Clock genes in three fish species from the family Salmonidae: QTL associations and synteny analyses
Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. 'Clock1' duplicates and a copy of 'NPAS2'-like gene were partially characterized by genomic sequencing and mapped using family-based indels/SNPs in rainbow trout (RT)('Oncorhynchus mykiss'), Arctic charr (AC)('Salvelinus alpinus'), and Atlantic salmon (AS)(' Salmo salar') mapping panels. 'Clock1' duplicates mapped to linkage groups RT-8/-24, AC-16/-13, and AS-2/-18. 'Clock3/NPAS2 '-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the 'Clock' gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci for life history and growth traits (i.e., reproduction and cell cycling). Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions, suggesting that functionally related or co-regulated genes are clustered in syntenic blocks.