Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.

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Using random PCR amplification followed by plasmid subcloning and DNA sequencing, we detected bocavirus related sequences in 9 out of 17 porcine stool samples. Using primer walking, we sequenced the nearly complete genomes of two highly divergent bocaviruses we provisionally named porcine bocavirus 1 isolate H18 (PBoV1-H18) and porcine bocavirus 2 isolate A6 (PBoV2-A6) which differed by 51.8% in their NS1 protein. Phylogenetic analysis indicated that PBoV1-H18 was very closely related to a ∼2 Kb central region of a porcine bocavirus-like virus (PBo-LikeV) from Sweden described in 2009. PBoV2-A6 was very closely related to the porcine bocavirus genomes PBoV-1 and PBoV2 from China described in 2010. Among 340 fecal samples collected from different age, asymptomatic swine in five Chinese provinces, the prevalence of PBoV1-H18 and PBoV2-A6 related viruses were 45–75% and 55–70% respectively, with 30–47% of pigs co-infected. PBoV1-A6 related strains were highly conserved, while PBoV2-H18 related strains were more diverse, grouping into two genotypes corresponding to the previously described PBoV1 and PBoV2. Together with the recently described partial bocavirus genomes labeled V6 and V7, a total of three major porcine bocavirus clades have therefore been described to date. Further studies will be required to elucidate the possible pathogenic impact of these diverse bocaviruses either alone or in combination with other porcine viruses.

A series of poly(vinylidene fluoride)-g-sulfonated polystyrene (PVDF-g-SPS) graft copolymers were systematically synthesized and examined with the focus of understanding how the polymer microstructure (backbone molecular weight, graft density, graft length, sulfonic acid concentration, ion exchange capacity, etc.) affects their morphology, water uptake, and proton conductivity under various environmental conditions (temperature and relative humidity). The synthesis of these relatively well-defined graft structures involves three reaction steps, including the preparation of PVDF copolymers containing a few mol% of chlorotrifluoroethylene (CTFE) units, the ATRP graft-from reaction to incorporate several polystyrene side chains, and the subsequent sulfonation reaction on the PS side chains. The PVDF-g-SPS graft copolymer with a combination of a high PVDF backbone molecular weight (M n >300 000 g/mol), very low SPS graft density (0.3 mol%), and high graft length (SPS content >30 mol%) presents an interesting material for the proton exchange membrane (PEM). This graft copolymer self-assembles into a microphase-separated morphology with randomly oriented long-range lamella/cylinder ionic channels (with small widths) that are imbedded in the hydrophobic semicrystalline PVDF matrix. This graft copolymer morphology offers a high ion exchange capacity (IEC = 2.75 mmol/g) and resistance to excessive water swelling, which yields notably higher proton conductivity than Nafion under 30−120 °C and high humidity conditions.