The complex quantitative barley–<Emphasis Type="Italic">Rhynchosporium secalis</Emphasis> interaction: newly identified QTL may represent already known resistance genes

Two barley populations, i.e. 135 doubled haploid (DH) lines of the cross 'Igri' (rrs1) x 'Triton' (Rrs1) (I x T) and 76 DH lines of the cross 'Post' x 'Vixen' (both rrs1) (P x V), were analysed to identify QTL for Rhynchosporium secalis resistance independent of the Rrs1 locus by using the single spore R. secalis isolate 271 (Rrs1-virulent). A major QTL with its positive allele derived from cv. 'Triton' was detected in the I x T population on chromosome 2HS explaining almost 80% of the phenotypic variance. Thus, it can be considered as an R-gene corresponding to the already described Rrs15(CI8288) on chromosome 2HS. In addition, two minor QTL were identified, one in the centromeric region of 6H in a highly polymorphic region with already several mapped R-genes and a second one at the end of the short arm of chromosome 7H which may be an allele of Rrs2 because of its chromosomal position. Regarding the DH population P x V different minor QTL were identified on chromosomes 6H and 7H. The first one is corresponding to the genomic region of the Rrs13 gene whereas the QTL on chromosome 7H maps in a genomic region where several R-genes against different pathogens have been localized. A comparison of both QTL analyses reveals no R. secalis isolate 271-specific resistance locus but leads to the hypothesis that two of the identified QTL may be alleles of the R-genes Rrs15(CI8288) and Rrs2.     

Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross

In this study, we considered five categories of molecular markers in clonal F₁ and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F₁ and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping (ICIM) of quantitative trait locus (QTL). The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple‐QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.     

The effect of an imprecise map on interval mapping QTLs

The statistical analysis of quantitative trait locus (QTL) experiments relies on the use of a linkage map of the markers genotyped. Such a map is, at best, a good estimate of the true map. Resources might be diverted into developing better marker maps or improved maps become available after the analysis, raising concerns over the original analysis. It is therefore important to understand the sensitivity of QTL analysis to map inaccuracy. We have used simulation methods to investigate the consequences of an incorrect map on the results of a QTL analysis using interval mapping. Backcross data sets were generated with a particular map and then analysed with both the correct map and incorrect maps. If the incorrect maps maintained the true linkage groups (i.e. no markers were incorrectly assigned to another linkage group), the accuracy of the map had little or no impact on the ability to detect QTLs, the true significance levels of the tests or the relative placement of QTLs. When a marker was incorrectly placed on another linkage group, there was a small increase in the level of the test. After adjusting for this increase, there was a decrease in power to detect a QTL near the misplaced marker. This decrease was of a similar magnitude to that found when using a single-marker analysis compared with interval mapping. These results mean that QTL analyses can proceed without the need for very accurate marker maps, and that estimated QTL positions can be translated onto updated maps without the need for reanalysis.     

BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.)

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.     

Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits

New microsatellites markers [simple sequence repeat (SSR)] have been isolated from rose and integrated into an existing amplified fragment-length polymorphism genetic map. This new map was used to identify quantitative trait locus (QTL) controlling date of flowering and number of petals. From a rose bud expressed sequence tag (EST) database of 2,556 unigenes and a rose genomic library, 44 EST-SSRs and 20 genomic-SSR markers were developed, respectively. These new rose SSRs were used to expand genetic maps of the rose interspecific F₁ progeny. In addition, SSRs from other Rosaceae genera were also tested in the mapping progeny. Genetic maps for the two parents of the progeny were constructed using pseudo-testcross mapping strategy. The maps consist of seven linkage groups of 105 markers covering 432 cM for the maternal map and 136 markers covering 438 cM for the paternal map. Homologous relationships among linkage groups between the maternal and paternal maps were established using SSR markers. Loci controlling flowering traits were localised on genetic maps as a major gene and QTL for the number of petals and a QTL for the blooming date. New SSR markers developed in this study will provide tools for the establishment of a consensus linkage map for roses that combine traits and markers in various rose genetic maps.     

植物QTL分析的理论研究进展

数量性状的表型是由数量性状基因座 ( Quantitative trait locus,QTL)和环境效应共同作用的结果。传统的数量遗传学采用统计学的方法由一级统计量和二级统计量描述处理 QTL的复合作用 ,估计各种遗传参数 (例如遗传力、遗传相关、遗传进度、有效因子数等 ) ,用于指导遗传育种实践。然而 ,在传统的数量遗传学分析中 ,往往假设数量性状受微效多基因控制 ,这些基因具有相同的并且是较微小的效应 ,所估计的遗传参数反映的是数量性状多基因系统的整体特征 ,其理论方法不能用于追踪研究和描述单个数量性状基因的作用。近年来 ,由于分子生物学技…     

Modeling segregation distortion for viability selection I. Reconstruction of linkage maps with distorted markers

Molecular markers have been widely used to map quantitative trait loci (QTL). The QTL mapping partly relies on accurate linkage maps. The non-Mendelian segregation of markers, which affects not only the estimation of genetic distance between two markers but also the order of markers on a same linkage group, is usually observed in QTL analysis. However, these distorted markers are often ignored in the real data analysis of QTL mapping so that some important information may be lost. In this paper, we developed a multipoint approach via Hidden Markov chain model to reconstruct the linkage maps given a specified gene order while simultaneously making use of distorted, dominant and missing markers in an F₂ population. The new method was compared with the methods in the MapManager and Mapmaker programs, respectively, and verified by a series of Monte Carlo simulation experiments along with a working example. Results showed that the adjusted linkage maps can be used for further QTL or segregation distortion locus (SDL) analysis unless there are strong evidences to prove that all markers show normal Mendelian segregation.     

Genetic dissection of grain weight in bread wheat through quantitative trait locus interval and association mapping

Genetic dissection of grain weight in bread wheat was undertaken through both genome-wide quantitative trait locus (QTL) interval mapping and association mapping. QTL interval mapping involved preparation of a framework linkage map consisting of 294 loci {194 simple sequence repeats (SSRs), 86 amplified fragment length polymorphisms (AFLPs) and 14 selective amplifications of microsatellite polymorphic loci (SAMPL)} using a bi-parental recombinant inbred line (RIL) mapping population derived from Rye Selection111 × Chinese Spring. Using the genotypic data and phenotypic data on grain weight (GW) of RILs collected over six environments, genome-wide single locus QTL analysis was conducted to identify main effect QTL. This led to identification of as many as ten QTL including four major QTL (three QTL were stable), each contributing >20% phenotypic variation (PV) for GW. The above study was supplemented with association mapping, which allowed identification of 11 new markers in the genomic regions that were not reported earlier to harbour any QTL for GW. It also allowed identification of closely linked markers for six known QTL, and validation of eight QTL reported earlier. The QTL identified through QTL interval mapping and association mapping may prove useful in marker-assisted selection (MAS) for the development of cultivars with high GW in bread wheat.     

Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in F2 intercross chickens.

Marek''s disease (MD) is a lymphoproliferative disease caused by the MD virus (MDV), which costs the poultry industry nearly $1 billion annually. To identify quantitative trait loci (QTL) affecting MD susceptibility, the inbred lines 6(3) (MD resistant) and 7(2) (MD susceptible) were mated to create more than 300 F2 chickens. The F2 chickens were challenged with MDV JM strain, moderately virulent) at 1 wk of age and assessed for MD susceptibility. The QTL analysis was divided into three stages. In stage 1, 65 DNA markers selected from the chicken genetic maps were typed on the 40 most MD-susceptible and the 40 most MD-resistant F2 chickens, and 21 markers residing near suggestive QTL were revealed by analysis of variance (ANOVA). In stage 2, the suggestive markers plus available flanking markers were typed on 272 F2 chickens, and three suggestive QTL were identified by ANOVA. In stage 3, using the interval mapping program Map Manager and permutation tests, two significant and two suggestive MD QTL were identified on four chromosomal subregions. Three to five loci collected explained between 11 and 23% of the phenotypic MD variation, or 32-68% of the genetic variance. This study constitutes the first report in the domestic chicken on the mapping of non-major histocompatibility complex QTL affecting MD susceptibility.     

油菜硫甙性状QTL 区间的加密和整合

目的:加密油菜控制硫甙性状QTL区间,并进行QTL整合预测候选基因。方法:利用生物信息学方法根据已知测序的白菜BAC序列信息设计引物,在油菜TN DH群体中进行多态性扩增和定位,并根据加密后构建的遗传连锁图重新检测QTL,进行QTL整合。结果:将根据白菜BAC设计的3对多态性标记成功定位到油菜控制硫甙性状QTL区间,进行QTL整合后将QTL置信区间进一步缩小,并判定了初步的候选基因。结论:充分利用白菜已测序的BAC或者基因组信息,将能加快油菜基础研究的步伐。     

Association mapping of drought tolerance-related traits in barley to complement a traditional biparental QTL mapping study

Key message

Association mapping of drought-related traits in barley was used to increase the density of existing QTL maps without recreating mapping populations.

Abstract

We used 109 spring barley genotypes exhibiting high or low drought tolerance to elucidate the associations between diversity array technology sequencing (DArTseq) and single nucleotide polymorphism (SNP) markers and various physiological parameters related to plant responses to drought conditions. The study was performed in controlled conditions (growth chambers), drought tolerance was phenotyped in the four-leaf seedlings. We identified 58 associations including 34 new markers (i.e., 16 DArTseq and 18 SNP markers). The results for three markers were consistent with the data obtained in an earlier traditional biparental QTL mapping study. The regions neighboring markers on linkage group 2H contained the highest number of significant marker–trait associations. Five markers related to the photosynthetic activity of photosystem II were detected on chromosome 4H. The lowest number of associations were observed for the sequences neighboring DArT markers on linkage group 6H. A chromosome 3H region related to water use efficiency and net photosynthesis rate in both biparental QTL, and association study, may be particularly valuable, as these parameters correspond to the ability of plants to remain highly productive under water deficit stress. Our findings confirm that association mapping can increase the density of existing QTL maps without recreating mapping populations.

     

利用三倍体胚乳遗传模型定位玉米籽粒淀粉含量QTL

在两种环境条件下种植以普通玉米自交系丹232和爆裂玉米自交系N04为亲本构建的259个F2:3家系群体, 采用SSR标记构建了包含183个标记的玉米遗传连锁图谱, 覆盖玉米基因组1 762.2 cM, 标记间平均距离为9.6 cM。利用三倍体胚乳遗传模型和区间作图方法对籽粒淀粉含量进行了QTL定位和遗传效应分析, 春、夏播条件下共检测到10个QTL, 春播条件下检测到的QTL在夏播均被检测到, 分别位于第1、3、4、5、7染色体上,可解释淀粉的表型总变异分别为36.84%和72.65%, 单个QTL解释表型变异介于4.74%~11.26%。在检测到的 QTL中, 有2个QTL的遗传作用方式在春播均表现为超显性, 而夏播分别为加性和部分显性; 其他2个为加性, 1个为部分显性, 5个为超显性。3个QTL的增效基因来自丹232, 其余QTL的增效基因均来自N04。     

Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F₂ population from ZL1929-4 × Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F₂ and F₃ generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F₂ population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.     

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     

Markov chain Monte Carlo for mapping a quantitative trait locus in outbred populations

A Bayesian approach is presented for mapping a quantitative trait locus (QTL) using the 'Fernando and Grossman' multivariate Normal approximation to QTL inheritance. For this model, a Bayesian implementation that includes QTL position is problematic because standard Markov chain Monte Carlo (MCMC) algorithms do not mix, i.e. the QTL position gets stuck in one marker interval. This is because of the dependence of the covariance structure for the QTL effects on the adjacent markers and may be typical of the 'Fernando and Grossman' model. A relatively new MCMC technique, simulated tempering, allows mixing and so makes possible inferences about QTL position based on marginal posterior probabilities. The model was implemented for estimating variance ratios and QTL position using a continuous grid of allowed positions and was applied to simulated data of a standard granddaughter design. The results showed a smooth mixing of QTL position after implementation of the simulated tempering sampler. In this implementation, map distance between QTL and its flanking markers was artificially stretched to reduce the dependence of markers and covariance. The method generalizes easily to more complicated applications and can ultimately contribute to QTL mapping in complex, heterogeneous, human, animal or plant populations.     

A comparison of interval mapping procedures including the QTL-cluster mapping

Using the deterministic sampling, patterns of the log-likelihood surfaces expected in some interval mapping procedures for estimating the position of, and the effect for, QTL(s) were investigated for the situations where a single QTL or closely linked QTLs are contained in a chromosome segment bracketed with two markers. The mapping procedures compared were the conventional, likelihood-based interval mapping (IM), the regression interval mapping (RIM), and the QTL-cluster mapping (CM) in which the conditional probabilities of transmission of the whole segment marked by the flanking markers were taken into consideration. The half-sib design was used here, and several cases of the true genetic model were considered, differing in the number of QTLs contained in the marker interval, the linkage phase for the sire, and the magnitude of the QTL(s) effect. For the true genetic models where a single QTL or closely linked QTLs being in coupling phase are contained in the interval, with (R)IM, clear global maxima of the log-likelihood were observed within the range of the marker interval. It was shown that the estimates of the QTL(s) effect at the marked segment level are expected to be unbiased. On the other hand, in a setting where the linkage phase for the linked QTLs located in the interval was different from coupling and repulsion, there was found a ridge along the interval for the log-likelihood surface with (R)IM, indicating the dependency between the estimates of the position of, and the effect for, the putative QTL. For this case, it was found that the position of the putative QTL could be estimated as that of one of the flanking markers, and the estimate of the QTL effect be biased. In contrast, it was revealed that CM is expected to provide the unbiased estimate of the QTL(s)-effect at the segment level for any case of the true genetic models considered here. If the aim is for marker-assisted selection rather than mapping closely linked QTLs individually, then the CM approach is considered to be useful.     

Genetic analysis of photoperiod sensitivity in a tropical by temperate maize recombinant inbred population using molecular markers

Photoperiod sensitivity is an important consideration in maize cultivation. Flowering time is affected by photoperiod and sensitivity to it limits the potential for successful exchange of germplasm across different latitudes. For resolving the genetic basis of photoperiod sensitivity in maize, a set of 207 recombinant inbred lines derived from a temperate and tropical inbred line cross was evaluated for 2 years in a long-day and short-day environment. Genetic linkage maps were constructed using 237 SSR markers with a total length 1,974.3 cM, and an average space between two makers of 8.33 cM. Twenty-nine QTL were detected for the five measured photoperiod sensitivity traits using composite interval mapping and multiple interval mapping. QTL for flowering time, plant height and leaf number, under long-day conditions, were found clustered on chromosome 10, while QTL for short-day conditions resided on chromosome 3. The QTL in the bin 10.04 region of chromosome 10 were detected associated with photoperiod sensitivity and related traits during long days. These results indicated that this region might contain an important photoperiod sensitivity element.     

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.     

Morphological traits defining species differences in wild relatives of maize are controlled by multiple quantitative trait loci

We analyzed the genetic basis of morphological differences between two wild species of teosinte (Zea diploperennis and Z. mays ssp. parviglumis), which are relatives of maize. These two species differ in a number of taxonomically important traits including the structure of the tassel (male inflorescence), which is the focus of this report. To investigate the genetic inheritance of six tassel traits, quantitative trait locus (QTL) mapping with 95 RFLP markers was employed on a population of 425 F2 plants. Each trait was analyzed by interval mapping (IM) and composite interval mapping (CIM) to identify and characterize the QTL controlling the differences in tassel morphology. We detected two to eight QTL for each trait. In total, 30 QTL with IM and 33 QTL with CIM were found for tassel morphology. QTL for several of the traits mapped near each other, suggesting pleiotropy and/or linkage of QTL. The QTL showed small to moderate magnitudes of effect. No QTL of exceptionally large effect were found as seen under domestication and in the case of some other natural species. Thus, the model involving major QTL of large effect seems not to apply to the traits and species analyzed. A mixture of QTL with positive and negative allelic effects was found for most tassel traits and may suggest a history of periodic changes in the direction of selection during the divergence of Z. diploperennis and Z. mays ssp. parviglumis or fixation of QTL alleles by random genetic drift rather than selection.     

A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation

Both inter- and intra-specific maps have been developed in eggplant (Solanum melongena L.). The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP) markers discriminating between the two eggplant mapping population parental lines '305E40' and '67/3'. A set of 347 de novo SNPs, together with 84 anchoring markers, were applied to the F(2) mapping population bred from the cross '305E40' x '67/3' to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL), of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.