QTL analysis of trichome-mediated insect resistance in potato

Genetic mapping of several components of a complex type of insect resistance has been undertaken as a means toward more efficient use of the valuable characteristics of a wild relative of potato. RFLP maps constructed on interspecific diploid progenies of Solanum tuberosum × S. berthaultii were used in conjunction with morphological, biochemical and biological phenotyping to identify quantitative trait loci (QTLs) contributing to trichome-mediated insect resistance. By superimposing QTL data for a wide range of phenotypes including biochemical assays, correlative and direct screens for insect resistance, and adaptation to the target environment on the genetic maps, we have addressed the organization, action and interaction of genes controlling the resistance mechanism. The outcome contributes to an understanding of the association between component traits and between desirable and undesirable features of the donor species generated in an applied breeding program. Research is proceeding toward the development of selectable markers for the introgression and transfer of this resistance among potato gene pools.     

QTL analysis of pest resistance in the wild tomato Lycopersicon pennellii: QTLs controlling acylsugar level and composition

Some accessions of Lycopersicon pennellii, a wild relative of the tomato Lycopersicon esculentum, are resistant to a number of important pests of cultivated tomato due to the accumulation of acylsugars, which constitute 90% of the exudate of type-IV trichomes in L. pennellii LA716. An interspecific F₂ population, created by the cross L. esculentum x L. pennellii LA 716, was surveyed for acylsugar accumulation and subjected to RFLP/QTL analysis to determine the genomic regions associated with the accumulation of acylglucoses, acylsucroses, and total acylsugars, as well as with acylglucoses as a percentage of total acylsugars (mole percent acylglucoses). Data were analyzed using MAPMAKER/QTL with and without a log₁₀ transformation. A threshold value of 2.4 (default value for MAPMAKER/QTL) was used, as well as 95% empirically derived threshold values. Five genomic regions, two on chromosome 2 and one each on chromosomes 3, 4 and 11, were detected as being associated with one or more aspects of acylsugar production. The L. esculentum allele is partially dominant to the L. pennellii allele in the regions on chromosomes 2 and 11, but the L. pennellii allele is dominant in the region on chromosome 3. Throughout this study, we report the comparative effects of analytical methodology on the identification of acylsugar QTLs. Similarities between our results and published results for the genus Solanum are also discussed.R. W. Doerge · S.-C. Liu · J. P. Kuai contributed equally to the paper, and we ordered randomly     

玉米RFLP连锁图谱构建及大斑病QTL定位

玉米大斑病菌存在有生理小种分化的现象,目前5个已定名的生理小种在我国均已发现,还有一些尚未定位名的新类群也出出现,提高玉米对大斑病的抗性,只有提高数量抗性才能达到目的,为了弄清楚玉米对大斑病数量抗性的基因数目及效效应,利用抗病自交5系P138和感病自交系缩3为亲本构建了F2：3家系群体,采用RFLP标记构建了包含了124个标记的玉米RFLP连锁图,覆盖玉米基因组1999．8cM,标记间平均距离为16．5cM,定位了玉米大斑病的病斑长,病斑宽和病斑面积的QTL分别为3、3、2个,其联合贡献率分别为58．1％、71．5％和27．5％,没有检测到病斑数／叶的QTL,其表现为单基因或者寡基因控制的性状,研究结果增加了对玉米大斑病的认识,对玉米抗大斑病育种具有重要的指导意义。     

Epistatic expression of quantitative trait loci (QTL) in soybean [Glycine max (L.) Merr.] determined by QTL association with RFLP alleles

Quantitative trait values for seed oil and protein content or for maturity were measured in recombinant inbred lines (RIL) of soybean derived from a cross between two soybean cultivars: Minsoy PI 27890 and Noir 1 PI 290136. Seed oil was found to be inversely correlated to protein content. By analyzing DNA from plants with extreme phenotypes, we were able to identify quantitative trait loci (QTL) for these traits as being linked to several restriction fragment length polymorphism (RFLP) loci, including R183 for oil and protein content and R79 for maturity. Cumulative distributions of trait values were graphed for those RIL with Minsoy alleles and for those with Noir 1 alleles. As already suggested by the alleles found associated with extreme phenotypes, the distributions were consistent with an independent and additive expression of the maturity QTL linked to R79. That is, the cumulative distributions for plants with Minsoy alleles and for plants with Noir 1 alleles were similar in shape, but the entire Noir 1 curve had been shifted to later maturity dates. In contrast, the trait distributions for a locus affecting oil and protein content linked to R183 were not compatible with an additive model. These results suggest that this approach can be used for rapid identification of QTLs with epistatic expression.     

Genetic models to estimate additive and non-additive effects of marker-associated QTL using multiple regression techniques

Summary The development of molecular markers has recently raised expectations for their application in selection programs. However, some questions related to quantitative trait loci (QTL) identification are still unanswered. The objectives of this paper are (1) to develop statistical genetic models for detecting and locating on the genome multi-QTL with additive, dominance and epistatic effects using multiple linear regression analysis in the backcross and F_n generations from the cross of two inbred lines; and (2) to discuss the bias caused by linked and unlinked QTL on the genetic estimates. Non-linear models were developed for different backcross and F_n generations when both epistasis and no epistasis were assumed. Generation analysis of marked progenies is suggested as a way of increasing the number of observations for the estimates without additional cost for molecular scoring. Some groups of progenies can be created in different generations from the same scored individuals. The non-linear models were transformed into approximate multivariate linear models to which combined stepwise and standard regression analysis could be applied. Expressions for the biases of the marker classes from linked QTL were obtained when no epistasis was assumed. When epistasis was assumed, these expressions increased in complexity, and the biases were caused by both linked and unlinked QTL.     

应用二种定位法比较不同世代水稻产量性状QTL的检测结果

应用珍汕97B／密阳46的F2和重组自交系（RIL）群体,建立RFLP连锁图,检测控制稻谷产量及其5个构成因子的QTL。结果表明,具有较大加性效应者,能同时在F2和RIL群体中检测到。而且,在重组自交系群体中,发现设重复的表型鉴定与基于单株的表型鉴定,对效应较高的QTL的检测影响不大。     

Use of QTL analysis in physiological research

Quantitative trait locus (QTL) analysis is a powerful approach to map and subsequently identify genes involved in complex traits. Here we describe the basic principles and recent achievements of this method, and its application in physiological research in plants. The rapidly increasing amount of molecular and “omics” data and genetic resources and tools, in model species (Arabidopsis) and crops, will greatly support and stimulate the use of this approach in the near future. Published in Russian in Fiziologiya Rastenii, 2007, Vol. 54, No. 1, pp. 15–21. The text was submitted by the authors in English.     

水稻子粒硒含量的遗传及QTL检测

富硒功能水稻具有富硒、优质、保健、防病、安全等特点,已成为当前研究的热点。子粒硒含量的QTL定位对研究富硒功能水稻的遗传育种具有重要的意义。以籼稻亲本奉新红米和明恢100杂交的145个株系的F2群体构建遗传连锁图谱,图谱拟合92个SSR标记位点,覆盖水稻基因组2187.5 cM,标记间平均遗传距离为23.7 cM,占水稻全基因组的49.2%。采用复合区间作图法,对水稻子粒硒含量进行QTL分析,在第5染色体上共检测到2个新的水稻子粒硒的QTL,对表型变异的贡献率分别为6.39%、8.01%。     

水稻QTL分析的研究进展

水稻许多重要的性状是由多基因控制的数量性状,经典的数量遗传学只能把数量性状作为一个整体进行研究。近年来．高密度分子标记连锁图的构建和有效的生物统计学方法的发展使人们对数量性状遗传基础的研究出现了革命性的变化。通过对不同群体内的个体或品系的分子标记基因型和表型数据的共分离分析,能对QTL进行检测和定位。本文对QTL定位的原理和方法进行了介绍,从QTL的数目和效应、上位性效应、QTL基因型与环境的互作、相关性状的QTL以及个体发育不同阶段的QTL等方面对水稻QTL分析的研究进展进行了综述。水稻基因组测序计划已经完成,本文还对基因组时代水稻QTL精细定位和克隆的方法进行了探讨,对QTL分析在水稻育种中的应用前景进行了展望。     

作物耐旱性QTL定位和分析的思路

干旱是非生物胁迫中对作物生长和产量影响最严重的胁迫之一.作物的耐旱性受数量性状位点(QTL)的控制,存在复杂的基因/QTL互作和与环境的互作.对作物耐旱相关性状QTL进行定位和分析是耐旱研究的重点之一.本文通过对目前研究中涉及到的作物耐旱性特点、耐旱QTL分析的技术路线与新方法,表型鉴定以及耐旱性QTL互作分析等方面进行了比较系统的阐述,旨在为作物耐旱性QTL定位及未来的分子标记辅助选择提供有益的借鉴.     

QTL mapping of resistance to Sporisorium reiliana in maize

We mapped and characterized quantitative trait loci (QTL) for resistance to Sporisorium reiliana. A population of 220 F₃ families produced from the cross of two European elite inbreds (D32, D145) was evaluated with two replications at a French location with high natural incidence of S. reiliana and at a Chinese location employing artificial inoculation. The 220 F₃ families were genotyped with 87 RFLP and seven SSR markers. Using composite interval mapping, we identified two different sets of 3 and 8 QTL for the French and the Chinese locations explaining 13% and 44% of respectively. Individual QTL explained up to 14% of σ^² _p. The 11 QTL mapped to eight maize chromosomes and displayed mostly additive or partial dominant gene action. Significant digenic epistatic interactions were detected for one pair of these QTL. Only a few QTL for S. reiliana were in common with QTL for resistance to Ustilago maydis and Puccinia sorghi, identified at a German location for the same population. Consequently, in our materials resistance to these three fungal pathogens of maize seems to be inherited independently. Received: 14. December 1998 / Accepted: 30 January 1999     

小麦早衰及其相关生理性状的QTL分析

利用RIL群体及其分子标记遗传图谱,对小麦早衰指标和与早衰相关的6个生理性状进行了QTL定位分析。小麦早衰指标中,检测到2个籽柆饱满度的加性QTL,分别位于3A和3B染色体,可解释表型变异的9.62%和18.30%。生理性状中,共检测到可溶性蛋白含量、SOD活性和POD活性3个性状的5个加性QTL,涉及2A、2B、2D、4A和6B等5条染色体,可解释表型变异的8.1%~49.56%。这些QTL间不存在连锁关系。     

Mapping multiple QTL of different effects: comparison of a simple sequential testing strategy and multiple QTL mapping

The aim of this study was to explore, by computer simulation, the mapping of QTLs in a realistic but complex situation of many (linked) QTLs with different effects, and to compare two QTL mapping methods. A novel method to dissect genetic variation on multiple chromosomes using molecular markers in backcross and F₂ populations derived from inbred lines was suggested, and its properties tested using simulations. The rationale for this sequential testing method was to explicitly test for alternative genetic models. The method consists of a series of four basic statistical tests to decide whether variance was due to a single QTL, two QTLs, multiple QTLs, or polygenes, starting with a test to detect genetic variance associated with a particular chromosome. The method was able to distinguish between different QTL configurations, in that the probability to `detect' the correct model was high, varying from 0.75 to 1. For example, for a backcross population of 200 and an overall heritability of 50%, in 78% of replicates a polygenic model was detected when that was the underlying true model. To test the method for multiple chromosomes, QTLs were simulated on 10 chromosomes, following a geometric series of allele effects, assuming positive alleles were in coupling in the founder lines For these simulations, the sequential testing method was compared to the established Multiple QTL Mapping (MQM) method. For a backcross population of 400 individuals, power to detect genetic variance was low with both methods when the heritability was 0.40. For example, the power to detect genetic variation on a chromosome on which 6 QTLs explained 12.6% of the genetic variance, was less than 60% for both methods. For a large heritability (0.90), the power of MQM to detect genetic variance and to dissect QTL configurations was generally better, due to the simultaneous fitting of markers on all chromosomes. It is concluded that when testing different QTL configurations on a single chromosome using the sequential testing procedure, regions of other chromosomes which explain a significant amount of variation should be fitted in the model of analysis. This study reinforces the need for large experiments in plants and other species if the aim of a genome scan is to dissect quantitative genetic variation.     

AFLA技术在经济动物中数量性状位点定位上的应用

简述了AFLP分子标记的原理、方法、特点和应注意的问题,QTL检测的方法和QTL定位的策略;综述了AFLP分子标记技术在经济动物中QTL定位方面的应用现状和前景。     

Mapping QTL controlling yield and yield components in a spring barley (Hordeum vulgare L.) cross using marker regression

An RFLP map constructed from 99 doubled haploid lines of a cross between two spring barley varieties (Blenheim × Kym) was used to localize quantitative trait loci (QTL) controlling grain yield and yield components by marker regression and single-marker analysis. Trials were conducted over three years. Genotype-by-year interaction was detected for plant grain weight and ear grain weight so they were analysed separately for each year. None was detected for thousand-grain weight and ear grain number so data were pooled over years. A total of eleven QTL were detected for plant grain weight over two years and fourteen for ear grain weight over three years. Seven QTL were detected for plot yield. The locus with the largest effect was on chromosome 2(2H)L and accounted for 19% of the variation in the progeny. Eight QTL were detected for thousand-grain weight and five for ear grain number. Many of the QTL detected were in comparable positions in each year. Yield and yield components were only partly correlated. Comparisons based on common RFLP markers showed that some QTL were found in positions similar to those identified in other studies. For a number of QTL the identification of linked markers provided suitable opportunities for marker-assisted selection and improvement of barley and reference markers with which to analyse the homoeologous chromosome regions of wheat and other cereals.     

小麦苗期水分利用效率及其相关性状的QTL分析

以小麦DH群体(旱选10号×鲁麦14)为研究材料,采用复合区间作图法,对小麦幼苗在水分胁迫及非胁迫条件下的水分利用效率(WUE)及其相关性状的QTL进行定位,并对比分析QTL的加性效应.两种水分条件下共检测到14个具显著加性效应的QTL,分布在2A、3A、4A、5A、6A、7A、1B、3B、3D染色体上,可解释表型变异的范围在6.36%～19.73%.其中,非胁迫(对照)条件下检测到10个QTL,包括2个单株WUE的QTL,5个地上部WUE的QTL,1个根系WUE的QTL及2个总耗水量的QTL;水分胁迫条件下上述性状各检测到1个QTL.对于同一性状没有检测到在两种水分条件下均位于同一标记区间的QTL,表明不同水分环境条件下同一性状的QTL表达模式是不同的.论文也讨论了可能用于标记辅助选择的QTL及其分子标记.     

Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design) was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design) consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study). Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study). Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26), protein yield (chromosome 26), protein content (chromosome 5), and somatic cell score (chromosome 2 and 19) with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.     

Comparative QTL mapping of resistance to Ustilago maydis across four populations of European flint-maize

 We mapped and characterized quantitative trait loci (QTLs) for resistance to Ustilago maydis and investigated their consistency across different flint-maize populations. Four independent populations, comprising 280 F₃ lines (A×B^I), 120 F₅ lines (A×B^II), 131 F₄ lines (A×C) and 133 F₄ lines (C×D), were produced from four European elite flint inbreds (A, B, C, D) and genotyped at 89, 151, 104, and 122 RFLP marker loci, respectively. All F_n lines were evaluated in field trials with two replications in five German environments. Genotypic variances were highly significant for the percentage of U. maydis infected plants (UST) in all populations, and heritabilities exceeded 0.69. Between five and ten QTLs were detected in individual populations by composite interval mapping, explaining between 39% and 58% of the phenotypic variance. These 19 different QTLs were distributed over all ten chromosomes without any clustering on certain chromosomes. In most cases, gene action was dominant or overdominant. Fourteen pairs of the detected QTLs for UST displayed significant digenic epistatic interactions, but only two of them did so after arcsin √UST/100 transformation. Significant QTL× environment interactions occurred frequently. Between two to four QTLs were common between pairs of populations. Population C×D was also grown in Chartres, a location with a high U. maydis incidence. Two out of six QTLs identified for Chartres were in common with QTLs detected across five German environments for C×D. Consequently, marker-assisted or phenotypic selection based on results from natural infection seem to be suitable breeding strategies for improving the resistance of maize to U. maydis. Received: 3 July 1998 / Accepted: 24 July 1998     

绵羊3号染色体的遗传连锁图谱构建及QTL定位

以四川凉山半细毛羊资源群体为研究对象, 选取位于绵羊3号染色体上的9个微卫星标记, 构建遗传连锁图谱, 用QTLExpress软件对影响绵羊生长发育的5个性状进行QTL定位分析。结果显示: (1) 9个微卫星标记的平均多态信息含量和平均群体杂合度分别为0.606 (0.378～0.738)、0.650 (0.404～0.766); (2) 连锁图谱总长为339.8 cM, 标记平均间距为42.5 cM, 略长于国际主要绵羊作图组织构建的图谱; (3) QTLExpress分析表明, 检测到影响羔羊断奶重、断奶日增重和成年体重的3个QTL, 分别位于99 cM、219 cM、273 cM处, 影响断奶日增重和成年体重的QTL都达到显著水平, 而影响羔羊断奶重的QTL未达到显著水平。