Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Background

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S₁ mapping population of the cultivar ‘Reikou’ with an IStraw90 Axiom® SNP array and previously published SSR markers.

Results

The ‘Reikou’ linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes.

Conclusions

Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3762-y) contains supplementary material, which is available to authorized users.

Draft genome sequence of subterranean clover, a reference for genus Trifolium

Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.

A Kirschner wire as a transverse-axis guide to improve acetabular cup positioning

PURPOSE

To compare cup-positioning accuracy in total hip arthroplasty (THA) with or without use of a Kirschner wire as a transverse-axis guide for pelvic alignment.

METHODS

Records of 18 men and 73 women (mean age, 60 years) who underwent primary THA with (n=49) or without (n=42) use of a Kirschner wire as a transverse-axis guide for pelvic alignment were reviewed. A 2.4-mm Kirschner wire as a transversea-xis guide was inserted to the anterior superior iliac spine and was parallel to a line linking the left and right anterior superior iliac spine. The safe zone for cup positioning was defined as 30º to 50° abduction and 10º to 30º anteversion. Of the 5 operative surgeons, 2 were classified as experienced (total surgical volume >300) and 3 as inexperienced (total surgical volume of <50). The proportion of patients with the cup in the safe zone was compared in patients with or without use of the transverse-axis guide and in experienced and inexperienced surgeons.

RESULTS

For inexperienced surgeons, the use of the transverse-axis guide significantly improved the proportion of patients with the cup in the safe zone from 90% to 100% for abduction, from 50% to 82.4% for anteversion, and from 40% to 82.4% for both. Patients with the cup inside or outside the safe zone were comparable in terms of body height, weight, BMI, subcutaneous fat thickness, incision length, and acetabular cup size.

CONCLUSION

The use of the transverse-axis guide improved the accuracy of cup positioning by inexperienced surgeons.

Coulomb Blockade in a Two-Dimensional Conductive Polymer Monolayer

Electronic transport was investigated in poly(3-hexylthiophene-2,5-diyl) monolayers. At low temperatures, nonlinear behavior was observed in the current-voltage characteristics, and a nonzero threshold voltage appeared that increased with decreasing temperature. The current-voltage characteristics could be best fitted using a power law. These results suggest that the nonlinear conductivity can be explained using a Coulomb blockade (CB) mechanism. A model is proposed in which an isotropic extended charge state exists, as predicted by quantum calculations, and percolative charge transport occurs within an array of small conductive islands. Using quantitatively evaluated capacitance values for the islands, this model was found to be capable of explaining the observed experimental data. It is, therefore, suggested that percolative charge transport based on the CB effect is a significant factor giving rise to nonlinear conductivity in organic materials.

Direct comparison of optical lattice clocks with an intercontinental baseline of 9000 km

We have demonstrated a direct frequency comparison between two ⁸⁷Sr lattice clocks operated in intercontinentally separated laboratories in real time. Two-way satellite time and frequency transfer technique, based on the carrier-phase, was employed for a direct comparison, with a baseline of 9000 km between Japan and Germany. A frequency comparison was achieved for 83,640 s, resulting in a fractional difference of (1.1±1.6)×10⁻¹⁵, where the statistical part is the largest contributor to the uncertainty. This measurement directly confirms the agreement of the two optical frequency standards on an intercontinental scale.

Matrix metalloprotease-9 activity in the cerebrospinal fluid and spinal injury severity in dogs with intervertebral disc herniation

We investigated whether matrix metalloproteinase (MMP)-9 expression in the cerebrospinal fluid (CSF) of dogs with intervertebral disc herniation (IVDH) is associated with the severity of neurological signs and prognosis. CSF from the cisterna magna (C-CSF) and the lumbar spine (L-CSF) of 34 dogs with IVDH was analyzed using zymography. Activity of MMP-9 in L-CSF was detected in 6 of 34 dogs with IVDH, often for more than 7 days after injury. MMP-9 activity was not detected from any of the C-CSF samples. Of the six cases that were MMP-9 positive, all four cases with grade V that had loss of deep pain were non-ambulatory 6 months after treatment. The remaining two cases with grade III and IV could recover mobility. In dogs with grade V thoracolumbar IVDH, MMP-9 expression in the CSF may indicate severe spinal cord injury with poor prognosis.

Needle traits of an evergreen, coniferous shrub growing at wind-exposed and protected sites in a mountain region: does Pinus pumila produce needles with greater mass per area under wind-stress conditions?

Snow depth is one of the most important determinants of vegetation, especially in mountainous regions. In such regions, snow depth tends to be low at wind-exposed sites such as ridges, where stand height and productivity are limited by stressful environmental conditions during winter. Siberian dwarf pine (Pinus pumila Regel) is a dominant species in mountainous regions of Japan. We hypothesized that P. pumila produces needles with greater mass per area at wind-exposed sites than at wind-protected sites because it invests more nitrogen (N) in cell walls at the expense of N investment in the photosynthetic apparatus, resulting in increased photosynthetic N use efficiency (PNUE). Contrary to our hypothesis, plants at wind-exposed site invested less resources in needles, as exhibited by lower biomass, N, Rubisco and cell wall mass per unit area, and had higher photosynthetic capacity, higher PNUE and shorter needle life-span than plants at a wind-protected site. N partitioning was not significantly different between sites. These results suggest that P. pumila at wind-exposed sites produces needles at low cost with high productivity to compensate for a short leaf life-span, which may be imposed by wind stress when needles appear above the snow surface in winter.

Climacteric-Like Disorders in Prostate Cancer Patients Treated With LHRH Agonists

We assessed long-term side effects with characteristics of female climacteric disorders in prostate cancer patients treated with luteinizing hormone-releasing hormone (LHRH) agonists. Such side effects are not considered to be serious, though they can significantly affect patient quality of life. Sixty-four prostate cancer patients treated with LHRH agonists and 30 benign prostatic hyperplasia patients, as a control group, were surveyed by questionnaire. The median age of the cancer patients was 74.9 years old, ranging from 60 to 94 years, and the median LHRH agonist dosing period was 16.5 months, ranging from 1 to 64 months. The results of the questionnaires were compared between the patients and the controls, as well as between different variables. Sixty (93.8%) of 64 patients claimed symptoms similar to female climacteric disorders. Further, more than 50% of the symptoms included in the questionnaire were reported by 14 (21.9%) of the patients. Symptoms reported by the patients were more severe than those by the controls. Hot flashes, sleep disturbance, and fatigue recorded high scores in the patient questionnaires as compared with those of the controls. In addition, as the term of LHRH agonist use increased, complaints of sweating or coldness in hands and feet increased. Patients without bone metastasis frequently experienced heaviness in the head and headaches compared to those with bone metastasis. The results of our questionnaire-based outcome study showed that side effects similar to female climacteric disorders in prostate cancer patients treated with LHRH agonists were more severe than in the control group, which could be detrimental to quality of life and general well-being.

Sacsin-related ataxia (ARSACS): expanding the genotype upstream from the gigantic exon

The authors describe a Japanese autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) patient with a compound heterozygous mutation (32627-32636delACACTGTTAC and 31760delT) in a new exon of the SACS gene. The new exons upstream of the gigantic one should be analyzed when a case is clinically compatible with ARSACS, even without any mutation in the gigantic exon.

An efficient construction of conditionally replicating adenoviruses that target tumor cells with multiple factors

Despite the enormous potential of conditionally replicating adenoviruses (CRAs), the time-consuming and laborious methods required to construct CRAs have hampered both the development of CRAs that can specifically target tumors with multiple factors (m-CRA) and the efficient analysis of diverse candidate CRAs. Here, we present a novel method for efficiently constructing diverse m-CRAs. Elements involving viral replication, therapeutic genes, and adenoviral backbones were separately introduced into three plasmids of P1, P2, and P3, respectively, which comprised different antibiotic resistant genes, different ori, and a single loxP (H) sequence. Independently constructed plasmids were combined at 100% accuracy by transformation with originally prepared Cre and specific antibiotics in specific Escherichia coli; transfection of the resulting P1+2+3 plasmids into 293 cells efficiently generated m-CRAs. Moreover, the simultaneous generation of diverse m-CRAs was achieved at 100% accuracy by handling diverse types of P1+2 and P3. Alternatively, co-transfection of P1+3 and P2 plasmids into Cre-expressing 293 cells directly generated m-CRA with therapeutic genes. Thus, our three-plasmid system, which allows unrestricted construction and efficient fusion of individual elements, should expedite the process of generating, modifying, and testing diverse m-CRAs for the development of the ideal m-CRA for tumor therapy.

Rapid disease progression correlates with instability of mutant SOD1 in familial ALS

Studies on the clinical course of familial ALS suggest that the duration of illness is relatively consistent for each mutation but variable among the different mutations. The authors analyzed the relative amount of mutant compared with normal SOD1 protein in the erythrocytes from 29 patients with ALS with 22 different mutations. Turnover of mutant SOD1 correlated with a shorter disease survival time.