Single tester triple test cross analysis in spring wheat

Summary Two experiments, each including the same 30 homozygous varieties of spring wheat plus one separate tester variety, were conducted in order to detect epistasis and to test and estimate the additive and dominance components of genetic variation for five quantitative traits: final plant height, spike length, number of spikelets per spike, 100-kernel weight and grain yield per plant. Epistasis played a significant role in the control of 100-kernel weight and yield per plant. There was a gratifyingly good agreement between the two independent methods (2¯B₁i — ¯f_1i — ¯P_i and 2¯B_ci — ¯F_1i) used to test the presence of epistasis. In both experiments, there was a remarkably uniform high dominance ratio for most of the traits studied indicating that this test cross design is equally sensitive to both additive and dominance genetic variation.     

Linkage of RAPD markers to NESTUR, a stem growth index in radiata pine seedlings

 Needle-to-stem unit rate (NESTUR) is a stem growth index of conifer seedlings that measures the efficiency of stemwood production per unit of foliage growth. The random amplified polymorphic DNA (RAPD) technique was applied to haploid DNA from the megagametophytes of a full-sib radiata pine cross to find markers linked to factors controlling the NESTUR trait. Using the bulked segregant analysis approach, 23 of 933 primers displayed putative linkage to factors controlling NESTUR. Based on the genotypic analysis of 174 individuals, two quantitative trait loci (QTLs) controlling NESTUR were identified at ANOVA P-levels of 0.01–0.001. The QTLs were identified by RAPD markers OPE-06₄₅₀ and OPA-10₁₂₀₀, which were linked to each other (r=7%), and UBC-333₅₅₀, which was not linked to the other two. Linkage to components of NESTUR (increments in stem diameter and stem volume) was demonstrated for UBC-333₅₅₀, while the others were not linked to NESTUR components. Received: 18 December 1996/Accepted: 24 January 1997     

Premature progression of anther early developmental programs accompanied by comprehensive alterations in transcription during high-temperature injury in barley plants

Kernel number per spike is one of the most important yield components of wheat. To map QTLs related to kernel number including spike length (SPL), spikelet number per spike (SPN), fertile spikelet number (FSPN), sterile spikelet number (SSPN) and compactness, and to characterize the inheritance modes of the QTLs and two-locus interactions, 136 recombinant inbred lines (RILs) derived from ‘Nanda2419’ x ‘Wangshuibai’ and an immortalized F₂ population (IF₂) generated by randomly permutated intermating of these RILs were investigated. QTL mapping made use of the previously constructed over 3300 cM linkage map of the RIL population. Three, five, two, two and six chromosome regions were identified, respectively, for their association with SPL, SPN, FSPN, SSPN, and compactness in at least two of the three environments examined. All compactness QTLs but one shared the respective intervals of QSpn.nau-5A and the SPL QTLs. Xcfd46–Xwmc702 interval on chromosome 7D was related to all traits but SSPN and had consistently the largest effects. The fact that not all the compactness QTL intervals were related to both SPL and SPN indicates that compactness is regulated by different mechanisms. Interval coincidence between QTLs of SPL and SPN and between QTLs of FSPN and SSPN was minimal. For all the traits, favorable alleles exist in both parents. Inheritance modes from additiveness to overdominance of the QTLs were revealed and two-locus interactions were detected, implying that the traits studied are under complex genetic control. The results could contribute to wheat yield improvement and better use of Wangshuibai and Nanda2419 the two special germplasms in wheat breeding program.     

Invasion of gene duplication through masking for maladaptive gene flow

Gene duplication can increase an organism's ability to mask the effect of deleterious alleles present in the population, but this is typically a small effect when the source of the genetic variation is mutation. Migration can introduce orders of magnitude more deleterious alleles per generation and may therefore be an important force acting on the structure of genomes. Using formal analytical methods, we study the invasion of haplotypes containing two copies of the resident allele, assuming that a single-locus equilibrium is already established in a continent-island model of migration. Provided that the immigrant allele can be completely masked by multiple functional gene copies, a new duplication will deterministically spread so long as duplicate haplotypes are, on average, fitter than single-copy haplotypes. When fitness depends on the number of immigrant allele copies and their masking ability then the threshold for invasion depends on the rate of immigration and the rate of recombination between the gene copies. Results from several special cases, including formation of protein dimers and Dobzhansky-Muller incompatibilities, suggest that duplications can invade in a wide range of selection regimes. We hypothesize that duplication in response to gene flow may provide an explanation for the high levels of polymorphism in gene copy number observed in natural populations.     

Multilocus selection in subdivided populations I. Convergence properties for weak or strong migration

The dynamics and equilibrium structure of a deterministic population-genetic model of migration and selection acting on multiple multiallelic loci is studied. A large population of diploid individuals is distributed over finitely many demes connected by migration. Generations are discrete and nonoverlapping, migration is irreducible and aperiodic, all pairwise recombination rates are positive, and selection may vary across demes. It is proved that, in the absence of selection, all trajectories converge at a geometric rate to a manifold on which global linkage equilibrium holds and allele frequencies are identical across demes. Various limiting cases are derived in which one or more of the three evolutionary forces, selection, migration, and recombination, are weak relative to the others. Two are particularly interesting. If migration and recombination are strong relative to selection, the dynamics can be conceived as a perturbation of the so-called weak-selection limit, a simple dynamical system for suitably averaged allele frequencies. Under nondegeneracy assumptions on this weak-selection limit which are generic, every equilibrium of the full dynamics is a perturbation of an equilibrium of the weak-selection limit and has the same stability properties. The number of equilibria is the same in both systems, equilibria in the full (perturbed) system are in quasi-linkage equilibrium, and differences among allele frequencies across demes are small. If migration is weak relative to recombination and epistasis is also weak, then every equilibrium is a perturbation of an equilibrium of the corresponding system without migration, has the same stability properties, and is in quasi-linkage equilibrium. In both cases, every trajectory converges to an equilibrium, thus no cycling or complicated dynamics can occur.      

Genetics of resistance to the pink stem borer (Sesamia nonagrioides) in maize (Zea mays)

Our knowledge of the genetics of resistance to the pink stem borer ( Sesamia nonagrioides ) in maize ( Zea mays ) is restricted to a few crosses among maize inbreds. The objectives of this study were to enlarge our understanding of the genetics of traits related to damage by pink stem borer and yield under infestation and to use generation means analyses to compare per se and testcross performance for detecting epistatic effects. All generations, either per se or crossed to testers, were evaluated in a 10 × 10 triple lattice design under artificial infestation with S. nonagrioides in 2005 and 2006. Most traits fit an additive–dominance model; but evidence for epistasis for resistance and yield under infestation was shown. Epistasis, in general, did not appear to play an important role in the inheritance of yield under pink stem borer infestation. However, the epistasis contribution to maize yield performance could be important in some outstanding crosses such as EP42 × A637. Testcross generation means revealed epistatic effects undetected by the generation means analysis, but neither method was able to eliminate dominance effects that could prevail over epistatic effects.     

Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions

With technological advances in genetic mapping studies more of the genes and polymorphisms that underlie Quantitative Trait Loci (QTL) are now being identified. As the identities of these genes become known there is a growing need for an analysis framework that incorporates the molecular interactions affected by natural polymorphisms. As a step towards such a framework we present a molecular model of genetic variation in sporulation efficiency between natural isolates of the yeast, Saccharomyces cerevisiae. The model is based on the structure of the regulatory pathway that controls sporulation. The model captures the phenotypic variation between strains carrying different combinations of alleles at known QTL. Compared to a standard linear model the molecular model requires fewer free parameters, and has the advantage of generating quantitative hypotheses about the affinity of specific molecular interactions in different genetic backgrounds. Our analyses provide a concrete example of how the thermodynamic properties of protein-protein and protein-DNA interactions naturally give rise to epistasis, the non-linear relationship between genotype and phenotype. As more causative genes and polymorphisms underlying QTL are identified, thermodynamic analyses of quantitative traits may provide a useful framework for unraveling the complex relationship between genotype and phenotype.     

GENETIC ARCHITECTURE OF METABOLIC RATE: ENVIRONMENT SPECIFIC EPISTASIS BETWEEN MITOCHONDRIAL AND NUCLEAR GENES IN AN INSECT

The extent to which mitochondrial DNA (mtDNA) variation is involved in adaptive evolutionary change is currently being reevaluated. In particular, emerging evidence suggests that mtDNA genes coevolve with the nuclear genes with which they interact to form the energy producing enzyme complexes in the mitochondria. This suggests that intergenomic epistasis between mitochondrial and nuclear genes may affect whole‐organism metabolic phenotypes. Here, we use crossed combinations of mitochondrial and nuclear lineages of the seed beetle Callosobruchus maculatus and assay metabolic rate under two different temperature regimes. Metabolic rate was affected by an interaction between the mitochondrial and nuclear lineages and the temperature regime. Sequence data suggests that mitochondrial genetic variation has a role in determining the outcome of this interaction. Our genetic dissection of metabolic rate reveals a high level of complexity, encompassing genetic interactions over two genomes, and genotype × genotype × environment interactions. The evolutionary implications of these results are twofold. First, because metabolic rate is at the root of life histories, our results provide insights into the complexity of life‐history evolution in general, and thermal adaptation in particular. Second, our results suggest a mechanism that could contribute to the maintenance of nonneutral mtDNA polymorphism.     

A SIMULATION OF WRIGHT'S SHIFTING-BALANCE PROCESS: MIGRATION AND THE THREE PHASES

Wright partitioned the shifting-balance process into three phases. Phase one is the shift of a deme within a population to the domain of a higher adaptive peak from that of the historical peak. Phase two is mass selection within a deme towards that higher peak. Phase three is the conversion of additional demes to the higher peak. The migration rate between demes is critical for the existence of phases one and three. Phase one requires small effective population sizes, hence low migration rates. Phase three is optimal under high migration rates that spread the most-fit genotype from deme to deme. Thus, a population-wide peak shift requires intermediate levels of migration. By altering the rates of phases one and three, migration affects the predominant direction of mass selection within a population. This study examines the degree to which migration, through its effects on phases one and three, determines the probability of a simulated population arriving at its genotypic optimum after 12,000 generations. These simulations reveal that there is a range of migration rates for which an entire population might be expected to shift to a higher peak. Below m = 0.001 peak shifts occur frequently (phases I and II) but are not successfully exported out of subpopulations (phase III), and above 0.01 peak shifts within demes (phase I and II), required to initiate phase III, become increasingly uncommon. Because it is unlikely that real populations will have uniform migration rates from generation to generation, the probable effects of varying migration rates on broadening the range of conditions producing peak shifts are discussed.     

A variety of epistatic interactions can occur between partially homologous transgene loci brought together by sexual crossing

Summary Epistatic interactions between unlinked transgene loci in tobacco plants were studied following sexual crosses between different transgenic lines. Three potential modifier transgene loci, which were structurally similar but integrated at different chromosomal locations, were tested for their ability to influence the expression of a partially homologous target transgene locus. After introduction of an individual modifier locus, the target locus could be either unaffected, completely inactivated and methylated or differentially sensitive, showing more complete inactivation and methylation when homozygous than when hemizygous. The implications of these results for inbreeding depression in plants are discussed.