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双语推荐：数量性状位点

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基因组学研究的主要目标是剖析复杂性状和疾病的遗传结构.数量性状位点(quantitative trait locus,QTL)定位和全基因组关联分析(genome-wide association study,GWAS)已经应用于遗传育种和药物研制,分析复杂性状和复杂疾病的遗传结构.本文回顾了分析复杂性状和复杂疾病的QTL定位和GWAS的作图方法和软件.PLINK,TASSEL,SNPassoc,GenABEL和ProbABEL是流行的软件,为GWAS提供了许多有用的功能.PLINK是目前最流行的开源全基因组关联分析的工具集,它聚合了用于分析SNP数据的许多功能.TASSEL是另一种流行的软件,整合了Q+K关联分析的诸多方法.SNPassoc、GenABEL和ProbABEL是应用于关联分析的开源代码R软件包.本文对上述提及的GWAS关联分析流行软件作了简要介绍,并介绍了新研制的QTXNetwork分析软件,它可分析QTL和GWAS定位数量性状SNP(QTS)、数量性状转录子(QTT)、数量性状蛋白子(QTP)和数量性状代谢子(QTM).本文还介绍了一些常用的分析软件,例如Windows QTL Cartographer,QTL Express,Map Manager QTX,R/qtl和QTLNetwork.
One of the key objectives in genomics studies is to understand genetic architecture of complex traits and diseases . Quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) mapping have been using to dissect genetic architecture of complex traits and diseases that assists in genetic breeding and drug discovery . In this paper , we reviewed QTL mapping and GWAS mapping methodologies and softwares for complex traits or diseases analysis . PLINK , TASSEL , SNPassoc , GenABEL and ProbABEL are most popular softwares providing many useful functions for GWAS mapping . PLINK is the highest popular open-source whole genome association analysis toolset , which implements a number of functions for SNP data analysis . TASSEL is another popular software , implements Q+K composite approach for association mapping . SNPassoc , GenABEL and ProbABEL are popular open source R packages using for association mapping . We have briefly described above popular softwares for GWAS mappi

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建立表达数量性状位点(eQTLs)与全基因组关联研究(GWAS)相结合的方法,可以为人类复杂疾病的病因学和复杂性状研究提供进一步的功能信息。在探索疾病的转录组,细胞的生长动态过程,人群的起源和多样化拟表型方面,这一方法,也为人们提供了一种较好的,有助于理解疾病发生机制和人类基因调控格局的研究手段。本综述将介绍在基因组时代eQTLs的应用及其意义。
Approaches that combine expression quantitative trait loci (eQTLs)and genome-wide association(GWA)studies are of-fering further functional information about the aetiology of complex human diseases and complex traits .These approaches-which take into account technological advances in resolving the transcriptome ,cell history and state ,population of origin and diverse endopheno-types-are providing better reach teqchniques to help us understand the architecture of disease and the landscape of gene regulation in humans.This review will introduce the application and significance of eQTLs on genome era.

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为了利用关联分析发掘与重要农艺性状相关的数量性状基因位点，本研究采用全基因组扫描的方法，利用分布在基因组上的60对SSR引物，对140份东北三省水稻种质资源进行群体结构和连锁不平衡分析。结果表明：本研究中东北粳稻可分为2个类群，线性和非线性组合中，都有一定的连锁不平衡存在。群体中，19．2％的标记位点可以观察到显著的LD（P〈0．05），其中第一类群和第二类群基于D’统计概率（P〈0．05）支持的LD成对位点比例分别为2．1％和16．6％。第2类群连锁不平衡衰减（D’〈0．5）所延伸的遗传距离变幅为0．32—120．4cM，回归方程为：y=-0．0276ln（x）＋0．3994。
To discover quantitative trait loci related to important agronomic traits via association analysis, popula-tion structure and linkage disequilibrium ( LD ) of 140 rice germplasm resources from northeast provinces were analyzed with 60 SSR markers located on chromosomes in this study. The results indicated that the population of japonica rice in northeast could be classified into 2 groups, and LD in the linear and non-linear combination occurred commonly. 19.2%of the SSR loci pairs significantly showed LD at P<0.05, where the sites based on D'' linkage disequilibrium of group 1 and group 2 were 2.1%and 19.1%, respectively. LD of second group was found to decay across a range from 0.32 to 120.4 cM, and the regression equation was y=-0.0276ln(x)+0.3994.

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为进一步增加特异性分子标记，填补棉花遗传图谱密度空隙，挖掘与纤维品质紧密相关的数量性状位点（QTLs）以陆地棉（Gossypium hirsutum L．）中棉所8号和海岛棉（Gossypium barbadense L．） Pima90杂交产生的 F2群体为材料，利用 SSR 标记对构建棉花遗传图谱及纤维品质性状 QTLs 定位进行研究。结果表明：构建了包含15个连锁群和102个标记位点（其中25个标记位点前人未曾报道）的连锁图谱，图谱总长642．1 cM，约占棉花基因组的14．4％，标记间平均距离为6．3 cM。15个连锁群中的6个分别被定位于5条染色体上，9个连锁群未定位于染色体上。应用复合区间作图法分析 F2单株和 F2∶3家系的纤维品质性状，检测到11个与纤维品质有关的 QTLs，包括 2个纤维长度（FL），4个马克隆值（FM），3个比强度（FS），2个伸长率（FE），分别解释表型变异的19．1％～24．8％、8．9％～16．9％、11．8％～19．0％和12．2％～34．3％。
In order to increase the linkage map markers of cotton,so as to fill the gap of genetic map density,and detect the QTLs related to fiber qualities,An F2 population from a cross between CRI 8 (Gossypium hirsutum)and Pima 90 (Gossypium barbadense )was used to construct the linkage map with simple sequence repeat (SSR).Results:This map included 102 markers distributing on 15 linkage groups (25 markers is not reported),covering 642.1cM,accounting for 14.4% of the cotton genome,and with an average distance of 6.3 cM between two markers.six out of 15 linkage groups were located on five chromosomes,and nine linkage groups were not located on any chromosomes.The fiber quality of the F2 plants and the F2∶3 family lines were analyzed by composite interval mapping and 11 quantitative trait loci of fiber quality were identified in the genetic map and these traits involved the QTLs of two fiber lengths, four fiber micronaires,three fiber strengths,two fiber elongations.The QTLs separatel

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通过运用灰色关联分析方法对国家棉花品种区域试验中的参试品种（系）邯郸点试验数据进行了主要数量性状与皮棉产量分析。结果表明：对棉花品种皮棉产量影响较大的因素是单株结铃数和衣分，各个因素对皮棉产量的影响程度依次为：单株结铃数〉衣分〉霜前花率〉始果枝节位〉单铃重〉果枝数〉株高〉籽指。
Main quantitative traits and lint yield were analyzed by grey correlation analysis in new cotton variety . The re-sults showed that :the numbers of bolls per plant and ginning outturn were the bigger influence factors to lint yield . The influ-ence degree to lint yields of every factor was as follows :the number of bolls per plant > ginning outturn > pre - frost yield > the first node of fruit branch > single boll weight > fruit branch number > stem height > seed index.

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以南方籼型杂交稻恢复系泸恢99和北方粳型超级稻沈农265杂交衍生的重组自交系群体(recombinant inbred lines, RILs)为试验材料,对株型性状(株高、穗长、分蘖和叶片性状)进行不同环境下的数量性状基因位点(quantitative trait locus, QTL)分析。共检测到39个相关 QTL,分布在水稻第1、第2、第3、第6、第7、第8和第9染色体上, LOD值介于2.50~16.90之间,有11个 QTL 能在两年中被检测到。株型相关的 QTL 在染色体上成簇分布,主要分布于第1、第6和第9染色体上,这可能与株型性状间显著或极显著相关有关。其中,在第9染色体上 RM3700B–RM7424区间存在1个 QTL 簇,含4个 QTL,即 qPH9、qPL9、qFLL9和 qSLL9,这4个 QTL 在2年中均被检测到。此外,进一步鉴定出5个能稳定表达的 QTL,其中, qPH8、qFLW6和 qSLW6效应较大。这些信息综合反映了株型相关性状遗传的复杂性,有助于更全面地了解和掌握株型性状的遗传基础。
A recombinant inbred lines (RILs) derived from the across between indica restorer line Luhui 99 and super japonica cultivar Shennong 265, was used to analyze the quantitative trait loci (QTLs) for plant height, panicle length, tillers, and leaf traits in 2012 and 2013. A total of 39 QTLs were detected on chromosomes 1, 2, 3, 6, 7, 8, and 9 with LOD score ranging from 2.50 to 16.90. Eleven of them were detected in both 2012 and 2013. Moreover, QTL clusters were detected on chromosomes 1, 6, and 9, which may be related to significant or highly significant correlations between plant type traits. Among them, the QTL cluster on chromosome 9 contained four QTLs, qPH9, qPL9, qFLL9, and qSLL9 in the interval between RM3700 and RM7424, and the four QTLs were detected in both years. In addition, five major QTLs were first reported, among which three QTLs (qPH8, qFLW6, and qSLW6) had the larger effect. The results facilitate further understanding of the genetic basis for plant height, p

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利用籼稻保持系骨干亲本岗46B与美国水稻品种Lemont多次回交培育的低垩白、窄粒株系K1075与岗46B构建F2群体,对稻谷粒长、粒宽、长宽比、粒厚、百粒重和垩白粒率进行数量性状位点(QTL)分析。6个性状在F2群体中均呈正态连续分布,属于典型的数量性状。除粒长与百粒重间没有显著相关性外,其他性状间均存在显著的正相关或负相关。采用SSR标记构建遗传连锁图,通过复合区间作图法共检测到14个控制稻谷粒形和垩白的QTL,包括2个控制粒长的QTL(qGL2和qGL5),2个控制粒宽的QTL(qGW5和qGW8),5个控制长宽比的QTL(qLWR2、qLWR5、qLWR6、qLWR8和qLWR12),1个控制粒厚的QTL(qGT5),1个控制百粒重的QTL(qHGW5)和3个控制垩白粒率的QTL(qPGWC5、qPGWC6和qPGWC8)。在这些位点中,岗46B等位基因增加粒宽、粒厚、粒重和垩白粒率,减小粒长和长宽比。控制粒宽、粒厚、粒重、垩白粒率和长宽比的主效QTL均位于第5染色体RM17990-RM18004-RM18068区间,这一结果与仅选择极端表型单株,采用连锁及连锁不平衡方法(LD)获得的结果一致。
To identify the genetic loci that control grain length,width,length-width ratio,thickness,100-grain weight and the percentage of grains with chalkiness (GL,GW,LWR,GT,HGW,PGWC),we constructed an F2 population by crossing an elite indica maintainer line Gang 46B(G46B)with K1075 ,an introgression line of G46B derived from multi-backcross with an US rice variety Lemont, with low percentage of chalkiness and narrow grain.All six investigated traits followed a continuous phenotypic distribution.Significantly positive or negative correlations were observed between all six traits,except the GL and GW.A genetic map was constructed with 30 simple sequence repeat (SSR)markers and a total of 14 QTLs for grain shape and chalkiness were detected by composite interval mapping (CIM).Among which,two were for GL (qGL2 and qGL5 ),two for GW (qGW5 and qGW8 ),five for LWR (qLWR2 ,qLWR5 ,qLWR6 ,qLWR8 and qLWR12 ),one for GT (qGT5 ),one for HGW (qHGW5 ),and three for PGWC (qPGWC5 ,qPGWC6 and qPGWC8 ).The G46

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选择已经获得的8个与大口黑鲈(Micropterus salmoides)生长性状相关的分子标记,其中4个单核苷酸多态性标记分别位于IGF-I、POU1F1、PSSIII和MSTN基因上,4个微卫星位点分别是JZL60、JZL67、MisaTpw76和MisaTpw117。从养殖群体中筛选出具有4个以上优势基因型数量的大口黑鲈亲鱼20尾进行群体繁殖,其中雌鱼9尾,雄鱼11尾。所产子代进行同塘饲养,9月龄时随机挑选288尾进行体质量测量与STR基因分型。结果显示:子代体质量为103~401 g,含有生长优势基因型的数量在1~6之间,含有1~6个生长优势基因型的个体其平均体质量依次为227.83、239.56、258.81、273.02、302.50和305.60 g,生长优势基因型的数量与大口黑鲈生长速度呈正相关。进一步分析表明子代中优势基因型的平均数量为2.99,相比亲本群体的优势基因型平均数量(2.36)得到提高。研究结果说明,利用有限的与生长相关的优势基因型进行聚合可以获得具有优良生长性状的大口黑鲈,也为下一步大口黑鲈分子标记辅助育种提供理论依据。
Gene pyramiding is a method of obtaining good varieties, which aims to produce individuals with one supe-rior economic trait, according to the optimal breeding scheme involving selection of favorable target alleles or linked markers after crossing basal populations and pyramiding them into a single individual. The largemouth bass (Microp-terus salmoides) is one of the most important freshwater fish in China. Previous research identified certain molecular markers related to growth traits. In this study, eight molecular markers including four single nucleotide polymorphisms (SNPs) and four simple sequence repeats (SSRs) related to the growth traits of largemouth bass were selected to amplify the genomic DNA of parent largemouth bass. The four SNPs were located in the IGF-I, POU1F1, PSSIII and MSTN genes;the four SSRs were located in the JZL60, JZL67, MisaTpw76 and MisaTpw117 genes. Twenty large mouth bass (9 females, 11 males) containing four or even more advantageous genotypes were sele

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【目的】黄瓜是世界十大蔬菜之一，单性结实是与黄瓜产量和品质密切相关的重要性状。对黄瓜单性结实进行研究，探明全雌性单性结实性状的遗传规律，并进行 QTL 定位，为进一步了解其分子机理和标记辅助育种奠定基础，也为黄瓜单性结实性状改良提供理论依据。【方法】试验采用对单株主、侧蔓各夹8朵雌花，待所有单株夹花结束后8—10 d 一次性调查单性结实座瓜的方法，通过计算单性结实百分率（单性结实瓜数/所夹雌花数×100%）来评价单性结实能力。利用全雌单性结实材料 EC1和雌雄同株非单性结实材料8419、14519分别构建的F2群体进行遗传分析。以 EC1×8419杂交得到的部分 F2为作图群体，利用9930和 gy14黄瓜全基因组测序开发的1335对 SSR 标记和双亲重测序开发的143对 Indel 标记引物进行多态引物筛选，采用 JionMap4.0软件进行遗传图谱构建，以该配组 F2﹕3家系群体为研究对象，利用 WinQTLcart2.5软件进行单性结实 QTL 检测。运用生物信息学的分析方法对初定位主效 QTL 区间进行候选基因分析。【结果】试材 EC1的单性结实遗传符合数量性状的特征，但与不同材料配组的后代群体分离偏向不同亲本。构建了一张含有7条染色体、116个 SSR 标记和9个 Indel 标记的连锁图谱，图谱总长度为802.9 cM，标记间平均距离6.3 cM。共检测到7个与单性结实相关的 QTL，分别为Parth1、Parth2-1、Parth2-2、Parth3-1、Parth3-2、Parth5、Parth7，分布在1、2、3、5、7染色体上。其中仅 Parth2-1在春、秋两季中均被检测到，LOD 值分别为9.0和6.2，贡献率为17.4%和10.2%，位于标记SSR00684-SSR22083之间，认为是控制单性结实的主效 QTL 位点。该区段的遗传距离为17.1 cM，物理距离2.9 Mb，包含307个基因，推测参与植物激素信号转导的基因 Csa2M035330.1和 Csa2M070880.1是与单性结实相关性较大的候选基因。其他位点都为微效位点。【结论】单性结实的遗传符合数量性状特征，位于2号染色体上的 Parth2-1是控制黄瓜单性结实性状的主效 QTL 位点。推测植物激素代谢通路中的基因是可能的候选基因。研究结果为单性结实主效基因的精细定位和克隆及分子标记辅助育种奠定了基础。
[Objective]Cucumber is one of the ten vegetables in the world and parhenocarpy is an important trait closely related to production and quality of cucumber. To explore the inheritance and QTL mapping for parthenocarpy in cucumber could provide a preliminary basis for further study on mechanism of parthenocarpy and molecular assistant selection breeding, and lay a theoretical foundation for breeding of parthenocarpy.[Method]In this study, The authers clipped eight female flowers on main stem and branches, respectively, for every individual plant and investigated parthenocarpic fruit once when all plants treament finished 8-10 days later to calculate the parthenocarpy percentage (numbers of parthenocarpis fruit/numbers of clipped female flower) in order toevaluate parthenocarpy ability. Two F2 progenies derived from two crosses between EC1, a gynoecious parthenocarpic line, and two monoecious non-parthenocarpic lines 8419 and 14519 were constructed to determine the inheritance o

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以郑58×PH4CV杂交种构成的6个世代群体为试验材料，在玉米灌浆期，取正常生长玉米植株以穗位处作为着力点测定与地面夹角呈60°时拉力。通过P1、P2、F1、F2、B1、B2共6个世代联合分析法，以玉米茎秆拉力为性状，研究控制玉米茎秆倒伏性的基因遗传分离规律。结果表明，分离世代F2和B1群体茎秆拉力数值呈多峰分布，并有一个主峰表现明显，B2群体茎秆拉力数值频率主要呈多峰分布。玉米茎秆拉力强度遗传为多基因数量性状控制，多基因遗传率较高，达到96.12%，说明要选育茎秆拉力强度较高的品系，基础试材非常关键，而且要注重早代试材的筛选。
Six generations of maize hybrids from Zheng58 ×PH4CV were used in the study, it took the normal growth plant located in ear as a point of pull strength measurement with ground in sixty angle in grouting period. F1, F2, B1, B2, P1 and P2 were used to study the inheritance of maize stem lodging with joint analysis of multiple generations. The results showed that maize stem pull strength tolerance trait presented multi-peak distribution in the F2 and B1 population and a peak performance obviously, a multi-peak distribution in B2 populations, indicated that the trait was quantitative in nature and controlled by polygene. The effects were important on maize stem lodging inheritance, and should be paid more attention in maize breeding.

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