| Teleosts is the most numerous and diversified group of vertebrates. Among them,catfish is a globally distributed species. The southern catfish(Silurus meridionalis),also called Chinese large-mouth catfish, is the largest catfish in China. It is also one of the most widely cultured catfish species for food consumption in China. There are many studies about southern catfish, most of them are relate to reproductive biology,comparative anatomy, physiological ecology and so on. While linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish. The construction of a linkage map provides an essential basis for identifying chromosomal regions and quantitative trait loci(QTLs) by genetic linkage analysis. It also serves as a link to the genomic information of model organisms and related non-model organisms by comparing their genomes to facilitate the discovery of candidate genes of non-model organism. Hence, the objective of this study was to construct a high-density linkage map using SNPs generated by next-generation Restriction-site-associated DNA sequencing(RAD)sequencing in the southern catfish for future genetic and genomic studies. The main results of the present study were listed as follows:1. An F1 population of 100 individuals was developed by intraspecific crossing between a wild, heterozygous pair of individuals. A total of 77,634 putative high-quality biallelic SNPs between the parents were discovered, consisting of 54.70%transitions(A/G and C/T) and 45.30% transversions(A/C, A/T, C/G and G/T)(transition/transversion ratio of 1.2). In addition, the A/G substitution was the commonest(27.50%) and C/G was the least common(6.16%). We randomly selected22 SNPs from 77,634 high-quality SNPs for validation of single nucleotide variations.PCR products were firstly analyzed on agarose gels to verify successful amplification,and the remaining PCR products were directly sequenced. Of these 22 SNPs, 16(73%)could be confirmed by Sanger sequencing. It indicated that the filter criteria used to identify the SNP in this study was able to filter out most false positive SNPs.2. We constructed a high-density genetic map in southern catfish based on RAD-seq. It consisted of 29 LGs comprising 26,714 SNPs, which corresponded to6,715 effective loci. The total map length was 5,918.31 cM, with a mean distance between markers of 0.89 cM. Moreover, the maximum interval between genetic RAD loci was 49.27 cM(LG6), while the minimum was 0.01 cM. The genetic length of each LG ranged from 62.59 cM(LG29) to 445.84 cM(LG4), with an average interval between loci of 0.44 ~ 1.77 cM. Moreover, LG24 was the densest, having 235 effective loci, with an average density of 0.44 cM, whereas LG29 had the least number of effective loci(only 125). Such a high-density linkage map providing detailed information on the genomic structure of an organism would be a valuable resource for comparative genomics and fine-scale QTL mapping in catfish.3. The linkage map of southern catfish had been constructed again by JoinMap 4.0to validate the previous linkage map. We selected 3772 SNPs from mapped markers with the interval < 0.3 cM for map construction. The results showed that: 1) Those two genetic linkage maps included the same number of groups(n = 29); 2) All of the linkage groups bettwen both genetic maps presented a one-to-one relationship, but the order of these markers were different between the two linkage maps; 3) The total map length between both linkage maps were different. We considered it may be caused by the different number of mapped markers. In a word, although there were some differences between the genetic maps which constructed by Lep-Map and JoinMap 4.0,they match up with each other in many ways. We considered the genetic map constructed in the present study is credible. |
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