Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane.

Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using FST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.

Enhanced dielectric permittivity and suppressed electrical conductivity in polyvinylidene fluoride nanocomposites filled with 4,4'-oxydiphenol-functionalized graphene.

Plastic film capacitors suffer from low charge storage capacity due to the low dielectric constant of the polymer (<10). We have devised a polyvinylidene fluoride (PVDF) composite film filled with small graphene oxide (GO) sheets that have aromatic molecules attached to their surfaces. The use of 4,4'-oxydiphenol molecules to functionalize graphene sheets is found to have a remarkable effect on enhancing the dielectric permittivity as well as reducing the electrical conductivity of the nanocomposite. When under an electric field, these molecules with an angled molecular geometry act as aligned electric dipoles to largely enhance the dielectric permittivity of the composite, reaching a level two orders of magnitude higher than that of the counterpart filled with blank graphene sheets. Also, the aromatic molecules on the graphene surface act as resistive barriers that block charge transfer between interconnected graphene sheets. As a consequence, the electric conductivity of the composite can be decreased by two orders of magnitude. The PVDF composite filled with functionalized graphene shows a percolation threshold of 13 wt% and a high dielectric constant of 1091 at 100 Hz at this point.

Genetic diversity based on SSR analysis of the cultured snakehead fish, Channa argus, (Channidae) in China.

The snakehead fish Channa argus is an important food fish in China. We identified six microsatellite loci for C. argus. These six microsatellite loci and four other microsatellite markers were used to analyze genetic diversity in four cultured populations of C. argus (SD, JX, HN, and ZJ) and determine their relationships. A total of 154 alleles were detected at the 10 microsatellite loci. The average expected and observed heterozygosities varied from 0.70-0.84 and 0.69-0.83, respectively, and polymorphism information content ranged between 0.66 and 0.82 in the four populations, indicating high genetic diversity. Population JX deviated from mutation-drift equilibrium and may have experienced a recent bottleneck. Analysis of pairwise genetic differentiation revealed FST values that ranged from 0.028 to 0.100, which indicates a moderate level of genetic differentiation. The largest distances were observed between populations HN and SD, whereas the smallest distances were obtained between populations HN and JX. Genetic clustering analysis demonstrated that the ZJ and HN populations probably share the same origin. This information about the genetic diversity within each of the four populations, and their genetic relationships will be useful for future genetic improvement of C. argus through selective breeding.

Cloning and characterization of the calreticulin gene in Asian seabass (Lates calcarifer).

Calreticulin (CRT) is a Ca2+-binding molecular chaperone in the endoplasmic reticulum. We cloned and characterized the CRT gene in an important marine food fish species Asian seabass (Lates calcarifer). The full-length DNA of the CRT gene was 2194 bp, including a complete open reading frame encoding 420 amino acid residues, a 113 bp 5'-untranslated region and an 818 bp 3'-untranslated region. The CRT gene contained nine exons and eight introns covering a total of 2772 bp genomic DNA from the start to stop codon. Ten single nucleotide polymorphisms (SNPs) were detected in introns and an exon in six individuals collected from five different locations. The CRT gene was assigned to linkage group 4 of the linkage map of Asian seabass. Quantitative real-time PCR revealed that the CRT gene was highly expressed in liver at the age of 1, 3 and 7 months under normal conditions, whereas its expression in liver reduced sharply after 0.5 to 2 h cold challenge at 16°C, and then increased slowly. A preliminary association analysis showed a significant (P < 0.001) association between the SNP6 in the CRT gene and the mortality after cold challenge at 16°C. Our results suggest that the CRT gene is associated with cold tolerance of Asian seabass and further investigation will be necessary to illustrate the underlying mechanisms.

Significant associations of polymorphisms in the prolactin gene with growth traits in Asian seabass (Lates calcarifer).

Prolactin (encoded by PRL) is a multifunctional hormone involved in osmoregulation, reproduction, growth, development, immunomodulation, endocrine and metabolic regulation. We cloned the full-length cDNA of Asian seabass PRL, searched for polymorphism in the DNA sequence, and conducted association analyses. Twelve SNPs and one 4-bp deletion were identified in PRL. The SNP c.264+127C>G was used for linkage mapping, and this gene was mapped to linkage group 11. The c.264+980_983delTTGT, c.264+127C>G, c.264+138T>G, c.264+269T>C and c.330C>G polymorphisms were genotyped in 521 individuals with growth trait records. Association analyses between single markers and growth traits revealed that the c.264+269T>C SNP was significantly associated with body weight (BW), total length (TL), standard length (SL) and Fulton's condition factor (KTL and KSL), while the other four were not. Analysis of haplotypes showed that there were 10 haplotypes and 22 haplotype combinations in the population. The differences of BW, TL, KTL and KSL among different haplotype combinations were significant.

Mapping QTL for an adaptive trait: the length of caudal fin in Lates calcarifer.

The caudal fin represents a fundamental design feature of fishes and plays an important role in locomotor dynamics in fishes. The shape of caudal is an important parameter in traditional systematics. However, little is known about genes involved in the development of different forms of caudal fins. This study was conducted to identify and map quantitative trait loci (QTL) affecting the length of caudal fin and the ratio between tail length and standard body length in Asian seabass (Lates calcarifer). One F1 family containing 380 offspring was generated by crossing two unrelated individuals. One hundred and seventeen microsatellites almost evenly distributed along the whole genome were genotyped. Length of caudal fin at 90 days post-hatch was measured. QTL analysis detected six significant (genome-wide significant) and two suggestive (linkage-group-wide significant) QTL on seven linkage groups. The six significant QTL explained 5.5-16.6% of the phenotypic variance, suggesting these traits were controlled by multiple genes. Comparative genomics analysis identified several potential candidate genes for the length of caudal fin. The QTL for the length of caudal fin detected for the first time in marine fish may provide a starting point for the future identification of genes involved in the development of different forms of caudal fins in fishes.

A standard panel of microsatellites for Asian seabass (Lates calcarifer).

Microsatellites are the most popular markers for parentage assignment and population genetic studies. To meet the demand for international comparability for genetic studies of Asian seabass, a standard panel of 28 microsatellites has been selected and characterized using the DNA of 24 individuals from Thailand, Malaysia, Indonesia and Australia. The average allele number of these markers was 10.82 +/- 0.71 (range: 6-19), and the expected heterozygosity averaged 0.76 +/- 0.02 (range: 0.63-1.00). All microsatellites showed Mendelian inheritance. In addition, eight standard size controls have been developed by cloning a set of microsatellite alleles into a pGEM-T vector to calibrate allele sizes determined by different laboratories, and are available upon request. Seven multiplex PCRs, each amplifying 3-5 markers, were optimized to accurately and rapidly genotype microsatellites. Parentage assignment using 10 microsatellites in two crosses (10 x 10 and 20 x 20) demonstrated a high power of these markers for revealing parent-sibling connections. This standard set of microsatellites will standardize genetic diversity studies of Asian seabass, and the multiplex PCR sets will facilitate parentage assignment.

Characterization and Optical Properties of the Single Crystalline SnS Nanowire Arrays.

The SnS nanowire arrays have been successfully synthesized by the template-assisted pulsed electrochemical deposition in the porous anodized aluminum oxide template. The investigation results showed that the as-synthesized nanowires are single crystalline structures and they have a highly preferential orientation. The ordered SnS nanowire arrays are uniform with a diameter of 50 nm and a length up to several tens of micrometers. The synthesized SnS nanowires exhibit strong absorption in visible and near-infrared spectral region and the direct energy gap E(g) of SnS nanowires is 1.59 eV.

Discovery of four natural clones in a crayfish species Procambarus clarkii.

Self-cloning is quite rare in shrimp, lobsters, crayfish and crabs. Here we report the discovery of four natural clones of red swamp crayfish (Procambarus clarkii), each containing 2-6 genetically identical individuals, during the genotyping of 120 individuals with five microsatellites. The four clones were heterozygote at most of the five microsatellite loci. Phylogenetic analysis using microsatellite genotypes suggests recent origin of the four clones. Sequencing a part of the mitochondrial gene Cox I confirmed that the four clones were from the species Procambarus clarkii.

Identification and verification of QTL associated with growth traits in two genetic backgrounds of Barramundi (Lates calcarifer).

Quantitative trait loci (QTL) affecting growth traits have previously been mapped in linkage groups (LG) 2, 3 and 23 of Barramundi (Lates carcalifer), but these QTL have not been verified in different genetic backgrounds and environments. Here, we report the identification and verification of QTL for growth traits on LG2, 3, 10 and 23 in F(1) families constructed using brooders from the Singapore Marine Aquaculture Center (MAC) and from wild stocks collected in Thailand (THAI). The previously detected QTL for body weight and length linked to marker Lca371 on LG2 were confirmed in both the MAC and THAI families, whereas other QTL previously mapped to LG3 and 23 were only detected in one of the two families. QTL for body weight and length were identified in the MAC family, but not in the THAI family, in a region where the insulin-like growth factor 2 (IGF2) and tyrosine hydroxylase 1 (TH1) genes are located on LG10. Significant epistatic interactions were identified between markers Lca287 on LG2 and IGF2 on LG10 for growth trait QTL in the MAC family, but not in the THAI family. Effects of the IGF2, TH1 and parvalbumin 1 candidate genes were family-specific. Our results indicate that some but not all QTL are family-specific in Barramundi.

Finite-size effect on magnetic properties in iron sulfide nanowire arrays.

We report the size effect on the magnetic properties in Fe(7)S(8) nanowire arrays. Samples with diameters in the range of 50-200 nm have been prepared by electrodeposition with AAO films. The Mössbauer measurement results show that four parameters (hyperfine fields, isomer shift, quadrupole splitting, full width at half-maximum) increased with decreasing the diameter of the nanowires. The magnetic properties were investigated. The hysteresis loop shape and the magnetization are dependent on the diameter of the nanowires. The thermomagnetic measurements on the as-synthesized nanowire samples and the corresponding bulk display a mixed-type curve and a Weiss-type curve, respectively.

Mutation rate and pattern of microsatellites in common carp (Cyprinus carpio L.).

Microsatellites are popular molecular markers in genetic and evolutionary studies. Their mutational dynamics have been extensively studied in humans and fruit flies, but few data were available in fish. By genotyping 55 individuals of a F1 pedigree, we investigated the mutation rates and patterns of 49 microsatellites in one of the most important fresh water fish species, the common carp (Cyprinus carpio L.). The overall mutation rate of the 49 loci was 5.56 x 10(-4)/locus/generation (95% confidence interval 1.52 x 10(-4) and 1.63 x 10(-3)). The change of allele size was between +2 to -5 repeat units, assuming that the mutation allele arose from the parental allele most similar in size to the mutant.

Isolation, characterization, and linkage analyses of 74 novel microsatellites in Barramundi (Lates calcarifer).

Barramundi (Lates calcarifer) is an important marine food fish species in Southeast Asia and Australia. Seventy-four novel microsatellites were isolated from a genomic DNA library enriched for CA repeats and were characterized in 24 unrelated individuals. Among the 74 microsatellites, 71 were polymorphic, with an average allele number of 7.0 +/- 3.6/locus. The average expected heterozygosity of these polymorphic markers was 0.66. Sixty-three of the 71 polymorphic microsatellites conformed to Hardy-Weinberg equilibrium. Linkage analyses were conducted in a reference family, leading to the assignment of 34 novel microsatellites and 16 published markers in 16 linkage groups. The novel microsatellites developed in this study will contribute significantly to the construction of a first-generation linkage map for mapping of quantitative trait loci in Barramundi, and supply a large choice of markers for studies on population genetics, stock management, and pedigree reconstruction.

Characterization of two parvalbumin genes and their association with growth traits in Asian seabass (Lates calcarifer).

Parvalbumins are extremely abundant in fish muscle and play an important role in muscle relaxation. In this study, two parvalbumin genes (PVALB1 and PVALB2) were cloned from Asian seabass (Lates calcarifer). The cDNAs for PVALB1 and PVALB2 were 840 and 667 bp respectively. Both genes consisted of five exons and four introns, encoded 109 amino acids, and were of beta lineage. Using real-time polymerase chain reaction, expression of PVALB1 was detected in all 10 tissues tested, with expression in brain, kidney, muscle and small intestine being 15- to 322-fold higher than in the other tissues. Expression of PVALB2 was detected only in muscle, brain and intestine, and was up to 10-fold lower than PVALB1 expression. A (CT)(17) microsatellite in the 3'-untranslated region of PVALB1 and three single nucleotide polymorphisms (SNPs) in the third intron of PVALB2 were identified. The microsatellite in PVALB1 was significantly associated with body weight and body length at 90 days post-hatch (P < 0.01), whereas the SNPs in PVALVB2 were not associated with these traits.

The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer).

We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.

Linear correlation between fractal dimension of EEG signal and handgrip force.

Fractal dimension (FD) has been proved useful in quantifying the complexity of dynamical signals in biology and medicine. In this study, we measured FDs of human electroencephalographic (EEG) signals at different levels of handgrip forces. EEG signals were recorded from five major motor-related cortical areas in eight normal healthy subjects. FDs were calculated using three different methods. The three physiological periods of handgrip (command preparation, movement and holding periods) were analyzed and compared. The results showed that FDs of the EEG signals during the movement and holding periods increased linearly with handgrip force, whereas FD during the preparation period had no correlation with force. The results also demonstrated that one method (Katz's) gave greater changes in FD, and thus, had more power in capturing the dynamic changes in the signal. The linear increase of FD, together with results from other EEG and neuroimaging studies, suggest that under normal conditions the brain recruits motor neurons at a linear progress when increasing the force.

Relationship between muscle output and functional MRI-measured brain activation.

The relationship between functional MRI (fMRI)-measured brain signal and muscle force and or electromyogram (EMG) is critical in interpreting fMRI data and understanding the control mechanisms of voluntary motor actions. We designed a system that could record joint force and surface EMG online with fMRI data. High-quality force and EMG data were obtained while maintaining the quality of the fMRI brain images. Using this system, we determined the relationship between fMRI-measured brain activation and handgrip force and between fMRI-measured brain signal and EMG of extrinsic finger muscles. Ten volunteers participated in the experiments (only seven subjects' data were analyzed due to excessive noise in the fMRI data of three subjects). The participants exerted 20%, 35%, 50%, 65%, and 80% of the maximal force. During each contraction period, handgrip force, surface EMG of the finger flexor and extensor muscles, and fMRI brain images were acquired. The degree of muscle activation (force and EMG) was directly proportional to the amplitude of the brain signal determined by fMRI in the entire brain and in a number of motor function-related cortical fields, including primary motor, sensory regions, supplementary motor area, premotor, prefrontal, parietal and cingulate cortices, and cerebellum. All the examined brain areas demonstrated a similar relationship between the fMRI signal and force. A stronger fMRI signal during higher force indicates that more cortical output neurons and/or interneurons may participate in generating descending commands and/or processing additional sensory information. The similarity in the relationship between muscle output and fMRI signal in the cortical regions suggests that correlated or networked activation among a number of cortical fields may be necessary for controlling precise static force of finger muscles.