A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map

et al. (2013) A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map. PLoS ONE 8(5): e63928. doi:10.1371/journal.pone.0063928 A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map Lan Zhao 0 Yan Zhang 0 Peifeng Ji 0 Xiaofeng Zhang 0 Zixia Zhao 0 Guangyuan Hou 0 Linhe Huo 0 Guiming Liu 0 Chao Li 0 Peng Xu 0 Xiaowen Sun 0 Laszlo Orban, Temasek Life Sciences Laboratory, Singapore 0 1 Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences , Beijing , China , 2 Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin , China , 3 College of Life Science and Technology, Dalian Ocean University , Dalian , China , 4 Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , China Background: Common carp (Cyprinus carpio) is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC)-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL) and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps. Results: The genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome. Conclusion: We integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BACassociated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for genetic improvement and modification. - Funding: This study was supported by the grants from National Department Public Benefit Research Foundation (No. 200903045), National High-tech Research & Development Program of China (No. 2009AA10Z105 and 2011AA100401), China Ministry of Agriculture 948 Program (No. 2010-Z11 and 2011-G12) and Research Foundation of Chinese Academy of Fishery Sciences (No. 2009B002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Common carp (Cyprinus carpio) originated in Eurasia and became one of the most important cultured fish species in the world with an annual global production of 3.4 million metric tons that accounts for nearly 14% of all freshwater aquaculture production in the world [1]. In addition to its economical importance, common carp is also considered as a model species for various studies on ecology [2], environmental toxicology [34], developmental biology [5], immunology [6], evolutionary genomics [7], nutrition [8] and physiology [3]. With increasing demand for the genome resources of this species efforts had been made in the past decades to unveil and understand the genome of common carp. As a result, the available genomic resources for common carp research have increased and include a large number of polymorphic loci, genetic markers [6,913], databases [14], genetic linkage maps for multiple generations [1517], expressed sequence tags (ESTs) and transcriptome sequences [18,19], a bacterial artificial chromosome (BAC) library [20], BAC end sequences (BES) [21], BAC-based physical maps [22], cDNA microarrays [2325] and whole genome exome data [26]. These resources have been used to analyze important genes and quantitative trait loci (QTL) related to various economic traits [2729] and for comparative analysis with other cyprinids [30]. The first generation of BAC-based physical maps of common carp was constructed using High Information Content Fingerprints (HICF) technology [31], which generated a total of 67,493 BAC clones assembled into 3,696 contigs with an average length of 476 kb and a N50 length of 688 kb representing approximately 1.76 Gb of the carp genome [22]. In parallel, the genetic linkage map of common carp was constructed based on 617 microsatellite markers [32]. However, it is important to integrate two types of maps and facilitate genome studies ranging from chromosomescale genome sequence assembly to position-based gene identification to improve important traits. Integration of both linkage and physical maps, is considered as an important step toward whole genome sequencing and assembly, especially for species with large and complex genomes, although it is a challenge to achieve complete genome-scale integration. Both physical and genetic linkage maps have been constructed for many aquaculture species in the past decades [33 39] and these maps have been partially integrated in catfish, rainbow trout and Atlantic salmon. For example, the first generation of integration map of rainbow trout was composed of 238 BAC contigs anchored to the genetic map, covering over 10% of the rainbow trout genome [40]. BAC-anchored SNP markers have been developed and used to anchor 73 BAC contigs to the Atlantic salmon genetic map [41]. In catfish, a total of 2,030 BAC end sequence (BES)-derived microsatellites from 1,481 physical map contigs were developed and used for map integration. These anchored 44.8% of the catfish BAC physical map contigs covering 52.8% of the genome [33,4246]. The genetic map is generally based on genome-wide markers, and the physical map is constructed based on the alignment of short DNA fragments. Integration of the two types of map will provide the essential tools to understand genomes in different scales, and will also facilitate whole genome sequencing and assembly. For instance, the integrated map of common carp in this study provides many more sequence tags fo (...truncated)