Levels Of Outcrossing Research Articles

Detection of relatedness in chemical alarm cues by a selfing vertebrate depends on population and the life stage producing the alarm cue

Aquatic prey have impressive abilities to extract information from a variety of chemical cues. For example, they can use the alarm cues released by wounded individuals during a predator attack to learn about predation risk, and they can also distinguish kin from non-kin individuals during interactions. However, it remains unclear whether animals can combine this information on predation risk with kin recognition of the particular individuals under threat. To examine how the relatedness of the individuals in alarm cue affects behaviour we used the self-fertilizing hermaphroditic mangrove rivulus (Kryptolebias marmoratus), in which lineages produce genetically identical offspring through selfing. We explored this in two populations that differ in their level of outcrossing. We measured activity before and after exposure to alarm cue made from individuals (either adults or embryos) from their own lineage or an unrelated lineage from the same population. Fish responded weakly to embryo alarm cues, but tended to reduce their activity more when the alarm cues were from an unrelated lineage compared to alarm cues from their own lineage, particularly in fish from the outcrossing population. In contrast, there was no effect of cue relatedness on the response to adult alarm cues but there was a strong population effect. Specifically, individuals from the outcrossing population tended to react more strongly to alarm cues compared to individuals from the predominantly selfing population. We discuss the potential roles of the major histocompatibility complex in cue detection, differences between adult vs embryo alarm cues in terms of concentration and information, and underlying differences among populations and genetic lineages in their production and detection of chemical cues. Whether this kin recognition offers adaptive benefits or is simply a consequence of being able to detect relatedness in living individuals would be an exciting area for future research.

Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae.

Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping-by-sequencing. Coalescent-based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide.

Point mutations including a novel Pro-197-Phe mutation confer cross resistance to acetolactate synthase (ALS) inhibiting herbicides in Lactuca serriola in Australia.

Control of prickly lettuce has become increasingly difficult for lentil growers in southern Australia due to widespread resistance to common herbicides, a lack of alternative herbicide options, and prolific production of highly mobile seed. This study aimed to quantify ALS-inhibiting herbicide resistance in the Mid North (MN) and Yorke Peninsula (YP) of South Australia, characterise the resistance mutations present, and investigate population structure and gene flow in this species. Resistance was identified in all populations tested, with average survival of 92% to chlorsulfuron and 95% to imazamox + imazapyr. Five different amino acid substitutions were identified at Proline-197 of the ALS gene. There was no significant difference in the LD50 between plants with these five different substitutions when treated with metsulfuron-methyl, however, imidazolinone resistance level was higher in plants with a phenylalanine substitution and lower in plants with a serine. Population structure based on 701 SNPs and 271 individuals provided evidence for both the independent evolution of the same mutation in different populations, as well as frequent short to medium distance dispersal accompanied by occasional long-distance dispersal events. The overall inbreeding coefficient (FIS ) was calculated at 0.5174, indicating an intermediate level of outcrossing despite the cross-pollination experiment showing only low outcrossing. In the structure analyses, most individuals from YP were assigned to a single cluster, whereas most individuals from MN were assigned 50% to each of two clusters, indicating some genetic differences between these two regions, but also evidence for dispersal between them. Use of imidazolinone herbicides has selected for mutations conferring higher levels of resistance, such as the Pro-197-Phe mutation, and resulted in further spread of resistance in this species. This article is protected by copyright. All rights reserved.

Insect Pollinator Monitoring in and around a Netted Plot of Apple Trees—Biosafety Implications for Genetically Engineered Fruit Trees

The complete netting of orchards is one strategy to protect fruit trees from pest and pathogen damage by reducing insect movement. When the cultivated trees were derived from genetic engineering (GE), reduced pollinator movement may also reduce outcrossing to cultivated or wild non-GE trees. We report on a field study over four years in a plot of apple tress supplied with insect side nets and covered with hail nets that were closed from shortly before flowering to harvest. A reduced number of arthropods in general, and large bees in particular, were recorded inside the netted plot compared with outside. However, wild bees colonized the plot before the net was closed and built up populations inside. An additional experiment demonstrated that small bees were able to cross the hail net. While the nets were effective in excluding large bees as active pollen vectors, the proportion of small bees acting as such remained unquantified. Furthermore, a companion study showed occasional cross-pollination events through the netting. For the field release of GE apple trees, acceptable levels of outcrossing thus need to be defined.

Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers.

Red clover (Trifolium pratense) is one of the most important fodder crops worldwide. The knowledge of genetic diversity among red clover populations, however, is under development. This study provides insights into its genetic diversity, using single nucleotide polymorphism (SNP) markers to define population structure in wild and cultivated red clover. Twenty-nine accessions representing the genetic resources available at NordGen (the Nordic gene bank) and Lantmännen (a Swedish agricultural company with a red clover breeding program) were used for this study. Genotyping was performed via SeqSNP, a targeted genotype by sequencing method that offers the capability to target specific SNP loci and enables de novo discovery of new SNPs. The SNPs were identified through a SNP mining approach based on coding sequences of red clover genes known for their involvement in development and stress responses. After filtering the genotypic data using various criteria, 623 bi-allelic SNPs, including 327 originally targeted and 296 de novo discovered SNPs were used for population genetics analyses. Seventy-one of the SNP loci were under selection considering both Hardy-Weinberg equilibrium and pairwise FST distributions. The average observed heterozygosity (HO), within population diversity (HS) and overall diversity (HT) were 0.22, 0.21 and 0.22, respectively. The tetraploids had higher average HO (0.35) than diploids (0.21). The analysis of molecular variance (AMOVA) showed low but significant variation among accessions (5.4%; P < 0.001), and among diploids and tetraploids (1.08%; P = 0.02). This study revealed a low mean inbreeding coefficient (FIS = −0.04) exhibiting the strict outcrossing nature of red clover. As per cluster, principal coordinate and discriminant analyses, most wild populations were grouped together and were clearly differentiated from the cultivated types. The cultivated types of red clover had a similar level of genetic diversity, suggesting that modern red clover breeding programs did not negatively affect genetic diversity or population structure. Hence, the breeding material used by Lantmännen represents the major genetic resources in Scandinavia. This knowledge of how different types of red clover accessions relate to each other and the level of outcrossing and heterozygosity will be useful for future red clover breeding.

One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species.

Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis – a narrow endemic, critically endangered plant species – we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uH E(0%missing data)=0.205, 95% CI (0.160, 0.250); uH E(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t (0%missing data)=0.883, SE±0.0483; t (30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F (0%missing data)=−0.145, 95% CI (−0.189, −0.101); F (30%missing data)=−0.105, 95% CI (−0.199, −0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.

Pollen limitation and xenia effects in a cultivated mass-flowering tree, Macadamia integrifolia (Proteaceae).

Pollen limitation is most prevalent among bee-pollinated plants, self-incompatible plants and tropical plants. However, we have very little understanding of the extent to which pollen limitation affects fruit set in mass-flowering trees despite tree crops accounting for at least 600 million tons of the 9200 million tons of annual global food production. We determined the extent of pollen limitation in a bee-pollinated, partially self-incompatible, subtropical tree by hand cross-pollinating the majority of flowers on mass-flowering macadamia (Macadamia integrifolia) trees that produce about 200 000-400 000 flowers. We measured tree yield and kernel quality and estimated final fruit set. We genotyped individual kernels by MassARRAY to determine levels of outcrossing in orchards and assess paternity effects on nut quality. Macadamia trees were pollen-limited. Supplementary cross-pollination increased nut-in-shell yield, kernel yield and fruit set by as much as 97, 109 and 92 %, respectively. The extent of pollen limitation depended upon the proximity of experimental trees to trees of another cultivar because macadamia trees were highly outcrossing. Between 84 and 100 % of fruit arose from cross-pollination, even at 200 m (25 rows) from orchard blocks of another cultivar. Large variations in nut-in-shell mass, kernel mass, kernel recovery and kernel oil concentration were related to differences in fruit paternity, including between self-pollinated and cross-pollinated fruit, thus demonstrating pollen-parent effects on fruit quality (i.e. xenia). This study is the first to demonstrate pollen limitation in a mass-flowering tree. Improved pollination led to increased kernel yield of 0.31-0.59 tons ha-1, which equates currently to higher farm-gate income of approximately $US3720-$US7080 ha-1. The heavy reliance of macadamia flowers on cross-pollination and the strong xenia effects on kernel mass demonstrate the high value that pollination services can provide to food production.

Multiple reproductive strategies of a spring ephemeral plant, Fritillaria maximowiczii, enable its adaptation to harsh environments

AbstractSpring ephemeral plants that experience harsh environments have developed specific reproductive characteristics. These characteristics are of great importance to the survival and reproduction of these species, particularly for rare and endangered plants. Fritillaria is a genus consisting of spring ephemeral plants with significant medicinal and ornamental value whose wild resources are highly threatened and whose reproductive characteristics and adaptative evolutionary mechanisms are still not well understood. Fritillaria maximowiczii is positioned at the most basal clade on the Fritillaria phylogenetic tree, whose reproductive characteristics remain obscure. In this study, we report the flowering dynamics, pollination biology and breeding system of F. maximowiczii. The flowering process of F. maximowiczii can be divided into seven stages. Based on the pollen/ovule ratio, the outcrossing index and a field pollination experiment on a natural population, F. maximowiczii showed high levels of outcrossing and self‐compatibility. Three types of pollinators were observed: two kinds of bumblebees, and spiders. Diverse herkogamy and dichogamy may have considerably improved its reproductive success rate. Furthermore, a special reproductive mode not previously reported in wild populations of Fritillaria, apomixis, was strongly suspected based on a high fruit setting rate (36.84%). Our study suggests F. maximowiczii has developed multiple reproductive strategies to adapt to harsh environments and ensure population reproduction, and the diverse reproductive mechanisms may be related to its primitive phylogenetic position in the genus. This study not only broadens our understanding of mechanisms of ecological adaptation in spring ephemeral plants but also provides key data for the conservation of Fritillaria.

Breeding Polyploid Varieties of Acacia: Reproductive and Early Growth Characteristics of the Allotetraploid Hybrid (Acacia mangium × A. auriculiformis) in Comparison with Diploid Progenitors

Diploid clones of the hybrid acacia (Acacia mangium × A. auriculiformis) are widely planted in Vietnam because of their high productivity, adaptability, and commercial wood yields. Polyploid breeding offers possibilities for further enhancing hybrid vigor and generating new high value genotypes. In a field trial, we compared three diploid hybrid clones with their respective colchicine-induced tetraploid lines. Flowering and seed production of each cytotype were observed and open pollinated seed collected for determination of outcrossing rate and ploidy, inbreeding depression and marker inheritance in the progeny. Comparisons are also made with published characteristics of autotetraploids derived from A. mangium. Compared with their corresponding diploid cytotypes, the allotetraploids flowered slightly later but more intensely; produced the same number of seeds per pod but larger seeds; and showed a greatly reduced level of outcrossing (an average of 14% compared with 87%). Inbreeding depression for height growth was less for progeny from the allotetraploid lines (17%) than for those from the original diploids (33%). 96% of seeds from the allotetraploid clones were also tetraploid, but we observed triploids at low frequency at both the seed and field progeny stages. The segregation of the molecular markers in outcrossed allotetraploid progenies demonstrated both disomic and tetrasomic inheritance, indicating that the hybrid behaves as a segmental allotetraploid. Results suggest that an open pollinated breeding strategy is a practical option for improving polyploid acacia hybrids.

Genetic characterization of global collection of flax (L. Usitatissimum L.) utilizing molecular marker

In assess the sufficient knowledge of genetic diversity, population structure and linkage disequilibrium were estimated among the three representative sub-population: Pop 1 (Indian accessions), Pop 2 (different species of Linum genus) and Pop 3 (exotic accessions) of flax using ISSR marker systems. A total of 118 number of alleles were amplified by eleven primers, with an average of 10.64 alleles per primer (100 bp −2072 bp). The maximum PIC value (0.25) was observed in the primer combination UBC808, which indicated that it as the most informative primer among the eleven primers to study genetic diversity among flax genotypes. The results of the AMOVA indicated that genetic variation within sub-populations (92%) was significantly higher than the variation among the sub-population (8%). According to the results of split network tree analysis, population structure and PCA, the total 264 flax accessions were distinctly clustered into eight genetic groups. Overall the mean LD value was less than the threshold level (r2 < 0.1) explaining that the population has a high level of outcrossing or gene flow. The knowledge generated through ISSR fingerprinting in this study has enhanced our conception of population structure and LD of the flax population, which has high implications for genetic improvement and association mapping.

Temporal diversification and no geographic population structure in the most abundant European ectomycorrhizal fungus Russula ochroleuca

Abstract Although Russula ochroleuca is a common ectomycorrhizal (ECM) species in European forests, its reproduction mode, dispersal range, and population structure remains unknown. Altogether, 462 fruit bodies from three spruce forests (two 15 km apart, one 230 km distant from the first two) were analysed using AFLP markers. A mixed mode of reproduction, with several large genets accompanied by a majority of single fruit body genets, was found. Low level of inbreeding (Fis = 0.0021–0.0072), low level of genetic differentiation among subpopulations (PhiPT = 0.037–0.190) and negligible isolation by distance (r = 0.033, P = 0.005) indicates effective spore dispersal and a high level of outcrossing across the sampled area. Finally, we discovered temporal diversification within this species, as evidenced by genetic differentiation between early (August) and late (September) fruiting genotypes.

How and When Does Outcrossing Occur in the Predominantly Selfing Species Medicago truncatula?

Empirical studies on natural populations of Medicago truncatula revealed selfing rates higher than 80%, but never up to 100%. Similarly, several studies of predominantly selfing species show variability in the level of residual outcrossing between populations and also between temporal samples of the same population. However, these studies measure global selfing rates at the scale of the population and we do not know whether there is intra-population variation and how outcrossing events are distributed, between genotypes, plants, flowers, or seeds. Theoretical studies predict the maintenance of residual outcrossing in highly selfing species due to environmental (e.g., pollen biology) and/or genetic determinants and decompositions of the variation in outcrossing rate using experimental data can be very informative to test these hypotheses. Here, we focus on one natural population of M. truncatula in order to describe precisely its mating system. In particular, we investigated the determinants of the selfing rate by testing for seasonal variations (environmental determinism) and variations between genotypes (genetic determinism). We measured selfing rates in maternal progenies from plants collected widely across a natural population. For each plant, we collected pods from flowers produced at the beginning and at the end of the flowering season to test for a seasonal variation in the outcrossing rate. For each collected offspring, we also estimated the likelihood that it was issued from a self-fertilization event and assessed the genetic component of variation of this mating system measure. We found a significant, albeit small, increase in outcrossing rate in progenies collected at the end [tm = 0.137 (SD = 0.025)] compared to those collected at the beginning [tm = 0.083 (0.016)] of the flowering season. A significant between genotypes variation in selfing rate was also detected, resulting in a heritability of 9% for the rate of residual outcrossing. Altogether, our work shows that despite a predominantly selfing reproductive mode, M. truncatula displays variation in residual outcrossing rate, and that this trait is likely under a complex determinism combining environmental and genetic factors. We discuss the evolutionary implications of our results for the population.

Biased Gene Conversion Constrains Adaptation in Arabidopsis thaliana.

Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better understand constraints on responses to both natural and human-mediated selection. Here, using whole-genome, transcriptome, and methylome data from >600 Arabidopsis thaliana individuals, we set out to identify important features influencing selective constraint. Our analyses reveal that multiple factors underlie the accumulation of maladaptive mutations, including gene expression level, gene network connectivity, and gene-body methylation. We then focus on a feature with major effect, nucleotide composition. The ancestral vs. derived status of segregating alleles suggests that GC-biased gene conversion, a recombination-associated process that increases the frequency of G and C nucleotides regardless of their fitness effects, shapes sequence patterns in A. thaliana Through estimation of mutational effects, we present evidence that biased gene conversion hinders the purging of deleterious mutations and contributes to a genome-wide signal of decreased efficacy of selection. By comparing these results to two outcrossing relatives, Arabidopsis lyrata and Capsella grandiflora, we find that protein evolution in A. thaliana is as strongly affected by biased gene conversion as in the outcrossing species. Last, we perform simulations to show that natural levels of outcrossing in A. thaliana are sufficient to facilitate biased gene conversion despite increased homozygosity due to selfing. Together, our results show that even predominantly selfing taxa are susceptible to biased gene conversion, suggesting that it may constitute an important constraint to adaptation among plant species.

Food/Feed and Environmental Risk Assessment of Genetically Modified Glufosinate-tolerant Oilseed Rape MS8, RF3 and MS8 x RF3 for Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/BE/96/01)

Food/Feed and Environmental Risk Assessment of Genetically Modified Glufosinate-tolerant Oilseed Rape MS8, RF3 and MS8 x RF3 for Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/BE/96/01)

Relationships between Nut Size, Kernel Quality, Nutritional Composition and Levels of Outcrossing in Three Macadamia Cultivars.

Tree nuts play an important role in healthy diets, but their economic value and nutritional quality may be affected by their size and paternity. We assessed relationships between nut size and kernel recovery, the incidence of whole kernels, fatty acid composition and mineral nutrient concentrations in three macadamia cultivars, “Daddow”, “816” and “A4”. We determined to what extent differences in nut size and quality were the result of different levels of cross- or self-paternity. Small nuts of all cultivars had lower kernel recovery than large nuts, and small nuts provided lower incidence of whole kernels in “Daddow” and “A4”. Small kernels had a lower relative abundance of the saturated fatty acid, palmitic acid, in all cultivars and higher relative abundance of the unsaturated fatty acid, oleic acid, in “Daddow” and “A4”. Small kernels had higher concentrations of many essential nutrients such as nitrogen and calcium, although potassium concentrations were lower in small kernels. Most nuts arose from cross-pollination. Therefore, nut size and kernel quality were not related to different levels of cross- and self-paternity. Identified cross-paternity was 88%, 78% and 90%, and identified self-paternity was 3%, 2% and 0%, for “Daddow”, “816” and “A4”, respectively. Small macadamia kernels are at least as nutritious as large macadamia kernels. High levels of cross-paternity confirmed that many macadamia cultivars are predominantly outcrossing. Macadamia growers may need to closely inter-plant cultivars and manage beehives to maximise cross-pollination.

Food, Feed and Environmental Risk Assessment of Glufosinatetolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing Under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Food, Feed and Environmental Risk Assessment of Glufosinatetolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing Under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Preliminary Environmental Risk Assessment of Genetically Modified Oilseed Rape MON 88302 for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (Application EFSA/GMO/BE/2011/101)

Preliminary Environmental Risk Assessment of Genetically Modified Oilseed Rape MON 88302 for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (Application EFSA/GMO/BE/2011/101)

Environmental Risk Assessment of Glufosinate-Tolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Environmental Risk Assessment of Glufosinate-Tolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Environmental Risk Assessment of Glufosinate-Tolerant Genetically Modified Oilseed Rape MS8, RF3 and MS8 x RF3 for Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/BE/96/01)

Environmental Risk Assessment of Glufosinate-Tolerant Genetically Modified Oilseed Rape MS8, RF3 and MS8 x RF3 for Import, Processing and Feed Uses under Directive 2001/18/EC (Notification C/BE/96/01)

Hybridization and geographic distribution shapes the spatial genetic structure of two co-occurring orchid species.

Multiple ecological and life-history traits shape the fine-scale spatial genetic structure (FSGS) of a given population. The occurrence in core versus peripheral populations, levels of outcrossing, pollen and seed dispersal, and hybridization are important biological properties that influence the kinship of individuals within populations. We examined spatial genetic structure within 15 populations of Epidendrum fulgens and E. puniceoluteum distributed along a linear gradient of Brazilian coastal vegetation, including both allopatric and sympatric populations where the two orchid species hybridize. We analyzed 581 mapped specimens using nine simple sequence repeat loci, aiming to investigate how geographic distribution and hybridization shape within-population FSGS. A significant increase in FSGS was found towards peripheral populations, compared to core populations. Analysis of short-distance and long-distance components of FSGS identified biparental inbreeding and higher levels of FSGS at peripheral populations, when compared to core populations. In contrast, the relatively high density of reproductive adults in core populations potentially leads to highly overlapping seed and pollen movement, decreasing FSGS. Hybridization was an important factor shaping within-population spatial genetic structure at sympatric sites, decreasing the FSGS observed in parental species. Our results indicate that different ecological forces act in concert to create a gradient of FSGS along species distribution ranges, shaped by extensive levels of intraspecific and interspecific gene exchange.