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Shenzhen, China

Wang Y.,Nanjing Agricultural University | Lu J.,Nanjing Agricultural University | Chen S.,CAS Institute of Genetics and Developmental Biology | Shu L.,BGIShenzhen | And 7 more authors.
Journal of Integrative Plant Biology

This study was designed to reveal the genome-wide distribution of presence/absence variation (PAV) and to establish a database of polymorphic PAV markers in soybean. The 33 soybeanwhole-genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518 (1.8%) overlapped with simple sequence repeats (SSRs) in BARCSOYSSR_1.0 database. In a random sample of 800 PAVs, 713 (89.13%) showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR (polymerase chain reaction) products showed better in PAVs than in SSRs, potential in accuratemarkerassisted allele selection. The association mapping results showed SSR+PAV was more powerful than any single marker systems. The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, andmay fit the materials with a range of per locus allele numbers, if jointly used with SSR markers. © 2014 Institute of Botany, Chinese Academy of Sciences. Source

Chen G.,Guangzhou University of Chinese Medicine | Zhang X.,BGIShenzhen | Li C.,Shenzhen Engineering Laboratory for GenomicsAssisted Animal Breeding | Lin Y.,Guangdong Second ProvincialTraditional Chinese Medicine Hospital | And 2 more authors.
Molecular Medicine Reports

Tanshinone IIA (TIIA) is widely used for the treatment of a number human diseases, including diabetic nephropathy (DN) (1). The present study was performed to examine the role of the transforming growth factor β (TGFβ)/p65 pathway under TIIA treatment in a glomerular mesangial cell model of DN. Firstly, it was identified that TIIA inhibited the proliferation of HBZY1 cells, while simultaneously suppressing the expression of TGFβ and p65. In addition, glucose-induced HBZY1 cells were treated with TIIA, siTGFβ and sip65. The results revealed that siTGFβ or sip65 were able to inhibit the proliferation of HBZY1 cells as well. Finally, the expression of TGFβ and p65 in a rat model of DN treated with TIIA was detected. The results demonstrated that renal hypertrophy and 24 h urinary protein excretion were ameliorated in TIIA-treated rats with DN. Furthermore, it was revealed that the protein levels of TGFβ and p65 were decreased in the DN rats following TIIA treatment. In conclusion, the present study demonstrated that TGFβ and p65 were activated by TIIA in HBZY1 cells. In addition, the expression of TGFβ and of p65 was downregulated in rats with DN treated with TIIA. Source

Yang H.,Anhui Agricultural University | Wei C.-L.,Anhui Agricultural University | Liu H.-W.,Anhui Agricultural University | Wu J.-L.,Anhui Agricultural University | And 10 more authors.

Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants. © 2016 Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

Evans J.D.,U.S. Department of Agriculture | Brown S.J.,Kansas State University | Hackett K.J.J.,U.S. Department of Agriculture | Robinson G.,University of Illinois at Urbana - Champaign | And 23 more authors.
Journal of Heredity

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind. © 2013 Published by Oxford University Press on behalf of The American Genetic Association 2013. This work is written by (a) US Government employee(s) and is in the public domain in the US. Source

Zhang M.,Anhui Medical University | Wu X.,BGIShenzhen | Wu X.,Southern Medical University | Lu W.,Anhui Medical University | And 6 more authors.
Iranian Journal of Basic Medical Sciences

Objective(s): Genome‐wide association studies have identified a number of genetic variants of telomerase reverse transcriptase (TERT), cleft lip and palate transmembrane1‐like (CLPTM1L) associated with the risk of bladder cancer. Rs401681 polymorphism in TERT‐CLPTM1L was of special interest for bladder cancer risk, whereas the results were inconclusive. Materials and Methods: Publications illustrating the association between rs401681 polymorphism and bladder cancer risk were collected from the Embase, PubMed and Google scholar. Three independent reviewers worked on the data extraction. The meta‐analysis was performed by STATA 12.0. The odds ratio (OR) with 95% confidence interval (CI) was calculated for these data. Results: Six case‐control studies were retrieved reporting a total of 9196 bladder cancer patients and 42570 controls. The strength of the relevance between rs401681 polymorphism and bladder cancer risk was evaluated by Stata 12.0 software. Rs401681[C] allele was identified marginally associated with increased bladder cancer risk, with per allele OR of 1.132 (95% CI=1.080‐1.187, Pheterogeneity=0.701); in the stratified analysis by ethnicity, the increased cancer risk was revealed in Asian and Caucasian groups. Moreover, we also revealed that rs401681 polymorphism was associated with an increased risk of bladder cancer in Asian population with three publications under allele model (OR=3.722, 95% CI=1.311‐10.568, P=0.014), whereas a decreased risk was identified in homozygote model (OR=0.692, 95% CI=0.513‐0.934, P= 0.016) and recessive model (OR=0.728, 95% CI=0.541‐0.980, P=0.036). Conclusion: In summary, our study provided evidence that rs401681 polymorphism is associated with the risk of bladder cancer. © 2015, Mashhad University of Medical Sciences. All rights reserved. Source

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