Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Abstract

A genetic linkage map of the channel catfish genome (N ¼ 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

“…Our linkage analysis successfully identified all 73 linkage groups. The linkage map provides high resolution, and the average recombination rate across all linkage groups in E. sinensis is 3.09 cM Mb − 1 , which is much higher than those reported in many other animals, such as mouse (0.5 cM Mb − 1 ), catfish (1.65 cM Mb − 1 ), zebrafish (1.35 cM Mb − 1 ), scallop (1.3 cM Mb − 1 ) and shrimp (1.9 cM Mb − 1 ) (Shimoda et al, 1999;Jensen-Seaman et al, 2004;Kucuktas et al, 2009;Huang et al, 2011;Baranski et al, 2014;Jiao et al, 2014). This suggests that QTLs, if identified, can be narrowed down to quite small genomic region in E. sinensis.…”

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

“…Furthermore, the high information content and transferability of microsatellite markers provide an important tool for integration of different maps and for comparative genomics studies (Xia et al, 2010;Yu et al, 2004). So far, first generation genetic maps with low or medium resolution have been reported for many aquaculture animals (e.g., Coimbraa et al, 2003;Li et al, 2003;Li et al, 2005;Li et al, 2006), and now microsatellites are extensively applied in the preparation of second generation genetic linkage maps in some economically important aquaculture fishes, such as tilapia (Lee et al, 2005), rainbow trout (Palti et al, 2012;Rexroad et al, 2008), Japanese flounder (Castaño-Sánchez et al, 2010;Song et al, 2012), channel catfish (Kucuktas et al, 2009;Ninwichian et al, 2012), grass carp (Xia et al, 2010) and common carp (Zhang et al, 2013;Zheng et al, 2011).…”

A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs

“…SNPs are the most frequent type of variation in the genome and provide powerful tools for linkage mapping, and for identifying complex traits in humans (Wang et al 1998) and other model organisms (Zimdahl et al 2004;Guryev et al 2006). However, the application of SNPs in linkage mapping of aquaculture fish is somewhat rare (Moen et al 2008;Kucuktas et al 2009;Castaño-Sánchez et al 2010).…”

“…These data provide valuable resources for comparative genomic analysis in related species, for example, one can use genomic information from model organisms for research projects in non-model species (Gebhardt et al 2003;Sarropoulou et al 2008) and identify regions of conserved syntenies (Woods et al 2005). Synteny has been demonstrated by comparative mapping among genomes of several farmed fish species: rainbow trout (Rexroad et al 2005), gilthead sea bream (Elena et al 2007), European seabass (Chistiakov et al 2008), catfish (Kucuktas et al 2009), grass carp (Xia et al 2010) and Asian seabass .…”