| We constructed an (AC)n-microsatellite-enriched library for large yellow croaker Pseudosciaena crocea (Richardson 1846) using the method of FIASCO. The rate of positive clones reached 66.4%,631 sequences containing microsatellite were obtained, and 413 primer pairs were designed. Eleven primer pairs were genotyped on 30 P. crocea individuals from Guangjingyang wild population (WP) in Fujian province and 38 individuals from Ningbo cultured population in Zhejiang province (CP). In WP, the average observed and expected heterozygosoties was 0.648 and 0.803, respectively, the average number of allele and polymorphism information content was 8.5 and 0.764, respectively. In CP, the average observed heterozygosoty, expected heterozygosoty and number of allele was 0.708,0.693 and 4.5, respectively. These results indicated that both WP and CP have low genetic diversity.Simple sequence repeat (SSR) markers were also obtained for the large yellow croaker Pseudosciaena crocea using 1205 expressed sequences tags (ESTs) from the NCBI database. The loci were screened in 30 specimens from a wild population in China. Sixteen of 48 loci were polymorphic, and they were amplified with the number of alleles per locus ranging from 3 to 11. Polymorphic information content ranged from 0.115 to 0.866. The number of successfully amplified loci in Pseudosciaena polyactis, Collichthys niveatus, Collichthys lucidus, Argyrosomus argentatus and Johnius grypotus was 14,12,11,7, and 6, respectively. These results showed that the amplification probability should correlate with their phylogenetic proximity to P. crocea.A mixed group of large yellow croaker Pseudosciaena crocea was constructed, whose parents (4♀×4♂) came from different populations. After they grew up to adults, parental allocation was conducted by using microsatellite markers. Two half-sib families were selected as mapping families to construct the genetic linkage maps of microsatellite markers using LINKMFEX software. The number of segregation makers was 115 and 224 in WC family and in CC family, respectively. Using the module MERGE of LINMFEX software, new linkage group orders were built for preexisting linkage group orders that were obtained from the two full-sib families. A total of 251 microsatellite markers were integrated into linkage maps, in which contained 47 EST-SSR markers. The composite female map contained 206 markers in 24 linkage groups, with an average of 8.6 markers per group, spanning 827.9 cM with an average interval 4.5 cM. The coverage of female map was 76.5%. For the composite male map,179 markers were assigned in 24 linkage groups, with an average of 7.5 markers per group. The total length of male map was 1000.4 cM with an average interval of 6.5 cM. The coverage of male map was 71.5%. The recombination frequency was greater in the female than that in the male with a female to male recombination frequency ratio of 0.1 to 3.6, with the average of 1.3:1.The location and effects of QTLs were estimated for total length, body length, body weight, body height trait using MapQTL 5.0 based on the composite maps of large yellow croaker. A total of 26 putative QTLs were located, including 7 for total length,6 for body length,7 for body height, and 6 for body weight. These QTLs were mapped in LG2, LG7, LGI0, LG11, LG17, and LG23. They were clustered on the composite maps of large yellow croaker, which means these growth-related traits shared the common genetic elements. The phenotypic variation explained by the QTLs for growth-related traits ranged from 6.5% to 73.0%. The association between phenotypic traits and genotypes of four allelic combinations from markers nearest to QTL was analyzed by ANOVA method, and 11 significant QTLs were found.
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