Developing Molecular Markers for Population and Quantitative Genetic Analysis of Seriola lalandi Using Transcriptome Sequencing

Developing breeding programs in new aquacultural species, such as Seriola lalandi is hampered by the lack of sufficient genomic resources required for assessing broodstock relationship. This is very important in marine species where it is not possible to keep family records during the first stages of development, due to communal spawning. We observed that when using markers from related Seriola species lead to an excess of homozygotes, likely due to the presence of mutations at primer sites. We have used whole body transcriptome sequencing of larvae (in excess of 60 millions reads per individual) in order to; Develop a marker panel of microsatellites and SNPs and to assess differential expression between normal and deformed individuals. Using de novo transcriptome assembly, 60K SNPs segregating, 10K indels and 3k microsatellites were discovered. A marker panel of 12 microsatelites and 24 SNPs was validated in vivo using broodstock DNA data. A large number of genes appear to be differentially expressed, between normal and deformed individuals, being interesting those related to jaw formation. Glycolisis, purine and fatty acid metabolic pathways could be predicted using KEGG. These results show the importance of further assessing the transcriptome of S. lalandi, in order to characterize the biology and performing sound breeding programs.