Development of microsatellite markers using next-generation sequencing for the fish Colossoma macropomum

• Published in: Molecular biology reports Vol. 45; no. 1; pp. 9 - 18
• Main Authors: Ariede, Raquel B., Freitas, Milena V., Hata, Milene E., Matrochirico-Filho, Vito A., Utsunomia, Ricardo, Mendonça, Fernando F., Foresti, Fausto, Porto-Foresti, Fábio, Hashimoto, Diogo T.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.02.2018; Springer Nature B.V
• Subjects: Animal Anatomy; Animal Biochemistry; Animals; Aquaculture - methods; Biomedical and Life Sciences; Characiformes - genetics; Chromosome Mapping - methods; Colossoma macropomum; Genetic markers; Genetic Variation; Genomes; Genotype & phenotype; Heterozygosity; High-Throughput Nucleotide Sequencing - methods; Histology; Immune system; Life Sciences; Microsatellite Repeats; Microsatellites; Morphology; Quantitative Trait Loci; Ribonucleic acid; Rivers; RNA; Sequence Analysis, DNA - methods; Short Communication; Species; NGS; Tambaqui; Aquaculture; SSR gene-associated
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-017-4134-z

Tambaqui ( Colossoma macropomum ) is a fish species from the Amazon and Orinoco Rivers, with favorable characteristics to the cultivation system and great market acceptance in South America. However, the construction of a genetic map for the genetic improvement of this species is limited by the low number of molecular markers currently described. Thus, this study aimed to validate gene-associated and anonymous (non-genic) microsatellites obtained by next generation sequencing (RNA-seq and whole genome shotgun—WGS, respectively), for future construction of a genetic map and search for quantitative trait loci (QTL) in this species. In the RNA-seq data, the observed and expected heterozygosity (H o and H e ) ranged from 0.09 to 0.73, and 0.09 to 0.85, respectively. In the WGS data, H o and H e ranged from 0.33 to 0.95, and 0.28 to 0.92, respectively. In general, the evaluation of 200 markers resulted in 45 polymorphic loci, of which 14 were gene-associated (RNA-Seq) and 31 were anonymous (WGS). Moreover, some markers were related to genes of the immune system, biological regulation/control and biogenesis. This study contributes to increase the number of molecular markers available for genetic studies in C. macropomum , which will allow the development of breeding programs assisted by molecular markers.