Signatures of selection in tilapia revealed by whole genome resequencing

Abstract

Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10–100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.

Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

“…Our study revealed that the LD level declined to 0.05 at 4000 Kb 294 inter-marker distance and that decay patterns were similar between populations ( Figure 295 4). A previous study conducted by Hong Xia et al, (2015) reported similar LD patterns 296 for GIFT tilapia stocks collected from South Africa, Singapore and China. Using 297 microsatellite loci Sukmanomon et al, (2012) estimated LD means in terms of 298 disequilibrium coefficient (D') of 0.05 for a GIFT population originally from the 299…”

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

“…The weight of tilapia fillet contributes heavily towards the yield per fish, which is an important parameter in the aquaculture industry1828. Here, we report the first methylome of skeletal muscle tissue, including sexually dimorphic DMRs, in hybrid tilapia, which is genetically close to Nile tilapia2122. We discovered that MAPK/ERK signaling pathway overexpression in male tilapia was associated with superior growth rate in male tilapia.…”

“…The superior growth rate of male tilapias has driven large sectors of the tilapia aquaculture industry to develop all-male tilapia populations for production using sex-reversal techniques18. In addition, the genome sequence of a Nile tilapia has been sequenced19, and other genomic resources, including microsatellites20, genome-wide SNPs2122, linkage maps232425 and QTL for important traits2526, are available. Hence, tilapia is a good model for studying the molecular mechanisms underlying SD.…”

Transcriptomic response to three osmotic stresses in gills of hybrid tilapia (Oreochromis mossambicus female × O. urolepis hornorum male)

“…Tilapia is an important commercial fish in China, which is euryhaline fish species and it is the second most important fish after carps in aquaculture [14]. Owing to ease of aquaculture, marketability and stable market prices, the production of tilapia has quadrupled over the past decade [15], and which is promoted and farmed in more than 100 countries and regions [16].…”