QTL Analysis for Yield Traits Related to Low Nitrogen Tolerance Using Backcrossing Recombinant Inbred Lines Derived from Dongxiang Wild Rice (Oryza rufipogon Griff.)

【Objective】Dongxiang wild rice (Oryza rufipogon Griff.) has strong low nitrogen tolerance and is an important germplasm for low nitrogen tolerance improvement. Identification of genes responsible for low nitrogen tolerance in Dongxiang wild rice is of great importance to understand molecular mechanisms of low nitrogen tolerance and develop rice varieties with low nitrogen tolerance. 【Method】Quantitative trait loci (QTLs) for plant height and yield traits under low and normal nitrogen conditions was identified using backcrossing recombinant inbred lines (BC1F12) derived from an interspecific cross Xieqingzao B // Dongxiang wild rice/Xieqingzao B and its genetic linkage. 【Result】A total of 57 QTLs were detected in 33 regions on all chromosome, except chromosome 4 and 8. They explained individually 3.17%~63.40% phenotypic variation, and 32 QTLs of them had favorable alleles derived from Dongxiang wild rice. Nineteen QTLs were simultaneously detected under both nitrogen treatments, and 38 QTLs were only identified under single nitrogen treatment, suggesting various genetic mechanisms in rice growth and yield formation under low and normal nitrogen conditions. 【Conclusion】Fourteen QTL clusters, 43 QTLs included, scattered on seven chromosomes, indicating the common genetic-physiological mechanisms behind different traits, and the QTL pyramiding for low nitrogen tolerance can be achieved by molecular marker-assisted selection.     

Genetic and physiological analysis of tolerance to acute iron toxicity in rice

Background

Fe toxicity occurs in lowland rice production due to excess ferrous iron (Fe²⁺) formation in reduced soils. To contribute to the breeding for tolerance to Fe toxicity in rice, we determined quantitative trait loci (QTL) by screening two different bi-parental mapping populations under iron pulse stresses (1,000 mg L⁻¹ = 17.9 mM Fe²⁺ for 5 days) in hydroponic solution, followed by experiments with selected lines to determine whether QTLs were associated with iron exclusion (i.e. root based mechanisms), or iron inclusion (i.e. shoot-based mechanisms).

Results

In an IR29/Pokkali F₈ recombinant inbred population, 7 QTLs were detected for leaf bronzing score on chromosome 1, 2, 4, 7 and 12, respectively, individually explaining 9.2-18.7% of the phenotypic variation. Two tolerant recombinant inbred lines carrying putative QTLs were selected for further experiments. Based on Fe uptake into the shoot, the dominant tolerance mechanism of the tolerant line FL510 was determined to be exclusion with its root architecture being conducive to air transport and thus the ability to oxidize Fe²⁺ in rhizosphere. In line FL483, the iron tolerance was related mainly to shoot-based mechanisms (tolerant inclusion mechanism). In a Nipponbare/Kasalath/Nipponbare backcross inbred population, 3 QTLs were mapped on chromosomes 1, 3 and 8, respectively. These QTLs explained 11.6-18.6% of the total phenotypic variation. The effect of QTLs on chromosome 1 and 3 were confirmed by using chromosome segment substitution lines (SL), carrying Kasalath introgressions in the genetic background on Nipponbare. The Fe uptake in shoots of substitution lines suggests that the effect of the QTL on chromosome 1 was associated with shoot tolerance while the QTL on chromosome 3 was associated with iron exclusion.

Conclusion

Tolerance of certain genotypes were classified into shoot- and root- based mechanisms. Comparing our findings with previously reported QTLs for iron toxicity tolerance, we identified co-localization for some QTLs in both pluse and chronic stresses, especially on chromosome 1.     

应用东乡野生稻回交重组自交系分析水稻耐低氮产量相关性状QTL

目的 东乡野生稻低氮耐性强,是水稻耐低氮育种的重要资源。鉴定东乡野生稻耐低氮基因对研究耐低氮遗传机制、培育耐低氮水稻品种具有重要意义。方法 利用协青早B//东乡野生稻/协BBC₁F₁₂回交重组自交系及其遗传图谱,应用Windows QTL Cartographer 2.5分析施氮肥和不施氮肥下的株高和产量相关性状QTL。结果 共检测到57个控制株高和产量性状的QTL,分布于10条染色体上的33个区域,单个QTL表型贡献率为3.17%~63.40%,其中32个QTL的增效等位基因来自东乡野生稻。19个QTL在施氮和未施氮条件下均检测到,38个QTL仅在单一环境下检测到显著效应,表明不同施氮水平下水稻性状的遗传机制不同。结论 43个QTL分别聚集于7条染色体上的14个QTL簇,表明不同性状涉及到共同遗传机制,并可通过分子标记辅助选择方法进行耐低氮有利等位基因的聚合育种。     

Molecular mapping of quantitative trait loci for zinc toxicity tolerance in rice seedling (Oryza sativa L.)

Excess zinc harms the growth of rice plants and zinc toxicity can easily occur in acid soils. The aim of the study was to map quantitative trait loci (QTLs) in rice for tolerance to zinc toxicity, using a recombinant inbred (RI) population derived from the cross of a japonica variety (Asominori: relatively tolerant to Zn²⁺ toxicity) with an indica variety (IR24, relatively susceptible), through 289 RFLP markers. The index scores of damage (representing Zn²⁺ toxicity tolerance), after irrigating rice seedlings with a 1000-ppm Zn²⁺ solution for 20 successive days, were examined for each RI line and its parental varieties. Continuous distributions and transgressive segregations of the index scores were observed in the RI population, suggesting that Zn²⁺ toxicity tolerance was a quantitatively inherited trait. Three QTLs for Zn²⁺ toxicity tolerance were detected on chromosomes 1, 3 and 10 and explained 21.9, 8.9 and 7.6%, respectively, of the total phenotypic variation. The results and the tightly linked molecular markers that flank the QTLs, detected in this study, will be useful in improving Zn²⁺ tolerance in rice. In addition, the genomic positions between QTLs for Zn²⁺ toxicity tolerance and the QTLs for other metal (Fe²⁺, Mn²⁺, Al³⁺) toxicity tolerances, from previous studies, are discussed.     

Identification of QTLs for Cadmium Tolerance During Seedling Stage and Validation of qCDSL1 in Rice

Cadmium(Cd)is a non-essential toxic metal that is harmful to plants.To investigate the genetic mechanism of Cd tolerance in rice,quantitative trait loci(QTLs)associated with Cd tolerance at the seedling stage were analyzed using a recombinant inbred line(RIL)population derived from a cross between PA64s and 93-11.A total of 36 QTLs associated with shoot length,root length,shoot dry weight,root dry weight and total dry weight were detected in Hangzhou and Lingshui of China.Among them,15 QTLs were identified under the control condition and 15 QTLs were identified under the Cd stress condition,and 6 QTLs for Cd tolerant coefficient were detected on chromosomes 1,3,7 and 9.The qCDSL1.1 and qCDSL1.2 were identified in Hangzhou and Lingshui,respectively,and had overlapping intervals on chromosome 1.To further confirm the effects of qCDSL1.1 and qCDSL1.2,we developed a chromosome segment substitution line(CSSL),CSSLqCDSL1,in 93-11 background harboring qCDSL1.1/qCDSL1.2 from PA64s.Compared to 93-11,CSSLqCDSL1 had increased shoot length under the Cd stress condition.These results pave the way for further isolation of those genes controlling Cd tolerance in rice and marker-assistant selection of rice elite varieties with Cd tolerance.     

水稻耐盐基因定位与克隆及品种耐盐性分子标记辅助选择改良研究进展

土壤盐渍化严重制约水稻生产发展,提高耐盐性已成为水稻育种的重要目标之一。挖掘水稻耐盐新基因,解析其分子作用机制可以为水稻耐盐性遗传改良奠定基础。本文从定位群体、耐盐性鉴定时期和鉴定方法、耐盐性评价指标、鉴定到的耐盐QTL、耐盐QTL的精细定位和图位克隆等方面,总结了近年来水稻耐盐QTL定位研究中所取得的进展;介绍了水稻耐盐/盐敏感突变体筛选和基因克隆以及耐盐性关联分析的研究近况;并对水稻耐盐性分子标记辅助选择改良的现状作了概述。     

水稻苗期耐热种质资源筛选及QTL定位

[目的]鉴定和筛选水稻极端耐热种质或基因,为培育耐高温水稻新品种提供技术支撑.[方法]以耐热等级和幼苗存活率为指标对不同类型水稻苗期耐热性进行鉴定评价,以筛选和鉴定耐热种质资源及主效QTL.[结果]不同类型水稻品种苗期耐热性存在明显差异,籼稻品种耐热性明显强于粳稻品种,籼稻和粳稻品种均存在极端耐热和极端敏感种质资源;共...     

Inheritance and QTL Mapping of Salt Tolerance in Rice

An F2 population derived from the cross between Jiucaiqing (japonica) and IR36 (indica) was used to analyze the inheritance of salt tolerance in rice by genetic model of major-genes plus polygenes, and to map the corresponding QTLs by SSR molecular markers. Rice plants of P1, P2, F1 and F2 at 5- to 6- leaf stage were treated under 140 mmol/L NaCI for 10 days. Three indices representing the ability of salt tolerance of rice seedlings were measured, including salt tolerance rating (STR), Na^ /K^ ratio in roots and dry matter weight of shoots (DWS). STR, Na^ /K^ and DWS were all controlled by two major genes with modification by polygenes. Heritability of these traits from major genes was 17.8, 53.3 and 52.3%, respectively. The linkage map constructed by 62 SSR molecular markers covered a total length of about 1 142 cM. There were three QTLs detected for STR located on chromosome 1, 5 and 9, two QTLs for DWS on chromosomes 8 and 9, and two QTLs for Na^ /K^ on chromosomes 2 and 6, one on each chromosome respectively. Single QTL accounted for 6.7 to 19.3% of phenotypic variation. Identification method of salt tolerance in rice and breeding of rice varieties with salt tolerance based on molecular markers assisted selection had been discussed.     

水稻对盐胁迫的响应及耐盐机理研究进展

我国土壤盐渍化问题日趋严重,在耕地红线内的盐碱地约有9.3×106 hm2,盐胁迫是制约粮食生产的主要非生物胁迫因子之一.水稻是盐碱地改良的先锋作物,全面深入了解水稻对盐胁迫的响应,对盐碱地水稻生产具有重要意义.本文概述了盐胁迫对水稻生长发育、产量和品质形成的影响;从渗透调节、离子平衡等生理层面以及基因层面阐述盐胁迫影...     

一个水稻铜锌SOD酶基因在应答亚砷酸盐胁迫中的作用

【目的】水稻Os08g44770.1基因编码一个铜锌SOD酶,但其在响应亚砷酸盐[As(Ⅲ)]胁迫中的生物学功能未知。本研究旨在深入揭示由该基因调控水稻砷耐性改变的分子机理并为水稻抗逆育种提供理论参考。【方法】以野生型日本晴(WT)和2个Os08g44770.1过表达转基因株系为试材,通过胁迫处理、生理指标测定和基因表达分析等,系统探究了转基因植株对As(Ⅲ)的耐受性表现,并初步揭示了其调控水稻砷耐性的生理和分子机理。【结果】与WT相比,过表达转基因株系对As(Ⅲ)更加敏感;转基因植株在砷胁迫下的根系相对伸长量、生物量(干质量)、叶绿素含量、根系细胞质膜完整性、叶片抗氧化程度等均显著低于WT;Os08g44770.1在砷处理后的WT和转基因植株叶片中的表达模式略有不同,但均表现为处理24 h时被显著诱导表达。【结论】过度表达Os08g44770.1基因可导致水稻的砷耐受性极显著下降。     

水稻生理特性与抗旱性的相关分析及QTL定位

利用籼稻品种IR64和粳稻品种Azucena杂交产生的包含110个加倍单倍体株系的群体,在干旱胁迫和正常水分条件下,连续在2004年和2005年于抽穗期分别测定了叶片水势、相对含水量、叶绿素含量(SPAD值)、游离脯氨酸含量、气孔导度和蒸腾速率,并于成熟期取样,计算抗旱系数。与正常水分状况下相比,干旱胁迫条件下叶片的游离脯氨酸含量的增加达极显著水平,干旱胁迫条件下叶片的相对含水量、水势、叶绿素含量和气孔导度的降低均达显著或极显著水平。相关分析表明,在干旱胁迫条件下,叶片相对含水量、叶片水势与抗旱系数呈显著或极显著正相关。 利用175个RFLP标记构建的遗传连锁图谱分析了与抗旱性相关的叶片生理指标,共检测到与抗旱性相关的6个生理指标的7个加性QTL,31对上位性QTL,其中有2个主效QTL、9对上位性QTL存在环境互作效应。在两种水分条件下检测到的QTL结果有较大差异,说明干旱胁迫对控制与抗旱性相关的叶片生理性状基因的表达有显著的影响。在6个抗旱相关生理指标中,检测到的控制叶片气孔导度和水势的QTL较多,有3个加性QTL和8对上位性QTL控制气孔导度,有8对上位性QTL控制水势。     

稻米垩白性状对高温耐性的QTL分析

【目的】本研究旨在筛选与稻米外观品质高温耐性连锁的分子标记,为稻米品质育种提供参考。【方法】以耐热水稻品系996和热敏感水稻品系4628为亲本构建的重组自交系为材料,采用垩白粒率耐热指数、垩白大小耐热指数和垩白度耐热指数为评价指标,对水稻垩白性状的高温耐性QTL进行检测。【结果】采用复合区间作图法两年共检测到垩白性状高温耐性QTL 24个,包括垩白粒率高温耐性QTL 8个,垩白大小高温耐性QTL 12个,垩白度高温耐性QTL 4个。其中,第6染色体上的2个垩白粒率高温耐性QTL和第7染色体上的2个垩白度高温耐性QTL在两年中重复检测到,且这2个稳定表达的垩白度位点与2015年检测到的第7染色体上的垩白粒率位点重合。另外,发现有4个QTL一因多效,同时影响垩白粒率、垩白大小及垩白度。【结论】控制垩白粒率耐热指数的q HTCGR6.1和控制垩白度耐热指数的q HTCD7.1是新的QTL。     

中国水稻育种百年发展与展望

水稻是中国最重要的口粮作物,新品种的培育与推广对水稻生产作出了重大贡献。中国现代水稻育种起步于20世纪20年代,已有百年历程,期间纯系育种、杂交育种、诱变育种和分子育种等技术成为技术主体,成就了矮化育种、杂交稻育种和超级稻育种三次突破,推进了全国水稻平均单产从20世纪50年代的200 kg/667 m²平台跃上了当前的470 kg/667 m²平台。展望未来百年的水稻产业需求,培育C4水稻、固氮水稻、耐盐碱水稻、耐旱水稻和一系杂交稻是水稻育种面临的重大任务。     

Flooding Tolerance in Rice: Focus on Mechanisms and Approaches

Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world,which results in huge economic loss.Approximately one-fourth of the global rice crops(approximately 40 million hectares)are grown in rainfed lowland plots that are prone to seasonal flooding.A great progress has been made during last two decades in our understanding of the mechanisms involved in adaptation and tolerance to flooding/submergence in rice.In this review,we summarized the physiological and molecular mechanisms that contribute to tolerance of flooding/submergence in rice.We also covered various features of flooding stress with special reference to rice plants,viz.different types of flooding stress,environmental characterisation of flood water,impact of flooding stress on rice plant and their morphological,physiological and metabolic responses under flooding.A brief discussion on the tolerance mechanism in rice exhibited to different types of flooding will be focused for the future crop improvement programme for development of flooding tolerant rice variety.     

Mapping of QTLs for Germination Characteristics under Non-stress and Drought Stress in Rice

Identification of genetic factors controlling traits associated with seed germination under drought stress conditions, leads to identification and development of drought tolerant varieties. Present study by using a population of F2：, derived from a cross between a drought tolerant variety, Gharib （indica） and a drought sensitive variety, Sepidroud （indica）, is to identify and compare QTLs associated with germination traits under drought stress and non-stress conditions. Through QTL analysis, using composite interval mapping, regarding traits such as germination rate （GR）, germination percentage （GP）, radicle length （RL）, plumule length （PL）, coleorhiza length （COL） and coleoptile length （CL）, totally 13 QTLs were detected under pole drought stress （-8 MPa poly ethylene glycol 6000） and 9 QTLs under non-stress conditions. Of the QTLs identified under non-stress conditions, QTLs associated with COL （qCOL-5） and GR （qGR-1） explained 21.28% and 19.73% of the total phenotypic variations, respectively Under drought stress conditions, QTLs associated with COL （qCOL-3） and PL （qPL-5） explained 18.34% and 18.22% of the total phenotypic variations, respectively. A few drought-tolerance-related QTLs identified in previous studies are near the QTLs detected in this study, and several QTLs in this study are novel alleles. The major QTLs like qGR-1, qGP-4, qRL-12 and qCL-4 identified in both conditions for traits GR, GP, RL and CL, respectively, should be considered as the important and stable trait-controlling QTLs in rice seed germination. Those major or minor QTLs could be used to significantly improve drought tolerance by marker-assisted selection in rice.     

Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings

Mercury (Hg) is one of the most toxic heavy metals to living organisms and its conspicuous effect is the inhibition of root growth.However,little is known about the molecular genetic basis for root growth under excess Hg2+ stress.To map quantitative trait loci (QTLs) in rice for Hg2+ tolerance,a population of 120 recombinant inbred lines derived from a cross between two japonica cultivars Yuefu and IRAT109 was grown in 0.5 mmol/L CaCl2 solution.Relative root length (RRL),percentage of the seminal root length in +HgCl2 to-HgCl2,was used for assessing Hg2+ tolerance.In a dose-response experiment,Yuefu had a higher RRL than IRAT109 and showed the most significant difference at the Hg2+ concentration of 1.5 μmol/L.Three putative QTLs for RRL were detected on chromosomes 1,2 and 5,and totally explained about 35.7% of the phenotypic variance in Hg2+ tolerance.The identified QTLs for RRL might be useful for improving Hg2+ tolerance of rice by molecular marker-assisted selection.     

Antioxidant Protection Mechanisms Reveal Significant Response in Drought-Induced Oxidative Stress in Some Traditional Rice of Assam,India

Drought tolerance levels and antioxidant protection mechanisms were evaluated for 21 traditional rice varieties of Assam, India, along with Sahbhagi Dhan (drought tolerant) and IR64 (drought sensitive) as controls. Drought was imposed in hydroponic culture with polyethylene glycol 6000 (PEG6000) that was initially standardized with different concentrations. All the rice varieties showed apparent decreases in growth characteristics under drought stress (initially at 15% for 7 d followed by 20% PEG6000 for 7 d in Yoshida medium). On the basis of standard evaluation score (SES), eight rice varieties showed high drought tolerance which were carried forward for further biochemical analyses. Based on different morpho- physiological parameters, SN03 (Bora), SN04 (Prosad Bhog), SN05 (Kola Joha), SN06 (Helash Bora), SN08 (Salihoi Bao), SN12 (Kola Amona), SN20 (Ronga Bora) and SN21 (Sok-Bonglong) were identified as promising drought tolerant varieties. The non-enzymatic antioxidants activities viz., glutathione, ascorbate and enzymatic antioxidant activities such as superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (GPX), ascorbate peroxidase (APX), glutathione reductase (GR) in shoots and roots of all the selected varieties revealed significant level of protection mechanisms as compared with controls. Enhancement in activities of the overall antioxidant enzymes including SOD, GPX, CAT, GR and APX under drought stress reflects their role in the adaptation process under water stress.     

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

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

Drought Tolerance in Rice: Focus on Recent Mechanisms and Approaches

Drought stress is a serious limiting factor to rice production,which results in huge economic losses.It is becoming a more serious issue with respect to the global climate change.Keeping in view of the current and forecasted global food demand,it has become essential to enhance the crop productivity on the drought-prone rainfed lands with priority.In order to achieve the production target from rainfed areas,there is a requirement of rice varieties with drought tolerance,and genetic improvement for drought tolerant should be a high priority theme of research in the future.Breeding for drought tolerant rice varieties is a thought-provoking task because of the complex nature and multigenic control of drought tolerant traits would be a major bottleneck for the current research.A great progress has been made during last two decades in our understanding of the mechanisms involved in adaptation and tolerance to drought stress in rice.In this review,we highlighted the recent progresses in physiological,biochemical and molecular adaptation of rice to drought tolerance.A brief discussion on the molecular genetics and breeding approaches for drought tolerance in rice will be focused for the future crop improvement program for development of drought tolerant rice varieties.     

Genetic Improvement of Rice for Bacterial Blight Resistance: Present Status and Future Prospects

The production and productivity of rice has been challenged due to biotic and abiotic factors. Bacterial blight (BB) disease, caused by Xanthomonas oryzae pv. oryzae, is one of the important biotic stress factors, which reduces rice production by 20%–50%. The deployment of host plant resistance is the most preferred strategy for management of BB disease, and breeding disease resistant varieties remains a very economical and effective option. However, it is difficult to develop rice varieties with durable broad-spectrum resistance against BB using conventional approaches alone. Modern biotechnological tools, particularly the deployment of molecular markers, have facilitated the cloning, characterization and introgression of BB resistance genes into elite varieties. At least 46 BB resistance genes have been identified and mapped from diverse sources till date. Among these, 11 genes have been cloned and characterized. Marker-assisted breeding remains the most efficient approach to improve BB resistance by introducing two or more resistance genes into target varieties. Among the identified genes, xa5, xa13 and Xa21 are being widely used in marker-assisted breeding and more than 70 rice varieties or hybrid rice parental lines have been improved for their BB resistance alone or in combination with genes/QTLs conferring tolerance to other stress. We review the developments related to identification and utilization of various resistance genes to develop BB resistant rice varieties through marker-assisted breeding.