Molecular Parentage Analysis Is Essential in Breeding Asian Seabass

Abstract

In aquaculture species, maintaining pedigree information and genetic variation in each generation is essential, but very difficult. In this study, we used nine microsatellites to genotype 2,520 offspring from four independent full-factorial crosses (10 males ×10 females) of Asian seabass to reconstruct pedigree and monitor the change of genetic variations. In all four crosses, over 96.8% of the offspring could be assigned to their parents, indicating the high power of the nine microsatellites for parentage assignment. This study revealed several interesting results: (1). In all four crosses, the contribution of parents to offspring was significantly uneven, and some dominant breeding fishes (i.e. brooders) were found; (2). In two mass crosses where the brooders were carefully checked for reproductive status, a majority (≥90%) of brooders contributed to offspring, whereas in another two crosses, where the brooders were randomly picked without checking reproductive status, only a few brooders (40.0–45.0%) produced offspring; (3). Females had more problems in successful spawning compared to males; and (4). In the two crosses where a few brooders produced offspring, there was a substantial loss in allelic (24.1–34.3%) and gene (20.5–25.7%) diversities in offspring, while in the other two crosses, the majority of allelic (96.8–97.0%) and gene diversities (94.8–97.1%) were maintained. These observations suggest that a routine molecular parentage analysis is required to maintain both allelic and gene diversity in breeding Asian seabass.

Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): Implications for management and resilience to climate change

“…The presence of related individuals in impoundments may be due to the use of relatively few breeders in hatcheries, the skewed contribution of breeders to offspring or a combination of these. Such skewed contribution is commonplace in aquaculture (Brown et al., ; Liu et al., ; Loughnan et al., ). To minimize unnaturally high levels of relatedness, we recommend that fish for stocking should be sourced from more broodstock matings than the current minimum of five pairs (NSW Department of Primary Industries ).…”

“…Microsatellite analyses of stocked impoundments in the MDB show they have little or no neutral genetic differentiation to localities in the natural river system (Faulks et al., ), as one would expect if broodfish are correctly being sourced. Management practices may also benefit from determining if impoundments include highly related individuals as this is a common issue in aquaculture (Brown, Woolliams, & McAndrew, ; Liu et al., ; Loughnan et al., ).…”

Parentage determination of yellow catfish (Pelteobagrus Fulvidraco) based on microsatellite DNA markers

“…As a molecular technique, parentage analysis based on SSRs has become an important booming science in aquaculture breeding program. For example, nine microsatellite markers were used for parentage analysis in the breeding of Asian seabass (Liu et al 2012), and ten microsatellite markers were selected for parentage determination in mandarin fish (Yang et al 2014). In present study, analysis of four genetic diversity parameters (N a , H o , H e and PIC) of nine SSRs suggested high levels of diversity within the populations, as their values ranging from 11 to 25, 0.822 to 0.958, 0.965 to 0.916 and 0.85 to 0.908 (Table 2).…”

“…Until now, microsatellite-based parentage identification technology is the most widely used and reliable method for the identification of genetic relationships among fish species, such as Asian seabass (Lates calcarifer) (Liu et al 2012), large yellow croaker (Larimichthys crocea) (Liu et al 2013), mandarin fish (Siniperca chuatsi) (Yang et al 2014), black-striped pipefish (Syngnathus abaster) (Hubner et al 2013) and Atlantic salmon (Salmo salar) (Norris et al 2000). And the rates of assignment success were 96.8 % for nine SSRs in Asian seabass, more than 99 % for seven SSRs in large yellow croaker, 94 % for ten SSRs in mandarin fish and 95 % for eight SSRs in Atlantic salmon, respectively.…”

Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs

“…Short tandem repeats (STRs, microsatellites) have been the recent and internationally preferred molecular markers to trace studbook information from the species down to the individual level in all types of organisms ranging from lianas (Lacombe et al, 2013) to fish (Liu et al, 2012), insects (Wong et al, 2012), birds (Hadfield et al, 2006;Guerier et al, 2012), and mammals (Cutullé et al, 2010;Stevanovic et al, 2010;Souza et al, 2012). Microsatellites with a high level of heterozygosity are relatively more powerful in assigning relatedness per locus than those with a low level of heterozygosity.…”