Additive Epistatic Effects Research Articles

Influence of the maize Sugary1 locus on genetics of economically important traits

Knowledge of genetic control of mutant viability is of great importance in maize breeding, particularly for mutants with deleterious effects. Little is known about the genetics of the viability of mutants and no previous report has been published concerning the genetic effects of the mutant sugary1 on agronomic traits. Our objective was to study the effects of the sweetcorn mutant sugary1 (su1) on the genetic effects of agronomic traits in two wild type corn backgrounds. Estimated genetic effects of agronomic traits in Su1 versus su1 plants were monitored through four successive selfpollination cycles in two separated mean generation designs. The first involved two Corn Belt inbred lines A619 and A632, while unrelated inbred lines EP42 and A631 were used for the second design. Parents, F1s, F2s, and backcrosses were crossed to the su1 inbred P39 as the donor of su1 and the 12 crosses were successively selfpollinated for 4 years. For each cross, Su1 and su1 seeds were separated and evaluated in 10 × 10 triple lattice designs. The Su1 plants showed higher performance than the su1 plants in almost all traits. The estimates of genetic effects of Su1 versus su1 plants were strongly affected by the su1 × wild type corn interactions. The introgression of su1 in wild type corn strongly affects the genetic effects of flowering time and, to a lesser stent, that of other plant or ear traits. Mutant viability is regulated by additive, dominance and digenic epistatic effects and the importance of those genetic effects depends on the genetic background and environmental conditions.

Rhizobiological Properties of Allelopathic Rice in Suppression of Weeds and Its Research Prospect

Two reviewed areas of the research include the genetic physiological and molecular ecological characteristics, and the allelochemical identification, rhizospheric biological process and mechanism of rice allelopathy. As a quantitative trait, the allelo-pathy is mediated by both genetic and environmental factors. QTLs for allelopathy are found mainly on chromosomes 2, 3, 8, 9, and 10 significantly interacting with the additive×additive epistatic effects and the environment. However, no relevant study has been reported concerning the correlation between the QTL genetics and allelochemical synthesis. Phenolic acids, terpenoids and flavonoids have been identified in laboratory to be the metabolites showing allelopathic potentials on the target weed (barnyardgrass). Since a concentration higher than what is normally required to exhibit the allelopathic effect in rice rhizospheric soils for phenolic acids, some researchers questioned its association with the allelopathy. On the other hand, our studies indicated that the rice allelopathic potential was enhanced under stress from the increased phenolic acids in soil. Furthermore, the gene ex- pression of phenylalanine ammonia-lyase (PAL-2-1) in the allelopathic rice, PI312777, was inhibited by the RNA interference (RNAi). The transgenic rice showed decreases in the phenolic acid concentration and the rhizospheric bacterial diversity as com-pared with its wild type (WT), especially for myxobacterium, whose population was significantly lowered. The results suggested that the phenolic acids might be regulated by PAL-2-1 gene, and then be released into the soil resulting in the chemotactic aggregation of the rhizosphere characteristic microbes. Some species of microorganisms with vast diversity existing in soil could conceivably degrade plant root exudates leaving little allelochemicals to be detected. The degradation and transformation by the rhizosphere microorganisms might have a coupling effect with the allelochemicals to result in the crop’s allelopathic effect on weeds as observed. Consequently, studying the rhizospheric biological process could eventually reveal the detailed mechanism of the rice allelopathy.

Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers

Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition, this study for the first time proposed a method to construct dominance relationship matrix using SNP markers and demonstrated it in detail. The proposed model was implemented to investigate the amounts of additive genetic, dominance and epistatic variations, and assessed the accuracy and unbiasedness of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects (MAD), and 4) a full model including all three genetic components (MAED). Estimates of narrow-sense heritability were 0.397, 0.373, 0.379 and 0.357 for models MA, MAE, MAD and MAED, respectively. Estimated dominance variance and additive by additive epistatic variance accounted for 5.6% and 9.5% of the total phenotypic variance, respectively. Based on model MAED, the estimate of broad-sense heritability was 0.506. Reliabilities of genomic predicted breeding values for the animals without performance records were 28.5%, 28.8%, 29.2% and 29.5% for models MA, MAE, MAD and MAED, respectively. In addition, models including non-additive genetic effects improved unbiasedness of genomic predictions.

Combining ability for resistance to soybean rust in F2 and F3 soybean populations

The impact of soybean rust (Phakopsora pachyrhizi) on soybean yields has been extensively studied. However, few studies have evaluated early generation segregating material under field conditions for soybean rust resistance to facilitate selection. The objective of this study was to estimate combining abilities for soybean rust resistance in the F2 and F3 populations at MUARIK and F3 populations simultaneously across five locations. Combining ability for soybean rust resistance was estimated from a half diallel cross of eight soybean using disease severity and sporulation rates as indices for resistance. A consistent contribution of additive gene action was observed at MUARIK across F2 and F3 despite high environment contribution to both severity and sporulation rate. The simultaneous evaluation of F3 populations in five diverse locations produced similar results with significant GCA effects for both traits. There were, however, greater genotypic effects to soybean rust severity and sporulation across the five test environments, although genetic systems of severity and sporulation rate acted independently. Additive and additive×additive epistatic gene effects were the most common form of GCA controlling resistance. Specific combining ability did not always contribute to soybean rust resistance. The positive correlation between parental severity, sporulation rate performance and GCA estimates suggested that selection of parents for soybean rust resistance breeding can be based on parental performance. Parental line UG 5 was the most outstanding producing the greatest number of resistant populations. This study underscores the importance of additive gene effects in the control of soybean rust severity and sporulation rate.

Mapping QTLs with epistatic effects and QTL × treatment interactions for salt tolerance at seedling stage of wheat

Quantitative trait loci (QTLs) with additive (a), additive × additive (aa) epistatic effects, and their treatmental interactions (at and aat) were studied under salt stress and normal conditions at seedling stage of wheat (Triticum aestivum L.). A set of 182 recombinant inbred lines (RILs) derived from cross Xiaoyan 54 × Jing 411 were used. A total of 29 additive QTLs and 17 epistasis were detected for 12 traits examined, among which eight and seven, respectively, were identified to have QTL × treatment effects. Physiological traits rather than biomass traits were more likely to be involved in QTL × treatment interactions. Ten intervals on chromosomes 1A, 1D, 2A (two), 2D, 3B, 4B, 5A, 5B and 7D showed overlapping QTLs for different traits; some of them represent a single locus affecting different traits and/or the same trait under both treatments. Eleven pairs of QTLs were detected on seemingly homoeologous positions of six chromosome groups of wheat, showing synteny among the A, B and D genomes. Ten pairs were detected in which each pair was contributed by the same parent, indicating a strong genetic plasticity of the QTLs. The results are helpful for understanding the genetic basis of salt tolerance in wheat and provide useful information for genetic improvement of salt tolerance in wheat by marker-assisted selection.

Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice.

Seed germination capability of rice is one of the important traits in the production and storage of seeds. Quantitative trait loci (QTL) associated with seed germination capability in various storage periods was identified using two sets of recombinant inbred lines (RILs) which derived from crosses between Milyang 23 and Tong 88-7 (MT-RILs) and between Dasanbyeo and TR22183 (DT-RILs). A total of five and three main additive effects (QTLs) associated with seed germination capability were identified in MT-RILs and DT-RILs, respectively. Among them, six QTLs were identified repeatedly in various seed storage periods designated as qMT-SGC5.1, qMT-SGC7.2, and qMT-SGC9.1 on chromosomes 5, 7, and 9 in MT-RILs, and qDT-SGC2.1, qDT-SGC3.1, and qDT-SGC9.1 on chromosomes 2, 3, and 9 in DT-RILs, respectively. The QTL on chromosome 9 was identified in both RIL populations under all three storage periods, explaining up to 40% of the phenotypic variation. Eight and eighteen pairs additive × additive epistatic effect (epistatic QTL) were identified in MT-RILs and DT-RILs, respectively. In addition, several near isogenic lines (NILs) were developed to confirm six repeatable QTL effects using controlled deterioration test (CDT). The identified QTLs will be further studied to elucidate the mechanisms controlling seed germination capability, which have important implications for long-term seed storage.

Impact of epistasis and QTL × environmental interaction on the oil filling rate of soybean seed at different developmental stages

The oil accumulation in the developing soybean seed has been shown to be a dynamic process with different rates and activities at different phases affected by both genotype and environment. The objective of the present study was to investigate additive, epistatic and quantitative trait loci (QTL) × environment interaction (QE) effects of the QTL controlling oil filling rate in soybean seed. A total of 143 recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were used in this study to obtain 2 years of field data (2004 and 2005). A total of 26 QTL with significantly unconditional and conditional additive (a) effect and/or additive × environment interaction (ae) effect at different filling stages were identified on 14 linkage groups. Among the QTL with significant a effects, 18 QTL showed positive effects and 6 QTL had negative effects on seed filling rate of oil content during seed development. A total of 29 epistatic pairwise QTL underlying seed filling rate were identified at different filling stages. About 28 pairs of the QTL showed additive × additive epistatic (aa) effects and 14 pairs of the QTL showed aa × environment interaction (aae) effects at different filling stages. QTL with aa and aae (additive × additive × environment) effects appeared to vary at different filling stages. Our results demonstrated that oil filling rate in soybean seed were under genetic, developmental and environmental control.

Componentes de variância e parâmetros genéticos em uma população multirracial Nelore-Angus sob enfoque Bayesiano

Os objetivos neste estudo foram utilizar um modelo animal multirracial para verificar a presença de heterogeneidade de variância genética entre as raças Angus e Nelore, avaliar a importância da variância devida à segregação entre essas duas raças e estimar os efeitos genéticos aditivos de raça, dominância e epistasia aditiva × aditiva. Foram utilizados neste estudo 4.016 registros de ganho de peso pós-desmame do rebanho de formação da raça Brangus-Ibagé da Embrapa Pecuária Sul, analisados por três modelos distintos: modelo animal multirracial com segregação, modelo animal multirracial sem segregação; e modelo animal tradicional. A heterose reduziu substancialmente em cruzamentos avançados. A variância genética média a posteriori da raça Angus (189 ± 26 kg²) foi maior que o dobro da obtida para a raça Nelore (82 ± 23 kg²) e a variância da segregação entre essas raças foi de 11 ± 5 kg². A alteração das estimativas das variâncias genéticas raciais foi insignificante quando a variância da segregação foi fixada em zero. Critérios bayesianos de escolha apontam o modelo multirracial sem segregação entre raças como uma alternativa parcimoniosa adequada para avaliação genética dessa população.

A non-parametric mixture model for genome-enabled prediction of genetic value for a quantitative trait

A Bayesian nonparametric form of regression based on Dirichlet process priors is adapted to the analysis of quantitative traits possibly affected by cryptic forms of gene action, and to the context of SNP-assisted genomic selection, where the main objective is to predict a genomic signal on phenotype. The procedure clusters unknown genotypes into groups with distinct genetic values, but in a setting in which the number of clusters is unknown a priori, so that standard methods for finite mixture analysis do not work. The central assumption is that genetic effects follow an unknown distribution with some "baseline" family, which is a normal process in the cases considered here. A Bayesian analysis based on the Gibbs sampler produces estimates of the number of clusters, posterior means of genetic effects, a measure of credibility in the baseline distribution, as well as estimates of parameters of the latter. The procedure is illustrated with a simulation representing two populations. In the first one, there are 3 unknown QTL, with additive, dominance and epistatic effects; in the second, there are 10 QTL with additive, dominance and additive×additive epistatic effects. In the two populations, baseline parameters are inferred correctly. The Dirichlet process model infers the number of unique genetic values correctly in the first population, but it produces an understatement in the second one; here, the true number of clusters is over 900, and the model gives a posterior mean estimate of about 140, probably because more replication of genotypes is needed for correct inference. The impact on inferences of the prior distribution of a key parameter (M), and of the extent of replication, was examined via an analysis of mean body weight in 192 paternal half-sib families of broiler chickens, where each sire was genotyped for nearly 7,000 SNPs. In this small sample, it was found that inference about the number of clusters was affected by the prior distribution of M. For a set of combinations of parameters of a given prior distribution, the effects of the prior dissipated when the number of replicate samples per genotype was increased. Thus, the Dirichlet process model seems to be useful for gauging the number of QTLs affecting the trait: if the number of clusters inferred is small, probably just a few QTLs code for the trait. If the number of clusters inferred is large, this may imply that standard parametric models based on the baseline distribution may suffice. However, priors may be influential, especially if sample size is not large and if only a few genotypic configurations have replicate phenotypes in the sample.

Impact of epistasis and QTL×environment interaction on the accumulation of seed mass of soybean (Glycine maxL. Merr.)

The accumulation of seed mass in soybean is affected by both genotype and environment. The aim of the present study was to measure additive, epistatic and quantitative trait locus (QTL) x environment (QE) interaction effects of QTLs on the development of 100-seed weight in a population of 143 F5 derived recombinant inbred lines (RILs) developed from the cross between the soybean cultivars 'Charleston' and 'Dong Nong 594'. Broad-sense heritability of 100-seed weight from 30 days (30D) to 80D stages was 0.58, 0.52, 0.62, 0.60, 0.66 and 0.57, respectively. A total of 17 QTLs with conditional additive (a) effect and/or conditional additive x environment interaction (ae) effect at specific stages were identified in ten linkage groups by conditional mapping. Of them, only 4 QTLs had significant a effect or ae effect at different stages of seed development. Among QTLs with significant a effect, five acted positively and six acted negatively on seed development. A total of 35 epistatic pairwise QTLs of 100-seed weight were identified by conditional mapping at different developmental stages. Five pairs of QTL showed the additive x additive epistatic (aa) effect and 16 QTLs showed the aa x environment interaction (aae) effect at the different developmental stages. QTLs with aa effect as well with their environmental interaction effect appeared to vary at different developmental stages. Overall, the results indicated that 100-seed weight in soybean is under developmental, genetic and environmental control.

Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that has been used for estimating the average degree of dominance of quantitative trait loci (QTL) and also for studying heterosis. In this study, we first develop a multiple-interval mapping (MIM) model for design III that provides a platform to estimate the number, genomic positions, augmented additive and dominance effects, and epistatic interactions of QTL. The model can be used for parents with any generation of selfing. We apply the method to two data sets, one for maize and one for rice. Our results show that heterosis in maize is mainly due to dominant gene action, although overdominance of individual QTL could not completely be ruled out due to the mapping resolution and limitations of NC design III. For rice, the estimated QTL dominant effects could not explain the observed heterosis. There is evidence that additive x additive epistatic effects of QTL could be the main cause for the heterosis in rice. The difference in the genetic basis of heterosis seems to be related to open or self pollination of the two species. The MIM model for NC design III is implemented in Windows QTL Cartographer, a freely distributed software.

Genetic analysis on aging-resistant in rice seed

Relative germination percentage, relative germination rate, and relative germination index were studied using P1, P2, and 350 lines of a RIL population from the japonica rice (Oryza sativa L. japonica) cross of Bing 8979/C Bao. By means of mixed major gene plus polygene inheritance models, genetic analysis showed that relative germination percentage, relative germination rate, and relative germination index were controlled by two major genes plus polygenes. Both major genes and polygenes showed additive-epistatic effects. The additive effects were larger than epistatic effects in the two major genes. The heritability of major genes was larger than that of polygenes in all the three traits, indicating that the three traits investigated in the present study were mainly governed by major genes.

Heterosis for Biomass-Related Traits in Arabidopsis Investigated by Quantitative Trait Loci Analysis of the Triple Testcross Design With Recombinant Inbred Lines

Arabidopsis thaliana has emerged as a leading model species in plant genetics and functional genomics including research on the genetic causes of heterosis. We applied a triple testcross (TTC) design and a novel biometrical approach to identify and characterize quantitative trait loci (QTL) for heterosis of five biomass-related traits by (i) estimating the number, genomic positions, and genetic effects of heterotic QTL, (ii) characterizing their mode of gene action, and (iii) testing for presence of epistatic effects by a genomewide scan and marker x marker interactions. In total, 234 recombinant inbred lines (RILs) of Arabidopsis hybrid C24 x Col-0 were crossed to both parental lines and their F1 and analyzed with 110 single-nucleotide polymorphism (SNP) markers. QTL analyses were conducted using linear transformations Z1, Z2, and Z3 calculated from the adjusted entry means of TTC progenies. With Z1, we detected 12 QTL displaying augmented additive effects. With Z2, we mapped six QTL for augmented dominance effects. A one-dimensional genome scan with Z3 revealed two genomic regions with significantly negative dominance x additive epistatic effects. Two-way analyses of variance between marker pairs revealed nine digenic epistatic interactions: six reflecting dominance x dominance effects with variable sign and three reflecting additive x additive effects with positive sign. We conclude that heterosis for biomass-related traits in Arabidopsis has a polygenic basis with overdominance and/or epistasis being presumably the main types of gene action.

Gene Effects for Parameters of Peanut bud necrosis virus (PBNV) Resistance in Peanut

The objective of this study was to determine relative importance of gene effects for PBNV incidence and PBNV severity evaluated at 30, 40, 50 and 60 days after planting. Eight generations of three crosses involved three parental lines were evaluated for disease incidence (percentage of infected plants) and disease severity under natural occurrence of PBNV infection in a randomized complete block design with six replications. Evaluations were carried out at 30, 40, 50 and 60 Days After Planting (DAP). The analysis followed Hayman's model and Gamble's notations were used to describe parameters of gene effects. Joint scaling test was used to determine adequacy of the model. Additive gene effect was the most important contribution to genetic variation in generation means for both disease incidence and disease severity in the cross ICGV 86388 x IC 10. Selection for lower disease incidence and disease severity in this cross is promising. Additive gene effect and additive x additive epistatic gene effect were also important but in lower magnitude in the cross ICGV 86388 x KK 60-1 for disease incidence at 60 DAP. The presence of significant dominance gene effect in this cross for disease incidence might hinder the progress from selection. The consistent and significant additive gene effect for disease severity might provide a better selection strategy. Additive gene effect was significant for disease incidence only in the cross IC 10 x KK 60-1 at 60 DAP. Additive x dominance epistatic gene effect was also significant at 40 DAP, but no genetic parameter was significant for disease severity. This cross is considered less promising.

2,3,7,8-Tetrachlorodibenzo-p-dioxin affects fluctuating asymmetry of molar shape in mice, and an epistatic interaction of two genes for molar size

Fluctuating asymmetry (FA), random variation between left and right sides in a bilaterally symmetrical character, is a commonly used measure of developmental instability that is expected to increase with increasing environmental stress. One potential stressor is 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a powerful toxicant known to disturb tooth development. In this study, mice in the F(2) generation produced from an intercross between two inbred strains (C57BL/6J and AKR/J) were exposed in utero to TCDD. We hypothesized that TCDD would increase FA in the molars of exposed mice over that of the control mice. In addition, we hypothesized that we would discover genes for molar size, shape or asymmetry whose expression would be affected by TCDD. We detected a very small, but significant, increase in FA of molar shape (but not size) in the TCDD-exposed mice compared to the control mice, although molar size and shape did not differ between these groups. Although we did not uncover any genes that acted differently in the TCDD exposed and control groups, we did identify two genes whose dominance by additive epistatic effect on molar size was affected by TCDD. We concluded that although TCDD may be affecting the expression of some genes governing the development of molars in our population of mice, FA of molar size and shape is not a particularly sensitive indicator of this effect.

The correlation between panicle angle and rice quality and genetic analysis on rice quality in japonica rice (Oryza sativa L.)

Linear correlation between panicle angle and 10 quality traits were studied by using P1, P2 and 349 lines of the RIL population in a cross of Bing 8979(erect panicle)/C bao (curve panicle) in japonica rice. We found that, there were no linear correlation between panicle angle and brown rice rate , head rice rate, chalky grain rate, chalkiness area, gelatinization temperature, gel consistency and apparent amylose content. The correlation coefficients between panicle angle and milled rice rate, between panicle angle and grain length, and between panicle angle and grain length/width ratio were 0.124*, 0.470** and 0.241** , respectively. By using major gene-polygene mixed inheritance models, genetic analyses showed that brown rice rate, milled rice rate and apparent amylose content were controlled by two major genes plus polygenes. The two major genes expressed additive effect and additive x additive effects. Head rice rate, grain length, grain length/width ratio and gel consistency were controlled by two major genes with additive-epistatic effects plus polygenes. Chalky grain rate, chalkiness area and gelatinization temperature were controlled by three major genes with additive-epistatic effects plus polygenes. Brown rice rate, milled rice rate, head rice rate, chalky grain rate, chalkiness area and gelatinization temperature traits were mainly governed by major genes. Grain length, grain length/width ratio, gel consistency and apparent amylose content traits were mainly governed by polygenes.

Genetic analysis of flowering and maturity time in high latitude spring wheat

Due to the short growing season in the high northern latitudes, the development of early maturing spring wheat (Triticum aestivum L.) cultivars is important to avoid frost damage which can lower production and quality. We investigated earliness of flowering and maturity, and some associated agronomic traits, using a set of randomly selected high northern latitude adapted spring wheat cultivars (differing in maturity) and their F1 and F2 crosses made in a one-way diallel mating design. The parents, and their F1 and F2 crosses were evaluated under field conditions over 2 years. Anthesis and maturity times were controlled by both vernalization response and earliness per se genes, mainly acting additively. Non-additive genetic effects were more important in controlling grain fill duration, grain yield and plant height. Additive × additive epistatic effects were detected for all traits studied except time to anthesis. Segregation analyses of the F2 populations for time to anthesis indicated the presence of different vernalization response genes. Molecular genetic analyses revealed the presence of Vrn-A1 and Vrn-B1 genes in the parental cultivars. Narrow-sense heritability was medium to high (60–86%) for anthesis and maturity times but low to medium (13–55%) for grain fill duration, plant height and grain yield. Selection for early flowering/maturity in early segregating generations would be expected to result in genetic improvement towards earliness in high latitude spring wheats. Incorporation of the vernalization responsive gene Vrn-B1 in combination with vernalization non-responsive gene Vrn-A1 into spring wheats would aid in the development of early maturing cultivars with high grain yield potential for the high latitude wheat growing regions of the northern hemisphere.

Genetic impacts of fiber sugar content on fiber characters in Sea Island cotton, Gossypium barbadense L.

A genetic model with additive effect, dominant effect, additive × additive effect, and their interaction with environment effect (GE) was employed to analyze the 2-year data of F1 and F2 hybrids from 5 × 4 diallel cross, whose parents were Sea Island cotton with different fruit branch types. Unconditional and conditional genetic variances were analyzed to demonstrate genetic impacts of fiber sugar content on fiber characters. Results of unconditional genetic variances showed that dominance × environment interaction effect and additive × additive epistatic effects mainly controlled the genetic variation of fiber sugar content, and environment influenced the inheritance of fiber sugar content. Fiber uniformity, fiber elongation, and fiber micronaire were mainly controlled by dominance × environment effects. Fiber strength was mainly controlled by the interaction of additive × additive epistatic effects and the environment. Analysis of correlation coefficients indicated that the varieties or hybrids with high-fiber sugar content had short fiber, low-fiber uniformity, strength, and fineness, which indicated the close co-variation between fiber quality traits and fiber sugar content. Relatively better fiber quality traits could be obtained effectively through selecting parents with low-fiber sugar. Fiber sugar content of different parents had different genetic effect on fiber quality traits.

Mapping QTL for Biomass Yield and Its Components in Rice ( Oryza sativa L.)

Addicive effects, additive by additive epistatic effects, and their environmental interactions of QTLs are important genetic components of quantitative traits. Genetic architecture underlying rice biomass yield and its two component traits (straw yield and grain yield) were analyzed for a population of 125 DH lines from an inter-subspecific cross of IR64/Azucena. The mixed-model based composite interval mapping approach (MCIM) was used to detect QTLs, There were 12 QTLs detected with additive main effects, 27 QTLs involved in digenic interaction with aa and/or aae effects, and 18 QTLs affected by environments with ae and/or aae effects. It was revealed that epistatic effects and QE interaction effects existed on biomass yield and its component traits in rice. In addition, the genetic basis of relationships among these traits were investigated. Four QTLs and one pair of epistatic QTLs were detected to be responsible for the positive correlation between biomass yield and straw yield. Three QTLs might be responsible for the negative correlation between straw yield and grain yield. This result could partially explain the genetic basis of correlation among the three traits, and provide useful information for genetic improvement of these traits by marker-assisted selection.

Conditional QTL mapping of oil content in rapeseed with respect to protein content and traits related to plant development and grain yield

Oil content in rapeseed (Brassica napus L.) is generally regarded as a character with high heritability that is negatively correlated with protein content and influenced by plant developmental and yield related traits. To evaluate possible genetic interrelationships between these traits and oil content, QTL for oil content were mapped using data on oil content and on oil content conditioned on the putatively interrelated traits. Phenotypic data were evaluated in a segregating doubled haploid population of 282 lines derived from the F(1) of a cross between the old German cultivar Sollux and the Chinese cultivar Gaoyou. The material was tested at four locations, two each in Germany and in China. QTLMapper version 1.0 was used for mapping unconditional and conditional QTL with additive (a) and locus pairs with additive x additive epistatic (aa) effects. Clear evidence was found for a strong genetic relationship between oil and protein content. Six QTL and nine epistatic locus pairs were found, which had pleiotropic effects on both traits. Nevertheless, two QTL were also identified, which control oil content independent from protein content and which could be used in practical breeding programs to increase oil content without affecting seed protein content. In addition, six additional QTL with small effects were only identified in the conditional mapping. Some evidence was apparent for a genetic interrelationship between oil content and the number of seeds per silique but no evidence was found for a genetic relationship between oil content and flowering time, grain filling period or single seed weight. The results indicate that for closely correlated traits conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the level of individual QTL. Furthermore, conditional QTL mapping can reveal additional QTL with small effects that are undetectable in unconditional mapping.