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。     

Mapping the genome of rapeseed (Brassica napus L.). II. Localization of genes controlling erucic acid synthesis and seed oil content

A F₁ microspore-derived DH population, previously used for the development of a rapeseed RFLP map, was analysed for the distribution of erucic acid and seed oil content. A clear three-class segregation for erucic acid content could be observed and the two erucic acid genes of rapeseed were mapped to two different linkage groups on the RFLP map. Although the parents of the segregating DH population showed no significant difference in seed oil content, in the DH population a transgressive segregation in oil content was observed. The segregation closely followed a normal distribution, characteristic of a quantitative trait. Using the program MAPMAKER/QTL, three QTLs for seed oil content could be mapped on three different linkage groups. The additive effects of these QTLs explain about 51% of the phenotypic variation observed for this trait in the DH population. Two of the QTLs for oil content showed a close association in location to the two erucic acid genes, indicating a direct effect of the erucic acid genes on oil content.     

Gene action,genetic variation,and GWAS: A user-friendly web tool

Fisher’s partitioning of genotypic values and genetic variance is highly relevant in the current era of genome-wide association studies (GWASs). However, despite being more than a century old, a number of persistent misconceptions related to nonadditive genetic effects remain. We developed a user-friendly web tool, the Falconer ShinyApp, to show how the combination of gene action and allele frequencies at causal loci translate to genetic variance and genetic variance components for a complex trait. The app can be used to demonstrate the relationship between a SNP effect size estimated from GWAS and the variation the SNP generates in the population, i.e., how locus-specific effects lead to individual differences in traits. In addition, it can also be used to demonstrate how within and between locus interactions (dominance and epistasis, respectively) usually do not lead to a large amount of nonadditive variance relative to additive variance, and therefore, that these interactions usually do not explain individual differences in a population.     

Epistasis and Its Contribution to Genetic Variance Components

We present a new parameterization of physiological epistasis that allows the measurement of epistasis separate from its effects on the interaction (epistatic) genetic variance component. Epistasis is the deviation of two-locus genotypic values from the sum of the contributing single-locus genotypic values. This parameterization leads to statistical tests for epistasis given estimates of two-locus genotypic values such as can be obtained from quantitative trait locus studies. The contributions of epistasis to the additive, dominance and interaction genetic variances are specified. Epistasis can make substantial contributions to each of these variance components. This parameterization of epistasis allows general consideration of the role of epistasis in evolution by defining its contribution to the additive genetic variance.     

QTL for phytosterol and sinapate ester content in <Emphasis Type="Italic">Brassica napus</Emphasis> L. collocate with the two erucic acid genes

Improving oil and protein quality for food and feed purposes is an important goal in rapeseed (Brassica napus L.) breeding programs. Rapeseed contains phytosterols, used to enrich food products, and sinapate esters, which are limiting the utilization of rapeseed proteins in the feed industry. Increasing the phytosterol content of oil and lowering sinapate ester content of meal could increase the value of the oilseed rape crop. The objective of the present study was to identify quantitative trait loci (QTL) for phytosterol and sinapate ester content in a winter rapeseed population of 148 doubled haploid lines, previously found to have a large variation for these two traits. This population also segregated for the two erucic acid genes. A close negative correlation was found between erucic acid and phytosterol content (Spearman’s rank correlation, r _s = −0.80^**). For total phytosterol content, three QTL were detected, explaining 60% of the genetic variance. The two QTL with the strongest additive effects were mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. For sinapate ester content four QTL were detected, explaining 53% of the genetic variance. Again, a close negative correlation was found between erucic acid and sinapate ester content (r _s = −0.66^**) and the QTL with the strongest additive effects mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. The results suggests, that there is a pleiotropic effect of the two erucic acid genes on phytosterol and sinapate ester content; the effect of the alleles for low erucic acid content is to increase phytosterol and sinapate ester content. Possible reasons for this are discussed based on known biosynthetic pathways. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Association mapping for quality traits in soft winter wheat

Improvement of end-use quality in bread wheat (Triticum aestivum L.) depends on a thorough understanding of the genetic basis of important quality traits. The main goal of our study was to investigate the genetic basis of 1,000-kernel weight, protein content, sedimentation volume, test weight, and starch concentration using an association mapping approach. We fingerprinted 207 diverse European elite soft winter wheat lines with 115 SSR markers and evaluated the genotypes in multi-environment trials. The principal coordinate analysis revealed absence of a clear population but presence of a family structure. Therefore, we used linear mixed models and marker-based kinship matrices to correct for family structure. In genome-wide scans, we detected main effect QTL for all five traits. In contrast, epistatic QTL were only observed for sedimentation volume and test weight explaining a small proportion of the genotypic variation. Consequently, our findings suggested that integrating epistasis in marker-assisted breeding will not lead to substantially increased selection gain for quality traits in soft winter wheat.     

Identifying quantitative trait locus by genetic background interactions in association studies

Association studies are designed to identify main effects of alleles across a potentially wide range of genetic backgrounds. To control for spurious associations, effects of the genetic background itself are often incorporated into the linear model, either in the form of subpopulation effects in the case of structure or in the form of genetic relationship matrices in the case of complex pedigrees. In this context epistatic interactions between loci can be captured as an interaction effect between the associated locus and the genetic background. In this study I developed genetic and statistical models to tie the locus by genetic background interaction idea back to more standard concepts of epistasis when genetic background is modeled using an additive relationship matrix. I also simulated epistatic interactions in four-generation randomly mating pedigrees and evaluated the ability of the statistical models to identify when a biallelic associated locus was epistatic to other loci. Under additive-by-additive epistasis, when interaction effects of the associated locus were quite large (explaining 20% of the phenotypic variance), epistasis was detected in 79% of pedigrees containing 320 individuals. The epistatic model also predicted the genotypic value of progeny better than a standard additive model in 78% of simulations. When interaction effects were smaller (although still fairly large, explaining 5% of the phenotypic variance), epistasis was detected in only 9% of pedigrees containing 320 individuals and the epistatic and additive models were equally effective at predicting the genotypic values of progeny. Epistasis was detected with the same power whether the overall epistatic effect was the result of a single pairwise interaction or the sum of nine pairwise interactions, each generating one ninth of the epistatic variance. The power to detect epistasis was highest (94%) at low QTL minor allele frequency, fell to a minimum (60%) at minor allele frequency of about 0.2, and then plateaued at about 80% as alleles reached intermediate frequencies. The power to detect epistasis declined when the linkage disequilibrium between the DNA marker and the functional polymorphism was not complete.     

Both additivity and epistasis control the genetic variation for fruit quality traits in tomato

The effect of a gene involved in the variation of a quantitative trait may change due to epistatic interactions with the overall genetic background or with other genes through digenic interactions. The classical populations used to map quantitative trait loci (QTL) are poorly efficient to detect epistasis. To assess the importance of epistasis in the genetic control of fruit quality traits, we compared 13 tomato lines having the same genetic background except for one to five chromosome fragments introgressed from a distant line. Six traits were assessed: fruit soluble solid content, sugar content and titratable acidity, fruit weight, locule number and fruit firmness. Except for firmness, a large part of the variation of the six traits was under additive control, but interactions between QTL leading to epistasis effects were common. In the lines cumulating several QTL regions, all the significant epistatic interactions had a sign opposite to the additive effects, suggesting less than additive epistasis. Finally the re-examination of the segregating population initially used to map the QTL confirmed the extent of epistasis, which frequently involved a region where main effect QTL have been detected in this progeny or in other studies.     

油菜油脂研究进展

油菜（Brassica napus）是世界范围内重要的油料作物,是植物油脂的第三大来源,其种植面积和总产量在油料作物中占有相当大的比例。我国油菜品种油脂含量普遍较国外低2—5个百分点,而油脂含量每增加1个百分点对产油量提高的贡献,相当于菜籽产量提高2．5个百分点。因此提高油菜油脂含量是解决油菜生产效益低的重要途径之一。本文综述了油菜油脂研究的状况,包括油脂积累的遗传学基础、油脂合成途径和调控、油脂含量的QTL定位及油脂含量与品质性状的遗传相关性,同时展望了油菜油脂研究前景,以期为油菜油脂含量的品种改良提供科学指导。     

油菜油脂研究进展

油菜(Brassica napus)是世界范围内重要的油料作物, 是植物油脂的第三大来源, 其种植面积和总产量在油料作物中占有相当大的比例。我国油菜品种油脂含量普遍较国外低2-5个百分点, 而油脂含量每增加1个百分点对产油量提高的贡献, 相当于菜籽产量提高2.5个百分点。因此提高油菜油脂含量是解决油菜生产效益低的重要途径之一。本文综述了油菜油脂研究的状况, 包括油脂积累的遗传学基础、油脂合成途径和调控、油脂含量的QTL定位及油脂含量与品质性状的遗传相关性, 同时展望了油菜油脂研究前景, 以期为油菜油脂含量的品种改良提供科学指导。     

应用中国和欧洲油菜建立的双二倍体群体对3个重要农艺性状的QTL定位以及与环境的互作分析

以中国的高油分自交系“高油”和欧洲高含油量品种“Sollux”的F1产生的282个株系组成的双二倍体(DH)群体为材料,在125个SSR标记座位构建的连锁图谱基础上,根据在中国和欧洲四个不同环境下的表型鉴定结果,采用混合线性模型基础上的QTL分析软件,对油菜3个重要农艺性状:株高,开花期和成熟期进行了数量性状基因座位(QTL)的联合定位分析,估测了这些QTL的加性、上位性以及与环境的互作效应。结果表明各性状均受多个加性、加加上位以及与环境互作的QTL控制。株高受多个QTL影响(12个位点具有加性或兼有环境互作效应,5个位点具有互作效应),以加性效应为主,加性效应总和可解释定位群体表型变异的75%左右,并多兼有上位性效应。12个主效QTL中,9个是“高油”等位基因相对“Sollux”有降低株高的作用,大多数加性×环境互作QTL的有效等位基因具有环境选择特异性。7个ae基因座位中,5个“高油”等位基因在杭州种植环境下,除一例外所有在德国环境下的互作基因座中,“Sollux”等位基因起着增加株高的作用,加加上位性主效总和为加性主效总和的三分之一。7个控制花期和8个控制成熟期的主效QTL中,分别有6个和5个是来自“高油”的等位基因相对“Sollux”具有提前开花和成熟的效应,这些QTL的效应总和占到性状表型变异的60%左右。5个位于第2和第12连锁群中的2个大效应QTL可能和已多次报导的VFN1和VFN3基因相近或相同。开花期和成熟期两性状均检测到显著的ae互作效应,双亲等位基因的效应在各环境下呈离散分布。位于14和19连锁群上的两个主效株高QTL同时也是控制开花期和油分含量的基因位点,因而利用这两个位点进行标记辅助筛选时要考虑到对油分含量的影响。控制成熟期的8个主效QTL中有3个同时也是控制开花期的基因座位,证实了开花期和成熟期高度正相关的遗传基础,两个生育性状均表现有较弱的QTL间加加上位互作,但以主效QTL的作用为主。     

Influence of Gene Interaction on Complex Trait Variation with Multilocus Models

Although research effort is being expended into determining the importance of epistasis and epistatic variance for complex traits, there is considerable controversy about their importance. Here we undertake an analysis for quantitative traits utilizing a range of multilocus quantitative genetic models and gene frequency distributions, focusing on the potential magnitude of the epistatic variance. All the epistatic terms involving a particular locus appear in its average effect, with the number of two-locus interaction terms increasing in proportion to the square of the number of loci and that of third order as the cube and so on. Hence multilocus epistasis makes substantial contributions to the additive variance and does not, per se, lead to large increases in the nonadditive part of the genotypic variance. Even though this proportion can be high where epistasis is antagonistic to direct effects, it reduces with multiple loci. As the magnitude of the epistatic variance depends critically on the heterozygosity, for models where frequencies are widely dispersed, such as for selectively neutral mutations, contributions of epistatic variance are always small. Epistasis may be important in understanding the genetic architecture, for example, of function or human disease, but that does not imply that loci exhibiting it will contribute much genetic variance. Overall we conclude that theoretical predictions and experimental observations of low amounts of epistatic variance in outbred populations are concordant. It is not a likely source of missing heritability, for example, or major influence on predictions of rates of evolution.     

Epistasis in the expression of relevant traits in cassava (Manihot esculenta Crantz) for subhumid conditions

There is limited knowledge on the inheritance of agronomic traits in cassava and the importance of epistasis for most crops. A nine-parent diallel study was conducted in subhumid environments. Thirty clones were obtained from each F1 cross. Each clone was represented by six plants, which were distributed in three replications at two locations. Therefore the same 30 genotypes of each F1 cross were planted in the three replications at the two locations. Analysis of variance suggested significant genetic effects for all variables analyzed (reaction to thrips, fresh root and foliage yields, harvest index, dry matter content, and root dry matter yield). Significant epistatic effects were observed for all variables, except harvest index. Dominance variance was always significant, except for dry matter content and dry matter yield. Additive variance was significant only for reaction to thrips. Results suggested that dominance plays an important role in complex traits such as root yield. The significance of epistasis can help us understand the difficulties of quantitative genetics models and QTLs in satisfactorily explaining phenotypic variation in traits with complex inheritance. Significant epistasis would justify the production of inbred parental lines to fix favorable allele combinations in the production of hybrid cassava cultivars.     

Dominance,overdominance and epistasis in Pisum sativum L.

Summary Dominant genes are the main cause of the heterosis induced by fasciated mutants of different lines of Pisum sativum. Most of these cases were originally interpreted by different authors as examples of monogenic overdominance. Several not-closely-linked genes appear to have mutated simultaneously in most of the fasciated lines. Although fasciation itself is recessive, other mutant characters, such as lateness, increased stem length (number and length of internodes) and, in part, seed production per plant, show dominant inheritance. The latter two features are, however, to a considerable extent suppressed in the fasciated lines by unfavourable gene-interactions (epistasis). Crossing these lines with non-fasciated ones shows that the epistatic genes are recessive and the dominant genes are then no longer hindered in their action. By eliminating the epistatic genes from the genomes of fasciated lines by recombination, the heterosis phenomenon has been fixed on six independent occasions for different lines. The fasciata genes themselves were found to be the most probable cause of these cases of recessive epistasis. The question whether different kinds of fasciation affect heterosis differently is examined. Recessive epistasis and dominance explain most of the quantitative distinctions between the different hybrids. In addition, one example of heterosis between non-fasciated lines is given and the possible meaning of the overall results for plant breeding and population genetics is mentioned.     

The impact of reducing fatty acid desaturation on the composition and thermal stability of rapeseed oil

Oilseed rape (Brassica napus) is the third largest source of vegetable oil globally. In addition to food uses, there are industrial applications that exploit the ability of the species to accumulate the very‐long‐chain fatty acid (VLCFA) erucic acid in its seed oil, controlled by orthologues of FATTY ACID ELONGASE 1 (Bna.FAE1.A8 and Bna.FAE1.C3). The proportion of polyunsaturated fatty acids (PUFAs) in rapeseed oil is predicted to affect its thermal stability and is controlled by orthologues of FATTY ACID DESATURASE 2, particularly Bna.FAD2.C5. Our aim was to develop rapeseed lines combining high erucic and low PUFA characters and to assess the impact on thermal stability of the oil they produce. The new type of rapeseed oil (high erucic low polyunsaturate; HELP) contained a substantially greater proportion of erucic acid (54%) compared with high erucic rapeseed oil (46%). Although the total VLCFA content was greater in oil from HELP lines (64%) than from high erucic rapeseed (57%), analysis of triacylglycerol composition showed negligible incorporation of VLCFAs into the sn‐2 position. Rancimat analysis showed that the thermal stability of rapeseed oil was improved greatly as a consequence of reduction of PUFA content, from 3.8 and 4.2 h in conventional low erucic and high erucic rapeseed oils, respectively, to 11.3 and 16.4 h in high oleic low PUFA (HOLP) and HELP oils, respectively. Our results demonstrate that engineering of the lipid biosynthetic pathway of rapeseed, using traditional approaches, enables the production of renewable industrial oils with novel composition and properties.     

Seed Structure Characteristics to Form Ultrahigh Oil Content in Rapeseed

Background

Rapeseed (Brassica napus L.) is an important oil crop in the world, and increasing its oil content is a major breeding goal. The studies on seed structure and characteristics of different oil content rapeseed could help us to understand the biological mechanism of lipid accumulation, and be helpful for rapeseed breeding.

Methodology/Principal Findings

Here we report on the seed ultrastructure of an ultrahigh oil content rapeseed line YN171, whose oil content is 64.8%, and compared with other high and low oil content rapeseed lines. The results indicated that the cytoplasms of cotyledon, radicle, and aleuronic cells were completely filled with oil and protein bodies, and YN171 had a high oil body organelle to cell area ratio for all cell types. In the cotyledon cells, oil body organelles comprised 81% of the total cell area in YN171, but only 53 to 58% in three high oil content lines and 33 to 38% in three low oil content lines. The high oil body organelle to cotyledon cell area ratio and the cotyledon ratio in seed were the main reasons for the ultrahigh oil content of YN171. The correlation analysis indicated that oil content is significantly negatively correlated with protein content, but is not correlated with fatty acid composition.

Conclusions/Significance

Our results indicate that the oil content of YN171 could be enhanced by increasing the oil body organelle to cell ratio for some cell types. The oil body organelle to seed ratio significantly highly positively correlates with oil content, and could be used to predict seed oil content. Based on the structural analysis of different oil content rapeseed lines, we estimate the maximum of rapeseed oil content could reach 75%. Our results will help us to screen and identify high oil content lines in rapeseed breeding.     

The mapping of epistatic effects onto a genealogical tree in haploid populations

In this paper we present a model that maps epistatic effects onto a genealogical tree for a haploid population. Prior work has demonstrated that genealogical structure causes the genotypic values of individuals to covary. Our results indicate that epistasis can reduce genotypic covariance that is caused by genealogical structure. Genotypic effects (both additive and epistatic) occur along the branches of a genealogical tree, from the base of the tree to its tips. Epistasis reduces genotypic covariance because there is a reweighting of the contribution of branches to the states of genotypes compared to the additive case. Branches near the tips of a genealogical tree contribute proportionally more genetic effects with epistasis than without epistasis. Epistatic effects are most numerous at basal positions in a genealogical tree when a population is constant in size and experiencing no selection, optimizing selection, diversifying selection or directional selection, indicating that epistatic effects are typically old. For a population that is growing in size, epistatic effects are most numerous at midpoints in a genealogical tree, indicating epistatic effects are of moderate age. Our results are important in that they suggest epistatic effects may typically explain deep (old) divergences and broad patterns of divergence that exist in populations, except in growing populations. In a growing population, epistatic effects may cause more within group divergence higher up in a tree and less between group divergence that is deep in a tree. The distribution of the number of epistatic effects and the expected variance and covariance in the number of epistatic effects is also provided assuming neutrality.     

The additive genetic variance after bottlenecks is affected by the number of loci involved in epistatic interactions

Abstract We investigated the role of the number of loci coding for a neutral trait on the release of additive variance for this trait after population bottlenecks. Different bottleneck sizes and durations were tested for various matrices of genotypic values, with initial conditions covering the allele frequency space. We used three different types of matrices. First, we extended Cheverud and Routman's model by defining matrices of "pure" epistasis for three and four independent loci; second, we used genotypic values drawn randomly from uniform, normal, and exponential distributions; and third we used two models of simple metabolic pathways leading to physiological epistasis. For all these matrices of genotypic values except the dominant metabolic pathway, we find that, as the number of loci increases from two to three and four, an increase in the release of additive variance is occurring. The amount of additive variance released for a given set of genotypic values is a function of the inbreeding coefficient, independently of the size and duration of the bottleneck. The level of inbreeding necessary to achieve maximum release in additive variance increases with the number of loci. We find that additive-by-additive epistasis is the type of epistasis most easily converted into additive variance. For a wide range of models, our results show that epistasis, rather than dominance, plays a significant role in the increase of additive variance following bottlenecks.     

Long-term selection for a quantitative character in large replicate populations of Drosophila melanogaster

Summary Six replicate lines of Drosophila melanogaster, which had been selected for increased abdominal bristle number for more than 85 generations, were assayed by hierarchical analysis of variance and offspring on parent regression immediately after selection ceased, and by single-generation realised heritability after more than 25 generations of subsequent relaxed selection.Half-sib estimates of heritability in 5 lines were as high as in the base population and much higher than observed genetic gains would suggest, excluding lack of sufficient additive genetic variance as a cause of ineffective selection in these lines. Also, there was considerable diversity among the six lines in composition of phenotypic variability: in addition to differences in the additive genetic component, one or more of the components due to dominance, epistasis, sex-linkage or genotype-environment interaction appeared to be important in different lines.Even after relaxed selection, single-generation realised heritabilities in four lines were as high as in the base population. As a large proportion of total genetic gain must have been made by fixation of favourable alleles, the compensatory increase of genetic variability has been sought in a genetic model involving genes at low initial frequencies, enhancement of gene effects during selection and/or new mutations.     

An olive oil-rich diet results in higher concentrations of LDL cholesterol and a higher number of LDL subfraction particles than rapeseed oil and sunflower oil diets

We investigated the effect of olive oil, rapeseed oil, and sunflower oil on blood lipids and lipoproteins including number and lipid composition of lipoprotein subclasses. Eighteen young, healthy men participated in a double-blinded randomized cross-over study (3-week intervention period) with 50 g of oil per 10 MJ incorporated into a constant diet. Plasma cholesterol, triacylglycerol, apolipoprotein B, and very low density lipoprotein (VLDL), intermediate density lipoprotein (IDL), and low density lipoprotein (LDL) cholesterol concentrations were 10;-20% higher after consumption of the olive oil diet compared with the rapeseed oil and sunflower oil diets [analysis of variance (ANOVA), P < 0.05]. The size of IDL, VLDL, and LDL subfractions did not differ between the diets, whereas a significantly higher number (apolipoprotein B concentration) and lipid content of the larger and medium-sized LDL subfractions were observed after the olive oil diet compared with the rapeseed oil and sunflower oil diets (ANOVA, P < 0.05). Total HDL cholesterol concentration did not differ significantly, but HDL(2a) cholesterol was higher after olive oil and rapeseed oil compared with sunflower oil (ANOVA, P < 0.05).In conclusion, rapeseed oil and sunflower oil had more favorable effects on blood lipids and plasma apolipoproteins as well as on the number and lipid content of LDL subfractions compared with olive oil. Some of the differences may be attributed to differences in the squalene and phytosterol contents of the oils.