Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat

Quantitative trait loci (QTLs) for plant height in wheat (Triticum aestivum L.) were studied using a set of 168 doubled haploid (DH) lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai’an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions (QEs). Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rht1 and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection (MAS).     

陆地棉产量性状的遗传效应及其与环境互作的分析

本研究根据加性-显性与环境互作的遗传模型, 分析了陆地棉10个杂交亲本和20个F1皮棉产量、单株铃数、单铃重、衣分和前期收花率的两年资料,估算了各项遗传方差分量和成对性状间各项遗传效应的相关。方差分析结果表明,衣分受基因型×环境互作效应影响较小,其它4个性状受基因型×环境互作影响较大,其中皮棉产量、单株铃数和前期收花率受显性×环境互作效应影响较大。遗传相关分析表明,皮棉产量与单株铃数、衣分和前期收花率加性相关系数值较大,皮棉产量与单株铃数、单铃重和前期收花率间存在较强的加性与环境互作负相关。皮棉产量与单株铃数、单铃重和前期收花率间存在显著的显性正相关,但与单株铃数、单铃重间存在显性与环境互作相关。 Abstract:Ten parents and their 20 F1s of upland cotton were analyzed for five yield traits in two years by a genetic model of additive-dominance with interaction effects.Genetic variance components and correlations were estimated.It was indicated that the gene by year effects interaction were small for lint percentage,but large for the other four traits,the dominance by year effects interaction were very large for lintvield,boll number and first picking percentage,especially.The additive correlation between lint yield with boll number,lint percentage and first picking percentage were significantly and high.The dominance correlations between lint yield and boll number,and between boll weight and first picking percentage were significantly too.The correlation of additive by year interaction between lint yield and boll number,boll weight and first picking percentage and those of dominance interaction by year between lint yield and boll number,boll weight were significant and large.The dominance correlation between boll number and boll weight were large too.     

玉米籽粒性状的遗传效应分析

采用二倍体胚和三倍体胚乳种子遗传模型及其分析方法,以5个玉米自交系及其配制的F1,F2,BC1,BC2世代为材料,研究5个玉米种子性状的胚直接效应、胚乳直接效应、母体效应和细胞质效应。分析结果表明,除粒宽外,各性状的遗传同时由细胞质效应和胚、胚乳、母体基因效应所控制,百粒重主要受胚乳和母体效应的影响,粒长的遗传以母体效应为主,粒宽和粒厚以胚乳效应为主。各部位籽粒百粒重的胚乳直接加性效应与母体加性效应的协方差达到显著或极显著水平,其余性状的胚、胚乳直接效应与母体效应间的协方差均不显著,通过母体植株的遗传表现可以对这些性状进行有效的选择。S22 是改良百粒重的优良亲本。 Abstract：The embryo,endosperm and cytoplasm effects of seven seed traits were studied by genetic model for diploid embryo and triploid endosperm plant seeds using five inbreds and their F1, F2, BC1 and BC2 generations. The estimates of genetic variance components indicated that the inheritance of all other kernel traits was controlled by the four effects except kernel width. The 100?kernel weight was mainly controlled by endosperm and maternal effects , and kernel length was controlled by the maternal effects,while endosperm conrrolled kernel width and kernel thickness. Except the significant or highly significant covariances between the endosperm direct additive and maternal additive effects for 100－kernel weight,all other traits between the embryo or endosperm direct effect and the maternal were not significant. So,maize inbreds could be developed by direct selection based on maternal plants for these traits. S22 was the best inbred of the improvement for kernel weight in this study.     

The Role of Viral Infection in Inducing Variability in Virus-Free Progeny in Tomato

The effect of virus-host interactions on subsequent generations is poorly understood. The evaluation of the effects of viral infection on inheritance of quantitative traits in the progeny of infected plants and elucidation of a possible relationship between chiasma frequency in the infected plants and variability of traits in the progeny were investigated. The current study involved genotypes of four intraspecific hybrids of tomato （Solanum lycopersicum L.）, their parental forms and two additional cultivars. Used as infection were the tobacco mosaic virus （TMV） and potato virus X （PVX）. The consequences of the effect of viral infection were evaluated based on chromosome pairing in diakinesis and/or by examining quantitative and qualitative traits in the progeny of the infected tomato plants. Tomato plants infected with TMV ＋ PVX were found to differ in chiasma frequency per pollen mother cell or per bivalent. Deviations have been observed for genotypes of both F1 hybrids and cultivars. At the same time, differences in mean values of the traits under study have only been found for progeny populations （F2-F4） derived from virus-infected F1 hybrids, but not in the case of progeny of the infected cultivars. The rate of recombinants combining traits of both parents increased significantly （2.22-8.24 times） in progeny populations of hybrids infected with TMV＋PVX. The above suggests that the observed effects could be the result of modification of recombination frequencies that can be manifested in heterozygous hybrids and make small contributions to variability in cases of ＇homozygous＇ tomato genotypes （i.e. cultivars）.     

Epistatic effect between ACACA and FABP2 gene on abdominal fat traits in broilers

Epistasis is generally defined as the interaction between two or more genes or their mRNA or protein products to influence a single trait. Experimental evidence suggested that epistasis could be important in the determination of the genetic architecture of complex traits in domestic animals. Acetyl-coenzyme A carboxylase alpha (ACACA) and fatty acid binding protein 2 (FABP2) are both key factors of lipogenesis and transport. They may play a crucial role in the weight variability of abdominal adipose tissue in the growing chicken. In this study, the polymorphisms of c.2292GA in ACACA and c.-561AC in FABP2 were detected among individuals from two broiler lines which were divergently selected for abdominal fat content. Epistasis between the two SNPs on abdominal fat weight (AFW) and abdominal fat percentage (AFP) was analyzed. The additive × additive epistatic components between these two SNPs were found significant or suggestively significant on both AFW and AFP in lean lines of the 9th and 10th generation; whereas, it was not significantly associated with either AFW or AFP in fat lines. At the same time, there were not any other significant epistatic components found in both generations or in both lines. Significant epistatic effects between these two SNPs found only in the lean lines could partly be due to the fact that the abdominal fat traits in these two experimental lines have been greatly modified by strong artificial selection. The results suggested that the epistasis mode may be different between the lean and fat chicken lines. Our results could be helpful in further understanding the genetic interaction between candidate genes contributing to phenotypic variation of abdominal fat content in broilers.     

甘蓝型油菜长角果变异体的遗传研究

用在中国发现的甘蓝型油菜长角果变异体的优良后代“鄂油长角”及短角果品种“中油821”为亲本,研究了角果长及与角果长密切相关的两个性状――千粒重和每果粒数的遗传。结果表明,角果长、千粒重、每果粒数3个性状受核基因控制,不存在任何形式的母性遗传。供试双亲间角果长性状存在2对基因的差异。长角果对短角果为显性。数量遗传分析表明,角果长、千粒重的遗传符合加性显性二基因互作模型,存在显著的上位性效应。角果长性状在两个基因座上呈联合分布,显性效应均大于加性效应,且存在超显性。千粒重性状以加性效应为主。 Abstract：Eryou long-pod,which was derived from the unique long-pod mutant discovered in China,was crossed with the commercial broad rapeseed cultivar Zhongyou 821.From the crossing six basic generations were generated for studying the genetical behaviors of pod length and two related characters i.e.1000?seed weight and seed number per pod.The results showed that the three characters were governed by nuclear genes.The difference in pod length between two parents was related to two loci.Generation mean analyses revealed that the 6?parameter mode was to interpret the inheritance of the characters studied and the epistasis was significant.Pod length mainly showed association of its genes and highly significant dominant effect,and even superdominant effect too.Meanwhile,additive effect was predominant in 1000-seed weight.     

Biology and life table studies of the oriental tobacco budworm,Helicoverpa assulta （Lepidoptera： Noctuidae）, influenced by different larval diets

Development, survivorship, pupal weight, oviposition, and life table parameters of the oriental tobacco budworm, Helicoverpa assulta Guenée, were evaluated in the laboratory on an artificial diet, pepper （Capsicumfrutescens L.）, and tobacco （Nicotiana tobacum L.）. We found that the average developmental time of immature stages was longest on tobacco （36.2 d）, intermediate on pepper （34.4 d）, and shortest on artificial diet （33.5 d）. Immature survival from egg to pupa varied from 31% on tobacco, 43% on pepper, and 74% on artificial diet. Pupal weight ranged from 197.4 mg/pupa on tobacco, 233.1 mg/pupa on pepper and 253.4 mg/pupa on artificial diet. The average numbers of eggs laid by adults reared as larvae on the artificial diet, pepper, or tobacco were 614, 421 and 334 eggs/female, respectively. Numbers of remaining eggs in ovaries of the adult females reared as larvae on the artificial diet, pepper, or tobacco were 16, 26, and 42 eggs/female, respectively. The longevity of adult females developed from larvae reared on the three diets was not significantly different, whereas the longevity of male adults from the larvae reared on artificial diet was longer （16.8 d） than that for males reared on tobacco （13.8 d） and pepper （13.3 d）. The intrinsic, finite, gross, and net rates of increase were highest for females reared as larvae on artificial diet, lowest for females emerging from larvae reared on tobacco, and intermediate for females emerging from larvae reared on pepper. Generation times and doubling time of H. assulta were shortest for larvae fed artificial diet, intermediate from larvae reared on pepper, and longest from larvae reared on tobacco. We concluded that the artificial diet was the most suitable larval diet ofH. assulta followed by pepper, and tobacco.     

家蚕胚胎期对高温干燥催青耐受性的遗传分析

本文运用完全双列杂交的方法,估测了家蚕在胚胎期对高温干燥催青条件耐受性的有关遗传参数。家蚕种对高温干燥催青的耐受性,在原种间和杂交组合间有明显差异。耐受性是一种遗传性性状,由遗传基因控制。经估算的广义遗传力大于狭义遗传力。有超显性现象。控制家蚕对高温干燥催青的耐受性的基因数目不少于两个。显性效应大于加性效应。显性效应为非单向性的。显性位点上的基因分布为不对称性。 Abstract:Some genetic parameters about endurance of silkworm to high temperature and low humidity condition during embryo stage were calculated in complete diallel crossing(6×6).There was clear variation in the endurance of both parents and F1 to the incubating condition of high temperature and low humidity.Endurance is a supper-dominant character controlled by genes not less than two.The generalized heritability is greater than narrow heritability .The effects of dominant genes were non-unidirection,with the dominant effect greater than additive effect.The distribution of genes on the location of the dominance is not symmetric.     

玉米耐铝性的遗传分析

以两个耐铝性不同的玉米自交系及它们的杂交和回交世代为材料,采用营养液培养方法,对玉米的耐铝性进行了遗传分析。结果表明,根系相对生物量具有较高的的遗传变异,其广义遗传率高达78.6%。但其狭义遗传率仅为15.4%,说明其遗传方式以显性效应为主。相反,地上部相对生物量具有相对较高的狭义遗传率（43.1%）,其遗传方式以加性效应为主。在0.1m mol/L Al3+ 胁迫条件下,根系总的和活跃的吸收比表面遗传率较低,说明此根系活力性状受环境影响较大。Abstract: The heredity of Al-tolerance was studied in different Al-tolerance of two inbred lines of maize and their F1, F2, B1 and B2 generations by the means of nutritional cultivation. The results indicated that the relative biomass(Al/CK) of root had high hereditary variance, the broad-sense heredity reached 78.6 %, but narrow-sense heredity only had 15.4 %. Its hereditary pattern mainly was dominant effects. On contrast, the relative biomass of shoot had high narrow-sense heredity (43.1%), it means that the hereditary pattern of relative biomass of shoot mainly was additive effects. On the hereditary ground of 0.1 mmol/L Al3+, the broad-sense heredity of total absorbing surface to volume ratio and active absorbing surface to volume ratio were 17.9 % and 36.4 %, and narrow-sense heredity of them were 10.0 % and 18.4 %. It means that the characters of root activity were obviously affected by environment.     

Additive and Over-dominant Effects Resulting from Epistatic Loci Are the Primary Genetic Basis of Heterosis in Rice

A set of 148 F9 recombinant inbred lines （RILs） was developed from the cross of an indica cultivar 93-11 and japonica cultivar DTI13, showing strong F1 heterosis. Subsequently, two backcross F1 （BCFI） populations were constructed by backcrossing these 148 RILs to two parents, 93-11 and DT713. These three related populations （281BCF1 lines, 148 RILs） were phenotyped for six yield-related traits in two locations. Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations. A total of 42 main-effect quantitative trait loci （M-QTLs） and 109 epistatic effect QTL pairs （E-QTLs） were detected in the three related populations using the mixed model approach. By comparing the genetic effects of these QTLs detected in the RILs, BCF1 performance and mid-parental heterosis （HMp）, we found that, in both BCF1 populations, the QTLs detected could be classified into two predominant types： additive and over-dominant loci, which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs. Further, we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations. All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.     

烤烟叶数、叶面积的遗传分析

以叶数较少、叶面积较小的烤烟品种丸叶为母本(P1),以叶数较多、叶面积较大的烤烟品种Coker319为父本,构建了6个世代分离群体,利用植物数量性状主基因+多基因混合遗传模型的联合分离分析方法,分析烤烟杂交组合丸叶×Co-ker319叶数、叶面积的遗传效应。结果表明:烤烟的叶数和叶面积均受2对加性-显性-上位性主基因+加性-显性-上位性多基因(E0)控制,其中叶数遗传以加性效应及显性×显性上位性效应为主,叶面积几种遗传效应差不多,其上位性效应>加性效应>显性效应,叶数和叶面积在B1世代的主基因遗传率分别为36.91%和2.13%,多基因遗传率分别为31.00%和19.53%,B2世代的主基因遗传率分别为51.60%和50.92%,多基因遗传率分别为16.84%和13.26%,F2世代的主基因遗传率分别为42.63%和30.32%,多基因遗传率分别为42.08%和12.18%,叶数和叶面积的主基因遗传率较高,适合在早代选择。     

猪产仔数性状基因效应与有效基因数的研究

利用太湖猪（Ｐ１）、长白猪（Ｐ２）、杂交一代（Ｆ１）、杂交二代（Ｆ２）、杂交三代（Ｆ３）;和回交一代（Ｂ２）等６个世代产仔数的材料,分析了猪产仔性状的基因效应和基因数。结果表明上位效应不显著,猪产仔数性状符合加性－显性遗传模式,受一个有效基因控制。太湖猪产仔数性状基因加性值比长白猪高１．３９头,太湖猪高产仔数基因对长白猪等位基因呈显性,显性度为０．８１。     

二棱大麦熟期性状的遗传研究

以甘木二条等7个二棱大麦品种进行不完全双列杂交,对其亲本、F1和F2的抽穗期,灌浆期和成熟期三个性状以1992和1995年（播种年份）的两年资料,采用加性-显性-上位性（ADAA）模型进行遗传分析．遗传方差分量的比率估算表明,三个性状都存在上位性作用．除灌浆期外,其余二性状还受显性和加性效应的作用,并以加性为主．显性效应和加性效应与环境的互作均达显著水平,基因效应的预测值表明采用P3（黔浙1号）和P4（浙农大3号）较易获得早熟后代．     

A new approach to the study of genetic variability of complex characters

A new approach to multivariate genetic analysis of complex organismal traits is developed. It is based on examination of the distribution of parental strains and the F1 and F2 hybrids in a multidimensional space, and the determination of the directions corresponding to heterozygosity, epistatic and additive gene effects. The effect of heterozygosity includes variability produced by interaction between and within heterozygous loci. The additive gene effects and the remaining epistatic interactions between the homozygous loci can be visualized separately from the effects of heterozygosity by an appropriate projection of the points in multidimensional space. In all, 20 morphological, physiological and behavioural characters and 21 craniometric measures were studied in crosses between two laboratory rat strains. Linear combinations of craniometric and of morphophysiological characters with a high narrow-sense heritability could be identified. These combinations characterized the organismal stress response, which had been selected for in one of the strains. The prospects for the practical application of the new approach and also for the evaluation of the contribution of the genetic diversity to phenotypic variability in animals in natural populations are discussed.     

Estimates of genetic variance in an F2 maize population

Maize (Zea mays L.) breeders have used several genetic-statistical models to study the inheritance of quantitative traits. These models provide information on the importance of additive, dominance, and epistatic genetic variance for a quantitative trait. Estimates of genetic variances are useful in understanding heterosis and determining the response to selection. The objectives of this study were to estimate additive and dominance genetic variances and the average level of dominance for an F2 population derived from the B73 x Mo17 hybrid and use weighted least squares to determine the importance of digenic epistatic variances relative to additive and dominance variances. Genetic variances were estimated using Design III and weighted least squares analyses. Both analyses determined that dominance variance was more important than additive variance for grain yield. For other traits, additive genetic variance was more important than dominance variance. The average level of dominance suggests either overdominant gene effects were present for grain yield or pseudo-overdominance because of linkage disequilibrium in the F2 population. Epistatic variances generally were not significantly different from zero and therefore were relatively less important than additive and dominance variances. For several traits estimates of additive by additive epistatic variance decreased estimates of additive genetic variance, but generally the decrease in additive genetic variance was not significant.     

Maternal effects and generation mean analysis of seed-oil content in cotton (Gossypium hirsutum L.)

Summary The nature of gene action and of maternal influence governing cottonseed oil attributes were determined with four lines, two each with high and low seed-oil percentage. For this purpose, P1, P2, F0, F1, F2 and alternative sets of BC1 and BC2 generations were analysed in six cross-combinations and their reciprocals. Marginal extents of heterosis for seed-oil percentage were noticeable in F1, with inbreeding depression in F2. Data from reciprocal backcrosses provided evidence in favour of maternal rather than cytoplasmic effects of seed-oil development. Relatively higher extents of heterosis, sizeable inbreeding depression and reciprocally unequal F2 averages were characteristic of the seed index trait, which often showed a reversal of effects from F1 to F2. Reverse reciprocal backcrosses exhibited some differences, including greater resemblance between the types, (A/B)A and (B/A)A, in addition to variable dose effects in seed index. Thus, the differences between F1 seed index values were not due to cytoplasmic influence. Positive heterotic effects for seed-oil index, especially among the backcrosses, ranged between 16.08% and 47.29% over midparent averages. Genetic component estimates from analysis of similar sets of crosses differing only in reciprocal backcrosses, and also from sets of reciprocal crosses between any two parental combinations, were inconsistent. Scaling tests detected presence of epistasis within and between a majority of cross-combinations. Despite reciprocal differences, additive gene effects for seed-oil percentage were significant in 7 out of 24 crosses, representing high x low, low x high and low x low seed-oil parents. Those were, however, accompanied by significant dominance effects of higher order. In crosses involving low seed-oil percentage parents SA1060 and SA229, all six components were detected significant, with opposite effects of dominance and dominance x dominance epistatic components. Significant additive components were also detected for seed index and seed-oil index in 7 and 5 out of 24 crosses, respectively. In the inheritance of seed index and seed-oil index, dominance effects were more important. Epistatic components of additive x additive, and to a lesser extent, those of dominant x dominant were found significant.     

Genetic divergence in adaptive characters between sympatric species of stickleback

This study explored the genetic basis of phenotypic differences between two sympatric species of ecologically and morphologically divergent sticklebacks (Gasterosteus aculeatus complex). The aim was to understand how many loci determine the differences and to what extent the differences are due to additive or nonadditive gene action. I reared the two parental species, F1 and F2 hybrids, and both backcrosses in the laboratory and measured the following quantitative characters: gill raker number and length (both involved in feeding), lateral plate number and pelvic spine length (both involved in predator defense), and growth (a fitness component). I then applied joint-scaling regression models to estimate composite additive, dominance and epistatic effects, and their contribution to divergence of parental lines. A simple additive model was sufficient for gill raker number and growth; additive and dominance effects contributed significantly to divergence in plate number and pelvic spine length; and additive, dominance, and epistatic effects contributed significantly to divergence in gill raker length. Wright's estimator for the number of loci for the four morphological characters ranged from 1 to 50. My results suggest that adaptive divergence between limnetic and benthic sticklebacks has taken place through a variety of genetic mechanisms specific to different traits. Though interspecific hybrids are completely fertile and viable in the laboratory, they are selected against in the wild. The pattern of inheritance for the traits examined here directly influences how well hybrids can exploit the two major resource environments in the wild.     

A comparison of the genetic basis of wing size divergence in three parallel body size clines of Drosophila melanogaster

Body size clines in Drosophila melanogaster have been documented in both Australia and South America, and may exist in Southern Africa. We crossed flies from the northern and southern ends of each of these clines to produce F(1), F(2), and first backcross generations. Our analysis of generation means for wing area and wing length produced estimates of the additive, dominance, epistatic, and maternal effects underlying divergence within each cline. For both females and males of all three clines, the generation means were adequately described by these parameters, indicating that linkage and higher order interactions did not contribute significantly to wing size divergence. Marked differences were apparent between the clines in the occurrence and magnitude of the significant genetic parameters. No cline was adequately described by a simple additive-dominance model, and significant epistatic and maternal effects occurred in most, but not all, of the clines. Generation variances were also analyzed. Only one cline was described sufficiently by a simple additive variance model, indicating significant epistatic, maternal, or linkage effects in the remaining two clines. The diversity in genetic architecture of the clines suggests that natural selection has produced similar phenotypic divergence by different combinations of gene action and interaction.     

Epistasis and genotype-by-environment interaction of grain protein content in durum wheat

Parental, F(1) , F (2) , BC (1) and BC (2) generations of four crosses involving four cultivars of durum wheat (Triticum durum Desf.) were evaluated at two sites in Tunisia. A three-parameter model was found inadequate for all cases except crosses Chili x Cocorit 71 at site Sidi Thabet and Inrat 69 x Karim at both sites. In most cases a digenic epistatic model was sufficient to explain variation in generation means. Dominance effects (h) and additive x additive epistasis (i) (when significant) were more important than additive (d) effects and other epistatic components. Considering the genotype-by-environment interaction, the non-interactive model (m, d, h, e) was found adequate. Additive variance was higher than environmental variance in three crosses at both sites. The estimated values of narrow-sense heritability were dependent upon the cross and the sites and were 0%-85%. The results indicate that appropriate choice of environment and selection in later generations would increase grain protein content in durum wheat.     

A complete solution for dissecting pure main and epistatic effects of QTL in triple testcross design

Epistasis plays an important role in genetics, evolution and crop breeding. To detect the epistasis, triple test cross (TTC) design had been developed several decades ago. Classical procedures for the TTC design use only linear transformations Z(1), Z(2) and Z(3), calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC design have been developed, these approaches do not provide a complete solution for dissecting pure main and epistatic effects. In this study, therefore, we developed a two-step approach to estimate all pure main and epistatic effects in the F(2)-based TTC design under the F(2) and F(∞) metric models. In the first step, with Z(1) and Z(2) the augmented main and epistatic effects in the full genetic model that simultaneously considered all putative QTL on the whole genome were estimated using empirical Bayes approach, and with Z(3) three pure epistatic effects were obtained using two-dimensional genome scans. In the second step, the three pure epistatic effects obtained in the first step were integrated with the augmented epistatic and main effects for the further estimation of all other pure effects. A series of Monte Carlo simulation experiments has been carried out to confirm the proposed method. The results from simulation experiments show that: 1) the newly defined genetic parameters could be rightly identified with satisfactory statistical power and precision; 2) the F(2)-based TTC design was superior to the F(2) and F(2:3) designs; 3) with Z(1) and Z(2) the statistical powers for the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; and 4) with Z(3) the estimation of pure epistatic effects required large sample size and family replication number. The extension of the proposed method in this study to other base populations was further discussed.