DNA isolation and amplification were performed following standard protocols in our laboratory (Premachandra et al., 2017a (link)). A panel of eight microsatellite markers were used to genotype the experimental fish (Whatmore et al., 2013 (link); Knibb et al., 2016 (link)). PCR products were separated by capillary electrophoresis on an AB 3500 Genetic Analyzer (Applied Biosystems). Fragment sizes were determined relative to an internal lane standard (GS-600 LIZ; Applied Biosystems) using GENEMARKER v1.95 software (SoftGenetics, State College, PA, United States) and double-checked manually. Parentage assignment was completed using COLONY software (Jones and Wang, 2010 (link)) with confidence scores of above 95%. The pedigree included 65 full-sib groups (16 dams and 31 sires), with the family size of 3–108 offspring. A total of 1,957 offspring out of 1,998 individuals were assigned to full- and half-sib families (Premachandra et al., 2017b (link)). In this study, representatives of large size families were sent to DArT Ptd. Ltd. in Canberra, Australia for sequencing. Seven hundred and fifty-two individual fish sequenced by DArT-seq technology platform contained 35 (full and half-sib) families varying in size between 2 and 39 (average family size = 17 fish).
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