Testing marker-based estimates of heritability in the wild

Marker-based estimates of heritability are an attractive alternative to pedigree-based methods for estimating quantitative genetic parameters in field studies where it is difficult or impossible to determine relationships and pedigrees. Here I test the ability of the marker-based method to estimate heritability of a suite of traits in a wild population of bighorn sheep (Ovis canadensis) using marker data from 32 microsatellite loci. I compared marker-based estimates with estimates obtained using a pedigree and the animal model. Marker-based estimates of heritability were imprecise and downwardly biased. The high degree of uncertainty in marker-based estimates suggests that the method may be sufficient to detect the presence of genetic variance for highly heritable traits, but not sufficiently reliable to estimate genetic parameters.     

A MARKER-BASED METHOD FOR INFERENCES ABOUT QUANTITATIVE INHERITANCE IN NATURAL POPULATIONS

A marker-based method for studying quantitative genetic characters in natural populations is presented and evaluated. The method involves regressing quantitative trait similarity on marker-estimated relatedness between individuals. A procedure is first given for estimating the narrow sense heritability and additive genetic correlations among traits, incorporating shared environments. Estimation of the actual variance of relatedness is required for heritability, but not for genetic correlations. The approach is then extended to include isolation by distance of environments, dominance, and shared levels of inbreeding. Investigations of statistical properties show that good estimates do not require great marker polymorphism, but rather require significant variation of actual relatedness; optimal allocation generally favors sampling many individuals at the expense of assaying fewer marker loci; when relatedness declines with physical distance, it is optimal to restrict comparisons to within a certain distance; the power to estimate shared environments and inbreeding effects is reasonable, but estimates of dominance variance may be difficult under certain patterns of relationship; and any linkage of markers to quantitative trait loci does not cause significant problems. This marker-based method makes possible studies with long-lived organisms or with organisms difficult to culture, and opens the possibility that quantitative trait expression in natural environments can be analyzed in an unmanipulative way.     

Estimates of genetic parameters and breeding values from western larch open-pollinated families using marker-based relationship

The availability and affordability of genetic markers made it possible to estimate quantitative genetic parameters without mating designs' structured pedigree. Here, we compared 4-year height's heritability and individuals' breeding values for a western larch common-garden population of 1,418 offspring representing 15 open-pollinated families from a 41-clone seed orchard using (a) classical pedigree models such as half- and full-sib families and (b) a molecular marker-based pedigree-free model using four pair-wise relationship estimation methods using eight informative SSR markers. The results highlighted the commonly observed inflated estimates of genetic parameters often obtained from half-sib analyses, as well as demonstrating some of the full-sib analyses' caveats. The pedigree reconstruction permitted the identification of selfed individuals, thus allowing evaluating the impact of selfing on marker-based genetic parameter estimation. The results demonstrated the utility of marker-based methods as an alternative to the classical pedigree-based approaches. Unlike the pedigree-based methods, the marker-based approach allowed better partitioning the variance components as well as separating the non-additive and additive genetic variance. The theoretical underpinning of the marker-based approach was discussed.     

Multilevel selection: the evolution of cooperation in non-kin groups

Hamiltons (1964a, 1964b) landmark papers are rightly recognized as the formal basis for our understanding of the evolution of altruistic traits. However, Hamiltons equation as he originally expressed it is simplistic. A genetically oriented approach to studying multilevel selection can provide insights into how the terminology and assumptions used by Hamilton can be generalized. Using contextual analysis I demonstrated that Hamiltons rule actually embodies three distinct processes, group selection, individual selection, and transmission genetics or heritability. Whether an altruistic trait will evolve depends the balance of all of these factors. The genetical approach, and particularly, contextual analysis provides a means of separating these factors and examining them one at a time. Perhaps the greatest issue with Hamiltons equation is the interpretation of r. Hamilton (1964a) interpreted this as relatedness. In this paper I show that what Hamilton called relatedness is more generally interpreted as the proportion for variance among groups, and that many processes in addition to relatedness can increase the variance among groups. I also show that the evolution of an altruistic trait is driven by the ratio of the heritability at the group level to the heritability at the individual level. Under some circumstances this ratio can be greater than 1. In this situation altruism can evolve even if selection favoring selfish behavior is stronger than selection favoring altruism.     

Potential bias in inbreeding depression estimates when using pedigree relationships to assess the degree of homozygosity for loci under selection

A potential bias in estimation of inbreeding depression when using pedigree relationships to assess the degree of homozygosity for loci under selection is indicated. A comparison of inbreeding coefficients based on either pedigree or genotypic frequencies indicated that, as a result of selection, the inbreeding coefficient based on pedigree might not correspond with the random drift of allelic frequencies. Apparent differences in average levels of both inbreeding coefficients were obtained depending on the genetic model (additive versus dominance, initial allelic frequencies, heritability) and the selection system assumed (no versus mass selection). In the absence of selection, allelic frequencies within a small population change over generations due to random drift, and the pedigree-based inbreeding coefficient gives a proper assessment of the accompanying probability of increased homozygosity within a replicate by indicating the variance of allelic frequencies over replicates. With selection, in addition to random drift, directional change in allelic frequencies is not accounted for by the pedigree-based inbreeding coefficient. This result implies that estimation of inbreeding depression for traits under either direct or indirect selection, estimated by a regression of performance on pedigree-based coefficients, should be carefully interpreted.Deceased     

Modification of the properties of a translocation in the German cockroach by selection

Summary A stock of Blattella germanica bearing the interchange T(3; 12)/3;12 was subjected to close inbreeding with selection for random disjunction at metaphase I. After 3–4 generations of selection, interchange quadrivalent chiasma frequency decreased, variability in free bivalent chiasma frequency increased sharply, and individuals with either random or directed disjunction were present in the stock. Random disjunction was modified from a ratio of 2112 (adj.-1; alt.-1; adj.-2; alt.-2) to a ratio of 1111. After 7–8 generations of selection, chiasma frequency appeared to stabilize at lower than normal levels and variability decreased for both quadrivalents and free bivalents. Directed disjunction was modified from a ratio of 2114 to 1112, and no individuals with the original high level of directed disjunction were detected. Chains-of-four tended to orient randomly, especially in individuals where the ring quadrivalents showed directed disjunction. Relaxation of inbreeding, but not selection, produced an increase in chiasma frequency and variability in both free bivalents and quadrivalents, but the modified ratios for both random and directed disjunction were retained. These results are discussed with respect to inbreeding effects and genetic control of chiasma frequency and metaphase I disjunction in interchange quadrivalents.     

Enzymic synthesis,chemical characterisation and Sda activity of GalNAcß1-4[NeuAcα2-3]Galß1-4GlcNAc and GalNAcß1-4[NeuAcα2-3]Galß1-4Glc

The tetrasaccharides GalNAcß1-4[NeuAc2-3]Galß1-4Glc and GalNAcß1-4[NeuAc2-3]Galß1-4GlcNAc were synthesised by enzymic transfer of GalNAc from UDP-GalNAc to 3-sialyllactose (NeuAc2-3Galß1-4Glc) and 3-sialyl-N-acetyllactosamine (NeuAc2-3Galß1-4GlcNAc). The structures of the products were established by methylation and¹H-500 MHz NMR spectroscopy. In Sd^a serological tests the product formed with 3-sialyl-N-acetyllactosamine was highly active whereas that formed with 3-sialyllactose had only weak activity.     

Puromycin enhances 20-hydroxyecdysone-induced protein synthesis in wing discs of Drosophila melanogaster

The effect of cycloheximide and puromycin on 20-hydroxyecdysone-induced protein synthesis in wing discs of Drosophila melanogaster has been studied by one-dimensional and two-dimensional SDS polyacrylamide electrophoresis. It is found that puromycin, but not cycloheximide, when applied simultaneously with the hormone enhanced the hormone-induced synthesis of the early and late proteins. However, when puromycin was applied after hormone treatment, only the late proteins were induced. The possible implication of these observations is discussed.     

Microspore cultures as donor tissue for the initiation of embryogenic cell suspensions in barley

We have initiated embryogenic cell suspension cultures of barley (Hordeum vulgare L.) Igri from isolated microspore cultures. Data were obtained on the time required for establishment, frequency of establishment, i.e. number of calluses out of the total number of initiations giving rise to suspensions, and embryogenic capacity of the suspension cultures. For comparison, establishment of embryogenic cell suspensions from callus derived from immature zygotic embryos of Igri, Dissa and Golden Promise was also carried out. The results revealed that embryogenic suspension cultures were established in half the time and with a seven-fold higher frequency from microspore cultures than from zygotic embryo-derived calluses. The suspension cultures were still capable of embryo formation after two years. However, only albino plantlets were regenerated. For comparison, long term callus cultures derived from microspores, anthers and zygotic embryos were established. From the anther and zygotic embryo-derived callus cultures green plants were continuously regenerated, whereas the microspore-derived callus cultures lost this ability after the second subculture.     

A comprehensive characterization of single-copy T-DNA insertions in the Arabidopsis thaliana genome

T-DNA flanking sequences were isolated from 112 Arabidopsis thaliana single-copy T-DNA lines and sequence mapped to the chromosomes. Even though two T-DNA insertions mapped to a heterochromatic domain located in the pericentromeric region of chromosome I, expression of reporter genes was detected in these transgenic lines. T-DNA insertion did not seem to be biased toward any of Arabidopsis' five chromosomes. The observed distribution of T-DNA copies in intergenic sequence versus gene sequence (i.e. 5-upstream regions, coding sequences and 3-downstream regions) appeared randomly. An evaluation of T-DNA insertion frequencies within gene sequence revealed that integration into 5-upstream regions occurred more frequently than expected, whereas insertions in coding sequences (exons and introns) were found less frequently than expected based on random distribution predictions. In the majority of cases, single-copy T-DNA insertions were associated with small or large rearrangements such as deletions and/or duplications of target site sequences, deletions and/or duplications of T-DNA sequences, and gross chromosomal rearrangements such as translocations. The accuracy of integration was similarly high for both left- and right-border sequences. These results may be called upon when making detailed molecular analyses of transgenic plants or T-DNA induced mutants.     

Analysis of pollen-tube growth in cultured maize silks

Summary In vitro pollen-tube growth in maize was studied using an in vitro pollination system. In the cut-silk method, ovaries with silks were placed on medium in vitro, whereafter the silk was cut and the upper part of the silk was pollinated. Pollen tubes were not able to bridge the space between the two silk parts. Even when silk parts were tightly connected, pollen tubes still were not able to pass the cut ends and reach the lower silk part. Pollen-tube growth rates and the direction of tube growth were not influenced by the presence or absence of an ovary. Prepollination did not have any influence on pollen-tube growth rate. Measurements of pollen-tube growth rate also showed that there was no population effect, i.e. growth rate was not stimulated by pollination with an excess of pollen grains. We found that the direction in which maize pollen grew was determined only by the positioning of the silk hairs.     

Comparative Analysis of the Mechanisms Underlying Nifedipine-Induced Blockade of Three Subtypes of T-Type Ca2+ Channels

We analyzed the effects of nifedipine on a family of recombinant low-threshold Ca²⁺ channels functionally expressed in Xenopus oocytes and formed by three different subunits (1G, 1H, and 1I). The 1G and 1I channels demonstrated a low sensitivity to nifedipine even in high concentrations (IC₅₀ = 98 and 243 M, maximum blocking intensity A_max = 25 and 47%, respectively). At the same time, the above agent effectively blocked channels formed by the 1H-subunit (IC₅₀ = 5 M and A_max = 41%). The nifedipine-caused effects were voltage-dependent, and their changes depended on the initial state of the channel. In the case of 1G-subunits, the blockade was determined mostly by binding of nifedipine with closed channels, whereas in the cases of 1H- and 1I-subunits this resulted from binding of nifedipine with channels in the activated and inactivated states. The obtained data allow us to obtain estimates of the pharmacological properties of the above three subtypes of recombinant channels and, in the future, to compare these characteristics with the properties of low-threshold Ca²⁺ channels in native cells.     

Multienvironment genomic variance decomposition analysis of open-pollinated Interior spruce (<Emphasis Type="Italic">Picea glauca</Emphasis> x <Emphasis Type="Italic">engelmannii</Emphasis>)

The advantages of open-pollinated (OP) family testing over controlled crossing (i.e., structured pedigree) are the potential to screen and rank a large number of parents and offspring with minimal cost and efforts; however, the method produces inflated genetic parameters as the actual sibling relatedness within OP families rarely meets the half-sib relatedness assumption. Here, we demonstrate the unsurpassed utility of OP testing after shifting the analytical mode from pedigree- (ABLUP) to genomic-based (GBLUP) relationship using phenotypic tree height (HT) and wood density (WD) and genotypic (30k SNPs) data for 1126 38-year-old Interior spruce (Picea glauca (Moench) Voss x P. engelmannii Parry ex Engelm.) trees, representing 25 OP families, growing on three sites in Interior British Columbia, Canada. The use of the genomic realized relationship permitted genetic variance decomposition to additive, dominance, and epistatic genetic variances, and their interactions with the environment, producing more accurate narrow-sense heritability and breeding value estimates as compared to the pedigree-based counterpart. The impact of retaining (random folding) vs. removing (family folding) genetic similarity between the training and validation populations on the predictive accuracy of genomic selection was illustrated and highlighted the former caveats and latter advantages. Moreover, GBLUP models allowed breeding value prediction for individuals from families that were not included in the developed models, which was not possible with the ABLUP. Response to selection differences between the ABLUP and GBLUP models indicated the presence of systematic genetic gain overestimation of 35 and 63% for HT and WD, respectively, mainly caused by the inflated estimates of additive genetic variance and individuals’ breeding values given by the ABLUP models. Extending the OP genomic-based models from single to multisite made the analysis applicable to existing OP testing programs.     

Segregation of allozymes in megagametophytes of viable seed from a natural population of jack pine,Pinus banksiana Lamb.

Summary Segregation ratios of allozymes in haploid female gametophytes obtained from viable seed were studied in a natural population of jack pine, Pinus banksiana. Stability of these ratios was assessed for three levels of the sexually reproductive crown as well as for four years of natural fertilization. Analyses of observed segregation ratios of four of five polymorphic isozyme loci showed good correspondence to the overall 11 ratios expected for simple Mendelian inheritance. Allozymes of glucose-6-phosphate dehydrogenase did not segregate in the expected 11 ratio. In addition, there were significant deviations from the expected segregation ratio for all the loci at some sampling positions on individual trees. Heterogeneity of segregation among trees, strata and years could be the result of pollen pool heterogeneity, segregation distortion and/or recessive lethal and semi-lethal gene combinations resulting in early embryo abortion. These types of segregation deviations in viable seed can affect the estimation of allele frequencies from bulked samples of a small number of individuals, the inference of heterozygosity/homozygosity of parental trees, and estimates of selfing rates.     

Relative family performance and variance structure of open-pollinated Douglas-fir seedlings grown in three competitive environments

Summary Open-pollinated Douglas-fir (Pseudotsuga menziesii var menziesii (Mirb.) Franco) families were tested in three contrasting competitive environments to test the hypothesis that relative performance as measured by total seedling dry weight is dependent upon distance or genotype of neighbors. The three competitive environmnts included (1) a mixture of individuals from all families planted at close spacing, (2) single (pure) family blocks planted at close spacing, and (3) individuals from all families planted at a wide, non-competitive spacing. Despite occasional large changes in rank between competitive environments and only moderate correlations of family means between competitive environments, the family x competitive environment interaction was non-significant. Furthermore, families did not differ significantly in competitive ability or density tolerance. The competitive environment in which seedlings were grown, however, had a large effect on estimates of variance components, which in turn led to large differences in estimates of heritability and genetic gain. Evaluation of families in mixture resulted in the largest estimates of heritability, while evaluation in pure family blocks resulted in the lowest. Analysis of correlated response to selection indicated that testing and selection in mixture result in the largest estimated gain, even if progeny of selected individuals are subsequently grown in a pure or non-competitive environment.Paper No. 2659 of the Forest Research Laboratory, Oregon State University     

Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in eucalyptus

Marker-based methods for estimating heritability and genetic correlation in the wild have attracted interest because traditional methods may be impractical or introduce bias via G x E effects, mating system variation, and sampling effects. However, they have not been widely used, especially in plants. A regression-based approach, which uses a continuous measure of genetic relatedness, promises to be particularly appropriate for use in plants with mixed-mating systems and overlapping generations. Using this method, we found significant narrow-sense heritability of foliar defense chemicals in a natural population of Eucalyptus melliodora. We also demonstrated a genetic basis for the phenotypic correlation underlying an ecological example of conditioned flavor aversion involving different biosynthetic pathways. Our results revealed that heritability estimates depend on the spatial scale of the analysis in a way that offers insight into the distribution of genetic and environmental variance. This study is the first to successfully use a marker-based method to measure quantitative genetic parameters in a tree. We suggest that this method will prove to be a useful tool in other studies and offer some recommendations for future applications of the method.     

Glyphosate in fisheries management

Glyphosate is the active ingredient of the broad-spectrum, translocated herbicide Roundup. Glyphosate is cleared for safe use in or near watercourses, being rated virtually non-toxic by the World Health Organisation. Trials in and alongside Irish fishery watercourses first commenced in 1989 and are continuing to date. The aim of this work is to evaluate the product's efficacy in clearing nuisance reed species in recreational fisheries. The longevity of control and impact on the habitat and its fauna is also investigated. Trials in canal fisheries have demonstrated the capacity of glyphosate to remove obstructive stands of reeds (mainly Schoenoplectus lacustris, Glyceria maxima, Phragmites australis, Sparganium erectum and Typha latifolia), so creating reed-free areas and swims for anglers. These swims remained open for three years following a single application. In 1992 a trial over a 3 km length of the River Boyne, a renowned salmonid fishery, was undertaken. The results clearly demonstrated the ability of glyphosate to provide long-term control of dense (354 shoots m^–2) Schoenoplectus infestations in a large watercourse. In the year following, less than one shoot per m² was present in the channel. In 1994 a small increase in density (7.6 shoots m^–2 was recorded, so enabling unobstructed angling in a stretch of river that had been virtually unfishable for years. Trout (Salmo trutta L.) and salmon (Salmo salar L.) also used the newly exposed gravels for spawning in the winter of 1993, thereby improving fish recruitment and production in the fishery.     

Norway spruce somatic embryogenesis: high-frequency initiation from light-cultured mature embryos

Somatic embryos and rooted plantlets have been regenerated from light-initiated embryogenic callus derived from mature embryos of Picea abies. Under a 16 h photoperiod, mature zygotic embryos were cultured on a modified half-strength Murashige & Skoog medium without NH₄NO₃ and supplemented with 5 mM glutamine, 4.5 M N6-benzyladenine and 10.7 M naphthaleneacetic acid or 10 M 2,4-dichlorophenoxyacetic acid. White translucent embryogenic callus, proliferating from the callusing hypocotyl region after 3 weeks incubation, was isolated from the green non-embryogenic tissue and subcultured for over 12 months. Upon transfer of the embryogenic callus through a specific sequence of media, somatic embryos proceeded to mature, elongating and forming rings of cotyledonary leaves similar to those of zygotic embryos. Transferred to medium without growth regulators, the somatic embryos germinated and produced plantlets with green cotyledons, elongated hypocotyls and primary roots.     

Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests

Nine microsatellite DNA markers (simple sequence repeats, SSRs) were used to estimate pairwise relationships among 597 Scots pine (Pinus sylvestris) trees as well as to generate a sibship structure for quantitative genetic parameters’ estimation comparison. The studied trees were part of an open-pollinated progeny test of 102 first-generation parents. Three methods were used to estimate variance components and heritabilities, namely, structured pedigree (half- and full-sib), marker-based pairwise relationships (four pairwise estimators), and a combined pedigree and marker-based relationship. In each of the three methods, the same animal model was used to compute variances except when marker-based relationship was used wherein we substituted the average numerator relationship matrix (i.e., pedigree-based matrix) with that computed based on markers’ pairwise relationships. Our results showed a high correlation in estimated breeding values between the pedigree (full-sib) and the combined marker-pedigree estimates. The marker-based relationship method produced high correlations when individual site data were analyzed. In contrast, the marker-based relationship method resulted in a significant decrease in both variance estimation and their standard errors which were in concordance with earlier published results; however, no estimates were produced when across-site analyses were attempted. We concluded that the combined pedigree method is the best approach as it represents the historical (pairwise) and contemporary (pedigree) relationships among the tested individuals, a situation that cannot be attained by any of the used methods individually. This method is dependent on the number and informativeness of the markers used.