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The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors. [ABSTRACT FROM AUTHOR]

For the purpose of revealing unique aspects of the electrical double layer (EDL) around nonspherical particles, we focus on a silica square platelike particle with well-defined shape, i.e., H−ilerite. Impedance measurements for suspensions of silica spherical and square platelike particles are performed to examine ion concentration polarization and its relaxation in their EDLs under ac electric fields that are high enough to orient H−ilerite to electric fields and form pearl chains of particles. For a silica spherical particle, the relaxation frequency of ion concentration polarization in EDL around the particles is independent of applied electric field strength and the volume fraction of the particles in suspension. The conductance ratios of silica particle suspension to its supernatant show a good linear relation against the volume fraction independently of applied electric field strength. For H−ilerite, at low electric field strength where there is neither electric orientation nor pearl chain formation, the conductance ratio also shows a linear relation against the volume fraction. The slope of the conductance ratio to the volume fraction increases and the relaxation frequency decreases as applied electric field strength increases. In addition, two linear relations with different slopes, where the slope becomes steep at higher volume fractions, appear in the plots of the conductance ratio against the volume fraction. Such a unique response of H−ilerite suspension to electric field can be explained by the electric orientation of H−ilerite accompanying pearl chain formation. [ABSTRACT FROM AUTHOR]

We have tackled in situ electric conductance measurements under microscopic observations for alignments of silica particles that are induced by ionic polarization of the electrical double layer (EDL) around the particles. Using the in situ conductance measurements, we have presented evidence that electro-osmotic flow at a vessel bottom/water interface would be coupled with the ionic polarization in the EDL of spherical silica particles settling at the bottom ( Langmuir2007, 23, 8797). In this study, we followed this phenomenon further. We altered the ζ potential of a platform of a glass plate on which a pearl chain of silica particles was formed under an ac electric field to control the mobility of electro-osmotic flow at the macroscopic interface of the platform/water. As the magnitude of the ζ potential of the platform increased, the surface distance between neighboring particles in the pearl chains decreased and the in situ conductance totally increased due to the enhancement of the dipole moments induced by the ionic polarizations of the particles. These results could be explained by considering that the electro-osmotic contribution to the surface conduction around the particles would be coupled with that occurring at the platform/water interface. [ABSTRACT FROM AUTHOR]

Counterions in an electric double layer (EDL) around a colloidal particle accumulate on one side of the EDL and are deficient on the other side under an electric field, resulting in an imbalance of ionic concentration in the EDL, that is to say, the ionic polarization of EDL. It is well known that the ionic polarization of EDL induces electric dipole moments whereby the alignments of colloidal particles (e.g., pearl chains) are formed under alternating electric fields. In this study, we focus on the effect of the frequency of applied electric fields (100 Hz−1 kHz) on the alignment of silica particles settling at the bottom of a silica glass vessel. In digital imaging analyses for pearl chains of silica particles, it is confirmed that surface distances between two neighboring particles decrease but the number of particles in a pearl chain increases as the frequency of the applied electric field is lowered from 1 kHz to 100 Hz. More interestingly, electrical conductance measurements suggest that the induced ionic polarization of EDL around silica particles at the bottom of the silica vessel is enhanced as the frequency is lowered from 1 kHz to 100 Hz, whereas the ionic polarization around isolated silica particles in uniform dispersions is alleviated by the relaxation of ionic concentration in the EDL as a result of the diffusion of counterions. This curious phenomenon can be explained by considering that the ionic polarization of EDL of silica particles at the bottom of a vessel is affected by the electro-osmosis of the silica surface at the bottom of the vessel. [ABSTRACT FROM AUTHOR]

The alignments of silica particles formed in sinusoidal electrical fields of 1 kHz were assessed using an optical microscope with measuring the electric conductance of a silica dispersion between two Pt electrodes in a vitreous silica glass cell. We confirmed that the electric conductance of the silica dispersion between the two electrodes in the cell reflected the surface conductance of the silica particles settling at the bottom of the cell. More interestingly, we observed that the electric conductance of the silica dispersion in the cell increased when pearl chains of the silica particle were formed along the direction of the electric field. However, no clear change in the electric conductance of the dispersion was observed at higher electric field strengths where a transition from pearl chains to zigzag band patterns and circulating movements of the silica particles in the zigzag bands formed. [ABSTRACT FROM AUTHOR]

Background: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results: To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions: Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture. [ABSTRACT FROM AUTHOR]

In this study, we confirmed that Vasconcellea cundinamarcensis resists Papaya leaf distortion mosaic virus (PLDMV), and used it to produce intergeneric hybrids with Carica papaya. From the cross between C. papaya and V. cundinamarcensis, we obtained 147 seeds with embryos. Though C. papaya is a monoembryonic plant, multiple embryos were observed in all 147 seeds. We produced 218 plants from 28 seeds by means of embryorescue culture. All plants had pubescence on their petioles and stems characteristic of V. cundinamarcensis. Flow cytometry and PCR of 28 plants confirmed they were intergeneric hybrids. To evaluate virus resistance, mechanical inoculation of PLDMV was carried out. The test showed that 41 of 134 intergeneric hybrid plants showed no symptoms and were resistant. The remaining 93 hybrids showed necrotic lesions on the younger leaves than the inoculated leaves. In most of the 93 hybrids, the necrotic lesions enclosed the virus and prevented further spread. These results suggest that the intergeneric hybrids will be valuable material for PLDMV-resistant papaya breeding. [ABSTRACT FROM AUTHOR]

Many host genes induced during compatible plant-pathogen interactions constitute targets of pathogen virulence factors that act to suppress host defenses. In order to identify Nicotiana tabacum L. genes for pathogen-induced proteins involved in susceptibility to the oomycete Phytophthora parasitica var. nicotianae, we used SuperSAGE technology combined with next-generation sequencing to identify transcripts that were differentially upregulated during a compatible interaction. We identified a pathogen-induced gene (NtPIP) that was rapidly induced only during the compatible interaction. Virus-induced gene silencing of NtPIP reduced the susceptibility of N. tabacum to P. parasitica var. nicotianae. Additionally, transient expression of NtPIP in the resistant species Nicotiana megalosiphon Van Heurck & Mull. Arg. compromised the resistance to P. parasitica var. nicotianae. This pathogen-induced protein is therefore a positive regulator of the susceptibility response against an oomycete pathogen in tobacco. [ABSTRACT FROM AUTHOR]

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spinytip- leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding. [ABSTRACT FROM AUTHOR]

There is no question that protein- and RNA-based measurements are complementary, but which approach has the highest return in the case of a non-model crop and what is the correlation between mRNA and proteins? We describe and evaluate in detail the advantages and pitfalls of both a proteomics and a transcriptomics approach. The information on the abundance of transcripts was obtained by serial analysis of gene expression (SAGE), while information on the abundance of proteins was obtained via two-dimensional gel electrophoresis. [ABSTRACT FROM AUTHOR]