DIFFERENTIATION AND INTEGRATION OF THE GENOME IN POPULATIONS OF THE MARINE COPEPOD TIGRIOPUS CALIFORNICUS

Geographically separated populations of the intertidal copepod Tigriopus californicus are sharply differentiated at several enzyme-encoding gene loci. Two studies were performed to investigate the extent to which the gene pools of local populations are organized into harmoniously interacting (or “coadapted”) gene complexes. In the first, the effects of interpopulation hybridization on development time were assessed. Results showed that while F₁ hybrids did not differ from parental lines, mean F₂ developmental times were as much as 50% longer. The second study used two unlinked enzyme polymorphisms as genetic markers to determine the genotypic specificity of F₂ hybrid breakdown. For two sets of parental populations, the relative viabilities of the different two-locus genotypes were determined from segregation ratios among the F₂ progeny. Sharp deviations from Mendelian ratios were observed; in the extreme, a block of genes marked by the Me^F allozyme from the LJ (La Jolla) population was found to be nearly lethal when homozygous in the F₂ of LJ × AB (Los Angeles) crosses. This same block of genes had a tenfold higher viability in crosses between LJ and SC (Santa Cruz). In the AB × LJ crosses, the two marker loci had independent (multiplicative) effects on viability. In the SC × LJ crosses, deviations from the multiplicative model were observed; the data indicate that parental homozygous genotypes have higher viability than predicted by independence, while nonparental homozygotes have lower than predicted viability. These results suggest that substantial integration of the genome has occurred within natural T. californicus populations.     

Prediction of hybrid grain yield performances in Indica Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) with effect-increasing loci

One hundred and fifty-one rice hybrids produced in two sets of half-dialell crosses and their parents (13 cytoplasmic male sterile lines and 19 restorers) were used to predict the F₁ performances of seven yield traits through the parental genetic distances (GD) based on SSR markers. The positive loci (PL) and effect-increasing loci (IL), which were screened from SSR polymorphic loci by the F₁ traits of 32 parents, together with total loci (TL), were utilized to estimate parental GD and the models were found to predict the traits of hybrids derived from different parents, fixed parents, and different environments, respectively. The results were as follows: (1) 550 polymorphic loci were detected from 174 SSR markers: a dendrogram based on these loci could separate all the sterile and restorer lines used in the present study, which indicated that parental genetic diversity of F₁ was large; (2) the correlations between F₁ traits and parental GDs based on IL ranged from 0.61 to 0.87 with a mean of 0.76, and they were higher than those on TL or on PL; (3) predictions based on IL for F₁ traits (except grain weight per plant) derived from different environments were ideal, but worse for F₁ traits derived from different parents; and (4) IL was more effective than TL and PL in predicting traits of F₁ with fixed parents, and predictions for fixed restorer combinations were more effective than those for fixed sterile line combinations. These results should facilitate molecular prediction for hybrid yield and other traits by means of both elite sterile and restorer lines.     

DNA divergence as a criterion of a sweet pepper (Capsicum annuum L.) selection for heterosis

The identification of perspective parental lines for the creation of high-yield hybrids is the most labor-consuming stage of selection, because it needs extensive trials of combining ability. Based on evaluation of the genetic divergence of the parental lines, the prediction accuracy of F₁ hybrids performance was investigated. The value of the divergence was calculated using biometric and molecular methods, such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD). Based on estimates of divergence, 10 lines were chosen for cyclic cross (scheme I) and testcross (scheme II). In most crosses, the F₁ hybrids were significantly superior to the parents in the main economically valuable traits. The level of heterosis was higher among hybrids of scheme I. Analysis of the relationship between parental divergence and F₁ performance showed that the hybrid productivity of scheme I was predetermined by ISSR divergence in 86%, and productivity was caused by RAPD divergence in 69%, whereas the F₁ yield of scheme II was not related to the value of genetic distances. Since the values of DNA divergence were closely associated both with midparent level and F₁ performance, we assumed that part of the polymorphic DNA fragments of the parental lines of scheme I is related to heterotic loci (HTL), which may be considered potential key markers for the heterotic selection of the sweet pepper.     

Influences of inbreeding and genetics on telomere length in mice

We measured telomere lengths of blood leukocytes in several inbred and outbred mammalian species, using a telomere-specific fluorescent probe and flow cytometry. Humans, non-human primates, and three outbred populations of Peromyscus mice (Peromyscus leucopus, Peromyscus maniculatus, and Peromyscus polionotus) have short telomeres. Two common strains of laboratory mice, C57BL/6J and DBA/2J, have telomeres several times longer than most other mammals surveyed. Moreover, the two inbred laboratory mouse strains display significantly different telomere lengths, suggesting the existence of strain-specific genetic determinants. To further examine the effects of inbreeding, we studied three Peromyscus leucopus inbred lines (GS109, GS16A1, and GS16B), all derived from the outbred P. leucopus stock. Telomeres of all three inbred lines are significantly lengthened relative to outbred P. leucopus, and the three lines display strain-specific significantly different telomere lengths, much like the C57BL/6J and DBA/2J strains of M. musculus. To further characterize the genetic inheritance of telomere length, we carried out several crosses to obtain hybrid F₁ mice between parental strains displaying the phenotype of long and short telomeres. In all F₁ mice assayed, peripheral blood leukocyte telomere length was intermediate to that of the parents. Additionally, we generated F₂ mice from a cross of the (P. leucopus outbred × GS16B)F₁. Based on the distribution of telomere length in the F₂ population, we determined that more than five loci contribute to telomere length regulation in Peromyscus. We concluded that inbreeding, through unknown mechanisms, results in the elongation of telomeres, and that telomere length for a given species and/or sub-strain is genetically determined by multiple segregating loci.     

Rapid genome‐wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome‐wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late‐season drought in California. These ancestor‐descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (F_ST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome‐wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution.     

Should maize doubled haploids be induced among F<Subscript>1</Subscript> or F<Subscript>2</Subscript> plants?

Maize (Zea mays L.) doubled haploid lines are typically produced from F₁ plants. Studies have suggested that the low frequency of recombinants in doubled haploids may reduce the response to selection. My objective was to determine if, for sustaining long-term response, doubled haploids should be induced in F₁ or F₂ plants during maize inbred development. In simulation experiments, I examined the response to multiple cycles of testcross selection among doubled haploid lines derived from F₁ plants (denoted by DH), doubled haploid lines derived from F₂ plants (DH_F2), and recombinant inbred (RI) lines derived by single-seed descent. For a trait controlled by 100 or more quantitative trait loci (QTL), the cumulative responses to selection were up to 4–6% larger among DH_F2 lines than among DH lines. The cumulative responses were up to 5–8% larger among RI lines than among DH lines. The QTL become unlinked as the number of QTL in a finite genome decreases, and the responses among RI, DH, and DH_F2 lines were equal or nearly equal when only 20 QTL controlled the trait. Metabolic-flux epistasis reduced the differences in the response among RI, DH, and DH_F2 lines. Overall, the results indicated that doubled haploids should be induced from F₂ plants rather than from F₁ plants. If year-round nurseries are used and new F₁ crosses for inbred development are initially created on a speculative basis, the development of doubled haploids from F₂ rather than F₁ plants should not cause a delay in inbred development.     

Drosophila simulans' response to laboratory selection for tolerance to a toxic food source used by its sister species D. sechellia

Drosophila sechellia is a specialist species which feeds and breeds on a toxic plant, Morinda citrifolia. All other Drosophila species are killed by ripe fruits of Morinda. D. simulans was subjected to laboratory selection for survival in presence of octanoic acid, the toxic compound of M. citrifolia. After 20 generations of selection, selected lines showed an increased tolerance to octanoic acid, although the response was small compared to the interspecific differences. The genetic response to selection was assessed by studying the changes in allele frequencies at 28 microsatellite loci. Three loci, located in three distinct genomic regions, showed changes in allele frequencies significantly different from what is expected under drift alone in the selected lines. An oligogenic determination for tolerance to octanoic acid is in agreement with published results based on interspecific crosses.     

Climatic adaptation and ecological divergence between two closely related pine species in Southeast China

Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra‐ and interspecific genetic variation at 25 climate‐related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two‐thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. F_ST outlier analysis identified six SNPs in five climate‐related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation‐with‐migration model indicated that gene flow between the species has been more restricted for climate‐related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species‐specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.     

Cryptic species in Diacyclops bicuspidatus (Copepoda:Cyclopoida): evidence from crossbreeding studies

The problem of cryptic species in Diacyclops bicuspidatus was examined using interpopulation crosses of four populations collected from a: (1) permanent flood lake in Kiev, Ukraine, (2) temporary pool in Kiev, (3) permanent pond in St. Petersburg, Russia (1200 km to north from Kiev) and (4) lake in Crimea (1100 km south of Kiev). The only interpopulation crosses to exhibit fertility were those between the St. Petersburg population and each of the two Kiev populations. The crosses between the Kiev and Crimea populations, between the St. Petersburg and Crimea populations, and between the two Kiev populations were sterile, as evidenced by either nonviable eggs, empty egg membranes or incomplete copulations. The F₁ hybrids resulting from the St. Petersburg permanent pond X Kiev flood lake cross were fertile and produced mature F₂ offspring. Some data on development times of parental and hybrid lines are presented. The St. Petersburg parental line showed development times almost twice as long as those of the Kiev flood lake population when reared at 10 °C and 20 °C in the laboratory. The F₁ offspring of the cross between St. Petersburg females and Kiev floodlake males showed similar development times to females of the St. Petersburg parental lines at both temperatures. The F₂ hybrids also showed development times that approximated those of the St. Petersburg parental line. These crossbreeding studies suggest the presence of cryptic species in the D. bicuspidatus inhabiting ecologically different populations in many parts of its large holarctic range.     

The genetic control of seven isozymic loci in Vicia faba L. Identification of lines and estimates of outcrossing rates between plants pollinated by bumble bees

A simplified and non-destructive method using starch gel electrophoresis has been developed on seeds to identify inbred lines of Vicia faba and assess outcrossing rates and gene dispersal in pollination experiments. Six enzyme systems (Alcohol dehydrogenase, Aspartate aminotransferase, Glucose-6-phosphate isomerase, Isocitrate dehydrogenase, Phosphogluconate dehydrogenase and Shikimate dehydrogenase) were analysed from parental lines, crosses performed between lines bearing dissimilar isozyme patterns in pollination cages with Bombus and F₂ progenies obtained from manual selfing of F₁ hybrids. The allozymes at each of the seven studied loci segregated in the expected Mendelian fashion and behaved in a co-dominant manner except for the Adh-2 locus where the only variant was a null allele. No evidence of genetic linkage was observed between at least 13 of the 15 pairs of the studied loci. Percentage of cross fertilisation by Bombus between seven pairs of inbred lines ranged between 1.7% and 28.3%. Pollen transfer between a donor line and a recipient line by two species of Bombus did not lead to differences in outcrossing rates (both about 8%). The new PGD marker with two loci at three alleles each is particularly discriminating and valuable in pollination studies and breeding of V. faba.     

Genomic evidence for population‐specific responses to co‐evolving parasites in a New Zealand freshwater snail

Reciprocal co‐evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population‐ or genotype‐specific evolutionary change. These host–parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co‐evolving host–parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its co‐evolving sterilizing trematode parasite, Microphallus sp., a textbook example of natural coevolution. We found that Microphallus‐infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population‐level co‐evolution is leading to population‐specific host–parasite interactions and evolutionary trajectories. We also used an F_ST‐based approach to identify a set of loci that represent promising candidates for targets of parasite‐mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population‐specific responses to co‐evolving infection in the P. antipodarum‐Microphallus interaction and provide new insights into the genomic basis of co‐evolutionary interactions in nature.     

Ontogeny of gene expression in Pomoxis (pisces: Centrarchidae)

The regulation of gene expression during embryogenesis was investigated in white and black crappie (Pomoxis spp.) and their reciprocal interspecific F₁ hybrids. The schedule of morphological development and the timing of isozyme expression were compared among the two species and both reciprocal maternal half-sibling F₁ hybrids. Although absolute rates of morphological development differed in response to incubation temperature, relative rates of morphological development (normalized to the onset of retinal pigment deposition) were similar among all crosses. Furthermore, these relative rates were similar to those previously documented for other centrarchid species. To assess differences in ontogenetic patterns of gene expression among the crosses, we examined expression for 39 enzymeencoding loci. Expression was not detected in the embryos for 16 loci due to low or nonexistent activity. Enzymatic activity from eight other loci were continuously detected throughout embryogenesis as a result of maternal enzyme in the egg. However, 15 loci initiated expression during the early development period investigated (fertilization through yolk sac absorption). We observed temporal variability in expression of these 15 loci among the crosses, either in the form of differential expression between parental species or as disturbances in the ontogeny of expression in interspecific hybrids. Such variability in expression suggests that some of the gene regulating mechanisms have diverged since Pomoxis species shared a common ancestral genome. © 1994 Wiley-Liss, Inc.     

Inheritance of photoperiod-induced flowering in three photoperiodic lines of Aeschynomene americana L.

Summary Induction of flowering by photoperiod was studied in the parental, F₁, F₂, and reciprocal backcross generations of crosses between three photoperiod-responsive Aeschynomene americana L. lines. Generation means appeared additive. Analysis with Mather and Jinks' scaling tests showed little or no epistasis and indicated that an additive-dominance model was adequate. Partitioning components of variation revealed that nearly all variation was additive genetic with dominance and environmental variation negligible. An additive genetic model with two loci, each with two alleles and all alleles having equal net effect, was tested using Power's partitioning method. Results demonstrated that the model fit the data and that there is a major additive genetic system controlling flowering in these crosses, with minor genetic and environmental influences present. Selection for flowering at a desired day length should be feasible.Accepted by A.R. HallauerFlorida Agricultural Experiment Station, Journal Series No. 9251     

Performance of recombinant inbred lines in Brussels sprouts (Brassica oleracea var. gemmifera)

Summary Performance of a random array of recombinant inbred lines derived by single seed descent from five different source populations of Brussels sprouts (Brassica oleracea var. gemmifera) is presented. A total of 2,356 lines were tested in trials during 1985 and 1986. Three of the source populations were derived from double crosses between F₁ hybrids. These hybrids show a considerable heterotic advantage over their inbred parents for the most important agronomic traits. The recombinant inbred lines performed, on average, less well than the parental inbred material, indicating that additive x additive genie interactions may make a significant contribution to the performance of current inbred material. Nevertheless, the very large variation among the recombinant inbred lines permitted many lines to be identified which outperformed the best parental inbred for all traits. Two lines outperformed the reference F₁ hybrid, Gower, for an index that included marketable yield and quality. Consideration was also given to the dangers of misinterpreting phenotypically based proportions. Accordingly, response equations were used to ascertain the real genetic progress that was made. Advance seemed small when compared with the large heterotic effect, which is consistent with the segregation of a large number of loci. The distribution of the recombinant inbred lines was compared to predictions made from early generation trials. There was broad agreement but significant discrepancies existed which, it is suggested, may arise from the effects of genotype-environment interactions.     

Growth performance of hybrid families by crossing selfed lines of Betula pendula Roth

Hybrid breeding is an effective approach in many agricultural crops. In allogamous tree species severe inbreeding depression and long reproductive cycles generally prohibit its use. However, three generations of selfing in silver birch (Betula pendula Roth) were obtained by forcing trees to flowering under greenhouse conditions. Hybrids were produced by crossing first-, second and third-generation selfed lines. The effects of different levels of parental inbreeding on the growth performance of hybrid families were observed in a 9-year-old field progeny test. Also, provenance crosses were carried out between selfed lines from different parts of Finland and several other European countries. Observations of growth performance of the provenance hybrids were made in the same trial. The results indicated that the mean stem volumes were significantly different between classes of parental in breeding coefficients (F_P) (P<0.0001), and were positively correlated with F_P (r=0.9106, P<0.05). Within-family variation of the hybrid families decreased with an increase of F_P. The performance of the provenance crosses between parents at a relatively close distance did not depart significantly from the standard controls. However, when the cross distance was extended far to the south, hybrids grew faster, indicating either higher heterozygosity or an extended growth period.     

Comparison of bread wheat lines selected by doubled haploid, single-seed descent and pedigree selection methods

 Yield performance of each group of ten spring bread wheat lines selected by doubled haploid (DH), single-seed descent (SSD) and pedigree selection (PS) methods from three F₁ crosses was compared with the aim of evaluating the DH method in breeding programs. Populations of 65–97 DH lines and 110 SSD lines per cross were used for selection. PS lines were developed by repeated selections from 1500 F₂ plants. Yield evaluation was performed at the F₆ generation of SSD and PS lines along with DH lines in a 2-year field experiment. It took only 2 years from the planting of wheat materials for DH production to the planting of selected DH lines for yield evaluation. There was no significant difference in grain yield between DH lines and PS lines selected from an F₁ cross whose parental varieties were closely related in their pedigrees. In two crosses with low coefficients of parentage and a large variation in their progenies, grain yield of selected DH lines was significantly lower than those of selected SSD and PS lines. These results confirm that the DH method can save time in obtaining recombinant inbred lines ready for yield evaluation. However, a larger DH population is required to achieve the same level of genetic advance with the PS method in crosses containing greater genetic variation. Received: 23 December 1997 / Accepted: 12 March 1998     

Idiosyncratic evolution of maternal effects in response to juvenile malnutrition in Drosophila

Maternal effects often affect fitness traits, but there is little experimental evidence pertaining to their contribution to response to selection imposed by novel environments. We studied the evolution of maternal effects in Drosophila populations selected for tolerance to chronic larval malnutrition. To this end, we performed pairwise reciprocal F₁ crosses between six selected (malnutrition tolerant) populations and six unselected control populations and assessed the effect of cross direction on larval growth and developmental rate, adult weight and egg‐to‐adult viability expressed under the malnutrition regime. Each pair of reciprocal crosses revealed large maternal effects (possibly including cytoplasmic genetic effects) on at least one trait, but the magnitude, sign and which traits were affected varied among populations. Thus, maternal effects contributed significantly to the response to selection imposed by the malnutrition regime, but these changes were idiosyncratic, suggesting a rugged adaptive landscape. Furthermore, although the selected populations evolved both faster growth and higher viability, the maternal effects on growth rate and viability were negatively correlated across populations. Thus, genes mediating maternal effects can evolve to partially counteract the response to selection mediated by the effects of alleles on their own carriers’ phenotype, and maternal effects may contribute to evolutionary trade‐offs between components of offspring fitness.     

RESPONSES AND CORRELATED RESPONSES TO ARTIFICIAL SELECTION ON THORAX LENGTH IN DROSOPHILA MELANOGASTER

Two sets of four replicate lines of Drosophila melanogaster were selected for large and small thorax with controls. F, progeny of crosses between the selected lines within each size category showed (a) a reduction in preadult viability in large lines relative to control and small lines when they were cultured at medium or high density in competition with a standard mutant marked competitor stock, and (b) an increase in larval development time in large lines relative to control and small lines. Natural selection for increased body size in adults may therefore be opposed by adverse effects on larval viability. The results are discussed in terms of the developmental mechanisms probably responsible for the change in body size. The preadult survival of the large and control lines was measured at three different temperatures, and there was no evidence for a significant interaction between size and temperature. The observed evolutionary increase in body size in response to reduced temperature in Drosophila must therefore involve either different genes from those subject to selection for size at a single temperature, or a fitness component other than preadult survival. There was no significant asymmetry in response to selection, and thorax length showed heterosis in crosses between the selected lines.     

Gene mutations in rye causing embryo lethality in hybrids with wheat: allelism and chromosomal localisation

In crosses between hexaploid wheat and inbred lines of rye, a small number of rye genotypes produce seeds carrying undifferentiated, non-viable embryos. Hybrids between such lines and those not showing this phenotype were used as pollen donors in crosses with bread wheat in order to determine the genetic basis of disturbed embryo development. A single gene, designated Eml-R1b, is causing this character. Molecular markers associated with F₂ genotypes derived from a contrasting rye inbred progeny were used for a linkage study. Recombinant inbred lines of an F₅ population served as testers. Eml-R1b maps to chromosome arm 6RL, along with two co-segregating microsatellite loci, Xgwm1103 and Xgwm732. Complementary interactions of deleterious genes in wheat and rye are discussed.     

Evolutionary ecology of learning: insights from fruit flies

Ecologically and evolutionarily oriented research on learning has traditionally been carried out on vertebrates and bees. While less sophisticated than those animals, fruit flies (Drosophila) are capable of several forms of learning, and have the advantage of a short generation time, which makes them an ideal system for experimental evolution studies. This review summarizes the insights into evolutionary questions about learning gained in the last decade from evolutionary experiments on Drosophila. These experiments demonstrate that Drosophila has the genetic potential to evolve a substantially improved learning performance in ecologically relevant learning tasks. In at least one set of selected populations, the improved learning generalized to a task other than that used to impose selection, involving a different behavior, different stimuli, and a different sensory channel for the aversive reinforcement. This improvement in learning ability was associated with reductions in other fitness-related traits, such as larval competitive ability and lifespan, pointing to evolutionary trade-offs for improved learning. These trade-offs were confirmed by other evolutionary experiments where a reduction in learning performance was observed as a correlated response to selection for tolerance to larval nutritional stress or for delayed aging. Such trade-offs could be one reason why fruit flies have not fully used up their evolutionary potential for learning. Finally, another evolutionary experiment with Drosophila provided the first direct evidence for the long-standing idea that learning can under some circumstances accelerate and in others slow down genetically based evolutionary change. These results demonstrate the usefulness of fruit flies as a model system to address evolutionary questions about learning.