Sequence-based GWAS meta-analyses for beef production traits

BACKGROUND

Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed summary statistics from sequence-based GWAS conducted with 54,782 animals from 15 purebred or crossbred populations. We combined the summary statistics for four growth, nine morphology, and 15 carcass traits into 16 MA, using both fixed effects and z-score methods.

RESULTS

The fixed-effects method was generally more informative to provide indication on potentially causal variants, although we combined substantially different traits in each MA. In comparison with within-population GWAS, this approach highlighted (i) a larger number of quantitative trait loci (QTL), (ii) QTL more frequently located in genomic regions known for their effects on growth and meat/carcass traits, (iii) a smaller number of genomic variants within the QTL, and (iv) candidate variants that were more frequently located in genes. MA pinpointed variants in genes, including MSTN, LCORL, and PLAG1 that have been previously associated with morphology and carcass traits. We also identified dozens of other variants located in genes associated with growth and carcass traits, or with a function that may be related to meat production (e.g., HS6ST1, HERC2, WDR75, COL3A1, SLIT2, MED28, and ANKAR). Some of these variants overlapped with expression or splicing QTL reported in the cattle Genotype-Tissue Expression atlas (CattleGTEx) and could therefore regulate gene expression.

CONCLUSIONS

By identifying candidate genes and potential causal variants associated with beef production traits in cattle, MA demonstrates great potential for investigating the biological mechanisms underlying these traits. As a complement to within-population GWAS, this approach can provide deeper insights into the genetic architecture of complex traits in beef cattle.

Evidence of mitochondrial alterations in primary cardiac stromal cells from arrhythmogenic cardiomyopathy hearts

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This research was funded by the Department of Innovation, Research and University of the Autonomous Province of Bolzano-South Tyrol (Italy), and by the Joint Project Südtirol- FWF (Italy-Austria) for A.R., J.T., A.M., R.P..

Background

Arrhythmogenic cardiomyopathy (ACM) is a genetic disease associated with sudden cardiac death and fibro-fatty replacement of myocardium. Recently, it has been demonstrated that oxidized lipid contributes to cardiac adipogenesis and that ACM hearts are characterized by an increase in oxidative stress.

Purpose

As mitochondria are an important source of reactive oxygen species (ROS) within mammalian cells, the present work aims to evaluate if increased oxidative stress observed in ACM hearts is associated with altered mitochondrial function.

Methods

The oxidative stress marker 4HNE was investigated together with the cardiomyocyte marker cardiac Troponin T on paraffin embedded human ventricular samples and analyzed by confocal microscopy.

Human primary cardiac stromal cells (CStCs), obtained from either right ventricle biopsies of ACM patients or healthy cadaveric tissue donor (CTR), were used as cellular model as they are known for their contribution to adipogenesis in the ACM pathology. CStCs were cultured either in basal medium or adipogenic medium (ADIPO) in presence or absence of 500 nM of the ROS scavenger MitoTEMPO.

After 7 days of adipogenic differentiation, intracellular lipid droplets accumulation and mitochondrial superoxide levels were measured in CStCs by confocal microscopy using BODIPY 493/503 (0.5 µM) and MitoSOX Red (5 µM) dyes, respectively.

The oxidative phosphorylation (OXPHOS) and fatty acid oxidation (FAO) were also evaluated in CStCs by high resolution respirometry.

Results

4HNE staining was increased in heart tissues from ACM patients compared to CTRs and particularly evident in non-cardiomyocyte cells. In agreement, a higher MitoSOX fluorescence intensity was found in ACM-CStCs compared to CTR-CStCs in ADIPO medium, confirming higher ROS presence in patient cells. The treatment with MitoTEMPO was efficient in reducing ROS abundance, strongly suggesting mitochondrial origin. Lipid accumulation in ACM-CStCs was also prevented by MitoTEMPO treatment.

Preliminary evidence further indicates that mitochondrial respiratory capacity is increased in ACM-CStCs versus CTR-CStCs exposed to adipogenic medium for 7 days. However, transmission electron microscopy analysis and Western blot analysis of Mfn1/2, Opa1, Fis1 and Drp1 did not show an evident alteration neither in mitochondria ultrastructure nor in the expression of proteins regulating mitochondrial dynamics.

Conclusions

Our data support an alteration of mitochondrial activity in CStCs from ACM patients, apparently not linked to a modified network or morphology of mitochondria but associated with a higher ROS production.

Long-range linkage disequilibrium in French beef cattle breeds

BACKGROUND

Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d'Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds.

RESULTS

We computed linkage disequilibrium (r²) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r² values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r² ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection.

CONCLUSIONS

We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.

Control of the single atom/nanoparticle ratio in Pd/C catalysts to optimize the cooperative hydrogenation of alkenes

Control of the single atom/nanoparticle ratio allows preparation of highly active Pd/C hydrogenation catalysts integrating the ultra-rational use of Pd.

Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Background

Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches.

Results

We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions.

Conclusions

Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0352-z) contains supplementary material, which is available to authorized users.

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Background

In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.

Results

In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.

Conclusions

To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users.

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

Background

The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

Results

Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.

Conclusions

This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

A physical map of the short arm of wheat chromosome 1A

Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

BACKGROUND

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

RESULTS

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

CONCLUSIONS

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.

Early surgical site infection in adult appendicular skeleton trauma surgery: a multicenter prospective series

INTRODUCTION

Surgical site infections (SSI) studies rely on an imprecise and debatable definition. The term "wound healing problems" (WHP), not necessarily septic, is also frequently cited. This study had the objectives of determining the frequency of early SSIs in traumatology, these terms eventual correlation, and the factors influencing onset.

PATIENTS AND METHODS

A multicenter prospective observational study was conducted in 12 centers. The exclusion criteria were open lesions as well as multiple injuries and multiple fractures (more than two fractures treated surgically). All patients were followed for the first three postoperative months until there was clinical certainty of healing and absence of infection. The presence of any WHP or SSI required a minimum follow-up of 1 year. WHP and SSI risk factors were determined using logistical regression adjusted on the centers.

RESULTS

Out of 1617 cases, 103 were complicated by a WHP and 22 by a SSI. The SSIs were mainly secondary to Staphylococcus infections. The factors predisposing the patients to WHP and SSI (p≤0.05) were age; the NNIS, ASA, and Parker scores; alcoholism; antiaggregant use; and the locoregional aspect at the time of injury. The 522 subcutaneous osteosyntheses "near the skin" resulted in 58 WHPs (11%) and 14 SSIs (2.7%); 13 of the 58 WHPs (22%) resulted in one SSI. Out of 707 deep osteosyntheses, 24 (3.4%) presented a WHP and seven (1%) a SSI; Four SSIs originated from a WHP. The 352 fractures of the trochanter were complicated by a WHP in 15 cases (5.5%) and a SSI in one case (0.4%) after interlocked nailing and two WHPs and two SSIs (2.5%) after screw and plate fixation. Of the 388 first-line arthroplasties, only the prostheses implanted for a proximal femur fracture presented complications: 21 WHPs (6%) and one SSI (0.02%). Of the 103 WHPs of the entire series, 18 became SSIs. In absence of WHP, the SSI rate was 0.2%, whereas the probability of a WHP evolving toward a SSI was 100 times higher. The only factor significantly associated with a WHP becoming a SSI was osteosynthesis material exposure.

DISCUSSION

This prospective study can be criticized on several points: the deliberately limited inclusion criteria, the short follow-up, and the possible subjectivity of the data collection. The SSI rates reported are for the most part in agreement with the literature. This study is innovative in traumatology given the large number of patients and the notion of WHP that was preferred over superficial infection. It demonstrates the relations between WHP and SSI, in particular for osteosyntheses near the skin.

LEVEL OF EVIDENCE

Level III.

Dual mobility cups hip arthroplasty as a treatment for displaced fracture of the femoral neck in the elderly. A prospective, systematic, multicenter study with specific focus on postoperative dislocation

INTRODUCTION

Displaced fractures of the femoral neck in the elderly are best treated with arthroplasty. The type of arthroplasty to be used, either hemi- or total hip arthroplasty, remains controversial as total hip replacements potentially have a higher rate of dislocation.

HYPOTHESIS

Dual mobility cups have a low dislocation rate when used to manage acute fractures of the femoral neck.

PATIENTS AND METHODS

In a multicenter prospective study conducted in France over an inclusion time of 3 months, all displaced fractures of the femoral neck treated with arthroplasty were operated on with insertion of a dual mobility cup. Patients had clinical and radiological assessment at 3, 6, and 9 months postoperative.

RESULTS

Two hundred and fourteen hips in 214 patients with a mean age of 83 years (range, 70-103 years) were included. None of the patients was lost to follow-up. The mortality rate after 9 months was 19%. Two patients (1%) had early postoperative infection successfully treated with lavage and antibiotics. Three patients (1.4%), operated through a posterior approach, presented one postoperative dislocation, all of which were posterior. Reduction was performed through closed external manipulation under general anesthesia. There was no recurrence of dislocation.

DISCUSSION

This low rate of dislocation after acute total hip replacement using dual mobility design cups favorably compares with hemiarthroplasties. Dual mobility cups might therefore be considered a valuable option to prevent postoperative dislocation when treating displaced intracapsular fractures of the proximal femur in elderly patients if a total hip replacement is recommended. Further study is needed before extending the indications for total hip arthroplasty following a fracture of the femoral neck, to assess the potential cost and complications of a longer procedure with its potential acetabular complication, and weigh them against the potential benefits.

Acetabular reconstruction using morselized allograft and a reinforcement ring for revision arthroplasty with Paprosky type II and III bone loss: survival analysis of 95 hips after 5 to 13 years

INTRODUCTION

Treatment of acetabular loosening and accompanying bone defects requires that the bone stock be rebuilt, the primary stability ensured, and the hip center of rotation restored to its anatomical location.

HYPOTHESIS

Acetabular reconstruction using morselized allograft and a reinforcement ring will meet these requirements and ensure medium-term survival.

PATIENTS AND METHODS

A retrospective study was performed on 95 acetabular revision cases (95 patients) performed between 1987 and 1995. The average age at revision was 69.5 years (42 to 86 years). Among these acetabular loosening cases, 12 cases had a type II Paprosky acetabular bone defect and 83 cases had a type III defect.

RESULTS

The average follow-up was 8 years (5 to 13 years). There were seven post-operative dislocations, three deep infections, and two cases of repeated acetabular loosening. The cumulative survival rate at 14 years was 77.9% (95% CI: 61.96% to 93.84%). The average Postel Merle d'Aubigné (PMA) score improved from 8 (range 6-11) preoperatively to 14.8 (range 8-18) at follow-up; the Harris score improved from 35.3 (range 11-52) to 71.1 (range 40-94) (P<0.001). Based on the parameters outlined by Ranawat, the optimal centre of rotation was restored in 45% of cases. Graft integration was found to be good in 60% of cases. The reinforcement ring had migrated in five cases, including two cases of acetabular loosening that required an additional revision. The functional result was better when the hip center of rotation was restored (P<0.05). Conversely, the position of the hip center of rotation had no effect on graft integration or acetabular fixation.

DISCUSSION

This series confirmed that acetabular reconstruction using morselized allograft and a reinforcement ring is effective in the medium term as a treatment for acetabular loosening with severe bone deficiency. It also revealed that restoring the hip center of rotation can improve functional results.

LEVEL OF EVIDENCE

Level IV, retrospective study.

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome

Background

Sequencing projects using a clone-by-clone approach require the availability of a robust physical map. The SNaPshot technology, based on pair-wise comparisons of restriction fragments sizes, has been used recently to build the first physical map of a wheat chromosome and to complete the maize physical map. However, restriction fragments sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs and mis-assembled BACs in such large and repetitive genomes. Whole Genome Profiling (WGP™) was developed recently as a new sequence-based physical mapping technology and has the potential to limit this problem.

Results

A subset of the wheat 3B chromosome BAC library covering 230 Mb was used to establish a WGP physical map and to compare it to a map obtained with the SNaPshot technology. We first adapted the WGP-based assembly methodology to cope with the complexity of the wheat genome. Then, the results showed that the WGP map covers the same length than the SNaPshot map but with 30% less contigs and, more importantly with 3.5 times less mis-assembled BACs. Finally, we evaluated the benefit of integrating WGP tags in different sequence assemblies obtained after Roche/454 sequencing of BAC pools. We showed that while WGP tag integration improves assemblies performed with unpaired reads and with paired-end reads at low coverage, it does not significantly improve sequence assemblies performed at high coverage (25x) with paired-end reads.

Conclusions

Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome. Moreover, WGP tag integration in sequence assemblies improves low quality assembly. However, to achieve a high quality draft sequence assembly, a sequencing depth of 25x paired-end reads is required, at which point WGP tag integration does not provide additional scaffolding value. Finally, we suggest that WGP tags can support the efficient sequencing of BAC pools by enabling reliable assignment of sequence scaffolds to their BAC of origin, a feature that is of great interest when using BAC pooling strategies to reduce the cost of sequencing large genomes.

Arthroscopic treatment of rotator cuff tear in the over-60s: repair is preferable to isolated acromioplasty-tenotomy in the short term

INTRODUCTION

The principal study objective was to compare clinical results for arthroscopic repair of rotator cuff tear and acromioplasty-tenotomy in patients aged over 60 years.

HYPOTHESES

Repair provides better clinical results than isolated acromioplasty-tenotomy. Shoulder function is improved when healing is obtained.

PATIENTS AND METHODS

One hundred and forty-two patients aged over 60 years (mean age, 67 years) presenting with reparable supraspinatus tear, extending to a greater or lesser degree to the infraspinatus, agreed to take part in a randomized prospective study. Fifteen were excluded from statistical analysis. All underwent acromioplasty and biceps tenotomy. They were randomly assigned to arthroscopic rotator-cuff repair (CR group) or not (AT group). The principal evaluation criterion was mean weighted Constant score at one year's follow-up. Healing in the CR group was assessed on ultrasound at one year.

RESULTS

The complications rate was 7.9%. Mean weighted Constant score was significantly better in group CR: 75.8%, versus 68.8% in AT. In the CR group, the 1-year healing rate was 67.6%. Healing significantly impacted mean weighted Constant score: 80% with healing, versus 66.9% in iterative tearing. Whatever the size of the tear, mean weighted Constant score was significantly better in patients with than without (no repair or iterative tear) tendon healing.

DISCUSSION

The study demonstrated the interest of arthroscopic rotator cuff repair in patients aged over 60 years. The benefit of repair compared to isolated acromioplasty-tenotomy depended on tendon healing.

LEVEL OF EVIDENCE

Randomized prospective study, level II.

Hip septic arthritis in children: assessment of treatment using needle aspiration/irrigation

INTRODUCTION

This retrospective series evaluated the surgical treatment of hip arthritis in children by needle aspiration-irrigation alone.

PATIENTS AND METHODS

Forty-three cases of septic hip arthritis were treated by needle aspiration-irrigation under general anesthesia associated with intravenous then oral administration of antibiotics. Clinical and biological criteria at admission, during hospitalization and at final follow-up were studied to identify any criteria carrying a predictive value for unsuccessful needle aspiration-irrigation.

RESULTS

Thirty-eight hips had a favorable outcome in this series, while secondary open arthrotomy was required in five hips for further irrigation. Common criteria found in the group requiring open arthrotomy were a diagnosis delay of at least 6 days between initial clinical symptoms and treatment as well as markedly abnormal biological results at admission. A threshold for the predictive value of certain variables was identified including C-reactive protein above 100, white polynuclear blood count above 15000, and sedimentation rate above 25 in the first hour and 50 in the second hour.

DISCUSSION

Treatment modalities for septic arthritis of the hip remain controversial in children and various techniques have been shown to be effective in the literature. Needle aspiration-drainage, the least invasive of these, has been shown to have good results, even in the hip, even though this is a deep, tight, joint which is known to be difficult to drain. Prognostic criteria are difficult to identify, however all authors agree that delayed treatment makes evacuation of intra-articular debris especially difficult.

CONCLUSION

Needle aspiration-irrigation is effective in septic arthritis of the hip, as long as basic principles are followed. Delayed treatment and certain biological criteria should be taken into account when selecting a treatment, since negative predictive criteria identified in this series were present in the five hips requiring secondary arthrotomy.

Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives

Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.

Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n approximately 12x approximately 115)

The genome of modern sugarcane cultivars is highly polyploid (approximately 12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Genetically modified coffee plants expressing the Bacillus thuringiensis cry1Ac gene for resistance to leaf miner

 A synthetic version of the cry1Ac gene of Bacillus thuringiensis has been used for the transformation of coffee species (Coffea canephora and C. arabica) to confer resistance to an important pest, the coffee leaf miner (Perileucoptera coffeella and other Leucoptera spp). Somatic embryos were co-cultivated with the LBA4404 strain of Agrobacterium tumefaciens containing the cry1Ac gene. More than 100 transformed plants from independent transformation events were obtained for each coffee genotype. The integration and expression of the cry1Ac gene was studied, and effective resistance of transgenic plants against leaf miner was verified in bioassays with the insects. These plants could represent a good opportunity to analyse the impact of genetic engineering of perennial crops for sustainable resistance to an obligate endocarpic pest using a B. thuringiensis insecticidal protein.

Considerations on the dynamics of fraud and shoplifting in adult female offenders

This paper compares two groups of adult female offenders involved in shoplifting and fraudulent behaviour. Twenty women were studied whose first offenses occurred in their mid-life period. The major findings conclude that an unresolved mourning or loss in the context of high stress and depression is one of the commonalities in the two groups. Another commonality is that a defined classical role for these women is conflictual and the relationship established with their spouses is a repetition of their relationship with their father. The authors suggest that these types of acting out in general are a depressive equivalent, and a larger sample could duplicate the findings and collect more precise data about the nature of the relationship in the family of origin to help these women feel better in their social role.

Thermodynamic properties of binary mixtures containing thiaalkanes. II. Thermal pressure coefficients of pure compounds at 298.15 K

An apparatus for the measurement of thermal pressure coefficients of pure compounds is described. The thermal pressure coefficient β of n-thiaalkanes R2S (R = CH3, C2H5, n-C3H7, n-C4H9, n-C7H15) and of dithiaalkanes R2S2 (R = CH3, C2H5, iso-C3H7) were measured at 298.15 K and at zero pressure. These experimental results in conjunction with data from literature for other compounds are compared using the reduced parameter of pressure P* proposed by Flory. The P* do not have regular values for the lower members of thiaalkanes series. One explanation of these irregularities is the different size of the molecules.

Excess heats of tri-n-alkylamines and tetraalkyl tin compounds in linear and branched alkanes: correlations of molecular orientations and steric hindrance effect

Excess heats of the following mixtures of trialkylamines and tetraalkyl tin compounds with branched and linear alkanes have been measured at 25 °C: five trialkylamines NR3 (R = C2H5, C3H7, C4H9, C10H21, C12H25) with six linear alkanes, n-C5, n-C6, n-C8, n-C10, n-C12, n-C16, and three highly branched alkanes, 2,2,4-trimethylpentane, 2,2,4,6,6-pentamethylheptane, and 2,2,4,4,6,8,8-heptamethylnonane (br-C16). Further measurements were carried out on tetrapropyl tin (SnPr4) with n-C8, n-C16, and br-C16.Measurements were made to obtain more information on the heats of disordering of long chain compounds and on an exothermic contribution to the heats coming possibly from the sterically hindered character of one of the components of the mixture. The three short-chain trialkylamines have large heats with the linear long alkanes and small heats with the branched alkanes. On the other hand, the two long-chain trialkylamines have very small heats with linear alkanes and large heats with the branched alkanes. These results are interpreted as indicating no change of liquid or solution 'structure' when two ordered compounds (long alkanes and long-chain amines) are mixed but a change of 'structure' when an ordered compound (long alkane or long-chain amine) is mixed with a non-ordered one (branched alkane or short-chain amine). The heat of disordering of n-hexadecane is obtained with many order breakers and found to depend to some extent on the expansion coefficient of the order breaker. HE values for the series of the shorter NR3 do not vary regularly with molecular weight but are smaller for the propyl (and possibly the ethyl) derivative. Similarly, HE of SnPr4 in n-C16, br-C16, and n-C8 are much lower than the corresponding heats with SnEt4 and SnBut4. This is attributed to the presence of the exothermic contribution to the heats, HE(steric hindrance). The X12 parameter of the Flory theory has been calculated and is interpreted in terms of the disorder and steric hindrance contributions to the heats.