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. 2025 Jul 16;15(14):2097.
doi: 10.3390/ani15142097.

Selection for Growth Performance in Oreochromis niloticus Across Different Aquatic Environments Using Growth Hormone Gene Polymorphisms

Fawzia S Ali  1 , Simone T Awad  1   2 , Mohamed Ismail  3 , Shabaan A Hemeda  2 , Abeer F El Nahas  2 , Eman M Abbas  1 , Ahmed Mamoon  4 , Hani Nazmi  1 , Ehab El-Haroun  5
Affiliations

Selection for Growth Performance in Oreochromis niloticus Across Different Aquatic Environments Using Growth Hormone Gene Polymorphisms

Fawzia S Ali et al. Animals (Basel). .

Abstract

The current work focused on the molecular selection of Oreochromis niloticus with improved growth performance through marker-trait associations between SNPs within the growth hormone gene (GH) and growth performance. A total of 155 fish of the same age were collected from three locations (Lake Brullus (B), the River Nile at El-Qanater El-Khairia (Q), and Lake Nasser (A)). The selected individual progenies were evaluated through gene expression analysis for growth, inflammatory, nervous, and immune-related genes. A total of nine SNPs and three InDels were significantly associated with morphometric characteristics. The phenotypic variance (R2) of the detected SNPs ranged between 2.6% and 36%. The best populations were A and Q, as they recorded the best growth performance and harboured the highest number of SNPs and InDels, in addition to a significant increase in body weight and length. Furthermore, their progenies documented the most promising gene expression patterns of all tested genes. The current research highlights the importance of molecular selection and the potential use of population-specific SNPs in tilapia breeding programs.

Keywords: Nile tilapia (Oreochromis niloticus); SNPs; growth hormone gene; larval gene expression; population structure; selective breeding.

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Conflict of interest statement

The authors declare no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Figures

Figure 1
Figure 1
Nile Tilapia sampling locations: Lake Brullus, El-Qanater (River Nile), and Lake Nasser, taken after [32].
Figure 2
Figure 2
Comparison of body length (A) and body weight (B) among male and female Nile tilapia (Oreochromis niloticus) from three different populations: Lake Nasser, El-Qanater, and Lake Brullus. Bars represent the mean ± SE. (*) indicate significant differences between groups based on a two-way ANOVA followed by Tukey’s post hoc test (p ≤ 0.05). Different lowercase letters above bars in panel A denote significant differences within the opposite sexes across locations.
Figure 3
Figure 3
SNPs with MAF > 1% within GH gene across 155 genotypes from six populations of Nile Tilapia.
Figure 4
Figure 4
SNP-based STRUCTURE analyses of Nile tilapia male and female genotypes: (A) The magnitude of ∆K as a function of K (i.e., the number of defined groups). (B) SNP-based STRUCTURE defined groups among six populations for K = 2. Yellow and blue are colors representing group 1 and group 2.
Figure 5
Figure 5
Boxplot diagrams depicting the genetic effects of SNPs with significant association with (A) body length and (B) body weight in Nile tilapia.
Figure 6
Figure 6
Haplotype block map for all nine SNPs. Linkage disequilibrium (LD) plots containing nine SNPs from the GH gene of Nile tilapia. LD is measured as D’, ranging from 0 to 1. D’ value equals 1 is depicted in red, and less than 1 is depicted in shades of pink/light red, light blue, and white. The black lines mark the identified blocks.
Figure 7
Figure 7
Ballon plot of the effect of SNP/InDel on the average body length (A) and body weight (B) in six broad stock populations of Nile tilapia. Females Lake Nasser (FA), females EL-Qanater (FQ), females Lake Brullus (FB), males Lake Nasser (MA), males EL-Qanater (MQ), and males Lake Brullus (MB).
Figure 8
Figure 8
Gene expression of growth-related genes, growth hormone (GH) (A), and insulin growth factor I (IGFI) (B) of Oreochromis niloticus larvae 72 h post-hatching. C is the control, B is Lake Brullus, A is Lake Nasser, and Q is El-Qanater F1. Different lowercase letters above bars denote significant differences between different larval groups (p < 0.05).
Figure 9
Figure 9
Gene expression of proinflammatory-related genes, interleukin 1 beta (IL1β) (A), interleukin 8 (IL8) (B), CXC2-chemokine (CXC2) (C), CC-chemokine (CC) (D), and tumor necrosis factor alpha (TNFα) (E) in Oreochromis niloticus larvae 72 h post-hatching. C is the control, B is Lake Brullus, A is Lake Nasser, and Q is El-Qanater F1. Different lowercase letters above bars denote significant differences between different larval groups (p < 0.05).
Figure 10
Figure 10
Gene expression of early immune system development-related gene, recombinant reactivating gene (Rag) (A), and early neural development-related gene, sacsin protein (sacs) (B) in Oreochromis niloticus larvae 72 h post-hatching. C is the control, B is Lake Brullus, A is Lake Nasser, and Q is El-Qanater F1. Different lowercase letters above bars denote significant differences between different larval groups (p < 0.05).
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