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。     

水稻条斑病抗性QTL的挖掘及相关基因的表达

条斑病是水稻(Oryza sativa)中的常见病害, 已经对我国粮食的高产稳产造成严重威胁。以典型籼稻台中本地1号与粳稻春江06的杂交F₁代花药培养双单倍体群体(DH)为材料, 用Xoc BLS256进行人工接菌, 对双亲及群体各株系的病斑长度进行测量和量化分析; 同时利用该群体业已构建的加密遗传图谱对病斑表型数据进行QTL作图分析。结果在水稻第2、4、5和8号染色体上共检测到4个效应值能区分开的QTL。对2号与5号染色体上2个较大的QTL区间内抗条斑病相关基因进行了表达分析, 结果表明这些基因在处理前后出现了不同程度的表达差异, 暗示这些基因可能是响应春江06与台中本地1号条斑病抗性差异的目标基因。研究结果为进一步克隆水稻条斑病抗性QTL奠定了重要基础。     

基于CSSL的水稻穗颈长度QTL的代换作图

水稻穗颈长度是影响杂交水稻制种产量提高的重要农艺性状之一。文章利用94个以籼稻品种9311为遗传背景、粳稻品种日本晴为染色体片段供体的覆盖全基因组的染色体片段置换系(Chromosome segment substi-tution lines, CSSL)为材料, 调查和分析CSSL群体及双亲的穗颈长度。结果表明: 在17个置换系中检测到8个控制水稻穗颈长度的数量性状位点(Quantitative trait loci, QTL), 分别位于第2、3、7、8、9和第11染色体; 利用代换作图法, 定位了其中的7个穗颈长度QTL; 其加性效应值介于0.10~3.20之间, 其中qPE-9和qPE-11的加性效应值较大, 平均效应值分别为3.15和2.95, 表现为主效基因特征; qPE-2-2、qPE-3-1、qPE-3-2、qPE-7和qPE-8等5个QTL被定位在小于10.0 cM的区段内。利用CSSL可以有效地鉴定水稻穗颈长度QTL, 这些QTL为分子标记辅助选育穗颈长度适中的水稻品系及其进一步的精细定位奠定了基础。     

图位克隆技术新型遗传学实验教学项目的设计与实践

染色体重组与连锁互换是遗传学教学的重点和难点。为使学生更好地理解此方面知识, 我们课题组前期利用图位克隆(map-based cloning)技术, 克隆了1个调控水稻(Oryza sativa)类病变表型的基因SPL5, 并基于此设计了一个新的综合型遗传学实验, 即利用DNA分子标记对基因进行定位。实验中学生利用水稻spl5突变体与野生型杂交获得的F₂代定位群体和多态性分子标记, 对spl5突变进行染色体连锁分析、初步定位和遗传作图。该教学实验不仅可有效促进学生对遗传学三大定律的理解, 而且对其开阔视野、提高解决问题和团队协作的能力也有促进作用。     

图位克隆技术新型遗传学实验教学项目的设计与实践

染色体重组与连锁互换是遗传学教学的重点和难点。为使学生更好地理解此方面知识, 我们课题组前期利用图位克隆(map-based cloning)技术, 克隆了1个调控水稻(Oryza sativa)类病变表型的基因SPL5, 并基于此设计了一个新的综合型遗传学实验, 即利用DNA分子标记对基因进行定位。实验中学生利用水稻spl5突变体与野生型杂交获得的F₂代定位群体和多态性分子标记, 对spl5突变进行染色体连锁分析、初步定位和遗传作图。该教学实验不仅可有效促进学生对遗传学三大定律的理解, 而且对其开阔视野、提高解决问题和团队协作的能力也有促进作用。     

玉米和水稻重要性状QTL的比较研究

在构建玉米分子标记连锁图和对重要性状进行QTL定位的基础上,以玉米和水稻的分子标记比较图谱为桥梁,分析了控制玉米和水稻F2：3群体重要农艺和产量性状QTL的共线性关系。研究结果表明：在玉米和水稻共线性的染色体区段,控制玉米株高、行数和行粒数的QTL与控制水稻株高、单株有效穗和每穗实粒数的QTL存在广泛的对应关系;在已定位的影响玉米株高等5个性状的45个QTL中,有16个与水稻“汕优63”群体中5个相同或相似性状所定位的38个QTL中的12个具有共线性关系。这一结果为利用水稻的基因组数据来定位、分离和克隆玉米重要性状的QTL提供了有益信息。同时发现,控制水稻某一个性状的QTL常常与控制玉米同一性状的两个QTL相对应,这一结果为玉米染色体是由水稻染色体加倍而来的理论假设提供了支持。研究还发现,不管是玉米还是水稻在染色体上都存在QTL的富集区域,而这些富集区域常常存在于相同的共线性区域,暗示着玉米和水稻控制相同或相似性状的QTL可能有着相同的起源。基于性状的比较基因组研究不但有助于新基因或QTL的发现、克隆和利用,同时还有助于研究不同物种间染色体的演变和进化规律。     

水稻籽粒γ-氨基丁酸含量的QTL定位分析

本研究以低含量γ-氨基丁酸的宁农黑粳为母本,高含量γ-氨基丁酸的高粱稻-1为父本,构建F2群体,获得了216个F2单株。利用130个SSR标记构建了一张F2群体的SSR标记连锁图谱,覆盖基因组长度为2406.9 cM,连锁群长度在129.5～360.7 cM之间,标记间的平均距离为18.5 cM,并进一步开展控制水稻γ-氨基丁酸含量的QTL定位研究。结果表明:共检测到7个QTL位点,分别位于第8号和第9号染色体上,其中qGABA8-2、qGABA8-3、qGABA9-1的贡献率依次为10%、11%和9%。对3个贡献率大的QTL位点进行复合区间作图,当LRS为25.6时,在RM342～RM515处可能存在较为可靠的QTL,初步将qGABA8定位在标记RM342与RM515之间的326 kb区间内。利用InDel标记对目标区间加密,将该区间进一步缩小到183 kb区间内,位于标记RM342和G121之间。本研究结果可进一步通过构建次级群体对该基因进行精细定位及图位克隆,同时,研究中筛选出的SSR标记和设计的InDel标记可快速筛选水稻育种材料中富γ-氨基丁酸的基因型,加快育种进程。     

作物数量性状基因图位克隆研究进展

对数量性状基因(QTL)的鉴定和克隆不仅有利于从分子水平上阐明作物重要农艺性状的形成机理,而且对于有效开展这些性状的分子育种,进一步提高作物增产潜力具有重要意义.近年来作物QTL图位克隆取得了重要突破,一批QTL被成功克隆,而模式植物基因组研究的快速发展则为作物QTL图位克隆技术带来了新的策略和方法.本文就相关研究的主要进展和发展趋势进行了综述.     

筛选和定位含水稻端粒相关序列的BAC克隆

根据水稻的端粒重复序列 ,设计了 2个引物 :(TTTAGGG) ₃ 和 (CCC TAAA) ₃ CCC ,利用单引物在水稻总DNA中进行PCR扩增 ,分别得到Tas1和Tas2 .这 2个片段在定位亲本间均无多态性 .Tas1的原位杂交表明该序列位于 2对染色体端部 .以Tas1为探针在所构建的水稻基因组BAC文库中筛选到 1个克隆 ,South ern杂交证明此克隆也包含序列Tas2 ,取该克隆中的单拷贝序列利用ZYQ/JX1 7DH群体将其定位在第 6号染色体的端部 .并对Tas1和Tas2在此克隆中的排列进行了初步研究     

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。     

An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL

Background

Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs) for QTL. Support interval (SI) methods based on the shape of the QTL likelihood curve have proven adequate for standard interval mapping, but have not been shown to be appropriate for use with composite interval mapping (CIM), which is one of the most commonly used QTL mapping methods.

Results

Based on a non-parametric confidence interval (NPCI) method designed for use with the Haley-Knott regression method for mapping QTL, a CIM-specific method (CIM-NPCI) was developed to appropriately account for the selection of background markers during analysis of bootstrap-resampled data sets. Coverage probabilities and interval widths resulting from use of the NPCI, SI, and CIM-NPCI methods were compared in a series of simulations analyzed via CIM, wherein four genetic effects were simulated in chromosomal regions with distinct marker densities while heritability was fixed at 0.6 for a population of 200 isolines. CIM-NPCIs consistently capture the simulated QTL across these conditions while slightly narrower SIs and NPCIs fail at unacceptably high rates, especially in genomic regions where marker density is high, which is increasingly common for real studies. The effects of a known CIM bias toward locating QTL peaks at markers were also investigated for each marker density case. Evaluation of sub-simulations that varied according to the positions of simulated effects relative to the nearest markers showed that the CIM-NPCI method overcomes this bias, offering an explanation for the improved coverage probabilities when marker densities are high.

Conclusions

Extensive simulation studies herein demonstrate that the QTL confidence interval methods typically used to positionally evaluate CIM results can be dramatically improved by accounting for the procedural complexity of CIM via an empirical approach, CIM-NPCI. Confidence intervals are a critical measure of QTL utility, but have received inadequate treatment due to a perception that QTL mapping is not sufficiently precise for procedural improvements to matter. Technological advances will continue to challenge this assumption, creating even more need for the current improvement to be refined.     

作物数量性状基因研究进展

分子生物技术的发展对作物数量性状基因（QTL）研究提供了条件,不同的定位群体各有其特点,相继出现的QTL定位也逐步完善。大量的研究揭示了QTL的基本特征,剖析了重要农艺4性状的遗传基础,给作物遗传改良带来了新的策略,不断深入的研究已经完成了特定的QTL的精细定位和克隆。本从QTL的定位群体,定位方法,研究现状,精细定位与克隆,以及QTL利用等方面对作物数量性状基因的研究进行了综述。     

Plant molecular diversity and applications to genomics

Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.     

控制玉米雄穗分枝数目和雄穗重的主效QTL的定位

利用2套具有共同亲本黄早四且分别含有230个及235个家系的F_2:3群体, 结合2年多点的表型鉴定, 运用完备复合区间作图方法对不同生态环境下(2007-北京、2008-北京、2007-河南、2008-河南、2007-新疆以及2008-新疆)的玉米雄穗分枝数和雄穗重进行QTL定位。同时, 利用基于混合线性模型的QTLNetwork-2.0软件进行基因×环境互作及上位性分析。6个环境下2个群体共检测到51个与雄穗分枝数和雄穗重相关的QTL(Q/H群体32个, Y/H群体19个), 其中包括7个主效QTL, 并在Q/H群体中确定了2个重要的QTL, 即位于7.01bin的Qqtpbn7-1和位于7.02bin的Qqtw7-2。对比2个群体的定位结果, 共挖掘到3个在不同遗传背景下的“一致性”QTL, 这些在不同环境及不同遗传背景下能够稳定存在的QTL可为玉米雄穗相关性状的生产应用以及精细定位提供有价值的参考。     

Identification of quantitative trait loci for physical and chemical properties of rice grain

Quantitative trait loci (QTL) associated with six physical traits of cooked rice and seven chemical properties of rice grain were identified using a recombinant inbred (RI) population of rice evaluated over 3 years at the National Honam Agricultural Research Institute in Korea. The RI population consisted of 164 lines derived from a cross between Milyang23 and Gihobyeo, and the genetic map consisted of 414 molecular markers. A total of 49 QTL were identified for the 13 physico-chemical properties using composite interval mapping. Of these, 13 QTL were identified for 2 or more years, while 36 were detected in only 1 year. Five QTL were identified over all 3 years and will be useful for marker-assisted improvement of rice grain quality in Korea. The two QTL with the highest LOD scores, adhesiveness1.2 and potassium content7.1, provide a valuable starting point for positional cloning of genes underlying these QTL.     

Identification of chromosomal regions associated with growth and carcass traits in an F3 full sib intercross line originating from a cross of chicken lines divergently selected on body weight

An F₃ resource population originating from a cross between two divergently selected lines for high (D+ line) or low (D− line) body weight at 8-weeks of age (BW55) was generated and used for Quantitative Trait Locus (QTL) mapping. From an initial cross of two founder F₀ animals from D(+) and D(−) lines, progeny were randomly intercrossed over two generations following a full sib intercross line (FSIL) design. One hundred and seventy-five genome-wide polymorphic markers were employed in the DNA pooling and selective genotyping of F₃ to identify markers with significant effects on BW55. Fifty-three markers on GGA2, 5 and 11 were then genotyped in the whole F₃ population of 503 birds, where interval mapping with GridQTL software was employed. Eighteen QTL for body weight, carcass traits and some internal organ weights were identified. On GGA2, a comparison between 2-QTL vs. 1-QTL analysis revealed two separate QTL regions for body, feet, breast muscle and carcass weight. Given co-localization of QTL for some highly correlated traits, we concluded that there were 11 distinct QTL mapped. Four QTL localized to already mapped QTL from other studies, but seven QTL have not been previously reported and are hence novel and unique to our selection line. This study provides a low resolution QTL map for various traits and establishes a genetic resource for future fine-mapping and positional cloning in the advanced FSIL generations.     

Interval-specific congenic strains (ISCS): An experimental design for mapping a QTL into a 1-centimorgan interval

A general experimental design that allows mapping of a quantitative trait locus (QTL) into a 1-cM interval is presented. The design consists of a series of strains, termed ``interval-specific congenic strains (ISCS)'. Each ISCS is recombinant at a specific 1-cM sub-interval out of an ordered set of sub-intervals, which together comprise a wider interval, to which a QTL was previously mapped. It is shown that a specific and previously detected QTL of moderate or even small effect can be accurately mapped into a 1-cM interval in a program involving a total of no more than 1000 individuals. Consequently, ISCS can serve as the ultimate genetic mapping procedure before the application of physical mapping tools for positional cloning of a QTL. Received: 2 August 1996 / Accepted: 28 October 1996     

Mapping of QTL for resistance to the Mediterranean corn borer attack using the intermated B73 × Mo17 (IBM) population of maize

The Mediterranean corn borer or pink stem borer (MCB, Sesamia nonagrioides Lefebvre) causes important yield losses as a consequence of stalk tunneling and direct kernel damage. B73 and Mo17 are the source of the most commercial valuable maize inbred lines in temperate zones, while the intermated B73 × Mo17 (IBM) population is an invaluable source for QTL identification. However, no or few experiments have been carried out to detect QTL for corn borer resistance in the B73 × Mo17 population. The objective of this work was to locate QTL for resistance to stem tunneling and kernel damage by MCB in the IBM population. We detected a QTL for kernel damage at bin 8.05, although the effect was small and two QTL for stalk tunneling at bins 1.06 and 9.04 in which the additive effects were 4 cm, approximately. The two QTL detected for MCB resistance were close to other QTL consistently found for European corn borer (ECB, Ostrinia nubilalis Hübner) resistance, indicating mechanisms of resistance common to both pests or gene clusters controlling resistance to different plagues. The precise mapping achieved with the IBM population will facilitate the QTL pyramiding and the positional cloning of the detected QTL.     

控制玉米雄穗分枝数目和雄穗重的主效QTL的定位

利用2套具有共同亲本黄早四且分别含有230个及235个家系的F2：3群体,结合2年多点的表型鉴定,运用完备复合区间作图方法对不同生态环境下（2007-北京、2008-北京、2007-河南、2008-河南、2007-新疆以及2008-新疆）的玉米雄穗分枝数和雄穗重进行QTL定位。同时,利用基于混合线性模型的QTLNetwork-2.0软件进行基因×环境互作及上位性分析。6个环境下2个群体共检测到51个与雄穗分枝数和雄穗重相关的QTL（Q/H群体32个,Y/H群体19个）,其中包括7个主效QTL,并在Q/H群体中确定了2个重要的QTL,即位于7.01bin的Qqtpbn7-1和位于7.02bin的Qqtw7-2。对比2个群体的定位结果,共挖掘到3个在不同遗传背景下的＂一致性＂QTL,这些在不同环境及不同遗传背景下能够稳定存在的QTL可为玉米雄穗相关性状的生产应用以及精细定位提供有价值的参考。     

植物数量性状基因的定位与克隆

作物的许多重要农艺性状属于数量性状, 鉴定和发掘控制数量性状的基因及其优异的等位变异, 并使之快速应用于育种实践是新时期作物科学家和育种学家所面临的重大课题。本文从QTL作图、QTL的精细定位与图位克隆、QTL近等基因系和染色体片断代换系的建立以及基于LD的关联分析等方面对植物数量性状的研究进展进行了讨论, 提出了以植物基因组学技术为平台, 将QTL作图与关联分析方法相结合, 是进行数量性状遗传机理研究同时服务于作物育种实践的有效途径。