Identifying wheat genomic regions for improving grain protein concentration independently of grain yield using multiple inter-related populations

Grain yield (GY) and grain protein concentration (GPC) are two major traits contributing to the economic value of the wheat crop. These are, consequently, major targets in wheat breeding programs, but their simultaneous improvement is hampered by the negative correlation between GPC and GY. Identifying the genetic determinants of GPC and GY through quantitative trait loci (QTL) analysis would be one way to identify chromosomal regions, allowing improvement of GPC without reducing GY using marker-assisted selection. Therefore, QTL detection was carried out for GY and GPC using three inter-connected doubled haploid populations grown in a large multi-environment trial network. Chromosomes 2A, 2D, 3B, 7B and 7D showed co-location of QTL for GPC and GY with antagonistic effects, thus contributing to the negative GPC–GY relationship. Nonetheless, genomic regions determining GPC independently of GY across experiments were found on chromosomes 3A and 5D and could help breeders to move the GPC–GY relationship in a desirable direction.     

Innate immune recognition of flagellin limits systemic persistence of Brucella

Brucella are facultative intracellular bacteria that cause chronic infections by limiting innate immune recognition. It is currently unknown whether Brucella FliC flagellin, the monomeric subunit of flagellar filament, is sensed by the host during infection. Here, we used two mutants of Brucella melitensis, either lacking or overexpressing flagellin, to show that FliC hinders bacterial replication in vivo. The use of cells and mice genetically deficient for different components of inflammasomes suggested that FliC was a target of the cytosolic innate immune receptor NLRC4 in vivo but not in macrophages in vitro where the response to FliC was nevertheless dependent on the cytosolic adaptor ASC, therefore suggesting a new pathway of cytosolic flagellin sensing. However, our work also suggested that the lack of TLR5 activity of Brucella flagellin and the regulation of its synthesis and/or delivery into host cells are both part of the stealthy strategy of Brucella towards the innate immune system. Nevertheless, as a flagellin‐deficient mutant of B. melitensis wasfound to cause histologically demonstrable injuries in the spleen of infected mice, we suggested that recognition of FliC plays a role in the immunological stand‐off between Brucella and its host, which is characterized by a persistent infection with limited inflammatory pathology.     

Intraspecific variation of recombination rate in maize

Background

In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation.

Results

Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between recombination rate and interference strength.

Conclusions

To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.     

Robust Demographic Inference from Genomic and SNP Data

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with , the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.     

Midcell Recruitment of the DNA Uptake and Virulence Nuclease,EndA, for Pneumococcal Transformation

Genetic transformation, in which cells internalize exogenous DNA and integrate it into their chromosome, is widespread in the bacterial kingdom. It involves a specialized membrane-associated machinery for binding double-stranded (ds) DNA and uptake of single-stranded (ss) fragments. In the human pathogen Streptococcus pneumoniae, this machinery is specifically assembled at competence. The EndA nuclease, a constitutively expressed virulence factor, is recruited during competence to play the key role of converting dsDNA into ssDNA for uptake. Here we use fluorescence microscopy to show that EndA is uniformly distributed in the membrane of noncompetent cells and relocalizes at midcell during competence. This recruitment requires the dsDNA receptor ComEA. We also show that under ‘static’ binding conditions, i.e., in cells impaired for uptake, EndA and ComEA colocalize at midcell, together with fluorescent end-labelled dsDNA (Cy3-dsDNA). We conclude that midcell clustering of EndA reflects its recruitment to the DNA uptake machinery rather than its sequestration away from this machinery to protect transforming DNA from extensive degradation. In contrast, a fraction of ComEA molecules were located at cell poles post-competence, suggesting the pole as the site of degradation of the dsDNA receptor. In uptake-proficient cells, we used Cy3-dsDNA molecules enabling expression of a GFP fusion upon chromosomal integration to identify transformed cells as GFP producers 60–70 min after initial contact between DNA and competent cells. Recording of images since initial cell-DNA contact allowed us to look back to the uptake period for these transformed cells. Cy3-DNA foci were thus detected at the cell surface 10–11 min post-initial contact, all exclusively found at midcell, strongly suggesting that active uptake of transforming DNA takes place at this position in pneumococci. We discuss how midcell uptake could influence homology search, and the likelihood that midcell uptake is characteristic of cocci and/or the growth phase-dependency of competence.     

Intraluminal thrombus and risk of rupture in patient specific abdominal aortic aneurysm – FSI modelling

Recent numerical studies of abdominal aortic aneurysm (AAA) suggest that intraluminal thrombus (ILT) may reduce the stress loading on the aneurysmal wall. Detailed fluid structure interaction (FSI) in the presence and absence of ILT may help predict AAA rupture risk better. Two patients, with varied AAA geometries and ILT structures, were studied and compared in detail. The patient specific 3D geometries were reconstructed from CT scans, and uncoupled FSI approach was applied. Complex flow trajectories within the AAA lumen indicated a viable mechanism for the formation and growth of the ILT. The resulting magnitude and location of the peak wall stresses was dependent on the shape of the AAA, and the ILT appeared to reduce wall stresses for both patients. Accordingly, the inclusion of ILT in stress analysis of AAA is of importance and would likely increase the accuracy of predicting AAA risk of rupture.     

Functional Gene Polymorphism to Reveal Species History: The Case of the CRTISO Gene in Cultivated Carrots

Background

Carrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO) has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history.

Methodology/Principal Findings

In this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group), and another one mainly from Europe (Western group). The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots.

Conclusion

The carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia material remains unclear.     

Mixing Plants from Different Origins to Restore a Declining Population: Ecological Outcomes and Local Perceptions 10 Years Later

Populations of the Large-flowered Sandwort (Arenaria grandiflora L.) in the Fontainebleau forest (France) have declined rapidly during the last century. Despite the initiation of a protection program in 1991, less than twenty individuals remained by the late 1990s. The low fitness of these last plants, which is likely associated with genetic disorders and inbreeding depression, highlighted the need for the introduction of non-local genetic material to increase genetic diversity and thus restore Fontainebleau populations. Consequently, A. grandiflora was introduced at three distant sites in the Fontainebleau forest in 1999. Each of these populations was composed of an identical mix of individuals of both local and non-local origin that were obtained through in vitro multiplication. After establishment, the population status (number of individuals, diameter of the plants, and number of flowers) of the introduced populations was monitored. At present, two populations (one of which is much larger than the other) persist, while the third one became extinct in 2004. Analyses of the ecological parameters of the introduction sites indicated that differences in soil pH and moisture might have contributed to the differences in population dynamics. This introduction plan and its outcome attracted interest of local community, with those who supported the plan and regarded its 10-year result as a biological success (i.e., persistent populations were created), but also those who expressed reservations or disapproval of the plan and its outcome. To understand this controversy, a sociological study involving 27 semi-structured interviews was carried out. From these interviews emerged three areas of controversy: alteration of the identity of the plant, alteration of the identity of its territory, and the biological and ethical consequences of the techniques used for the experimental conservation.     

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

Objective

Characterization of HIV-1 sequences in newly infected individuals is important for elucidating the mechanisms of viral sexual transmission. We report the identification of transmitted/founder viruses in eight pairs of HIV-1 sexually-infected patients enrolled at the time of primary infection (“recipients”) and their transmitting partners (“donors”).

Methods

Using a single genome-amplification approach, we compared quasispecies in donors and recipients on the basis of 316 and 376 C2V5 env sequences amplified from plasma viral RNA and PBMC-associated DNA, respectively.

Results

Both DNA and RNA sequences indicated very homogeneous viral populations in all recipients, suggesting transmission of a single variant, even in cases of recent sexually transmitted infections (STIs) in donors (n = 2) or recipients (n = 3). In all pairs, the transmitted/founder virus was derived from an infrequent variant population within the blood of the donor. The donor variant sequences most closely related to the recipient sequences were found in plasma samples in 3/8 cases and/or in PBMC samples in 6/8 cases. Although donors were exclusively (n = 4) or predominantly (n = 4) infected by CCR5-tropic (R5) strains, two recipients were infected with highly homogeneous CXCR4/dual-mixed-tropic (X4/DM) viral populations, identified in both DNA and RNA. The proportion of X4/DM quasispecies in donors was higher in cases of X4/DM than R5 HIV transmission (16.7–22.0% versus 0–2.6%), suggesting that X4/DM transmission may be associated with a threshold population of X4/DM circulating quasispecies in donors.

Conclusions

These suggest that a severe genetic bottleneck occurs during subtype B HIV-1 heterosexual and homosexual transmission. Sexually-transmitted/founder virus cannot be directly predicted by analysis of the donor’s quasispecies in plasma and/or PBMC. Additional studies are required to fully understand the traits that confer the capacity to transmit and establish infection, and determine the role of concomitant STIs in mitigating the genetic bottleneck in mucosal HIV transmission.     

Variations of the mandibular shape in extant hominoids: Generic, specific, and subspecific quantification using elliptical fourier analysis in lateral view

While a number of studies have documented the mandibular variations in hominoids, few focused on evaluating the variation of the whole outline of this structure. Using an efficient morphometrical approach, i.e. elliptical Fourier analysis, mandibular outlines in lateral view from 578 adult hominoids representing the genera Hylobates, Pongo, Gorilla, Pan, and Homo were quantified and compared. This study confirms that elliptical Fourier analysis provides an accurate characterization of the shape of the mandibular profile. Differences in mandibular shape between hominoid genera, species, subspecies, and to a lesser extent between sexes were demonstrated. Mandibles in great apes and hylobatids subspecies were generally less distinct from each other than were species. However, the magnitudes of differences among subspecies of Gorilla and Pongo approached or exceeded those between Pan troglodytes and P. paniscus. The powerful discrimination between taxa from the genus down to subspecific level associated to the relatively low level of intrageneric mandibular polymorphism in great apes provides strong evidences in support of the taxonomic utility of the shape of the mandibular profile in hominoids. In addition, morphological affinities between Pongo and Pan and the clear distinction between Homo and Pan suggest that the mandibular outline is a poor estimate of phylogenetic relationships in great apes and humans. The sexual dimorphism in mandibular shape exhibits two patterns of expression: a high degree of dimorphism in Gorilla, Pongo, and H. s. syndactylus and a relatively low one in modern humans and Pan. Besides, degree of mandibular shape dimorphism can vary considerably among closely related subspecies as observed in gorillas, arguing against the use of mandibular shape dimorphism patterns as characters in phylogenetic analyses. However, the quantification of the mandibular shape and of the variations among hominoids provides an interesting comparative framework that is likely to supply further arguments for a better understanding of the patterns of differentiation between living hominoids.