic background, LTG is under the control of a number of QTL, each of relatively small effect, and is spread over six chromosomes. The most stable of these QTL was for GR, mapping to a segment of chromosome 11 which also carries a QTL for GI. On chromosome 2, qGR-2 not only controlled GR, but also was associated with GI and MGT. Significant differences in LTG were detected between 'Asominori' and some CSSL harbouring qGR-2 or qGR-11 .     

Mapping quantitative trait loci and expressed sequence tags related to brown planthopper resistance in rice

To map genes responsible for brown planthopper (BPH) resistance in rice, a rice genetic map was constructed based on a recombinant inbred line population from a cross between a BPH‐resistant line ‘B5’ and a susceptible variety ‘Minghui 63’. Four quantitative trait loci (QTLs) for BPH resistance were detected. ESTs differentially regulated by BPH feeding were isolated by suppressive subtractive hybridization (SSH) and assigned to chromosomes based on RFLP mapping and searches of the rice genome database. The distribution of ESTs showed some clustering, and some ESTs are related to known QTLs and known BPH resistance genes. These findings suggest that the mapping of differentially induced ESTs may be a useful strategy for the identification of candidate plant defence genes, which could be beneficial in the development of a BPH‐resistant rice variety.     

控制水稻RIL群体化感作用的QTL定位研究

此研究以“莱蒙”（弱化感）和“多拉”（强化感）水稻杂交产生的重组自交系（recombinant inbred lines,RILs）及其亲本为供体植物,并以稻田主要杂草稗草为受体植物,采用迟播共培法测定与各家系及亲本共培稗草的根长,并转化成抑制率来表征化感作用。结果表明群体及亲本根长抑制率基本呈正态分布,且用它来表征化感作用是适合的。运用分子标记技术构建了该群体的遗传图谱,共97个分子标记,覆盖水稻12条连锁群。QTL定位检测到控制水稻化感作用的5个QTL,分别位于1、1、5、9、9号连锁群,解释了23.97%、15.21%、13.89%、18.63%、6.64%的遗传变异。进一步证实水稻化感作用存在主效QTL,同时为分子育种提供依据。     

籼粳交稻米品质性状杂种优势的遗传分析

用胚乳性状遗传模型和分析方法对籼粳交稻米品质性状的杂种优势进行了遗传分析,结果表明：各品质性状都具有一定的杂种优势,其中碱消值和蛋白质含量的优势较强。直链淀粉含量和胶稠度的优势较弱。不同性状杂种优势的遗传原因不同,直接显性和母体显性对杂种优势的贡献大小因性状而异,但总的来说,母体显性对籼粳杂种Ｆ２籽粒品质性状的杂种优势具有重要的意义,细胞质效应对部分性状（如胶稠度、蛋白质含量）的群体平均优势有一定