Identification of Transcriptome-Derived Microsatellite Markers and Their Association with the Growth Performance of the Mud Crab (Scylla paramamosain)

Abstract

Microsatellite markers from a transcriptome sequence library were initially isolated, and their genetic variation was characterized in a wild population of the mud crab (Scylla paramamosain). We then tested the association between these microsatellite markers and the growth performance of S. paramamosain. A total of 129 polymorphic microsatellite markers were identified, with an observed heterozygosity ranging from 0.19 to 1.00 per locus, an expected heterozygosity ranging from 0.23 to 0.96 per locus, and a polymorphism information content (PIC) ranging from 0.21 to 0.95 per locus. Of these microsatellite markers, 30 showed polymorphism in 96 full-sib individuals of a first generation family. Statistical analysis indicated that three microsatellite markers were significantly associated with 12 growth traits of S. paramamosain. Of these three markers, locus Scpa36 was significantly associated with eight growth traits, namely, carapace length, abdomen width (AW), body height (BH), fixed finger length of the claw, fixed finger width of the claw, fixed finger height of the claw, meropodite length of pereiopod 2, and meropodite length of pereiopod 3 (MLP3) (P<0.05). Locus Scpa75 was significantly associated with five growth traits, namely, internal carapace width, AW, carapace width at spine 8, distance between lateral spine 2 (DLS2), and MLP3 (P<0.05). Locus Spm30 was significantly associated with BH, DLS2, and body weight (P<0.05). Further analysis suggested a set of genotypes (BC at Scpa36, BC and BD at Scpa75, and AC at Spm30) that have great potential in the selection of S. paramamosain for growth traits. These findings will facilitate the development of population conservation genetics and molecular marker-assisted selective breeding of S. paramamosain and other closely related species.

First genetic linkage map for the mud crab (Scylla paramamosain) constructed using microsatellite and AFLP markers

“…In the present study, a total of five type I microsatellite loci were found to be polymorphic using a G 1 family. The genetic diversity (mean H O = 0.50) was much lower than that of type II loci (mean H O = 0.76; Ma et al, 2010), and even lower than that of type I loci developed in a previous study (mean H O = 0.68; Ma et al, 2014a). Aside from the major reason of microsatellite loci themselves, this difference may be due to the types and sizes of populations (wild, cultured, or a single family) used.…”

“…In order to acquire as many markers as possible, we first developed polymorphic microsatellite markers from the transcriptome, using a previously described method (Ma et al, 2014a). Then, we collected all published microsatellite markers for S. paramamosain (Xu et al, 2009;Ma et al, 2011a,b,c;Cui et al, 2011b;Yao et al, 2012;Song et al, 2013;Ma et al, 2014a,b).…”

“…In order to boost molecular marker-assisted selection (MAS) for S. paramamosain, a microsatellite-PCR based parentage assignment technique was created successfully, with a success rate of 95% (Ma et al, 2013b). Growth performance-related microsatellite markers were developed in S. paramamosain, and the genotypes with the most potential were also identified (Ma et al, 2014a). In addition, a large number of transcriptome resources, including functional genes, single nucleotide polymorphisms (SNPs), and microsatellites have been developed (Gao et al, 2014;Ma et al, 2014b).…”

First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics

“…Next‐generation sequencing has recently been used to identify transcriptome‐derived microsatellites (SSRs) and polymorphic nucleotide positions such as SNPs, and it is considered a time‐saving, highly efficient approach (Li et al ; Ma et al . ; Wang et al . ).…”

Development of polymorphic microsatellite markers in Sardinella aurita by 5′-anchored PCR technique

“…Isolation and utilization of microsatellite markers has been carried out in many species (Wang et al 2009;Ma et al 2011Ma et al , 2014. Currently, no polymorphic microsatellite markers have been reported for S. aurita.…”