Quantitative Trait Loci Differentiating the Outbreeding Mimulus Guttatus from the Inbreeding M. Platycalyx

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6-28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect.     

大豆遗传图谱的构建和若干农艺性状的QTL定位分析

大豆许多重要农艺性状都是由微效多基因控制的数量性状,对这些数量性状进行QTL定位是大豆数量性状遗传研究领域的一个重要内容.本研究利用栽培大豆科新3号为父本、中黄20为母本杂交得到含192个单株的F2分离群体,构建了含122 个SSR标记、覆盖1719.6cM、由33个连锁群组成的连锁遗传图谱.利用复合区间作图法,对该群体的株高、主茎节数、单株粒重和蛋白质含量等农艺性状的调查数据进行QTL分析,共找到两个株高QTL,贡献率分别为9.15%和6.08%;两个主茎节数QTL,贡献率分别为10. 1%和8.6%;一个蛋白质含量QTL,贡献率为9.8%;一个单株粒重QTL,贡献率为11.4% .通过遗传作图共找到与所定位的4个农艺性状QTL连锁的6个SSR标记,这些标记可以应用于大豆种质资源的分子标记辅助选择,从而为大豆分子标记辅助育种提供理论依据.     

Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum

The identification of quantitative trait loci (QTLs) affecting agronomically important traits enable to understand their underlying genetic mechanisms and genetic basis of their complex interactions. The aim of the present study was to detect QTLs for 12 agronomic traits related to staygreen, plant early development, grain yield and its components, and some growth characters by analyzing replicated phenotypic datasets from three crop seasons, using the population of 168 F₇ RILs of the cross 296B × IS18551. In addition, we report mapping of a subset of genic-microsatellite markers. A linkage map was constructed with 152 marker loci comprising 149 microsatellites (100 genomic- and 49 genic-microsatellites) and three morphological markers. QTL analysis was performed by using MQM approach. Forty-nine QTLs were detected, across environments or in individual environments, with 1–9 QTLs for each trait. Individual QTL accounted for 5.2–50.4% of phenotypic variance. Several genomic regions affected multiple traits, suggesting the phenomenon of pleiotropy or tight linkage. Stable QTLs were identified for studied traits across different environments, and genetic backgrounds by comparing the QTLs in the study with previously reported QTLs in sorghum. Of the 49 mapped genic-markers, 18 were detected associating either closely or exactly as the QTL positions of agronomic traits. EST marker Dsenhsbm19, coding for a key regulator (EIL-1) of ethylene biosynthesis, was identified co-located with the QTLs for plant early development and staygreen trait, a probable candidate gene for these traits. Similarly, such exact co-locations between EST markers and QTLs were observed in four other instances. Collectively, the QTLs/markers identified in the study are likely candidates for improving the sorghum performance through MAS and map-based gene isolations.     

Epistasis affecting litter size in mice

Litter size is an important reproductive trait as it makes a major contribution to fitness. Generally, traits closely related to fitness show low heritability perhaps because of the corrosive effects of directional natural selection on the additive genetic variance. Nonetheless, low heritability does not imply, necessarily, a complete absence of genetic variation because genetic interactions (epistasis and dominance) contribute to variation in traits displaying strong heterosis in crosses, such as litter size. In our study, we investigated the genetic architecture of litter size in 166 females from an F2 intercross of the SM/J and LG/J inbred mouse strains. Litter size had a low heritability (h2 = 12%) and a low repeatability (r = 33%). Using interval-mapping methods, we located two quantitative trait loci (QTL) affecting litter size at locations D7Mit21 + 0 cM and D12Mit6 + 8 cM, on chromosomes 7 and 12 respectively. These QTL accounted for 12.6% of the variance in litter size. In a two-way genome-wide epistasis scan we found eight QTL interacting epistatically involving chromosomes 2, 4, 5, 11, 14, 15 and 18. Taken together, the QTL and their interactions explain nearly 49% (39.5% adjusted multiple r2) of the phenotypic variation for litter size in this cross, an increase of 36% over the direct effects of the QTL. This indicates the importance of epistasis as a component of the genetic architecture of litter size and fitness in our intercross population.     

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactions

Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used for genetic mapping and phenotypic evaluations. An all-marker interval mapping method was used for scanning the genome for the presence of QTL and single-factor ANOVA was used for estimating QTL-by-environment interactions. A modest number of QTL were detected per trait, with individual QTL explaining up to 9.5% of the phenotypic variation. Two QTL-by-treatment interactions were found for growth initiation, whereas several QTL-by-treatment interactions were detected among growth cessation traits. This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants.     

Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum [Sorghum bicolor (L.) Moench]

Sorghum, a cereal of economic importance ensures food and fodder security for millions of rural families in the semi-arid tropics. The objective of the present study was to identify and validate quantitative trait loci (QTL) for grain yield and other agronomic traits using replicated phenotypic data sets from three post-rainy dry sorghum crop seasons involving a mapping population with 245 F₉ recombinant inbred lines derived from a cross of M35-1 × B35. A genetic linkage map was constructed with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers. The QTL analysis for 11 traits following composite interval mapping identified 91 QTL with 5–12 QTL for each trait. QTL detected in the population individually explained phenotypic variation between 2.5 and 30.3 % for a given trait and six major genomic regions with QTL effect on multiple traits were identified. Stable QTL across seasons were identified. Of the 60 genic markers mapped, 21 were found at QTL peak or tightly linked with QTL. A gene-based marker XnhsbSFCILP67 (Sb03g028240) on SBI-03, encoding indole-3-acetic acid-amido synthetase GH3.5, was found to be involved in QTL for seven traits. The QTL-linked markers identified for 11 agronomic traits may assist in fine mapping, map-based gene isolation and also for improving post-rainy sorghum through marker-assisted breeding.     

Identification of QTL for maize resistance to common smut by using recombinant inbred lines developed from the Chinese hybrid Yuyu22

Common smut in maize, caused by Ustilago maydis, reduces grain yield greatly. Agronomic and chemical approaches to control such diseases are often impractical or ineffective. Resistance breeding could be an efficient approach to minimize the losses caused by common smut. In this study, quantitative trait loci (QTL) for resistance to common smut in maize were identified. In 2005, a recombinant inbred line (RIL) population along with the resistant (Zong 3) and susceptible (87-1) parents were planted in Beijing and Zhengzhou. Significant genotypic variation in resistance to common smut was observed at both locations after artificial inoculation by injecting inoculum into the whorl of plants with a modified hog vaccinator. Basing on a genetic map containing 246 polymorphic SSR markers with an average linkage distance of 9.11 cM, resistance QTL were analysed by composite interval mapping. Six additive-effect QTL associated with resistance to common smut were identified on chromosomes 3 (three QTL), 5 (one QTL) and 8 (two QTL), and explained 3.2% to 12.4% of the phenotypic variation. Among the 6 QTL, 4 showed significant QTL x environment (Q x E) interaction effects, which accounted for 1.2% to 2.5% of the phenotypic variation. Nine pairs of epistatic interactions were also detected, involving 18 loci distributed on all chromosomes except 2, 6 and 10, which contributed 0.8% to 3.0% of the observed phenotypic variation. However, no significant epistasis x environment interactions were detected. In total, additive QTL effects and Q x E interactions explained 38.8% and 8.0% of the phenotypic variation, respectively. Epistatic effects contributed 15% of the phenotypic variation. The results showed that besides the additive QTL, both epistasis and Q x E interactions formed an important genetic basis for the resistance to Ustilago maydis in maize.     

A composite method for mapping quantitative trait loci without interference of female achiasmatic and gender effects in silkworm,Bombyx mori

The silkworm, Bombyx mori, is an economically important insect that was domesticated more than 5000 years ago. Its major economic traits focused on by breeders are quantitative traits, and an accurate and efficient QTL mapping method is necessary to explore their genetic architecture. However, current widely used QTL mapping models are not well suited for silkworm because they ignore female achiasmate and gender effects. In this study, we propose a composite method combining rational population selection and special mapping methods to map QTL in silkworm. By determining QTL for cocoon shell weight (CSW), we demonstrated the effectiveness of this method. In the CSW mapping process, only 56 markers were used and five loci or chromosomes were detected, more than in previous studies. Additionally, loci on chromosomes 1 and 11 dominated and accounted for 35.10% and 15.03% of the phenotypic variance respectively. Unlike previous studies, epistasis was detected between loci on chromosomes 11 and 22. These mapping results demonstrate the power and convenience of this method for QTL mapping in silkworm, and this method may inspire the development of similar approaches for other species with special genetic characteristics.     

Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) investigated with joint linkage association mapping

Epistatic interactions may contribute substantially to the hybrid performance of sugar beet. The main goal of our study was to dissect the genetic basis of eight important physiological and agronomic traits using two different biometrical models for joint linkage association mapping. A total of 197 genotypes of an elite breeding population were evaluated in multi-location trials and fingerprinted with 194 SNP markers. Two different statistical models were used for the genome-wide scan for marker–trait associations: Model A, which corrects for the genetic background with markers as cofactors and Model B, which additionally models a population effect. Based on the extent of linkage disequilibrium in the parental population, we estimated that for a genome-wide scan at least 100 equally spaced markers are necessary. We mapped across the eight traits 39 QTL for Model A and 22 for Model B. Only 11% of the total number of QTL were identified based on Models A and B, which indicates that both models are complementary. Epistasis was detected only for two out of the eight traits, and contributed only to a minor extent to the genotypic variance. This low relevance of epistasis implies that in sugar beet breeding the prediction of performance of three-way hybrids is feasible with high accuracy based on the means of their single crosses.     

The inheritance and evolution of leaf pigmentation and pubescence in teosinte

To investigate the genetic mechanisms that underlie morphological evolution in natural populations, we employed QTL mapping to dissect the inheritance of leaf sheath characters that distinguish Chalco from Balsas teosinte. Abundant macrohairs (trichomes) and intense anthocyanin accumulation are found in Chalco teosinte sheaths whereas Balsas teosinte leaf sheaths are green and glabrous. These character states may represent adaptations to the cooler highland (Chalco) vs. warmer middle-elevation (Balsas) climates. QTL mapping in multiple populations revealed a mix of major- and minor-effect QTL affecting both sheath color (anthocyanin) and macrohair abundance. The major QTL for macrohairs accounts for 52% of the parental difference. Epistatic interactions were detected between the major-effect QTL and multiple other QTL for both traits, accounting for substantial portions of phenotypic variance. Developmental analyses suggest that regulatory program changes underlie the phenotypic differences. Sheath anthocyanin QTL are clearly associated with b1 and a3, both of which are regulators of anthocyanin biosynthesis. Our findings suggest that changes in a small number of QTL can lead to morphological evolution by modulating existing developmental programs.     

The genetic architecture of immune defense and reproduction in male Bombus terrestris bumblebees

Understanding the architecture of genetic variation, that is the number, effect, location, and interaction, of genes responsible for phenotypic variability in nature is important for the understanding of microevolutionary processes. In this study, we have used a quantitative trait loci (QTL) approach to uncover the genetic architecture of fitness-relevant traits associated with reproduction and immune defense in male Bombus terrestris bumblebees. Three male reproductive investment traits, the number and length of the produced sperm and the size of the accessory glands, were studied. Two branches of the insect innate immune system, the activation of the Phenoloxidase-cascade and the hemolymph's antibacterial activity, were investigated. We found that variation in most of the studied traits is based on a network of minor QTLs and epistatic interactions. Unexpectedly, there was no evidence for phenotypic or genetic trade-offs between the presumably costly investment in immune defense and reproductive effort in this population for the measured traits. In fact, we found a positive correlation, both, in phenotype and genetic architecture for the number of produced sperm and antibacterial activity against an insect pathogen. A major finding for all traits analyzed was that the epistatic interactions accounted for a major proportion of the explained phenotypic variance. Especially for traits involved in immune defense, this pattern highlights the possible role of parasites in the evolution and maintenance of recombination and sexual reproduction.     

Estimating the genetic architecture of quantitative traits

Understanding and estimating the structure and parameters associated with the genetic architecture of quantitative traits is a major research focus in quantitative genetics. With the availability of a well-saturated genetic map of molecular markers, it is possible to identify a major part of the structure of the genetic architecture of quantitative traits and to estimate the associated parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the genetic architecture parameters, including the number, genomic positions, effects and interactions of significant QTL and their contribution to the genetic variance. With multiple traits and multiple environments involved in a QTL mapping experiment, pleiotropic effects and QTL by environment interactions can also be estimated. We review the method and discuss issues associated with multiple interval mapping, such as likelihood analysis, model selection, stopping rules and parameter estimation. The potential power and advantages of the method for mapping multiple QTL and estimating the genetic architecture are discussed. We also point out potential problems and difficulties in resolving the details of the genetic architecture as well as other areas that require further investigation. One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating.     

Genetic dissection of a modern sugarcane cultivar ( Saccharum spp.).II. Detection of QTLs for yield components

The genetics of current sugarcane cultivars ( Saccharum spp.) is outstandingly complex, due to a high ploidy level and an interspecific origin which leads to the presence of numerous chromosomes belonging to two ancestral genomes. In order to analyse the inheritance of quantitative traits, we have undertaken an extensive Quantitative Trait Allele (QTA) mapping study based on a population of 295 progenies derived from the selfing of cultivar R570, using about 1,000 AFLP markers scattered on about half of the genome. The population was evaluated in a replicated trial for four basic yield components, plant height, stalk number, stalk diameter and brix, in two successive crop-cycles. Forty putative QTAs were found for the four traits at P = 5 x 10(-3), of which five appeared in both years. Their individual size ranged between 3 and 7% of the whole variation. The stability across years was improved when limiting threshold stringency. All these results depict the presence in the genome of numerous QTAs, with little effects, fluctuating slightly across cycles, on the verge to being perceptible given the experimental resolution. Epistatic interactions were also explored and 41 independent di-genic interactions were found at P = (5 x 10(-3))(2). Altogether the putative genetic factors revealed here explain from 30 to 55% of the total phenotypic variance depending on the trait. The tentative assignment of some QTAs to the ancestral genomes showed a small majority of contributions as expected from the ancestral phenotypes. This is the first extensive QTL mapping study performed in cultivated sugarcane.     

Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations

It has long been recognized that epistasis or interactions between non-allelic genes plays an important role in the genetic control and evolution of quantitative traits. However, the detection of epistasis and estimation of epistatic effects are difficult due to the complexity of epistatic patterns, insufficient sample size of mapping populations and lack of efficient statistical methods. Under the assumption of additivity of QTL effects on the phenotype of a trait in interest, the additive effect of a QTL can be completely absorbed by the flanking marker variables, and the epistatic effect between two QTL can be completely absorbed by the four marker-pair multiplication variables between the two pairs of flanking markers. Based on this property, we proposed an inclusive composite interval mapping (ICIM) by simultaneously considering marker variables and marker-pair multiplications in a linear model. Stepwise regression was applied to identify the most significant markers and marker-pair multiplications. Then a two-dimensional scanning (or interval mapping) was conducted to identify QTL with significant digenic epistasis using adjusted phenotypic values based on the best multiple regression model. The adjusted values retain the information of QTL on the two current mapping intervals but exclude the influence of QTL on other intervals and chromosomes. Epistatic QTL can be identified by ICIM, no matter whether the two interacting QTL have any additive effects. Simulated populations and one barley doubled haploids (DH) population were used to demonstrate the efficiency of ICIM in mapping both additive QTL and digenic interactions.     

玉米杂交种掖单13号的SSR连锁图谱构建与叶夹角和叶向值的QTL定位与分析

为了增加单位面积产量, 玉米育种者已经开始了更密植更紧凑株型的选育。叶夹角和叶向值是评价玉米株型的重要指标。本研究以掖478×丹340的500个F2单株为作图群体, 构建了具有138个位点的SSR标记连锁图谱, 图谱总长度为1 394.9 cM, 平均间距10.1 cM。利用397个F2：3家系对叶夹角和叶向值进行QTL定位分析, 结果表明: 叶夹角和叶向值分别检测到6和8个QTL, 累计解释表型变异41.0%和60.8%, 单个QTL的贡献率在2.9%~13.6%之间。与叶夹角和叶向值有关的基因主要作用方式为加性和部分显性。此外两个性状共检测到9对上位性互作位点, 表明上位性互作在叶夹角和叶向值的遗传中也起较重要的作用。     

胡萝卜(Daucus carota L.)中主要胡萝卜素和番茄红素含量的QTL分析

以高胡萝卜素自交系P50006和HCM A.C.为亲本构建的F2群体为作图群体,对胡萝卜中α-胡萝卜素、α-胡萝卜素、总胡萝卜素和番茄红素含量进行QTL定位及遗传分析。结果表明,α、β-胡萝卜素、总胡萝卜素和番茄红素含量的广义遗传力分别为0.75、0.50、0.31和0.93。遗传图谱包含91个SRAP(Sequence-related amplified polymorphism)标记,分布于9个连锁群,总长度502.9cM,标记间平均距离5.5cM。除α-胡萝卜素含量外,α-胡萝卜素、总胡萝卜素和番茄红素含量分别检测到1个主效QTL,均为加性遗传效应,分别解释表型变异为12.79%、12.87%和14.61%。此外,α-胡萝卜素和番茄红素含量还分别检测到1对上位性QTL,最大遗传效应分别为显性×加性互作和显性×显性互作,分别解释表型变异为15.1%和6.5%。文章中与QTL连锁的分子标记可用于高胡萝卜素、番茄红素的种质筛选和聚合育种。     

Quantitative trait loci mapping in five new large recombinant inbred line populations of Arabidopsis thaliana genotyped with consensus single-nucleotide polymorphism markers

Quantitative approaches conducted in a single mapping population are limited by the extent of genetic variation distinguishing the parental genotypes. To overcome this limitation and allow a more complete dissection of the genetic architecture of complex traits, we built an integrated set of 15 new large Arabidopsis thaliana recombinant inbred line (RIL) populations optimized for quantitative trait loci (QTL) mapping, having Columbia as a common parent crossed to distant accessions. Here we present 5 of these populations that were validated by investigating three traits: flowering time, rosette size, and seed production as an estimate of fitness. The large number of RILs in each population (between 319 and 377 lines) and the high density of evenly spaced genetic markers scored ensure high power and precision in QTL mapping even under a minimal phenotyping framework. Moreover, the use of common markers across the different maps allows a direct comparison of the QTL detected within the different RIL sets. In addition, we show that following a selective phenotyping strategy by performing QTL analyses on genotypically chosen subsets of 164 RILs (core populations) does not impair the power of detection of QTL with phenotypic contributions >7%.     

QTL for tuber morphology traits in diploid potato

A diploid, potato mapping population consisting of 149 individuals was assessed in three consecutive years for important agronomic and quality traits: tuber shape, regularity of tuber shape, eye depth, mean tuber weight, and tuber flesh color. Analysis of variance showed that the genotype had the largest influence on the phenotypic scores but effect of the genotype × year interactions was also strong. Using this data and an existing genetic map, a quantitative trait loci (QTL) analysis was conducted. From four to seven QTL were detected for each trait except tuber flesh color, which was determined by a major QTL on chromosome III explaining 76.8% of the trait variance. Additionally, a minor QTL for flesh color was localized on chromosome II. For the other traits, significant QTL were detected: for tuber shape on chromosome X, for regularity of tuber shape on chromosome III, for eye depth on chromosome IV, and for tuber weight on chromosome I. Some detected QTL confirmed previous studies, but new ones were also identified.     

Identification of QTLs Conferring Resistance to Deltamethrin in Culex pipiens pallens

Culex pipiens pallens is the most abundant Culex mosquito species in northern China and is an important vector of bancroftian filariasis and West Nile virus. Deltamethrin is an insecticide that is widely used for mosquito control, however resistance to this and other insecticides has become a major challenge in the control of vector-borne diseases that appear to be inherited quantitatively. Furthermore, the genetic basis of insecticide resistance remains poorly understood. In this study, quantitative trait loci (QTL) mapping of resistance to deltamethrin was conducted in F₂ intercross segregation populations using bulked segregation analysis (BSA) and amplified fragment length polymorphism markers (AFLP) in Culex pipiens pallens. A genetic linkage map covering 381 cM was constructed and a total of seven QTL responsible for resistance to deltamethrin were detected by composite interval mapping (CIM), which explained 95% of the phenotypic variance. The major QTL in linkage group 2 accounted for 62% of the variance and is worthy of further study. 12 AFLP markers in the map were cloned and the genomic locations of these marker sequences were determined by applying the Basic Local Alignment Search Tool (BLAST) tool to the genome sequence of the closely related Culex quinquefasciatus. Our results suggest that resistance to deltamethrin is a quantitative trait under the control of a major QTL in Culex pipiens pallens. Cloning of related AFLP markers confirm the potential utility for anchoring the genetic map to the physical map. The results provide insight into the genetic architecture of the trait.     

长蓝猪QTL定位资源群建立及其遗传分析

利用高度选育的8头瘦肉型长白猪为父本,16头中国优良地方品种蓝塘猪为母本,采用远交系杂交的F2代设计方法,建立包括8头F1公猪、40头F1母猪和232头F2个体的猪资源群体。资源群体的遗传分析表明,所测定的32个性状都有一定的变异,主要经济性状的变异系数都在10％以上。进一步的方差组分估计表明,主要经济性状的加性遗传方差较大。在所测定6号染色体连锁群的22个微卫星DNA标记中,12个表现有多态性,全群平均杂合度为0.53,多态信息含量为0.46,能较好地为QTL检测提供信息。因此,F2代有较好的分离状态,有可能利用该资源群体检测到较多的QTL。