QTL mapping of the root traits and their correlation analysis with drought resistance using DH lines from paddy and upland rice cross

A Double Haploid (DH) population, 116 plants, derived from the cross between Japonica upland rice IRAT109 and paddy rice Yuefu, planted in PVC pipe under upland ecosystem in 2001 and 2002, was used in this study. Seven root traits, including basal root thickness (BRT), total root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), ratio of root fresh weight to shoot fresh weight (RFW/SFW) and ratio of root dry weight to shoot dry weight (RDW/SDW), were studied. Using index of drought resistance (IDR), the ratio of yield under upland ecosystem to yield under lowland ecosystem of DH lines, as the criteria of drought resistance, and correla-tion analysis between root traits and IDR, showed that BRT, MRL and RN were significantly correlated with IDR. High IDR lines had thicker BRT, longer MRL and less RN than low IDR lines. A molecular linkage map with 94 RFLP markers and 71 SSR markers covering 1535.1 cM was pro-duced. QTLs and G譋 interactions for BRT, RN, MRL, RFW, RDW, RFW/SFW and RDW/SDW were obtained based on the constructed molecular linkage map and soft-ware QTLmapper version 1.0. A total of 18 additive QTLs and 18 pairs of epistatic QTLs associated with root traits were detected. There were nine additive QTLs and two pairs of epistatic QTLs performed significant interactions with environment. Some QTLs with high general contribution and no G譋 interaction were obtained. Two pairs of epistatic QTLs mrl3 and mrl8, brt3 and brt11a controlling MRL and BRT had high general contributions of 21.51% and 13.03% respectively. An additive QTL and a pair of epistatic QTLs controlling RFW and RDW had high general contributions of 13.50% and 25.64% respectively. Marker assisted selec-tion (MAS) for rice drought resistance based on QTL with high general contribution, low G譋 interaction and tightly linkage with IDR were also discussed.     

Analysis of rice blast resistance genes by QTL mapping

Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several minor genes. Its complexity and the mutable characteristic of rice blast isolates both hinder the development of the blast resistance research. The article here tried to explore the resistance gene distribution on rice chromosomes and the way of function. Totally 124 QTLs have been identified against 20 isolates using Cartographer software with a ZYQ8/JX17 DH population, which separately are at 100 loci of 72 marker intervals on 12 rice chromosomes. Of them, 16 QTLs were determined by the isolate HB-97-36-1. 82 QTLs (66.13%) are from the resistant parent alleles, ZYQ8, while 42 QTLs (33.87%) are from the susceptible parent alleles, JX17. In comparison of their positions on chromosome, most QTLs are clustered together and distributed nearby the major genes especially the regions on chromosomes 1, 2, 8, 10 and 12. Each QTL could account for the resistance variation between 3~2%-68.64%. And, a positional QTL might display the resistance to several different isolates with different contributions.     

Identification of salt-tolerance QTL in rice (Oryza sativa L.)

Quantitative trait loci (QTLs) controlling salt-tolerance at the seedling stage in rice (Oryza sativa L.) were identified by interval mapping (SIM) and composite interval mapping (CIM) using a doubled haploid population ZJDH and its high resolution genetic linkage map. The population was derived from an inter-subspecific cross between an indica variety Zhaiyeqing8 (ZYQ8) and a japonica variety Jingxi17 (JX17). Analysis of survival days of seedlings treated with 0.7% NaCI revealed that a major salt-tolerance quantitative trait locus (QTL), Std, was present between markers RG612 and C131 on chromosome 1 when using both MAPMAKER/QTL 1.1 and PLABQTL 1.0 (SIM). Its allele which contributes to salt-tolerance was from ZYQ8. In addition, seven more QTLs which give additive effect on salt-tolerance are identified when using PLABQTL (CIM), and most of them were from JX17.     

Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (Oryza sativa L.) grown at two nitrogen levels

In this study,we used 127 double haploid (DH) lines to analyze agricultural traits of rice.The DH lines,derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture,contained 160 RFLP and 83 SSR markers.Unconditional and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at five growth stages that were grown at two nitrogen levels.Fourteen PH and 13 TP unconditional QTL were identified in the different growth stages,including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) conditions.The conditional QTL for 14 genomic regions under LN/HN con-ditions showed that there was a significant effect on PH and TP across the different stages.Only one conditional QTL,ph2-3,was unable to be detected in unconditional mapping.More QTL were detected in the first four rice growth stages than in the final stage.Further-more,a line from the DH mapping population,DH78,was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) characters.The gene dftl was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a map-based cloning strategy.The location of dftl coincided with the mapping region of the small-LOD peak,QTL ph2 and tp2,which were identified in plants grown in low-nitrogen conditions.Further backcrossing and fine-mapping successfully delimited the dftl locus to a 91 kb region.     

Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (Oryza sativa L.)grown at two nitrogen levels

In this study, we used 127 double haploid (DH) lines to analyze agricultural traits of rice. The DH lines, derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture, contained 160 RFLP and 83 SSR markers. Unconditional and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at ?ve growth stages that were grown at two nitrogen levels. Fourteen PH and 13 TP unconditional QTL were identified in the di?erent growth stages, including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) conditions. The conditional QTL for 14 genomic regions under LN/HN conditions showed that there was a significant effect on PH and TP across the different stages. Only one conditional QTL, ph2-3, was unable to be detected in unconditional mapping. More QTL were detected in the ?rst four rice growth stages than in the final stage. Furthermore, a line from the DH mapping population, DH78, was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) characters. The gene dft1 was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a mapbased cloning strategy. The location of dft1 coincided with the mapping region of the small-LOD peak, QTL ph2 and tp2, which were identified in plants grown in low-nitrogen conditions. Further backcrossing and fine-mapping successfully delimited the dft1 locus to a 91 kb region.     

Genetic analysis of rice allelopathy

A double haploid population derived from anther culture of ZYQ8/JX17,a typical indica and japonica hybrid,was used in this study.The inhibited effect of water-soluble extract of 123 DH pure lines leaves on the lettuce roots growth was investigated,and the QTLs analysis of rice allelopathy was carried out.Totally,four QTLs related to rice allelopathy were detected,and they were on chromosomes,3,9,10 and 12,respectively.The LOD scores were 3.40,2.68,2.75 and 3.08,respectivel.Among them,additive effects of the QTLs on chromosomes 3 and 10 were 1.65 and 1.43,on chromosomes 9 and 12 were-1.44 and -1.58 respectively.Allelopathy characteristics of another three common rice varieties were also studied.     

水稻苗期形态性状的QTL定位

采用苗期形态性状上有着明显差异的粳稻Asominori和籼稻IR24杂交产生的重组自交系（RILs）为材料,经营养液培养后,对水稻苗期形态相关的6个数量性状：最大根长（MRL）、苗高（SH）、根干重（RDW）、茎（叶）干重（SDW）、总重（TW）以及根/茎（叶）干重比（RSR）进行了数量性状位点（QTL）定位分析.结果共检测到影响6个形态性状的8个QTL位点,分别位于水稻的第2,4,10和11染色体上,其贡献率为9.79%～22.90%.并发现位于第4染色体上的控制根/茎（叶）干重比的qRSR-4和根干重的qRDW-4的2个位点以及位于第10染色体上的控制茎（叶）干重的qSDW-10和总重的qTW-10的2个位点分别位于同一分子标记区间.研究结果对水稻苗期形态性状QTL的精细定位及培育理想株型具有一定的应用价值.     

QTL analysis of the rice seedling cold tolerance in a double haploid population derived from anther culture of a hybrid betweenindica andjaponica rice

A doubled haploid population, derived from anther culture of F₁ hybrid between a typicalindica cv. and ajaponica cv. has been used to investigate the seedling cold tolerance (SCT) in growth cabinet. By dynamically analyzing every day’s survival percentages of the parents and DH lines under 7-d cold plus 9-d normal temperature condition, the quantitative trait loci (QTLs) for SCT have been mapped based on a molecular linkage map constructed from this population. The results show that two parents had significant differences in SCT and the segregation of SCT in DH lines was basically a continuous distribution with most serious injury on the 6th d of the cold treatment. A total of 4 QTLs for SCT have been identified on chromosomes 1, 2, 3 and 4 respectively. The additive effects of qSCT-1, qSCT-2 and qSCT-3 have been contributed by thejaponica cv JX17, but that of qSCT-4 has been contributed by theindica cv ZYQ8. The mechanism of SCT seems complicated since the above 4 QTLs detected at different stages during the treatment. Further study on the genotypes for these SCT QTLs in the DH lines shows transgressive segregation. It is demonstrated that the lines with stronger SCT over JXI7 have 3–4 loci for SCT. Integration of these QTLs into an appropriate variety may lead to a successful rice breeding program for cold tolerance.     

QTL analysis of rice low temperature germinability

A double haploid population, derived from anther culture of F1 hybrid between a typical indica and a japonica (ZYQ8/JX17), has been used to investigate the low temperature germinability (LTG) at 15 ℃. The low temperature germinability of two parents was significantly different. In 6-11 d, the germination percentage of ZYQ8 was higher than that of JX17. In 12-16 d, the germination percentage of JX17 was higher than that of ZYQ8. The quantitative trait loci (QTLs) of every day for low temperature germinabilityhave been mapped based on a molecular linkage map constructed from this population. In 8-11 d, qLTG-9 was identified in C397B-RZ617B on chromosome 9, the additive effect was positive, showing that, the allele from JX17 could increase low temperature germinability. In 12-16 d, qLTG-4 was mapped between RG908 and CT563 on chromosome 4, the additive effect was negative, showing that the allele from ZYQ8 could increase low temperature germinability. These two QTLs were detected at different stages, showing the complexity of the mechanism of low temperature germinability.     

水稻芒长及其分布特征相关QTL的定位

水稻芒的性状与驯化过程密切相关,具体表现为芒长短和芒的分布等．利用一个无芒品种越光（轮回亲本）和一个有芒品种Kasalath杂交产生的回交重组自交系群体,在上海、海南两地对芒长和芒的分布（芒出现比例）进行了相关分析及其相关基因（QTL）定位,结果发现这两个性状间存在显著的正相关．共检测到影响这两个性状的12个QTL,分布在6条染色体上的7个区域,贡献率介于2．90％-53．24％,其正效应大多来自有芒亲本Kasalath,但也有3个QTL正效应来自无芒亲本越光,并对这个现象产生的原因进行了讨论．本研究检测到的QTL及其两侧的分子标记可以用于水稻驯化的研究和理想型无芒品种分子辅助育种．     

Starch RVA profile parameters of rice are mainly controlled byWx gene

Quantitative trait locus (QTLs) mapping for rapid visco analyser (RVA) profile parameters has been carried out by using a double haploid (DH) population derhred from a cross betweenindica variety Zhai-Ye-Qing 8 andjaponica variety Jing-Xi 17 and its genetic linkage map. The results indicate that the segregation of the RVA profiles is continually distributed among the DH lines, and some DH lines show transgressive segregation for all the parameters. A major QTL,Waxy (Wx) gene on chromosome 6 which controls the amylose synthesis, has been detected significantly for 5 traits: hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), consistency viscoslty (CSV) and setback viscoslty (SBV). Therefore, the RVA profile parameters are mainly controlled byWx gene. Other 3 and 2 QTLs have also been identified for BDV and SBV, respectively, and two of them share the same region on chromosomes 1 and 5. However, the peak viscosity (PKV) is controlled by a minor QTL on chromosome 12, qPKV-12.     

水稻萌发期耐Cu2+胁迫的QTL定位

以典型籼粳交(春江06/台中本地1号)双单倍体(DH)群体为材料,经100μmol/L CuSO4溶液对其双亲及DH群体进行处理,考察了DH群体及其双亲的耐铜性,并利用业已构建的分子连锁图谱进行了数量性状基因座(QTL)区间分析.共检测到23个QTLs,其中与铜胁迫有关的QTL有7个,分别位于水稻第1,2,3和7染色体上;贡献率最大的QTL为qTGR-2,变异解释率为14.60%,其增效等位基因来自台中本地1号;芽质量的QTL qTSW-1增效等位基因来自春江06;余下的几个耐铜胁迫的QTL增效基因均来自台中本地1号.同时,在3号染色体上检测到了一个QTL,可显示发芽率受铜胁迫抑制的程度.     

QTL analysis of flag leaf in barley （Hordeum vulgate L.） for morphological traits and chlorophyll content

To understand genetic patterns of the morphological and physiological traits in flag leaf of barley, a double haploid （DH） population derived from the parents Yerong and Franklin was used to determine quantitative trait loci （QTL） controlling length, width, length/width, and chlorophyll content of flag leaves. A total of 9 QTLs showing significantly additive effect were detected in 8 intervals on 5 chromosomes. The variation of individual QTL ranged from 1.9% to 20.2%. For chlorophyll content expressed as SPAD value, 4 QTLs were identified on chromosomes 2H, 3H and 6H; for leaf length and width, 2 QTLs located on chromosomes 5H and 7H, and 2 QTLs located on chromosome 5H were detected; and for length/width, I QTL was detected on chromosome 7H. The identification of these QTLs associated with the properties of flag leaf is useful for barley improvement in breeding programs.     

Detecting quantitative trait loci for water use efficiency in rice using a recombinant inbred line population

Breeding rice with high water use efficiency (WUE) can ameliorate water shortage through water-saving irrigation.However,WUE is a complex quantitative trait and very few studies have been conducted to measure WUE directly.In this study,a recombined inbred line population derived from a cross between an indica lowland rice and upland japonica rice was used to dissect the genetic control of WUE by fine-monitored water supply experiments.Quantitative trait loci (QTL) were scanned for 10 traits including heading date (HD),water-consumption per day (water/d),shoot weight gain per day (shootw/d),root weight gain per day (rootw/d),kernel weight gain per day (kernelw/d),average WUE at whole plant level (WUEwhole/d),average WUE for up-ground biomass (WUEup/d),average WUE for grain yield (WUEyield/d),average economic index (econindex/d),and average root/shoot ratio per day (ratio/d).The results show that most of the traits were significantly correlated to each other.Twenty-four QTL (LOD ≥ 2.0) were detected for econindex,econindex/d,WUEyield,WUEyield/d,WUEup,WUEup/d,WUEwhole,WUEwhole/d,kernelw,kernelw/d,rootw,and water/d by composite interval mapping.These QTLs are located on chromosomes 1,2,4,6,7,8,and 12.Individual QTLs accounted for 4.97%-10.78% of the phenotypic variation explained.Some of these QTLs overlapped with previously reported drought resistance QTLs detected in this population.These results provide useful information for further dissection of the genetic basis and marker-assisted selection of WUE in rice.     

Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.     

Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.     

The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs

Since the first publication of quantitative trait locus (QTL) localization using molecular markers[1], a large number of QTLs have been identified in different ge- netic backgrounds and environments. Affected by many factors, such as marker sets, experime…     

控制水稻剑叶形态相关性状的数量基因位点(QTL)的定位

水稻籽粒中一半以上的碳水化合物来自剑叶的光合作用，剑叶形态改良一直是水稻株型育种的一个重要目标．利用一个日本主要种植的粳稻品种越光（轮回亲本）和一个印度的籼稻品种Kasalath杂交产生的回交重组自交系群体（backcross recombinant inbred lines，BILs）对剑叶形态中的3个主要性状（剑叶长、叶宽以及其叶面积）进行了相关分析及其数量基因位点（quantitative trait loci，QTL）的定位．研究表明，控制剑叶形态的3个主要性状间存在极显著的正相关，并检测到影响3个性状的8个QTL，分布在第1，3，4，6条染色体上，贡献率介于4．94％～22．07％，其中第4染色体上C1016标记和第6染色体上C556标记附近的共有6个QTL，其两侧的紧密分子标记在水稻株型分子育种上具有一定应用价值．     

Statistical method for mapping QTLs for complex traits based on two backcross populations

Most important agronomic and quality traits of crops are quantitative in nature.The genetic variations in such traits are usually controlled by sets of genes called quantitative trait loci (QTLs),and the interactions between QTLs and the environment.It is crucial to understand the genetic architecture of complex traits to design efficient strategies for plant breeding.In the present study,a new experimental design and the corresponding statistical method are presented for QTL mapping.The proposed mapping population is composed of double backcross populations derived from backcrossing both homozygous parents to DH (double haploid) or RI (recombinant inbreeding) lines separately.Such an immortal mapping population allows for across-environment replications,and can be used to estimate dominance effects,epistatic effects,and QTL-environment interactions,remedying the drawbacks of a single backcross population.In this method,the mixed linear model approach is used to estimate the positions of QTLs and their various effects including the QTL additive,dominance,and epistatic effects,and QTL-environment interaction effects (QE).Monte Carlo simulations were conducted to investigate the performance of the proposed method and to assess the accuracy and efficiency of its estimations.The results showed that the proposed method could estimate the positions and the genetic effects of QTLs with high efficiency.     

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

Aluminum (A1) 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 A1 sensitive lowland indica rice variety IR1552 and an A1 tolerant upland japonica rice variety Azucena, was used for mapping quantitative trait loci (QTLs) for A1 tolerance. Three QTLs for relative root length (RRL) were detected on chromosome 1,9, 12, respectively, and 1 QTL for root length under A1 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 A1 tolerance. This interval provides an important start point for isolating genes responsible for A1 tolerance and understanding the genetic nature of Al tolerance in rice. Four A1 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.