Comparison and analysis of QTLs for grain and hull thickness related traits in two recombinant inbred line(RIL) populations in rice(Oryza sativa L.)

Grain traits are major constraints in rice production, which are key factors in determining grain yield and market values. This study used two recombinant inbred line（RIL） populations, RIL-JJ（japonica/japonica） and RIL-IJ（indica/japonica） derived from the two crosses Shennong 265/Lijiangxintuanheigu（SN265/LTH） and Shennong 265/Luhui 99（SN265/LH99）. Sixty-eight quantitative trait loci（QTLs） associated with 10 grain traits were consistently detected on the 12 chromosomes across different populations and two environments. Although 61.75% of the QTLs clustered together across two populations, only 16.17% could be detected across two populations. Eight major QTLs were detected on the 9, 10 and 12 chromosomes in RIL-JJ under two environments, a novel QTL clustered on the 10 chromosome, q GT10, q BT10 and q TGW10, have a higher percentage of explained phenotypic variation（PVE） and additive effect; 15 major QTLs were detected on the 5, 8, 9, and 11 chromosomes in RIL-IJ under two environments, a novel clustered QTL, q GT8 and q TGW8, on the 8 chromosome have a higher additive effect. Finally, the analysis of major QTL-BSA mapping narrowed the q TGW10 to a 1.47-Mb region flanked by simple sequence repeat markers RM467 and RM6368 on chromosome 10. A comparison of QTLs for grain traits in two different genetic backgrounds recombinant inbred line populations confirmed that genetic background had a significant impact on grain traits. The identified QTLs were stable across different populations and various environments, and 29.42% of QTLs controlling grain traits were reliably detected in different environments. Fewer QTLs were detected for brown rice traits than for paddy rice traits, 7 and 17 QTLs for brown rice out of 25 and 43 QTLs under RIL-JJ and RILIJ populations, respectively. The identification of genes constituting the QTLs will help to further our understanding of the molecular mechanisms underlying grain shape.

Mapping of three QTLs for seed setting and analysis on the candidate gene for qSS-1 in rice(Oryza sativa L.)

The lower seed setting is one of the major hindrances which face grain yield in rice. One of the main reasons to cause low spikelet fertility （seed setting） is male sterility or pollen abortion. Notably, pollen abortion has been frequently observed in advanced progenies of rice. In the present study, 149 BC2F6 individuals with significant segregation in spikelet fertility were generated from the cross between N040212 （indica） and Nipponbare （japonica） and used for primary gene mapping. Three QTLs, qSS-1, qSS-7 and qSS-9 at chromosomes 1, 7 and 9, respectively, were found to be associated with seed setting. The recombinant analysis and the physical mapping information from publicly available resources exhibited that the qSS-1, qSS-7 and qSS-9 loci were mapped to an interval of 188, 701 and 3741 kb, respectively. The seed setting responsible for QTL qSS-1 was further fine mapped to 93.5 kb by using BC2F7 population of 1 849 individuals. There are 16 possible putative genes in this 93.5 kb region. Pollen vitality tests and artificial pollination indicated that the male gamete has abnormal pollen while the female gamete was normal. These data showed that low seed setting rate relative to qSS-1 may be caused by abnormal pollen grains. These results will be useful for cloning, functional analysis of the target gene governing spikelet fertility （seed setting） and understanding the genetic bases of pollen sterility.

Mapping QTLs for Heat Tolerance in Rice (Oryza sativa L. ) at Heading Stage Using Chromosome Segment Substitution Lines

In the present study, a japonica rice （ Oryza sativa L. ） variety Nipponbare, an indica variety 9311 and a set of chromosome segment substitution lines （CSSLs） which were generated using Nipponbare as the recipient parent and 9311 as the donor parent were used as the experimental materials. The CSSLs were grown in 2012 （normal temperature condition） and 2013 （high temperature condition） in Yangzhou, Jiangsu, and were used to map the quantitative trait loci （QTLs） for heat tolerance, based on the heat tolerance index [ （The seed setting rate under normal temperature condition -The seed setting rate under high temper- ature condition） / The seed setting rate under normal temperature condition]. As a result, three QTLs related to heat tolerance in rice were mapped on chromo- somes 2, 4 and 12, respectively. They had LOD （logarithm of rntds） scores of 2.56, 4.02 and 2.79, and contributian rates of 4.95%, 7.99% and 5.44%. Among them, qHT12.1 showed positive effect, while qHT2.1 and qHT4. t showed negative effect on heat tolerance. The results lay a foundation for the fine mapping and cloning of the QTLs and genes related to heat tolerance, and for the breeding of heat-tolerant rice varieties.

Mapping QTLs for Salt Tolerance at Seeding Stage of Landrace Rice (Oryza sativa L.)

[Objectives] The identification of salt tolerant genetic loci in rice can provide a research basis for the molecular mechanism of salt tolerance and gene resources for improving salt tolerant cultivars. [Methods] Recombinant inbred lines(RILs) derived from Zhaxima, an indica landrace variety from Yunnan Province and Nanjing 46, an elite japonica variety with superior grain quality from Jiangsu Province were used. The salt tolerance at seeding stage in the RIL population was investigated as the phenotypic value. [Results] Combined with the linkage map, a total of 4 QTLs were detected: qSST-1, qSST-3, qSST-5 and qSST-11, located in rice chromosomes 1, 3, 5 and 11, respectively. All positive alleles were from the parent Nanjing 46. Three QTLs among them were not included in chromosome intervals the same as cloned rice salt tolerance genes, and thus were described as new candidate gene loci associated with seeding-stage salt tolerance. [Conclusions] This study provides important information for further exploration and utilization of new salt tolerant QTLs in rice. It is of great significance for improving the utilization of saline land in China and ensuring the stable rice production.

不同遗传背景及环境中水稻(Oryza sativa L.)穗长的QTLs和上位性分析

以粳稻Azucena为父本与舢稻IR64杂交发展的一双单倍体（DH）群体，与籼稻IR1552杂交发展的一重组自交系（RI）群体为材料，应用分子标记图谱对2个群体在大田和盆栽2个环境下的穗长进行QTLs及上位性效应分析。DH群体中共检测到6个穗长QTLs，位于第1、4条染色体上的3个QTLs，在2个环境中稳定表达，未检测到上位性效应，加性效应为穗长遗传主效应。R1群体中，共检测到3个穗长QTLs及6对互作效应位点，位于策4条染色体上的1个QTL及位于第1、12条染色体上的2个互作位点在2个环境中稳定表达，上位性效应表现为遗传主效应。在2个群体中均检测到的与穗长相关的1个QTL位于第4条染色体RG163～RZ23区间内，遗传正效应等位基因来源于Azucena；位于第1条染色体与RG323连锁的位点在DH群体中表现为1个QTL，但在RI群体中表现为互作位点。

QTLs for Rice Leaf Chlorophyll Content Under Low N Stress

Quantitative trait loci (QTLs) for chlorophyll content of a rice leaf weremapped on to the molecular marker linkage map of a double-haploid (DH) population derived from across between two rice varieties 'IR64' and 'Azucena' in both nutrient solutionand soil cultureexperiments to detect rice nitrogen nutrition status under low N stress A chlorophyll meter was usedto measure the soil plant analysis development (SPAD) value of the topmost fully expanded leaf asthe index of chlorophyll content thatexpressed nitrogen status in rice plants. Totally 3 QTLs forSPAD values, two on chromosome 3 located at interval RG179-CDO337 and RG348-RZ329, respectively, andone on chromosome 10 at interval RZ500-RG134, were detected under stressed conditions of low N inthe soil and/or nutrient solution culture experiments. One QTL located at interval RG179-GDO337 onchromosome 3 associated with a relative change in SPAD value from a high N level to a low N level inthe soil culture experiment was also detected.Based on the different responses to low N stressbetween the two parents, it was supposed that the QTLs identified in this study associated withnitrogen efficiency in rice at low N levels might be useful in applying marker technology to ricebreeding programs.

Influence of Epistasis and QTL×Environment Interaction on Heading Date of Rice(Oryza sativa L.)

QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a double haploid （DH） population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%-4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.

Advances in Physiological-biochemical and Genetic Mechanisms of Seed Aging in Rice(Oryza sativa L.)

Reasons causing or accelerating seed aging are mainly damage of mem- branes, DNA and proteins, decline of protein synthesis capacity and excessive ac- cumulation of reactive oxygen species. With the application of natural aging or artifi- cial aging methods, it was reported that quantitative trait loci （QTLs） of seed stora- bility in rice were widely distributed on the chromosomes except the 10th chromo- some. In this paper, we reviewed the progresses in the research on physiological- biochemical and genetic mechanisms of seed aging, and analyzed the existing problems and developing prospect in molecular breeding of rice with improved seed storability, in order to provide reference for the basic research and genetic improve- ment of rice seed storabUity.

Bulked Segregant Analysis to Detect QTL Related to Heat Tolerance in Rice(Oryza sativa L.) Using SSR Markers

The study was undertaken to assess the genetic effect of quantitative trait loci （QTLs） conferring heat tolerance at flowering stage in rice. A population consisting of 279 F2 individuals from the cross between 996, a heat tolerant cultivar and 4628, a heat-sensitive cultivar, was analyzed for their segregation pattern of the difference of seed set rate under optimal temperature condition and high temperature condition. The difference of seed set rate under optimal temperature condition and high temperature condition showed normal distribution, indicating the polygenic control over the trait. To identify main effect of QTL for heat tolerance, the parents were surveyed with 200 primer pairs of simple sequence repeats （SSR）. The parental survey revealed 30% polymorphism between parents. In order to detect the main QTL association with heat tolerance, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The association of putative markers identified based on DNA pooling from selected segregants was established by single marker analysis （SMA）. The results of SMA revealed that SSR markers, RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively, accounted for 17 and 3% of the total variation respectively. The heat tolerance during flowering stage in rice was controlled by multiple gene. The SSR markers, RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively, accounted for 17 and 3% of the total variation respectively. The two genetic loci, especially for RM3735 on chromosome 4, can be used in marker-assistant-selected method in heat tolerance breeding in rice.

Genotypic Difference in the Responses of Seedling Growth and Cd Toxicity in Rice(Oryza sativa L.)

The experiment was carried out to study the genotypic difference in the responses of seed germination, growth and physiological characters of rice seedlings to Cd toxicity. The result showed that the germination was slightly stimulated under low Cd concentration （0.01-1.5 mM Cd）, while severely depressed under higher Cd concentration （2.0 mM）. Rice seedlings exposed to 0.01 mM Cd showed slight increases in plant height, root volume, biomass and chlorophyll concentration. These parameters were significantly reduced when Cd level in the medium was increased to 0.5 mM, and meanwhile corresponding increase in superoxide dismutase （SOD） and peroxidase （POD） activities, and MDA （malondialdehyde） content was observed. However, SOD and POD activities declined when plants were exposed to 1 mM Cd when compared with those under 0.5 mM Cd. Cadmium addition lowered Fe, Cu and Mn concentrations in roots and shoots. There was significant genotypic difference in the response of these parameters to Cd stress. Under Cd stress, Xiushui 110 had the least inhibition of growth and increase in MDA content, higher shoot Cd concentration, and greatest increase in POD and SOD activities, indicating its higher tolerance to Cd toxicity, while Bing 9914 had the greatest reduction of growth, and Zn, Cu, Fe, and Mn contents, but greatest increase in MDA content, and least increase in activities of antioxidative enzymes, indicating its sensitivity to Cd toxicity.

Identification of Quantitative Trait Locus for Overwintering Germinability in Rice(Oryza sativa L.)

312 recombinant inbred lines （RILs） in F9 from a cross between a overwintering cold-tolerant germplasm resource Glutinous rice 89-1（Gr 89-1） and a cold-sensitive variety Shuhui 527 was used for quantitative trait locus （QTL） analysis. The scores of percent ratooning germinability （PRG） and overwintering germinability （POG） were evaluated. The overwintering germination rate of axillary buds was scored to represent the overwintering germinability. Two significant QTLs （qPRG-4 and qPRG-7） on chromosomes 4 and 7 were detected and explained 8.3 and 7.2% of the total phenotypic variation, respectively. Three significant QTLs （qPOG-2, qPOG-3 and qPOG-7） were identified and mapped on chromosomes 2, 3, and 7, respectively. These QTLs contributed 9.6, 6.7, and 17.8% of phenotypic variations, respectively. A comparative analysis using SSR markers closely linked to the three QTLs for the overwintering revealed cold-tolerant individuals, which harbour the Glutinous rice 89-1 alleles at RM7110, RM250, RM418, and RM232, had a high percent overwintering germinability, while cold-sensitive individuals, which carry Shuhui 527 alleles at these loci, had a low percent overwintering germinability in the F2 population of Shuhui 527/Glutinous rice 89-1. This study demonstrated the utility of these SSR markers for selection of overwintering germinability genotypes.

Responses of Contrasting Rice (Oryza sativa L.) Genotypes to Salt Stress as Affected by Nutrient Concentrations

The study was conducted to investigate the effects of applying different concentrations of the macronutrients K＋,Ca2＋,and Mg2＋ on the responses of contrasting rice（Oryza sativa L.） genotypes under salt stress.A solution culture experiment was conducted in a phytotron at the International Rice Research Institute（IRRI）,under controlled temperature and humidity and natural sunlight.When subjected to salt stress of 100 mmol L-1 using NaCl,the salt tolerant genotypes FL478 and IR651,accumulated less Na＋ and maintained lower ratios of Na＋/K＋,Na＋/Ca2＋,and Na＋/Mg2＋ than the sensitive genotypes IR29 and Azucena.These tolerant genotypes also had higher concentrations of K＋ in their shoots and greater root and shoot biomass and green leaf area.Tolerant genotypes also maintained much lower concentration of Na＋ and lower and more favorable ratios of Na＋/K＋,Na＋/Ca2＋,and Na＋/Mg2＋ in their active and developing tissues.Salt tolerance and shoot and root growth of both tolerant and sensitive genotypes were enhanced considerably when higher concentrations of Ca2＋ and Mg2＋ were applied in culture solution.The concentration of Na＋ and the ratios of Na＋/K＋,Na＋/Ca2＋,and Na＋/Mg2＋ in shoots also declined significantly.The beneficial effects of higher calcium were greater than that of magnesium and application of higher concentration of K＋ seems to have minor effects.Responses to salinity in rice can therefore be considerably enhanced through proper nutrient management,by increasing the concentrations of nutrient elements that have favorable effects such as Ca2＋ and Mg2＋.Calcium is particularly more effective than both magnesium and potassium,and can be applied at relatively larger quantities in salt affected soils.

QTL Mapping and Epistasis Analysis for Yield Traits in an RIL Population of Rice(Oryza sativa L.)

A genetic linkage map consisting of 168 DNA markers was constructed based on a recombinant inbred line(RID population derived from a cross between a high yielding indica variety, Zhong156, and a low yielding indica variety, Gumeil. The markers on the linkage map were distributed on all 12 chromosomes and covered 1 447. 9 cM of the genome. The parents and 304 RILs were grown in China National Rice Research Institute(CNRRI), Hangzhou, China, in 2001, over two seasons in a randomized block design. The statistic software of QTL Mapper 1.01 was applied to detect quantitative trait loci(QTLs)and additive by environment(AE)interactions for yield traits, including panicle length, number of panicles per plant, number of spikelets per panicle, number of filled grains per panicle, fertility and kilo-grain weight. A total of 30 QTLs with significant additive effects located on all chromosomes, except chromosomes 5 and 9, and two QTLs with significant AE interactions, were detected. Thirty-one interactions of QTLs showing significant additive by additive epistatic effects for yield traits were also detected. Genetic contributions were generally lower for QTLs showing epistatic effects compared with QTLs showing additive effects. No significant interactions between epistasis and environment were detected.

Analysis of QTL for Seed Dormancy and Their Response to Dry Heat Treatment in Rice (Oryza sativa L.)

Quantitative trait loci (QTL) controlling seed dormancy in rice were identified usingrecombinant inbred lines (RILs) population derived from the cross between a japonicavariety Kinmaze and an indica variety DV85. Seeds of two parental cultivars and each RILwere harvested in 35d after heading. The germination percentage of these seeds at 30℃for 7 days were measured as the degree of seed dormancy. QTL analysis was performed withWindows QTL Cartographer 1.13a program by composite interval mapping. A total of four QTLfor seed dormancy were detected on chromosome 2 (two regions), 5 and 11, respectively.Phenotypic variation explained by each QTL ranged from 8.37 to 17.40%. Responses of suchloci to a dormancy-breaking treatment with dry heat were further detected. The resultsshowed that two alleles of qDOR-2-1 and qDOR-5 from DV85 as well as the allele of qDOR-11 from Kinmaze increased the seed dormancy, which seemed to be easily broken by dry heattreatment. Such loci of seed dormancy may be applied to rice genetic improvement. Theallele of qDOR-2-2 from DV85 increased the seed dormancy, which could not be broken bydry heat treatment.

Two Novel QTLs for Heading Date Are Identified Using a Set of Chromosome Segment Substitution Lines in Rice(Oryza sativa L.)

Heading date in rice is a typical quantitative trait controlled by multiple quantitative trait loci （QTLs）. It is mainly regulated by environmental factors such as photoperiod and temperature （Izawa, 2007）. Many QTLs for heading date have been identified using different mapping populations and methods （http：// www.gramene.org/qtl）. Up to date, several major heading date QTLs have been cloned by map-based cloning strategy （Yano et al., 2000; Takahashi et al., 2001; Kojima et al., 2002; Doi et al., 2004; Xue et al., 2008; Wei et al., 2010; Yan et al.,

QTL analysis of leaf photosynthetic rate and related physiological traits in rice(Oryza sativa L.)

Photosynthesis is one of the most important factors that influence the biomass and yield. Recently, more attention has been paid to genetic study on rice photosynthesis and rice breeding for the physiological traits related to high efficient photosynthesis. Chlorophyll content, stomatal resistance, and transpiration rate were very important physiological traits related to photosynthesis. But until now, no genetic study on these traits has been reported. A DH population derived from anther culture of ZYQ8/JX17, a typical indica/japonica hybrid was developed,

Comparison of QTLs for rice seedling morphology under different water supply conditions

The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice （Oryza sativa L.） and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid （DH） rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism （RFLP） and 76 microsatellite （SSR） markers. A total of 32 putative QTLs were associated with the four seedling traits： average of three adventitious root lengths （ARL）, shoot height （SH）, shoot biomass （SW）, and root to shoot dry weight ratio （RSR）. Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXPI, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.

Comparative mapping of QTLs for Al tolerance in rice and identification of positional Al-induced genes

Aluminum (Al) toxicity is the major factor limiting crop productivity in acid soils. In this study, a recombinant inbreed line (RIL) population derived from a cross between an Al sensitive lowland indica rice variety IR1552 and an Al tolerant upland japonica rice variety Azucena, was used for mapping quantitative trait loci (QTLs) for Al tolerance. Three QTLs for relative root length (RRL) were detected on chromosome 1, 9, 12, respectively, and 1 QTL for root length under Al stress is identical on chromosome 1 after one week and two weeks stress. Comparison of QTLs on chromosome 1 from different studies indicated an identical interval between C86 and RZ801 with gene(s) for Al tolerance. This interval provides an important start point for isolating genes responsible for Al tolerance and understanding the genetic nature of Al tolerance in rice. Four Al induced ESTs located in this interval were screened by reverse Northern analysis and confirmed by Northern analysis. They would be candidate genes for the QTL.

Molecular Mapping of QTLs for Drought Related Traits at Seedling Stage under PEG Induced Stress Conditions in Rice

Differential response of seedling characteristics under water stress conditions is known to be associated with drought resistance in rice and elucidation of its genetics could be of help in breeding for tolerance to the stress. A recombinant inbred population derived from the cross between a semi-dwarf variety IR64 and landrace INRC10192 was grown in hydroponic culture and phenotyped for varied responses of seedlings to water deficit imposed by poly ethylene glycol (PEG). The ratio between mean value of seedling trait under stress and control conditions was used for assessing drought tolerance. In all 19 putative QTL relating to five seedling traits viz., shoot length, maximum root length, shoot dry weight, root dry weight and root to shoot dry weight ratio under PEG induced stress conditions were identified confirms that the traditional tall landraces as the one chosen for the study posses hitherto unexploited drought tolerant genes and utilization of them as potential donors in breeding for yield enhancement would be rewarding. They might be useful for improving drought resistance of rice by marker assisted selection/breeding.

Fine mapping of qHUS6.1,a quantitative trait locus for silicon content in rice(Oryza sativa L.)

Silicon is essential for optimal growth of rice(Oryza sativa L.).This study was conducted to fine map qHUS6.1,a quantitative trait locus(QTL) for rice hull silicon content previously located in the interval RM510-RM19417 on the short arm of chromosome 6,and to analyze the effect of this QTL on the silicon content in different organs of rice.Selfed progenies of a residual heterozygous line of rice were detected using 13 microsatellite markers in the vicinity of qHUS6.1.Three plants with overlapping heterozygous segments were selected.Three sets of near isogenic lines(NILs) were developed from the selfed progenies of the 3 plants.They were grown in a paddy field and the silicon contents of the hull,flag leaf,and stem were measured at maturity.Based on analyses of the phenotypic distribution and variance among different genotypic groups in the same NIL set,a significant genotypic effect was shown in the NIL set that was heterogenous in the interval RM19410-RM5815,whereas a significant effect was not found in the remaining 2 NIL sets that were heterogenous in either of the intervals RM4923-RM19410 or RM19417-RM204.On comparison among the physical positions of the 3 heterogenous segments,qHUS6.1 was delimited to a 64.2-kb region flanked by RM19410 and RM19417 that contains nine annotated genes according to the genome sequence of Nipponbare.This QTL showed strong effects on all of the three traits tested,and the enhancing alleles were always derived from the paternal line Milyang 46.The present study will facilitate the cloning of qHUS6.1 and the exploration of new genetic resources for QTL fine mapping.