Genome-scan analysis for quantitative trait loci in an F2 tilapia hybrid

A. Cnaani, N. Zilberman, S. Tinman, G. Hulata, M. Ron

Research output: Contribution to journalArticlepeer-review

84 Scopus citations


We searched for genetic linkage between DNA markers and quantitative trait loci (QTLs) for innate immunity, response to stress, biochemical parameters of blood, and fish size in an F2 population derived from an interspecific tilapia hybrid (Oreochromis mossambicus x O. aureus). A family of 114 fish was scanned for 40 polymorphic microsatellite DNA markers and two polymorphic genes, covering ∼80% of the tilapia genome. These fish had previously been phenotyped for seven immune-response traits and six blood parameters. Critical values for significance were P <0.05 with the false discovery rate (FDR) controlled at 40%. The genome-scan analysis resulted in 35 significant marker-trait associations, involving 26 markers in 16 linkage groups. In a second experiment, nine markers were resampled in a second family of 79 fish of the same species hybrid. Seven markers (GM180, GM553, MHC-I, UNH848, UNH868, UNH898 and UNH925) in five linkage groups (LG 1, 3, 4, 22 and 23) were associated with stress response traits. An additional six markers (GM47, GM552, UNH208, UNH881, UNH952, UNH998) in five linkage groups (LG 4, 16, 19, 20 and 23) were verified for their associations with immune response traits, by linkage to several different traits. The portion of variance explained by each QTL was 11% on average, with a maximum of 29%. The average additive effect of QTLs was 0.2 standard deviation units of stress response traits and fish size, with a maximum of 0.33. In three linkage groups (LG 1, 3 and 23) markers were associated with stress response, body weight and sex determination, confirming the location of QTLs reported by several other studies.

Original languageEnglish
Pages (from-to)162-172
Number of pages11
JournalMolecular Genetics and Genomics
Issue number2
StatePublished - Sep 2004
Externally publishedYes

Bibliographical note

Funding Information:
Acknowledgements The authors thank Thomas D. Kocher for allowing the use of data on the tilapia linkage map and microsat-ellite sequences before they were published. This study was supported by the Israel Science Foundation (Grant no. 418/99-1), and has been carried out in compliance with the current laws governing genetic experimentation in Israel


  • Genome scan
  • Microsatellites
  • Oreochromis
  • Quantitative trait loci (QTLs)
  • Tilapia


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