基于高密度遗传图谱的水稻萌发耐淹性QTL定位

通过对水稻萌发耐淹性进行QTL定位和稳定位点的聚合效应分析,可以为萌发耐淹性基因的精细定位及后续分子辅助育种奠定基础。本研究利用一个包含144份家系的强萌发耐淹性粳型杂草稻WR-4与籼稻品种广百香占的F2:3定位群体,基于1K m GPS SNP芯片构建了一个包含825个Bin标记的高密度遗传图谱,利用完备区间作图法共检测到10个萌发耐淹性QTL,分布于水稻第3、4、7、8、9和10染色体上,LOD值介于3.6～21.3之间,可解释3.0%～21.1%的表型变异。其中,具有较高LOD值和贡献率的2个主效QTL(q GS4-1和q GS7-1)能够被重复检测到,是后续基因克隆的候选位点。根据Bin标记分型结果将不同子代在两个稳定QTL区间内分为WR型和广百香占型,在F2:3群体中进行聚合效应分析,发现聚合增效等位基因数量越多的家系,其淹水条件下的胚芽鞘越长,这些携带多个耐性QTL的株系可为分子育种培育耐低氧萌发水稻新品种提供亲本资源。     

基于单片段代换系的水稻芽期耐冷QTL定位和聚合北大核心CSCD

芽期耐冷性是华南双季稻地区水稻育种的一个重要目标。虽然水稻芽期耐冷QTL的标记定位已取得了一定的进展,但是这些QTL/基因尚未在水稻育种中得到有效的应用。定位稳定表达的芽期耐冷QTL,开展QTL聚合育种是水稻芽期耐冷性育种取得突破的关键。在本研究中,利用以粳稻IR65598-112-2为供体,籼稻华粳籼74为受体构建的单片段代换系(SSSL)开展芽期耐冷QTL定位,并进行聚合育种。通过评价SSSL与受体华粳籼74的芽期耐冷性差异,定位了2个稳定的芽期耐冷QTLs(qCTBB-3和qCTBB-12)。试验表明,分别携带有耐冷QTL qCTBB-3和qCTBB-12的SSSL在冷处理后都比华粳籼74表现出更高的幼苗成活率。通过代换作图,发现在qCTBB-3区间存在2个紧密连锁的耐冷QTLs(qCTBB-3a和qCTBB-3b)。利用本研究携带qCTBB-3a/qCTBB-3b的单片段代换系和前期研究鉴定出的芽期耐冷QTL qCTBB-6的单片段代换系为亲本进行杂交,通过分子标记辅助选择,获得了2份含有这3个QTL的聚合系。耐冷性评价表明,来源于两个供体/亲本的QTL不存在显著的上位性效应,聚合系的芽期耐冷性较亲本显著增强。可见,通过聚合芽期耐冷QTLs qCTBB-3a/qCTBB-3b和qCTBB-6能显著提高水稻芽期的耐冷性,获得的QTL及三耐冷QTL聚合系为水稻芽期耐冷性分子育种提供了优良的基因资源和亲本材料。     

5 个籼稻背景的高代回交置换系的置换片段分析

以轮回亲本籼稻品种9311(Oryz a sativa ssp. indica ‘Yangdao 6’)为对照, 选用132个亲本间有多态性的SSR标记, 对以粳稻品种日本晴(Oryz a sativa ssp. japonica 'Nipponbare’)为供体的5个高代回交置换系的农艺性状及置换片段进行分析。5个置换系在粒长、粒宽、千粒重、剑叶长、株高及落粒性等方面与籼稻品种9311之间有极显著差异, 其余性状与籼稻品种9311间的差异不显著; 从置换系中检测出8个置换片段, 总长度为236.0 cM, 平均长度为29.5 cM; 从置换片段上检出包括2个千粒重、1个粒长、1个粒宽、1个剑叶长、1个株高和1个落粒性共7个QTLs , 分别分布在水稻第1、3、5、6和第10染色体上。其中, 第1染色体上控制剑叶长的QTL和第6染色体上控制株高的QTL可能是新发现的QTLs。实验结果进一步丰富了置换系群体的数量和质量, 也为QTLs 的精细定位及分子设计育种奠定了基础。     

水稻籽粒锌含量的QTL 定位

锌元素的营养失衡已成为影响人类健康的最重要因素之一, 籽粒锌含量的QTL(quantitative trait loci)定位对研究富锌水稻的遗传育种具有重要的意义。以水稻(Oryza sativa L.)亲本奉新红米和明恢100杂交的145个株系的F2群体为实验材料, 利用92个SSR(simple sequence repeat)标记对水稻籽粒锌含量进行了QTL定位, 共检测到3个QTLs , 分别定位于第3、6和11染色体上, 对表型变异的贡献率分别为4.97%、12.75%和7.74%。其中位于第3染色体上的分子标记RM186和RM168之间的QZN3对表型变异的贡献率最大, 其增效等位基因来自亲本明恢100, 表现为部分显性。3个QTLs 的联合贡献率为25.46%, 具有基因累加效应。该研究结果有利于深入理解水稻锌含量的遗传基础, 为锌含量的QTL精细定位、基因克隆和分子标记辅助选择提供依据。     

5个籼稻背景的高代回交置换系的置换片段分析

以轮回亲本籼稻品种9311（Oryza sativassp.indica‘Yangdao6’）为对照,选用132个亲本间有多态性的SSR标记,对以粳稻品种日本晴（Oryzasativassp.japonica‘Nipponbare’）为供体的5个高代回交置换系的农艺性状及置换片段进行分析。5个置换系在粒长、粒宽、千粒重、剑叶长、株高及落粒性等方面与籼稻品种9311之间有极显著差异,其余性状与籼稻品种9311间的差异不显著;从置换系中检测出8个置换片段,总长度为236.0cM,平均长度为29.5cM;从置换片段上检出包括2个千粒重、1个粒长、1个粒宽、1个剑叶长、1个株高和1个落粒性共7个QTLs,分别分布在水稻第1、3、5、6和第10染色体上。其中,第1染色体上控制剑叶长的QTL和第6染色体上控制株高的QTL可能是新发现的QTLs。实验结果进一步丰富了置换系群体的数量和质量,也为QTLs的精细定位及分子设计育种奠定了基础。     

长江下游不同类型水稻分蘖期耐淹能力比较

在分蘖期对长江下游稻作区主栽的9个水稻品种进行大田模拟没顶淹涝处理,研究淹涝胁迫对水稻植株农艺性状、生理指标和产量性状的影响,比较分析了常规粳稻、杂交籼稻和杂交粳稻对淹水胁迫环境适应性的差异.结果表明:淹水胁迫4d后,水稻株高及顶部全展3片叶长均比对照有不同程度的增加,伸长程度为杂交粳稻＞杂交籼稻＞常规粳稻.杂交粳稻的茎蘖数、绿叶数和地上部干质量损失率分别为18.0％、41.4％、13.2％,显著小于常规粳稻;杂交籼稻则介于杂交粳稻和常规粳稻之间,且整株死亡率显著低于常规粳稻.常规粳稻叶片中丙二醛(MDA)含量比对照增加1.91 μmol·g-1 FM,超氧化物歧化酶(SOD)和过氧化氢酶(CAT)活性明显降低;杂交粳稻和杂交籼稻MDA含量分别降低2.32和2.10 μmol·g-1 FM,SOD和CAT活性显著提高.不同类型品种的减产程度差异显著,常规粳稻的产量损失率达到38.5％,显著高于杂交粳稻和杂交籼稻,杂交粳稻产量损失率仅为4.1％.长江下游水稻分蘖期的耐淹涝能力为杂交粳稻强于杂交籼稻,常规粳稻的耐淹能力最低.     

水稻籼粳交DH群体苗期耐冷性基因的分子标记定位

水稻苗期低温冷害导致的烂秧现象是水稻生产中重要的限制因素之一。以一个水稻籼粳交(圭630／02428)DH群体为材料,在幼苗3叶1心时用10℃低温处理3d,随后恢复培养,以恢复培养5d后的秧苗成活率(％)为指标,鉴定该DH群体的苗期耐冷性。利用已构建的RFLP连锁图谱和基于混合线性模型的定位软件QTLMapper1.0对水稻苗期耐冷性进行QTL分析,检测到控制水稻苗期耐冷性的3个QTLs,分别位于第3、11、12染色体上,贡献率分别为7．9％、18．3％和24.4％,其增效等位基因均来自于亲本“02428”。同时检测到控制水稻苗期耐冷性的上位性互作位点8个,分散分布于第2、7、8、9、11染色体上,其中有2对互作的贡献率在15％左右,这2对互作的增效基因型均为来自2个亲本的重组基因型。苗期耐冷性在2个亲本间差异很大,在DH群体中呈现出连续变异,有明显的超亲分离。这些结果表明,水稻苗期耐冷性是受多基因控制的数量性状,基因的上位性互作是其重要的遗传基础之一。     

籼粳稻杂交后代花时性状的QTL分析

研究典型籼稻品种‘七山占’和典型粳稻品种‘秋光’杂交衍生的重组自交系群体及其双亲的花时性状,并用该群体的分子连锁图谱进行QTL分析,共检测到6个与水稻花时性状相关的QTL,包括1个始花时QTL、3个盛花时QTL和2个终花时QTL,分别位于第1、2、7、8、10和12染色体,单个QTL的贡献率在7.08%～26.95%之间。有4个增效等位基因来源于粳型亲本‘秋光’,2个来源于籼型亲本‘七山占’。     

水稻RIL群体苗期耐冷性QTL分析

水稻苗期冷害是影响早春季节和高纬度地区水稻成苗和秧苗生长的重要限制因素之一。为了鉴定控制水稻苗期耐冷性的QTL,研究采用了1个水稻“粳籼交”重组自交系(RIL)群体,结合1张高密度分子遗传图谱,对3叶期幼苗经过10℃冷处理3d、恢复培养2d和4d时的秧苗存活率进行复合区间作图。亲本Lemont和特青的苗期耐冷性具有极显著差异,Lemont的苗期耐冷性很强,而特青对低温敏感。在重组自交系群体中,苗期耐冷性表现为连续变异,在两个方向上均出现大量超亲分离。共检测到5个水稻苗期耐冷性QTL,分别位于水稻1、3、8和11号染色体上,单个QTL对性状的贡献率为7％～21％。其中,4个QTL的增效基因来源于亲本Lemont,另1个QTL的增效基因来源于亲本特青。2个主效QTL(qSCT-3和qSCT-8)分别位于3号染色体标记区间RM282-RM156和8号染色体标记区间RM230—RM264,对性状的贡献率达到或接近20％,被检测到的LOD值显著较高,其增效基因均来自于耐冷性亲本Lemont。研究结果进一步揭示了水稻苗期耐冷性QTL具有丰富的位点多样性,表明耐冷性普遍较强的粳稻是发掘苗期耐冷性优异基因的主要稻种资源。     

水稻籽粒锌含量的QTL定位

锌元素的营养失衡已成为影响人类健康的最重要因素之一,籽粒锌含量的QTL（quantitative trait loci）定位对研究富锌水稻的遗传育种具有重要的意义。以水稻（Oryzasativa L．）亲本奉新红米和明恢100杂交的145个株系的F2群体为实验材料,利用92个SSR（simple sequence repeat）标记对水稻籽粒锌含量进行了QTL定位,共检测到3个QTLs,分别定位于第3、6和11染色体上,对表型变异的贡献率分别为4．97％、12．75％和7．74％。其中位于第3染色体上的分子标记RM186和RM168之间的QZN3对表型变异的贡献率最大,其增效等位基因来自亲本明恢100,表现为部分显性。3个QTLs的联合贡献率为25．46％。具有基因累加效应。该研究结果有利于深入理解水稻锌含量的遗传基础,为锌含量的QTL精细定位、基因克隆和分子标记辅助选择提供依据。     

Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice

Salt tolerance was evaluated at the young seedling stage of rice (Oryza sativa L.) using recombinant inbred lines (MG RILs) from a cross between Milyang 23 (japonica/indica) and Gihobyeo (japonica). 22 of 164 MG RILs were classified as tolerant with visual scores of 3.5-5.0 in 0.7% NaCl. Interval mapping of QTLs related to salt tolerance was conducted on the basis of the visual scores at the young seedling stage. Two QTLs, qST1 and qST3, conferring salt tolerance, were detected on chromosome 1 and 3, respectively, and the total phenotypic variance explained by the two QTLs was 36.9% in the MG RIL population. qST1 was the major QTL explaining 27.8% of the total phenotypic variation. qST1 was flanked by Est12-RZ569A, and qST3 was flanked by RG179-RZ596. The detection of new QTLs associated with salt tolerance will provide important information for the functional analysis of rice salt tolerance.     

Identification of Quantitative Trait Loci for Grain Appearance and Milling Quality Using a Doubled-Haploid Rice Population

Improving grain quality, which is composed primarily of the appearance of the grain and its cooking and milling attributes, is a major objective of many rice-producing areas in China. In the present study, we conducted a marker-based genetic analysis of the appearance and milling quality of rice （Oryza sativa L.） grains using a doubled-haploid population derived from a cross between the indica inbred Zhenshan 97 strain and the japonica inbred Wuyujing 2 strain. Quantitative trait locus （QTL） analysis using a mixed linear model approach revealed that the traits investigated were affected by one to seven QTLs that individually explained 4.0%-30.7% of the phenotypic variation. Cumulatively, the QTL for each trait explained from 12.9% to 61.4% of the phenotypic variation. Some QTLs tended to have a pleiotropic or location-linked association as a cause of the observed phenotypic correlations between different traits. Improvement of the characteristics of grain appearance and grain weight, as well as an improvement in the milling quality of rice grains, would be expected by a recombination of different QTLs using marker-assisted selection.     

Identification of Quantitative Trait Loci for ABA Sensitivity at Seed Germination and Seedling Stages in Rice

Abscisic acid (ABA) is one of the important plant hormones, which plays a critical role in seed development and adaptation to abiotic stresses. The sensitivity of rice (Oryza sativa L.) to exogenous ABA at seed germination and seedling stages was investigated in the recombinant inbred line (RIL) population derived from a cross between irrigated rice Zhenshan 97 and upland rice IRAT109, using relative germination vigor (RGV), relative germination rate (RGR) and leaf rolling scores of spraying (LRS) or culturing (LRC) with ABA as sensitivity indexes. The phenotypic correlation analysis revealed that only RGV at germination stage was positively correlated to ABA sensitivity at seedling stage. QTL detection using composite interval mapping (CIM) and mixed linear model was conducted to dissect the genetic basis of ABA sensitivity, and the single-locus QTLS detected by both methods are in good agreement with each other. Five single QTLs and six pairs of epistatic QTLs were detected for ABA sensitivity at germination stage. Eight single QTLs and five pairs of epistatic QTLs were detected for ABA sensitivity at seedling stage. Two QTLs were common between LRS and LRC; and one common QTL was detected for RGV, LRS and LRC simultaneously. These results indicated that both single and epistatic loci were involved in the ABA sensitivity in rice, and the genetic basis of ABA sensitivity at seed germination and seedling stage was largely different.     

Mapping QTLs of root morphological traits at different growth stages in rice

Roots are a vital organ for absorbing soil moisture and nutrients and influence drought resistance. The identification of quantitative trait loci (QTLs) with molecular markers may allow the estimation of parameters of genetic architecture and improve root traits by molecular marker-assisted selection (MAS). A mapping population of 120 recombinant inbred lines (RILs) derived from a cross between japonica upland rice 'IRAT109' and paddy rice 'Yuefu' was used for mapping QTLs of developmental root traits. All plant material was grown in PVC-pipe. Basal root thickness (BRT), root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW) and root volume (RV) were phenotyped at the seedling (I), tillering (II), heading (III), grain filling (IV) and mature (V) stages, respectively. Phenotypic correlations showed that BRT was positively correlated to MRL at the majority of stages, but not correlated with RN. MRL was not correlated to RN except at the seedling stage. BRT, MRL and RN were positively correlated to RFW, RDW and RV at all growth stages. QTL analysis was performed using QTLMapper 1.6 to partition the genetic components into additive-effect QTLs, epistatic QTLs and QTL-by-year interactions (Q x E) effect. The results indicated that the additive effects played a major role for BRT, RN and MRL, while for RFW, RDW and RV the epistatic effects showed an important action and Q x E effect also played important roles in controlling root traits. A total of 84 additive-effect QTLs and 86 pairs of epistatic QTLs were detected for the six root traits at five stages. Only 12 additive QTLs were expressed in at least two stages. This indicated that the majority of QTLs were developmental stage specific. Two main effect QTLs, brt9a and brt9b, were detected at the heading stage and explained 19% and 10% of the total phenotypic variation in BRT without any influence from the environment. These QTLs can be used in breeding programs for improving root traits.     

Mapping of QTLs associated with cold tolerance during the vegetative stage in rice

Low-temperature stress is an important factor affecting the growth and development of rice (Oryza sativa L.) in temperate and high-elevation areas. Cold stress may cause various seedling injuries, delayed heading and yield reduction due to spikelet sterility. In this study, 181 microsatellite marker loci were used to identify quantitative trait loci (QTLs) associated with cold tolerance at the vegetative stage in 191 recombinant inbred lines (RILs) derived from a cross of a cold-tolerant temperate japonica cultivar (M-202) with a cold-sensitive indica cultivar (IR50). Different temperature regimes were applied in growth chambers on 191 RILs. The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling and late vegetative stages. In this study a major QTL was identified on chromosome 12, designated as qCTS12a, that was closely associated with cold-induced necrosis and wilting tolerance, and accounted for 41% of the phenotypic variation. A number of QTLs with smaller effects were also detected on eight rice chromosomes.     

A major locus for submergence tolerance mapped on rice chromosome 9

Submergence stress is a widespread problem in rice-growing environments where drainage is impeded. A few cultivars can tolerate more than 10 days of submergence, but the genes conferring this tolerance have not been identified. We used randon-amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers to map submergence tolerance in 169 F₂ plants and the resulting F₃ families of a cross between a tolerant indica rice line, IR40931-26, and a susceptible japonica line, PI543851. IR40931-26 inherited strong submergence tolerance from the unimproved cultivar FR13A. Eight-day old F₃ seedlings were submerged for 14–16 days in 55-cm deep tanks, and tolerance was scored after 7 days recovery on a scale of 1 (tolerant) to 9 (susceptible). The tolerant and susceptible parents scored 1.5 and 8.4, respectively, and the F₃ means ranged from 1.6 to 8.9. Two bulks were formed with DNA from F₂ plants corresponding to the nine most tolerant and the nine most susceptible F₃ families. Of 624 RAPD primers used to screen the bulks, five produced bands associated with either tolerance or susceptibility. These markers were mapped to a region of chromosome 9 by linkage to RFLP markers. A submergence tolerance quantitative trait locus (QTL), here designatedSub1, was located ca. 4 cM from the RFLP marker C1232 and accounted for 69% of the phenotypic variance for the trait.     

Molecular mapping of quantitative trait loci in japonica rice.

Rice (Oryza sativa L.) molecular maps have previously been constructed using interspecific crosses or crosses between the two major subspecies: indica and japonica. For japonica breeding programs, however, it would be more suitable to use intrasubspecific crosses. A linkage map of 129 random amplified polymorphic DNA (RAPD) and 18 restriction fragment length polymorphism (RFLP) markers was developed using 118 F2 plants derived from a cross between two japonica cultivars with high and low seedling vigor, Italica Livorno (IL) and Labelle (LBL), respectively. The map spanned 980.5 cM (Kosambi function) with markers on all 12 rice chromosomes and an average distance of 7.6 cM between markers. Codominant (RFLP) and coupling phase linkages (among RAPDs) accounted for 79% of total map length and 71% of all intervals. This map contained a greater percentage of markers on chromosome 10, the least marked of the 12 rice chromosomes, than other rice molecular maps, but had relatively fewer markers on chromosomes 1 and 2. We used this map to detect quantitative trait loci (QTL) for four seedling vigor related traits scored on 113 F3 families in a growth chamber slantboard test at 18 degrees C. Two coleoptile, five root, and five mesocotyl length QTLs, each accounting for 9-50% of the phenotypic variation, were identified by interval analysis. Single-point analysis confirmed interval mapping results and detected additional markers significantly influencing each trait. About two-thirds of alleles positive for the putative QTLs were from the high-vigor parent, IL. One RAPD marker (OPAD13720) was associated with a IL allele that accounted for 18.5% of the phenotypic variation for shoot length, the most important determinant of seedling vigor in water-seeded rice. Results indicate that RAPDs are useful for map development and QTL mapping in rice populations with narrow genetic base, such as those derived from crosses among japonica cultivars. Other potential uses of the map are discussed. Key words : QTL mapping, RAPD, RFLP, seedling vigor, japonica, Oryza sativa.     

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。     

水稻外观品质的数量性状基因位点分析

利用由98个家系组成的Nipponbare(粳)／Kasalath(秒)∥Nipponbare回交重组自交系(backcross inbred lines,BILs)群体(BC1F9)及其分子连锁图谱,采用复合区间作图的方法,在2个不同年份对粒长、粒宽、粒形、垩白率、垩白大小、垩白度和透明度等7个稻米外观品质性状的数量性状基因位点(Quantiative trait loci,QTL)进行了定位分析。共定位到33个四QTLs,单个性状QTL数目在4-7个之间,以垩白率最多,为7个;粒长和垩白大小次之,为5个;其他性状均为4个,表明该组合外观品质是由多基因控制的数量性状。单个QTL对性状变异解释率粒长为6．2％-15．2％,粒宽为8．3％-32．5％,长宽比为6．8％-19．8％,垩白率为6．4％-28．5％,垩白大小为6．1％-16．9％,垩白度为9．3％-17．2％,透明度为5．6％-25．2％．QTL在染色体上成集中分布的特点,第3染色体C1488-C563、第5染色体R830-R3166和R1436-R2289、第6染色体R2147-R2171均有3个以上的QTLs分布。比较2年的检测结果表明,外观品质性状的QTL定位都受环境影响,但不同性状受影响的程度差异很大。粒长和粒形的QTL定位受环境影响很小,垩白率、垩白大小和垩白度的QTL定位受环境影响很大。