Construction of a genetic linkage map for silver carp (Hypophthalmichthys molitrix)

Abstract

For silver carp (Hypophthalmichthys molitrix), a combined microsatellite (or simple sequence repeat) and amplified fragment length polymorphism (AFLP) sex average linkage map was constructed. A total of 483 markers (245 microsatellites and 238 AFLPs) were assigned to 33 linkage groups. The map spanned 1352.2 cM, covering 86.4% of the estimated genome size of silver carp. The maximum and average spaces between 420 loci were 21.5 cM and 3.2 cM, respectively. The length of linkage groups ranged from 3.6 cM to 98.5 cM with an average of 41.0 cM. The number of markers per group varied from 2 to 44 with an average of 14.6. The AFLP markers significantly improved the integrity of microsatellite-based linkage groups and increased the genome coverage and marker evenness. A genome-wide recombination suppression was observed in male. In an extreme case, six microsatellites co-segregated in male, but spanned a 45.1 cM region in female.

Comparative transcriptomic analyses of two bighead carp ( Hypophthalmichthys nobilis ) groups with different growth rates

“…Microsatellite markers have been widely used in genetic map construction and QTL analyses in aquaculture (Zhang et al, 2010;Laghari et al, 2013;Laine et al, 2013;Zhu et al, 2015). In bighead carp, few genetic studies have employed microsatellites in genetic map construction (Liao et al, 2007).…”

QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp ( Hypophthalmichehys nobilis )

“…These microsatellite markers were recruited from four sources: (1) 800 bighead carp markers (Arsd) and 1912 silver carp markers (Hysd) were developed from genome sequencing (Guo et al, 2013b;Zhu et al, 2014), (2) 406 markers (HysdE) were developed through silver carp transcriptome sequences , (3) 775 markers were developed from three microsatellite-enriched genomic libraries, with 559 from bighead carp assigned with the prefixes 'ArGA' and 'ArGT' (Guo et al, 2013b;Zhu et al, 2014), 216 from silver carp assigned with the prefixes 'HyGT' (Guo et al, 2013b;Zhu et al, 2014), (4) 432 microsatellites which were developed and used in silver carp genetic map with the prefixes 'Hym' (Zhang et al, 2010) were also applied in this study.…”

A second generation genetic linkage map for silver carp (Hypophthalmichehys molitrix) using microsatellite markers

“…These SSRs were named using their original nomenclatures with the prefixes of "Hym" (Zhang et al, 2010;Zhang et al, 2011), "Ar" (Cheng et al, 2008), "BL" (Liao et al, 2007a), "Hmo" (Gheyas et al, 2006), and "Cid" ).…”

“…Approximately 600 SSR sequences for silver carp are available in GenBank or other public databases. A few first-generation genetic maps have been previously reported for silver carp, primarily based on AFLP markers and limited number of SSRs, resulting in relatively low resolution and more linkage groups than expected (Liao et al, 2007b;Zhang et al, 2010Zhang et al, , 2011. A well-defined genetic map with co-dominant DNA markers is not available for this species.…”