Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)

BACKGROUND: A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. RESULTS: The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. CONCLUSIONS: The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species

Waterways to Greenways: A Case Study in Shangjie, Zhengzhou, Henan, China

This case study introduces how we used a water sensitive approach to plan a storm water and sponge city project, which expanded into a holistic green infrastructure project. The project is in the Shangjie district in city of Zhengzhou, Henan China. The whole site is 61.16 km² including several waterways. The city is expanding into areas that were previously agricultural. Developers and city both desire to improve the ecological value of the city to boost the economic growth of the Shangjie district. The main goal for the client is to transform the existing industrial city into a more resilient and livable ecological region. Our approach is to holistically solve the region\u27s increasing demand for flood control and storm water management, and to improve ecological and recreational values along these riparian corridors. We propose additional waterways and water bodies to act as green infrastructure, then link the greenways to existing or proposed parks to form a comprehensive greenway network. Our multidisciplinary team conducted detailed investigations and collaborated extensively. The team consists of hydraulic engineers, civil engineers, environmental planners, landscape planners, urban planners, economic planners, and others. We used a variety of technologies, including GIS, Infoworks, remote sensing technology, MIKE model, and lab tests