Abstract
BackgroundCommon 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.ResultsThe 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.ConclusionWe integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated 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.
Highlights
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]
A number of bacterial artificial chromosome (BAC)-anchored microsatellite markers were developed for genetic linkage map construction, with some of them having been used for genetic linkage map construction previously [32], which provided us with the first batch of BAC-anchored genetic markers for map integration
A total of 244 BAC-anchored microsatellite markers were successfully mapped onto the genetic linkage map, anchoring 169 physical map contigs and 46 single BAC clones, equivalent to 144.06 Mb of the common carp genome
Summary
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]. The available genomic resources for common carp research have increased and include a large number of polymorphic loci, genetic markers [6,9,10,11,12,13], databases [14], genetic linkage maps for multiple generations [15,16,17], 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 [23,24,25] 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 [27,28,29] and for comparative analysis with other cyprinids [30]. The objective of this study was to integrate the currently available BAC-based physical and genetic maps
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
