Multi-trait GWAS using imputed highdensity genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

- Multi-trait GWAS using imputed high- density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia.
- Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species.
- Conclusions: The high-resolution mtGWAS presented here allowed the identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia.
- The most important body traits in Nile tilapia are body weight measured at a spe- cific age (e.g.
- To the best of our knowledge, no previous studies have shown the use of imputation to high-density SNP genotypes, in a combination with mtGWAS, to un- cover putative causative genetic variants associated with body traits in aquaculture species.
- The objective of this study was to use mtGWAS and high-density SNP geno- types to increase the accuracy and power to identify both QTLs and genes associated with eight body traits in Nile tilapia..
- Most of the lead SNPs were on LG01, LG03 and LG12 for ADG, BWH, WW, HW, HON and BLH.
- Table 1 Descriptive statistics for phenotypic values of body traits recorded in a breeding Nile tilapia population.
- Some of these genes have been associated with body traits in previous studies.
- Previous studies have identified loci and candidate genes associated with growth-related traits in aquaculture species .
- Table 2 Genetic parameters and comparison of association results between single- and multi-trait GWAS for Nile tilapia.
- 1 Correlation of SNP effects (standard error) among eight body traits in Nile tilapia.
- Table 3 Genomic regions and the closest candidate genes for the top five lead SNPs associated with body traits based on multi- trait GWAS in Nile tilapia.
- Table 3 Genomic regions and the closest candidate genes for the top five lead SNPs associated with body traits based on multi- trait GWAS in Nile tilapia (Continued).
- 2 Manhattan plot for multi-trait GWAS (mtGWAS) for eight body traits in Nile tilapia.
- Manhattan plots of SNPs associated with: a Average daily gain.
- The x-axis presents genomic coordinates along chromosomes 1 – 23 in Nile tilapia.
- 2), probably due to the polygenic architecture of these traits in Nile tilapia.
- suggesting that part of the genetic variation that affects body traits might be explained by loci on Table 4 Genes intercepted by a lead SNP associated with body traits based on multi-trait GWAS in Nile tilapia.
- Some lead SNPs identified in this study were located close or intercepted several strong functional candidate genes associated with body and growth-related traits in previous studies.
- In catfish COL4A1 was identified within QTLs associated with body length and body length of the fish without the head.
- We also found strong candidate genes intercepted by lead SNPs that may contribute to a better understanding of the biological mechanisms controlling body traits in Nile tilapia.
- We found a lead SNP associated with ADG on LG15, located in an in- tronic region of the FUT8 gene, which has been associ- ated with ADG (from birth to six months-age) in a sheep population from Iran [48].
- Two lead SNPs associated with BWH and HON were found on LG17, in an intronic and exonic region of the NUP107 gene which plays an important role in the de- velopment of vertebrate embryos.
- We found a lead SNP that intercepts the SLC4A2 gene, a strong biological candidate for waste weight in Nile tilapia.
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- ADAMTS9 is responsible for the regulation of the epidermal growth factor receptor (EGFR) and TGF-β1 [62, 63].
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- A lead SNP associated with FY intercepted the HEG1 gene, located in LG16.
- In a comparative transcriptomic analysis aimed to identify differentially expressed genes related to product performance and meat quality from the longissi- mus dorsi in sheep, Cheng et al.
- The functional relation- ship between these genes and the variation in growth-related traits in Nile tilapia is unclear.
- Thus, the function of the identified genes and their potential relationship with body traits in Nile tilapia must be better characterized..
- We used dense genotypic information to refine associ- ation mapping analysis for body traits in Nile tilapia and found that mtGWAS provided substantial improvements in the number of significant SNPs identified when com- pared to stGWAS.
- results can provide further knowledge and a better un- derstanding of genetic variants and genes underlying complex body traits in Nile tilapia..
- The single-trait genome wide association analyses (stGWAS) were performed using the mlma option of the software GCTA v.
- This multi-trait approach can increase the power to detect loci in any of the traits assessed.
- Genes located within 100 kb upstream and downstream of the lead SNP were considered putative candidate genes associated with the trait.
- Manhattan plot for single- trait GWAS (stGWAS) for body traits in Nile tilapia.
- Manhattan plots of SNPs associated with: (A) Average daily gain.
- The x-axis presents gen- omic coordinates along chromosomes 1 – 23 in Nile tilapia.
- Summary results from genotype quality control of whole-genome sequence (WGS), imputed WGS genotypes, and 50 K single nucleotide polymorphism (SNP) chip for Nile tilapia..
- Genomic regions and candidate genes for all lead SNPs associated with body traits based on multi-trait GWAS for Nile tilapia.
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