Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia

Abstract

Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

Effects of photoperiod on growth performance and melanogenesis pathway for skin pigmentation of Malaysian red tilapia

“…Red tilapia are known for their red colour, while the colour for Malaysian red tilapia varies from red to pink, pink/red and red with black spots (Zhu et al, ). In this study, all fish used for the experiment were pink at the start (whole pink body), whereas after 78 days of experiment changes in colour based on different photoperiods were observed.…”

“…However, red tilapia farming is challenged by pigmentation differences and colour variations especially during overwintering (Zhu et al, ). Luckily, previous studies established the melanogenesis pathway of Malaysian red tilapia and identified several key genes (such as tyrosinase [ tyr ], tyrosine‐related protein 1 [ tyrp‐1 ], solute carrier family 7 member 11 [ slc7a11 ] and SRY‐related HMG‐Box 10 [ sox 10 ]), which are involved in the process of melanin synthesis (Zhu et al, ). Moreover, the expression of slc7a11 and tyr genes involved in melanogenesis is re‐regulated by nutrition (Wang et al, ).…”

“…This study investigated the effects of photoperiods (light and darkness lengths) on the growth performance and melanogenesis pathway of Malaysian red tilapia. Malaysian hybrid tilapia was chosen based on its growth retardation and pigmentation differences during breeding (Wang et al, ; Zhu et al, ). We aimed to get information about colour variations of red tilapia during photoperiod changes.…”

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

“…In evolutionary studies, analysis of transcript abundance is by far the most common functional genomic assay performed but many other factors can be measured including: DNA methylation, chromatin configuration, RNA splicing, RNA synthesis rate, protein-DNA interactions, histone modifications and enhancer-core promoter interactions (Bailey and Batailon, 2016;Zhu et al, 2016). Experimental approaches are now available to test the impact of functional gene changes on traits both at the molecular and organismal level (Turner et al, 2010).…”

“…Both phenotypic plasticity and genetic changes, in a complementary manner or independently, can contribute to this process (Jones et al, 2012;Kozak et al, 2014). Previous investigations have suggested that initial responses result from behavioral and/or phenotypic plasticity which is then followed by genetic assimilation (Wray, 2013;Feldman et al, 2016;Zhu et al, 2016). …”