Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.

BackgroundTreatment of diabetes mellitus with Traditional Chinese Medicine has a long history. The aim of this study is to establish the safety and efficacy of traditional Chinese medicine combined with glibenclamide to treat type 2 diabetes mellitus.MethodsIn a controlled, double blind, multicentre non-inferiority trial, 800 patients with unsatisfactory glycemic control (fasting glucose 7–13 mmol/L and HbA1c 7–11%) were randomly assigned to receive Xiaoke Pill, a compound of Chinese herbs combined with glibenclamide, or Glibenclamide in two study groups – drug naive group, and patients previously treated with metformin monotherapy (metformin group). Outcome measures at 48 weeks were the incidence and rate of hypoglycemia, mean difference in HbA1c, and proportion of patients with HbA1c<6.5%.FindingsIn drug naïve group, the total hypoglycemia rate and the mild hypoglycemic episode in the Xiaoke Pill arm were 38% (p = 0.024) and 41% (p = 0.002) less compared to Glibenclamide arm; in Metformin group, the average annual rate of hypoglycemia was 62% lower in Xiaoke Pill arm (p = 0.003). Respective mean changes in HbA1c from baseline were −0.70% and −0.66% for Xiaoke Pill and Glibenclamide, with a between-group difference (95% CI) of −0.04% (−0.20, 0.12) in the drug naïve group, and those in metformin group were −0.45% and −0.59%, 0.14% (−0.12, 0.39) respectively. The respective proportions of patients with a HbA1c level <6.5% were 26.6% and 23.4% in the drug naïve group and 20.1% and 18.9% in the metformin group.InterpretationIn patients with type 2 diabetes and inadequate glycaemic control, treatment with Xiaoke Pill led to significant reduction in risk of hypoglycemia and similar improvements in glycemic control after 48 weeks compared to Glibenclamide.Trial RegistrationChinese Clinical Trial Register number, ChiCTR-TRC-08000074

Inhibition of protein tyrosine phosphatase 1B (PTP1B) activity has been considered to be a promising therapy approach to treat type 2 diabetes. In this work, a novel PTP1B activity inhibitor, named FYGL (Fudan-Yueyang-G. lucidum), was screened from the fruiting bodies of Ganoderma lucidum and showed an efficient PTP1B inhibitory potency with IC₅₀ = 5.12 ± 0.05 μg/mL. FYGL is a water-soluble macromolecular proteoglycan with a protein to polysaccharide ratio of 17:77 and a viscosity-average molecular weight (M(η)) of 2.6 × 10⁵. The type 2 diabetic mice treated orally by FYGL showed an obvious decrease in plasma glucose level compared with the diabetic controls without drug treatment, comparable with that of diabetic mice treated with metformin, a clinical drug. The toxicity of FYGL is very low. The results indicate that FYGL may serve as a drug candidate or a health-care food for diabetic therapy or protection.

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F(ST)) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such a Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei's genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.

Previously, we screened a proteoglycan for anti-hyperglycemic, named FYGL, from Ganoderma Lucidum. For further research of the antidiabetic mechanisms of FYGL in vivo, the glucose homeostasis, activities of insulin-sensitive enzymes, glucose transporter expression and pancreatic function were analyzed using db/db mice as diabetic models in the present work. FYGL not only lead to a reduction in glycated hemoglobin level, but also an increase in insulin and C-peptide level, whereas a decrease in glucagons level and showed a potential for the remediation of pancreatic islets. FYGL also increased the glucokinase activities, and simultaneously lowered the phosphoenol pyruvate carboxykinase activities, accompanied by a reduction in the expression of hepatic glucose transporter protein 2, while the expression of adipose and skeletal glucose transporter protein 4 was increased. Moreover, the antioxidant enzyme activities were also increased by FYGL treatment. Thus, FYGL was an effective antidiabetic agent by enhancing insulin secretion and decreasing hepatic glucose output along with increase of adipose and skeletal muscle glucose disposal in the late stage of diabetes. Furthermore, FYGL is beneficial against oxidative stress, thereby being helpful in preventing the diabetic complications.

SummaryThe Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole‐genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor‐joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome‐wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.

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Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reducedrepresentation sequencing method. After imputation and quality control, 60 850 highconfidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH-related variables were compared between imputed and non-missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction-related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.