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Zhu A.-X.,Nanjing Normal University | Zhu A.-X.,State Key Laboratory Cultivation Base of Geographical Environment Evolution | Zhu A.-X.,CAS Institute of Geographical Sciences and Natural Resources Research | Zhu A.-X.,University of Wisconsin - Madison | And 14 more authors.
International Journal of Geographical Information Science

The vast accumulation of environmental data and the rapid development of geospatial visualization and analytical techniques make it possible for scientists to solicit information from local citizens to map spatial variation of geographic phenomena. However, data provided by citizens (referred to as citizen data in this article) suffer two limitations for mapping: bias in spatial coverage and imprecision in spatial location. This article presents an approach to minimizing the impacts of these two limitations of citizen data using geospatial analysis techniques. The approach reduces location imprecision by adopting a frequency-sampling strategy to identify representative presence locations from areas over which citizens observed the geographic phenomenon. The approach compensates for the spatial bias by weighting presence locations with cumulative visibility (the frequency at which a given location can be seen by local citizens). As a case study to demonstrate the principle, this approach was applied to map the habitat suitability of the black-and-white snub-nosed monkey (Rhinopithecus bieti) in Yunnan, China. Sightings of R. bieti were elicited from local citizens using a geovisualization platform and then processed with the proposed approach to predict a habitat suitability map. Presence locations of R. bieti recorded by biologists through intensive field tracking were used to validate the predicted habitat suitability map. Validation showed that the continuous Boyce index (Bcont(0.1)) calculated on the suitability map was 0.873 (95% CI: [0.810, 0.917]), indicating that the map was highly consistent with the field-observed distribution of R. bieti. Bcont(0.1) was much lower (0.173) for the suitability map predicted based on citizen data when location imprecision was not reduced and even lower (−0.048) when there was no compensation for spatial bias. This indicates that the proposed approach effectively minimized the impacts of location imprecision and spatial bias in citizen data and therefore effectively improved the quality of mapped spatial variation using citizen data. It further implies that, with the application of geospatial analysis techniques to properly account for limitations in citizen data, valuable information embedded in such data can be extracted and used for scientific mapping. © 2015 Taylor & Francis. Source

Dondup D.,Chinese Academy of Agricultural Sciences | Dondup D.,Tibet Academy of Agricultural and Animal science | Dong G.,Wuhan Polytechnic University | Xu D.,Chinese Academy of Agricultural Sciences | And 7 more authors.
Molecular Breeding

Knowledge of the allelic variation and epistatic interaction of vernalization genes is crucial to understanding seasonal growth habit and adaptability of genetic resources in cultivated (Hordeumvulgare) and wild (Hodeumspontaneum) barley. In this research, 1398 Chinese barley accessions were characterized with molecular markers for vernalization genes HvVRN1 and HvVRN2. Different combinations of haplotypes at these two vernalization genes were present at different frequencies in wild barley, landraces and modern cultivars. All of the HvVRN1 haplotypes except HvVRN1-7 (V1-7) and HvVRN1-Hs (V1-Hs) were identified in the Chinese barley collection chosen for this study. Haplotype V1-8 occurred at the highest frequency in spring V1 alleles, and V1-1, V1-4 and V1-8 had broad geographic distributions in China. Haplotypes V1-2 and V1-3 are restricted to modern cultivars as they were introduced from exotic germplasm. A total of 18 HvVRN1/HvVRN2 multilocus haplotypes were identified. Most of the HvVRN1/HvVRN2 haplotypes were present in materials from the Yellow-Huai River Valley and Middle-Lower Yangtze Valley ecological zones, birthplace of Chinese farming. The predominant combinations in landraces were V1-8/V2 and v1/V2, but v1/v2 made up the highest proportion of modern cultivars. Haplotypes V1-5/v2, V1-10/V2 and V1-9/V2 showed a correlation with region. Our results confirmed the presence or absence of conserved regulatory elements and the length of the first intron of HvVRN1 plays a determinant role in the vernalization requirement of barley. This study provides useful information for breeding and utilization of Chinese barley germplasm. © 2016, Springer Science+Business Media Dordrecht. Source

Zhang G.-R.,Shanghai Key Laboratory of Agricultural Genetics and Breeding | Zhang G.-R.,Nanjing Agricultural University | Yu R.-S.,Shanghai Key Laboratory of Agricultural Genetics and Breeding | Zeng J.-Y.,Tibet Academy of Agricultural and Animal science | And 7 more authors.

Aims: To develop an effective diagnostic kit, based on a competitive ELISA-based system (cELISA), for detecting serum antibody against peste des petits ruminants virus (PPRV). Methods: Epitope peptides of the nucleocapsid (N) protein of Tibetan PPRV were synthesized chemically and injected into rabbits to prepare hyperimmune antisera. Test sera were incubated simultaneously with hyperimmune antisera and added to the wells of ELISA plates coated previously with recombinant N protein. Horseradish peroxidase-conjugated goat anti-rabbit antibody was employed to detect the quantity of hyperimmune antisera combined with recombinant N protein. Results: A cELISA has been developed for monitoring PPRV infections with a cutoff value of 35. Relative sensitivity and specificity values of the epitope-based cELISA were 96.18 and 91.29%, respectively, when compared with a commercial cELISA kit in a test involving 1,039 serum samples. Conclusion: We report an efficient method for preparing antibody suitable for incorporation into a cELISA that can be used routinely for the detection of PPRV antibodies in serum samples. The method eliminated the requirement for virus culture and monoclonal antibody preparation, reduced the biorisk posed by virus-dependent manipulations, and the performance of the resultant cELISA compared favorably with a commercially available cELISA kit. Copyright © 2012 S. Karger AG, Basel. Source

Shen Y.,Nanjing Agricultural University | Shen J.,Nanjing Agricultural University | Dawadondup,Nanjing Agricultural University | Dawadondup,Tibet Academy of Agricultural and Animal science | And 7 more authors.
Molecular Breeding

Blue wheat grain contains different groups of pigments that can be used for making specialty foods or as food colorants. Thinopyrum bessarabicum, a wild relative of wheat, carries a blue-grained gene on chromosome 4J. In this study, we analyzed the mitotic chromosomes of 159 F7 lines derived from the cross between Triticum aestivum cv. Chinese Spring (CS) and a CS-Th. bessarabicum amphiploid by using multi-color fluorescence in situ hybridization, genomic in situ hybridization, and newly developed chromosome 4J-specific DNA markers. Intact chromosome 4J and various 4J chromosomal segments were identified in the 159 lines. The blue-grained gene of Th. bessarabicum was physically localized to the region between the centromere and FL0. 52 on chromosome arm 4JL. The chromosomal location of this gene differed from the location of previously reported blue-grained genes. In addition, a strong dosage effect was observed with this gene. These results suggest that the blue-grained gene in Th. bessarabicum represents a novel gene locus for blue aleurone, designated BaThb. The wheat lines and 4J chromosome-specific molecular markers developed in this study will facilitate the introgression and utilization of BaThb for wheat nutritional quality improvement. © 2012 Springer Science+Business Media B.V. Source

Zhang G.-R.,Nanjing Agricultural University | Zeng J.-Y.,Tibet Academy of Agricultural and Animal science | Zhu Y.-M.,Shanghai Key Laboratory of Agricultural Genetics and Breeding | Dong S.-J.,Shanghai Key Laboratory of Agricultural Genetics and Breeding | And 5 more authors.

The full-length gene encoding the nucleocapsid (N) protein of the virus (PPRV) responsible for an outbreak of peste des petits ruminants in Tibet in 2007 was synthesized in two stages using overlapping PCR without the need for viral genomic cDNA as template. The full-length N gene was successfully expressed in Escherichia coli, and the purified gene product bound to monoclonal antibody raised against PPRV N protein. Furthermore, it was able to replace recombinant B-N antigen as the coating antigen in a commercial ELISA kit prepared with another PPRV strain. Recombinant protein was employed as the coating antigen to develop an indirect ELISA for PPRV antibody detection in the sera of infected small ruminants. Antibody detection was optimal at a 1:200 serum dilution and an antigen concentration of 3.2 μg/ml, and the positive threshold (cutoff) value of the assay was 2.18. Analysis of 697 serum samples revealed the sensitivity and specificity of the indirect ELISA to be 96.7 and 96.1%, respectively, compared with a commercially available ELISA test. Copyright © 2011 S. Karger AG, Basel. Source

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