基于混池测序的抗玉米灰斑病QTL定位

玉米灰斑病是由玉米尾孢菌(Cercospora zeine)和玉蜀黍尾孢菌(Cercospora zeae-maydis)引起的真菌性病害,是世界范围内重要的玉米叶部病害之一。以玉米灰斑病抗病自交系Suwan1和感病自交系HM01构建的BC1F1群体为研究材料,在自然发病条件下通过对BC1F1群体中玉米灰斑病的抗性鉴定,选择30株抗病材料和30株感病材料分别构建DNA抗、感混池。在对两个混池进行高通量测序后,通过质量控制和数据分析得到两个极端混池中的变异信息。利用高质量SNP标记对应的两个混池中测序深度差异进行统计检验,成功鉴定了29个玉米灰斑病抗性QTL (quantitative trait loci)。利用MaizeGDB网站在29个抗病QTL内共搜索到2 768个基因,通过Phytozome网站与拟南芥和水稻基因组进行同源比对,在1号、5号和10号染色体上分别确定了1个基因作为抗玉米灰斑病的候选基因。     

水稻籽粒镉积累QTL定位及候选基因分析

水稻(Oryza sativa)是全世界重要的经济作物之一, 稻田镉(Cd)污染和镉积累问题严重威胁世界水稻的产量和品质以及人类健康, 如何降低水稻中镉积累已成为热点问题。以籼稻品种华占(HZ)为父本、粳稻品种热研2号(Nekken2)为母本, 连续自交多代后得到120个重组自交系群体, 对其镉积累进行检测和分析, 同时利用遗传图谱进行QTL作图。结果共检测到7个QTLs, 分别位于水稻第2、3、9和12号染色体上, 其中1个LOD值高达4.97。对这些QTL区间内与耐金属离子胁迫相关的候选基因进行定量分析, 发现LOC_Os02g50240、LOC_Os02g52780、LOC_Os09g31200、LOC_Os09g35030和LOC_Os09g37949这5个基因在双亲间的表达量差异显著, 结合亲本对不同金属离子的浓度积累数据, 推测LOC_ Os02g50240、LOC_Os09g31200及LOC_Os09g35030的高表达可能极大地提高了水稻对镉离子的吸收和胁迫耐受能力。通过QTL挖掘和分析, 发现这些基因与水稻籽粒的镉积累有关, 可能影响水稻耐镉胁迫的能力。研究结果为进一步筛选和培育耐镉胁迫的水稻品种创造了条件, 为阐明水稻镉积累的分子调控机制奠定了基础。     

水稻对叶瘟和穗瘟部分抗性的遗传分析

在一个水稻籼籼交重组自交系群体中,选用由感病株系构成的2个亚群体和2个不同的稻瘟病菌小种,进行了水稻对叶瘟部分抗性的QTL定位,还选用由感病而且抽穗期相近的株系构成的亚群体和另一个病菌小种,进行了水稻对穗瘟部分抗性的QTL定位,将病叶面积百分比(DLA)、病斑大小(LS)和病斑数(LN)作为对叶瘟部分抗性的性状,将病斑长度(LL)和孢子量(CA)作为对穗瘟部分抗性的性状。所构建的图谱包含168个标记。应用QTLMapper 1．01b,共检测到11个表现主效应的QTL和28对双因子互作,有3个表现主效应的QTL参与对同一性状的互作。QTL的主效应对单一性状的贡献率为4．7％～38．8％,而上位性效应对单一性状的贡献率为16．0％～51．7％,QTL的主效应对大多数性状的贡献率小于互作效应,表明互作效应对于部分抗性的重要作用。对穗瘟部分抗性的两个性状LL和CA,所检测到QTL总效应的贡献率分别达到70．6％和82．6％,表明由排除了主效抗病基因的感病株系组成的亚群体适合于进行部分抗性QTL定位。     

水稻白叶枯病抗性基因定位及其小种专化性

利用 3个致病性不同的水稻白叶枯病菌小种 ,对由Lemont/特青培育的 31 5个F₁₀ 重组自交系群体进行抗性基因 (QTL)RFLP分析 .共发现 1个主基因、1 0个QTL及 9对互作位点与白叶枯病菌抗性有关 .其中 ,主基因Xa4定位于第 1 1染色体上 .Xa4对CR4和CX0 8表现显性主基因遗传 ,但对CR6则表现为一个主要的加性QTL的作用 .主基因小种专化性明显大于QTL .QTL之间以及QTL与主基因之间效应累加 ,共同提供抗病性的强度和稳定性 .在感病亲本中 ,亦存在抗性QTL .因此 ,来源不同的中抗材料可能是水平抗性的良好基因源 .研究还表明 ,所定位的QTL与其他研究发现的抗不同病原菌的基因 (QTL)处于相近的染色体位置 ,意味着它们可能是同一抗性基因族的成员 .     

水稻条纹叶枯病抗性位点的检测和效应分析

利用111个家系组成的热研2号(Oryza sativa subsp. japonica ‘Reyan2’)/ Mi lyang23(Oryza sativa subsp. indica ‘Mi lyang23’)重组自交系(recombinant inbred l ines, RIL)群体(F7), 采用重病区田间自然接种方法, 以病情指数作为条纹叶枯病的表型值, 鉴定了2个亲本及111个RIL家系对条纹叶枯病的抗性。使用QTL Cartographer 软件复合区间作图法, 对水稻(Oryza a sativa)条纹叶枯病抗性基因进行了QTL分析。结果检测到2个抗水稻条纹叶枯病的QTL, 分别位于第2和第11染色体上, 其中第11染色体上的QTL贡献率为19.58%, 表明这是一个主效的QTL, 该QTL及其附近的分子标记, 可以用于水稻条纹叶枯病抗性分子标记辅助育种。     

水稻条纹叶枯病抗性位点的检测和效应分析

利用111个家系组成的热研2号（Oryza sativa subsp．japonica‘Reyan2’）／Milyang23（Oryza sativa subsp．indica‘Milyang23’）重组自交系（recombinant inbred lines,RIL）群体（F7）,采用重病区田间自然接种方法,以病情指数作为条纹叶枯病的表型值,鉴定了2个亲本及111个RIL家系对条纹叶枯病的抗性。使用QTL Cartographer软件复合区间作图法,对水稻（Oryza sativa）条纹叶枯病抗性基因进行了QTL分析。结果检测到2个抗水稻条纹叶枯病的QTL,分别位于第2和第11染色体上,其中第11染色体上的QTL贡献率为19．58％,表明这是一个主效的QTL,该QTL及其附近的分子标记,可以用于水稻条纹叶枯病抗性分子标记辅助育种。     

水稻籽粒维生素E QTL挖掘及候选基因分析

维生素E (V_E)是稻米营养品质的重要指标。水稻(Oryza sativa)是我国种植最广泛的粮食作物, 增加其籽粒的V_E含量是实现国民营养强化的一条便捷有效的途径。该研究以籼稻华占(HZ)为父本, 粳稻热研2号(Nekken2)为母本, 构建120个重组自交系(RILs)群体。采用高效液相色谱法(HPLC)对RILs群体的V_E各组分含量进行测定, 并基于构建的高密度分子遗传图谱进行QTL定位, 谱系分析后挖掘到122个V_E总量和分量相关QTLs, 分布在12条染色体上。其中qT3α/to2-1的LOD值高达10.32, qT3α2-1的LOD值高达9.91, 另有多个控制各异构体含量的主效QTLs, 且区间内包含OsGGR1、OsGGR2、OsTC及OsγTMT等V_E生物合成基因。通过qRT-PCR检测亲本中V_E合成基因的表达量, 发现在华占中候选基因的表达量均极显著高于热研2号, 推测这些基因的高表达是华占生育酚及生育三烯酚含量高于热研2号的原因。研究挖掘到的QTL数目较多, LOD值也较大, 为进一步筛选和培育高V_E含量的水稻新品种奠定了分子基础, 同时为揭示水稻V_E生物合成的分子调控机制提供了重要基因资源。     

水稻对白叶枯病和细菌性条斑病的抗性遗传研究进展

水稻白叶枯病和水稻细菌性条斑病是由稻黄单胞细菌(Xanthomonas oryzae)不同致病变种引起的两种最重要的水稻细菌性病害。发掘和利用抗性基因,培育抗病品种是防治这两种病害的最有效手段之一。本文分别综述了这两种高度相关的病害的抗性遗传研究进展,包括已发掘和利用的主效抗性基因特点及目前国内外对这两种病害的抗性QTL定位研究进展,为水稻抗白叶枯病和细菌性条斑病育种研究提供有用信息。     

水稻对白叶枯病Xanthomonas oryzae pv.Oryzae水平抗性的数量性状位点(QTL)定位

利用“Lemont/特青”重组自交系（RI）群体研究了水稻对白叶枯病致病菌株CR6的水平抗性。双亲和F1均为感病,重组自交系（RILs）的病斑长度（LL）为带有明显双向超亲的连续变异,显示出典型的多基因遗传特征。部分重组自交系（约占总数90％）对CR6表现高水平抗性（LL≤3cm）。利用由178个良好分离的RFLP标记构建的饱和连锁图,鉴定出11个数量形状位点（QTLs）和3对互作位点解释了RI群体的大部分病斑变异。抗性QTLs定位于水稻第2、3、4、8、9、10、11、12等8条染色体。在来自特青的Xa－4位点上检测到一个有很大加性效应的QTL。其余10个QTLs的抗性等位基因有7个来自特青,3个来自Lemont。研究结果表明多个数量性状位点和失效主基因（Xa－4）残效的累加效应构成了对白叶枯病水平抗性的遗传基础,是重要的抗性组成部分。可以预期在DNA标记的辅助下,这些数量性状位点与主效抗性基因的组合将使水稻品种具有持久抗病性。     

烟草品种Beinhart1000-1抗黑胫病基因的QTL定位

为研究烟草黑胫病不同亲本来源的抗性遗传规律,定位抗性基因位点,本研究利用抗黑胫病品种Beinhart1000-1构建了220个F2分离群体。通过病圃接种鉴定和遗传分析,确定Beinhart1000-1对烟草黑胫病的抗性由多基因控制。利用筛选到的70对稳定SSR引物对烟草黑胫病抗性进行了QTL分析,绘制了一张包含14条染色体的遗传连锁图谱,且定位到5个与烟草黑胫病抗性紧密相关的QTLs,分别在2、3、3、6、12号染色体上,其贡献率分别为6.2%、6.0%、6.7%、5.6%和5.1%。此结果使烟草黑胫病抗性研究进一步深入,推进了烟草黑胫病分子标记辅助选择。     

Genetic analysis of leaffolder resistance in rice

A double haploid(DH)population,which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid 'CJ06'/'TN1',was used to investigate the genetic basis for rice leaffolder resistance.Using a constructed molecular linkage map,five QTLs for rolled leaves were detected on chromosomes 1,2,3,4,and 8.The positive alleles from CJ06 on chromosomes 3,4,and 8 in-creased the resistance to rice leaffolder,and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolde...     

Mapping quantitative trait loci associated with arsenic accumulation in rice (Oryza sativa)

The quantitative trait loci (QTLs) associated with arsenic (As) accumulation in rice were mapped using a doubled haploid population established by anther culture of F1 plants from a cross between a Japonica cultivar CJ06 and an Indica cultivar TN1 (Oryza sativa). Four QTLs for arsenic (As) concentrations were detected in the map. At the seedling stage, one QTL was mapped on chromosome 2 for As concentrations in shoots with 24.4% phenotypic variance and one QTL for As concentrations in roots was detected on chromosome 3. At maturity, two QTLs for As concentrations in grains were found on chromosomes 6 and 8, with 26.3 and 35.2% phenotypic variance, respectively. No common loci were detected among these three traits. Interestingly, the QTL on chromosome 8 was found to be colocated for As concentrations in grain at maturity and shoot phosphorus (P) concentrations at seedling stage. These results provide an insight into the genetic basis of As uptake and accumulation in rice, and will be useful in identifying genes associated with As accumulation.     

Genetic analysis of leaffolder resistance in rice

A double haploid(DH)population,which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid'CJ06'/'TN1',was used to investigate the genetic basis for rice leaffolder resistance.Using a constructed molecular linkage map,five QTLs for rolled leaves were detected on chromosomes 1,2,3,4,and 8.The positive alleles from C J06 on chromosomes 3,4,and 8 in-creased the resistance to dee leaffolder,and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolder.The interactions between QTLs were identified and tested,and four conditional interactions were acquired for resistance to rice leaffolder.These loci were located on chromosomes 2,9,10,and 11,respectively.QTL pyramiding indicated that the positive alleles affect resis-tance to leaffolder.The prospective application of this data in rice breeding was also discussed.     

水稻叶片水势的QTL定位与候选基因分析

为探究叶片水势(LWP)相关基因在水稻(Oryza sativa)抗旱中的作用及其遗传机制,以热研2号(Nekken2)和华占(HZ)为亲本以及构建的120个重组自交系(RILs)群体为实验材料,对水稻分蘖期叶片水势进行检测,并利用前期基于高通量测序构建的分子遗传连锁图谱进行数量性状基因座(QTL)分析。结果表明,共检...     

Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid (DH) population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus (QTL) for three related traits of panicle-layer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniformity in two locations: Hangzhou (HZ) and Hainan (HN). A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH -4 and qTPH -8 were co-located with the QTLs for qLPH -4 and qLPH -8, which were only significant in the HZ environment, whereas the qTPH -6 and qLPH -6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD -10-1 and qPLD -10-2, were closely linked to qTPH-10 , and they might have been at the same locus. One QTL, qPLD -3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD -3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD -3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice.     

ARCHIPELAGO: a dedicated resource for exploiting past, present, and future genomic data on disease resistance regulation in rice

Large amounts of expression data dealing with biotic stresses in rice have been produced in the past 5 years. Here, we extensively review approximately 70 publications and gather together information on more than 2,500 genes of the rice defense arsenal. This information was integrated into the OryGenesDB database. Several genes (e.g., metallothioneins and PBZ1) appear to be hallmarks of rice-pathogen interactions. Cross-referencing this information with the rice kinome highlighted some defense genes and kinases as possible central nodes of regulation. Cross referencing defense gene expression and quantitative trait loci (QTL) information identified some candidate genes for QTL. Overall, pathogenesis-related genes and disease regulators were found to be statistically associated with disease QTL. At the genomic level, we observed that some regions are richer than others and that some chromosomes (e.g., 11 and 12), which contain a lot of resistance gene analogs, have a low content of defense genes. Finally, we show that classical defense genes and defense-related genes such as resistance genes are preferentially organized in clusters. These clusters are not always coregulated and individual paralogs can show specific expression patterns. Thus, the rice defense arsenal has an ARCHIPELAGO-like genome structure at the macro and micro level. This resource opens new possibilities for marker-assisted selection and QTL cloning.     

基于元分析的抗玉米丝黑穗病QTL比较定位

以玉米遗传连锁图谱IBM2 2005 Neighbors为参考图谱,通过映射整合不同试验中的抗玉米丝黑穗病QTL,构建QTL综合图谱。在国内外种质中,共发现22个抗病QTL,分布在除第7染色体外的9条玉米染色体上。采用元分析技术,获得2个“一致性”抗病QTL,图距分别为8.79 cM和18.92cM。从MaizeGDB网站下载“一致性”QTL区间内基因和标记的原始序列;采用NCBI网站在线软件BLASTx通过同源比对在2个“一致性”QTL区间内初步获得4个抗病位置候选基因。借助比较基因电子定位策略,将69个水稻和玉米抗性基因定位于玉米IBM2图谱上,在2个“一致性”QTL区间内分别发现1个水稻抗性基因,初步推断为抗病位置候选基因。本文结果为抗玉米丝黑穗病QTL精细定位和分子育种提供了基础。     

粳稻子预44中稻瘟病数量抗性位点分析

稻瘟病是世界范围内影响水稻(Oryza sativa)生产的主要病害。抗稻瘟病基因的发掘和育种利用是控制稻瘟病经济、环保的有效措施。为了揭示云南地方水稻品种子预44广谱持久抗瘟机制, 利用江南香糯和子预44杂交构建的F₇重组自交群体, 采用苗期稻瘟病菌自然诱发接种法, 通过调查田间抗瘟性表型数据, 结合基因型数据对子预44中的数量抗瘟性位点进行了分析。结果表明, 在连锁系数(logarithm of odds, LOD)大于2.0的域值上, 共检测出13个QTLs, 分别位于第1、2、6、8、12号染色体上。不同位点表型贡献值差异较大, 范围为5.8%-21.9%, 其中8号染色体上标记RM72-RM404之间的QTLs可解释约61.9%的表型变异, 很可能为一个主效抗瘟QTL位点。多个位点的主效和微效抗性相结合可能是子预44持久稻瘟病抗性的分子基础。