The effects of mating design on introgression between chromosomally divergent sunflower species

Population genetic theory suggests that mating designs employing one or more generations of sib-crossing or selfing prior to backcrossing are more effective than backcrossing alone for moving alleles across linkage groups where effective recombination rates are low (e.g., chromosomally divergent linkages). To test this hypothesis, we analyzed the effects of chromosomal structural differences and mating designs on the frequency and genomic distribution of introgressed markers using the domesticated sunflower, Helianthus annuus, and one of its wild relatives, H. petiolaris, as the experimental system. We surveyed 170 progeny, representing the end products of three different mating designs (design I, P-F₁-BC₁-BC₂-F₂-F₃; design II, P-F₁-F₂-BC₁-BC₂-F₃; and design III, P-F₁-F₂-F₃-BC₁-BC₂), for 197 parental RAPD markers of known genomic location. Comparison of observed patterns of introgression with expectations based on simulations of unrestricted introgression revealed that much of the genome was protected from introgression regardless of mating design or chromosomal structural differences. Although the simulations indicated that all markers should introgress into multiple individuals in each of the three mating designs, 20 of 58 (34%) markers from collinear linkage groups, and 112 of 139 (81%) markers from rearranged linkage groups did not introgress. In addition, the average size of introgressed fragments (12.2 cM) was less than half that predicted by theoretical models (26–33 cM). Both of these observations are consistent with strong selection against introgressed linkage blocks, particularly in chromosomally divergent linkages. Nonetheless, mating designs II and III, which employed one and two generations of sib-mating, respectively, prior to backcrossing, were significantly more effective at moving alleles across both collinear and rearranged linkages than mating design I, in which the backcross generations preceded sib-mating. Thus, breeding strategies that include sib-crossing, in combination with backcrossing, should significantly increase the effectiveness of gene transfer across complex genic or chromosomal sterility barriers.     

The function of Notch signalling in segment formation in the crustacean Daphnia magna (Branchiopoda)

Ten years ago we showed for the first time that Notch signalling is required in segmentation in spiders, indicating the existence of similar mechanisms in arthropod and vertebrate segmentation. However, conflicting results in various arthropod groups hampered our understanding of the ancestral function of Notch in arthropod segmentation. Here we fill a crucial data gap in arthropods and analyse segmentation in a crustacean embryo. We analyse the expression of homologues of the Drosophila and vertebrate segmentation genes and show that members of the Notch signalling pathway are expressed at the same time as the pair-rule genes. Furthermore, inactivation of Notch signalling results in irregular boundaries of the odd-skipped-like expression domains and affects the formation of segments. In severe cases embryos appear unsegmented. We suggest two scenarios for the function of Notch signalling in segmentation. The first scenario agrees with a segmentation clock involving Notch signalling, while the second scenario discusses an alternative mechanism of Notch function which is integrated into a hierarchical segmentation cascade.     

Hydrocarbons Are Essential for Optimal Cell Size,Division, and Growth of Cyanobacteria

Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that Synechococcus sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.Cyanobacteria (oxygenic photosynthetic bacteria) are found in nearly every environment on Earth and are major contributors to global carbon and nitrogen fixation (Galloway et al., 2004; Zwirglmaier et al., 2008). They are distinguished among prokaryotes in containing multiple internal thylakoid membranes, the site of photosynthesis, and a large protein compartment, the carboxysome, involved in carbon fixation. Despite these extra features, cyanobacteria can be as small as 0.6 µm in diameter (Raven, 1998).All cyanobacteria with sequenced genomes encode the pathway for the biosynthesis of hydrocarbons, implying an important, although as-yet-undefined, role for these compounds (Lea-Smith et al., 2015). The major forms are C15-C19 alkanes and alkenes, which can be synthesized from fatty acyl-acyl-carrier proteins (ACPs) by one or other of two separate pathways (Fig. 1; Schirmer et al., 2010; Mendez-Perez et al., 2011). The majority of species produce alkanes and alkenes via acyl-ACP reductase (FAR) and aldehyde deformylating oxygenase (FAD; Schirmer et al., 2010; Li et al., 2012; Coates et al., 2014; Lea-Smith et al., 2015). Cyanobacterial species lacking the FAR/FAD pathway synthesize alkenes via olefin synthase (Ols; Mendez-Perez et al., 2011; Coates et al., 2014; Lea-Smith et al., 2015). This suggests that hydrocarbons produced by either pathway serve a similar role in the cell. Homologs of FAR/FAD or Ols are not present in other bacteria or plant and algal species. However, C15-C17 alkanes and alkenes, synthesized by an alternate, uncharacterized pathway, were recently detected in a range of green microalgae, including Chlamydomonas reinhardtii, Chlorella variabilis NC64A, and several Nannochloropsis species (Sorigué et al., 2016). In C. reinhardtii, hydrocarbons were primarily localized to the chloroplast, which originated in evolution from a cyanobacterium that was engulfed by a host organism (Howe et al., 2008). Hydrocarbons may therefore have a similar role in cyanobacteria, some green microalgae species, and possibly a broader range of photosynthetic organisms.Open in a separate windowFigure 1.Hydrocarbon biosynthesis is encoded in all sequenced cyanobacteria. Detailed are the two hydrocarbon biosynthetic pathways, indicated in blue and red, respectively, in cyanobacteria. The number of species encoding the enzymes in each pathway is indicated.Hydrocarbons act as antidesiccants, waterproofing agents, and signaling molecules in insects (Howard and Blomquist, 2005) and prevent water loss, ensure pollen viability, and influence pathogen interactions in plants (Kosma et al., 2009; Bourdenx et al., 2011). However, the function of hydrocarbons in cyanobacteria has not been determined. Characterization of cyanobacterial hydrocarbon biosynthesis pathways has provided the basis for investigating synthetic microbial biofuel systems, which may be a renewable substitute for fossil fuels (Schirmer et al., 2010; Choi and Lee, 2013; Howard et al., 2013). However, secretion of long-chain hydrocarbons from the cell into the medium, which is likely essential for commercially viable production, has not been observed in the absence of a membrane solubilization agent (Schirmer et al., 2010; Tan et al., 2011). Cyanobacterial hydrocarbons also have a significant environmental role. Due to the abundance of cyanobacteria in the environment, hydrocarbon production is considerable, with hundreds of millions of tons released into the ocean per annum following cell death (Lea-Smith et al., 2015). This production may be sufficient to sustain populations of hydrocarbon-degrading bacteria, which can then play an important role in consuming anthropogenic oil spills (Lea-Smith et al., 2015).Here, we investigated the cellular location and role of hydrocarbons in both spherical Synechocystis sp. PCC 6803 (Synechocystis) and rod-shaped Synechococcus sp. PCC 7002 (Synechococcus) cells. We developed a model of the cyanobacterial membrane, which indicated that hydrocarbons aggregate in the middle of the lipid bilayer and, when present at levels observed in cells, lead to membrane swelling associated with pools of hydrocarbon. This suggested that alkanes may facilitate membrane curvature. In vivo measurements of Synechococcus thylakoid membrane conformation are consistent with this model.     

Genetic architecture of a selection response in Arabidopsis thaliana

Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life-history and fitness-related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map-based population genetic data to study how selection acts on standing genetic variation in populations.     

Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana

Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation for this observed variation is the action of heterogeneous natural selection in the wild. Here we report that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. At one QTL, the allele that enhanced the viability of fall-germinating seedlings in North Carolina reduced the fecundity of spring-germinating seedlings in Rhode Island. Several other QTL experienced strong directional selection, but only in one site and seasonal cohort. Thus, different loci were exposed to selection in different natural environments. Selection on allelic variation also depended upon the genetic background. The allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus. Moreover, alternative alleles at each of these loci caused reversals in the allelic fitness effects of a QTL closely linked to TFL1, a candidate developmental gene displaying nucleotide sequence polymorphism consistent with balancing selection. Thus, both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.     

Quantitative trait loci for inflorescence development in Arabidopsis thaliana

Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler x Col and Cvi x Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi x Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.     

External morphology of limb development in the amphipod <Emphasis Type="Italic">Orchestia cavimana</Emphasis> (Crustacea,Malacostraca, Peracarida)

The external morphology of limb development in Orchestia cavimana is examined by scanning electron microscopy and fluorescence staining from the appearance of the first limb buds until hatching. As other amphipods, O. cavimana undergoes direct development and the degree of segmental differentiation shows a more or less continual decrease in anteroposterior direction. Limbs form ventrally as small buds, which elongate and divide into podomeres early in development. This early subdivision largely corresponds with the limb segmentation of the hatchling. When the post-naupliar limbs start to develop, the germ band begins to split into two halves along the midline, so that the trunk limbs transiently occupy a very dorsolateral position. After the germ band has closed again, the differentiation into the characteristic amphipodan tagmata (cephalothorax, pereon, pleon) takes place and the limb podomeres lose their round-shape. The late embryo is covered by a so-called intermediate cuticle, which is formed after an embryonic moult and shed after hatching. The early development of O. cavimana reveals the Anlage of a vestigial seventh pleonic segment that is assumed to belong to the ground pattern of malacostracans, but is retained as a free, limbless segment only in adult Leptostraca. A transient subdivision of the proximal segment of the pleopods suggests the occurrence of a coxa and a basis in these limbs. The mandible attains its upright, adult position via a characteristic bending process that is strikingly similar to that in Archaeognatha (Insecta).     

Functional alterations after cardiac sodium-calcium exchanger overexpression in heart failure

The sodium-calcium exchanger (NCX) is discussed as one of the key proteins involved in heart failure. However, the causal role and the extent to which NCX contributes to contractile dysfunction during heart failure are poorly understood. NCX overexpression was induced by infection with an adenovirus coding for NCX, which coexpressed green fluorescence protein (GFP) (AdNCX) by ex vivo gene transfer to nonfailing and failing rabbit cardiomyocytes. Myocardial gene transfer in rabbits in vivo was achieved by adenoviral delivery via aortic cross-clamping. Peak cell shortening of cardiomyocytes was determined photo-optically. Hemodynamic parameters in vivo were determined by echocardiography (fractional shortening) and tip catheter [maximal first derivative of left ventricular (LV) pressure (dP/dt(max)); maximal negative derivative of LV pressure (-dP/dt(max))]. Peak cell shortening was depressed after NCX gene delivery in isolated nonfailing and in failing cardiomyocytes. In nonfailing rabbits in vivo, basal systolic contractility (fractional shortening and dP/dt(max)) and maximum rate of LV relaxation (-dP/dt(max)) in vivo were largely unaffected after NCX overexpression. However, during heart failure, long-term NCX overexpression over 2 wk significantly improved fractional shortening and dP/dt(max) compared with AdGFP-infected rabbits, both without inotropic stimulation and after beta-adrenergic stimulation with isoproterenol. -dP/dt(max) was also improved after NCX overexpression in the failing rabbits group. These results indicate that short-term effects of NCX overexpression impair contractility of isolated failing and nonfailing rabbit cardiomyocytes. NCX overexpression over 2 wk in vivo does not seem to affect myocardial contractility in nonfailing rabbits. Interestingly, in vivo overexpression of NCX decreased the progression of systolic and diastolic contractile dysfunction and improved beta-adrenoceptor-mediated contractile reserve in heart failure in rabbits in vivo.