| Yellow catfish(Pelteobagrus fulvidraco Richardson), a member of the family Bagridae of order Siluriformes, is widely distributed in most of water systems in China. Due to its high-quality meat, yellow catfish has become increasing important as a high-value species in aquaculture. Basic knowledge on the genetic diversity, population structure and linkage map of yellow catfish is essential to the effective conservation of wild germ plasm resource, further studies of genetics and marker-assisted breeding in this species. Here, we developed microsatellite loci from yellow catfish, and estimated the genetic diversity and population structure of the yellow catfish for 12 wild populations (N = 460 individuals from ten lakes and two rivers) based on eight polymorphic microsatellite markers. Meanwhile, a primary genetic linkage map of yellow catfish was also constructed. The main contents include:(1) Isolation of microsatellite loci from yellow catfish by FIASCO protocolTwenty microsatellite loci from yellow catfish(Pelteobagrus fulvidraco Richardson) have been isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol, sixteen loci were polymorphic and four ones were monomorphic. Those polymorphic loci were characterized by genotyping 40 individuals. The observed number of alleles ranged from 3 to 11 with an average of 5.4 of each locus. The expected and observed heterozygosities ranged from 0.6372 to 0.8770 with a mean value of 0.7521 and from 0.1250 to 0.9500 with a mean value of 0.5990, respectively. And the polymorphic information content indexes were varied from 0.3841 to 0.8809 with an average of 0.6534. Among these polymorphic microsatellite loci, ten ones conformed to Hardy-Weinberg Equilibrium. These microsatellite markers would be useful for investigating the genetic diversity and population structure of yellow catfish.(2) Development of type I makers of yellow catfish based on Public Data BaseFive microsatellite loci were obtained based on sequences of six microsatellite-containing genes by searching Genbank. Among these loci, three ones were polymorphic. The observed number of alleles ranged from 2 to 4. The expected and observed heterozygosities ranged from 0.4949 to 0.7516 and from 0.5750 to 0.9750, respectively. And the polymorphic information content indexes were varied from 0.3693 to 0.6940. Only one polymorphic loci conformed to Hardy-Weinberg Equilibrium. These typeⅠmarkers would play an important role in map construction, QTL analysis, gene mapping and marker-assisted selection of yellow catfish.(3) Population structure and genetic diversity of the yellow catfish inferred from microsatellite markersWe estimated the genetic diversity and population structure of the yellow catfish for 12 wild populations (N=460 individuals from ten lakes and two rivers) based on eight polymorphic microsatellite markers. The expected and observed heterozygosities of these populations ranged from 0.6222 to 0.6940 and from 0.4489 to 0.9611, respectively. The mean number of alleles and the number of effective alleles were varied from 3.2794 to 4.1543 and from3.1 to 4.4, respectively. These genetic indices indicated the genetic diversity of wild yellow catfish populations was at a high level. However, the population XJR sampled from Xijiang River of Guangdong Province showed lowest level of genetic diversity and monomorphism at locus Pf428 was detected while other populations showing polymorphism at the locus.Cluster analysis revealed three clusters that reflected geographical separation and isolation, for each cluster represented one geographic group. Population XJR being located in Xijiang River in southern China formed a separate cluster. The large cluster included almost all populations in the middle and lower reaches of Yangtze River Basin with only one exception (the population CHL). Population CHL and the other two populations (HLJR and HZL) whose sits belong to northern river system of China formed the third cluster. AMOVA showed that a major portion (82.29%) of the total genetic variation resulted from the within-populations component, while among geographic groups variation and the variance among population within groups accounted for 11.69% and 6.02% of the total genetic variation, respectively. The differenciation among three geographic groups were highly significant (FST=0.1771, P<0.001). However, when we further analyzed correlation between genetic and geographical distances with the Mantel test, the result showed no significant correlation between genetic and geographical distances (r=0.3937, R2=0.155, P=0.9200).(4) A primary linkage map of yellow catfish based on AFLP and microsatellite markersGenetic linkage map is useful for genetic improvement and selective breeding of yellow catfish. Linkage maps were constructed using an intraspecific F1cross and amplified fragment length polymorphism (AFLP) markers.411 AFLP markers produced from eighty-one selected AFLP primer combinations and fifteen microsatellite markers were polymorphic in either of the parents and segregated in the progeny. Among these segregating markers,100 were mapped to 13 linkage groups, six triplets and seven doublets of the male map, covering a total of 1142.2 cM. The total length of male framework map was 813.2 cM with an average marker spacing of 14.2 cM. And 75 markers were assigned to six linkage groups, seven triplets and thrirteen doublets of the female map, covering a total of 1115.8 cM. The total length of female framework map was 612.2 cM with an average marker spacing of 28.3 cM. None of the fifteen microsatellite markers was assigned to the genetic maps. The estimated genome length of P. fulvidraco was 1951.7 cM for the male and 2180.4 cM for the female, respectively. Genome coverage was estimated to be 41.67% and 28.08% for the female and male framework maps respectively, rising to 58.53% (male) and 51.18% (female) when associated markers were included.The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map and mapping of economically important genes. |
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