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. 2025 Feb;38(2):209-222.
doi: 10.5713/ab.24.0187. Epub 2024 Jun 25.

A novel p.127Val>Ile single nucleotide polymorphism in the MTNR1A gene and its relation to litter size in Thin-tailed Indonesian ewes

Mutasem Abuzahra  1 , Mohammed Baqur S Al-Shuhaib  2 , Dwi Wijayanti  3 , Mustofa Helmi Effendi  4 , Imam Mustofa  5 , Ikechukwu Benjamin Moses  6
Affiliations

A novel p.127Val>Ile single nucleotide polymorphism in the MTNR1A gene and its relation to litter size in Thin-tailed Indonesian ewes

Mutasem Abuzahra et al. Anim Biosci. 2025 Feb.

Abstract

Objective: The primary objective was to identify and characterize the single nucleotide polymorphisms (SNPs) within the MTNR1A gene sequence in Thin-tailed Indonesian ewes to assess the possible association of MTNR1A gene polymorphism with litter size trait.

Methods: Forty-seven Thin-tailed Indonesian sheep were selected for the study. Genotyping involved collecting blood samples, and sequencing exon 2 of the MTNR1A gene.

Results: The study identified 19 novel SNPs, with 10 being non-synonymous variations, in the MTNR1A gene of Thin-tailed Indonesian ewes. One non-synonymous SNP (rs1087815963) showed a significant association with litter size, with the GC genotype exhibiting a higher average litter size than the GG genotype. The deleterious impact of p.Val127Ile SNP was predicted by various in silico tools that predicted a highly damaging effect of p.Val127Ile SNP on the structure, function, and stability of MTNR1A. Docking reactions showed a critical involvement of this locus with the binding with melatonin.

Conclusion: In conclusion, the results of our study suggest that rs1087815963 has a remarkable negative impact on the MTNR1A with a putative alteration in the binding with melatonin. Therefore, the implementation of the novel p.Val127Ile could be a useful marker in marker-assisted selection.

Keywords: Genetic Diversity and Farmed Animals; Litter Size; MTNR1A; Single Nucleotide Polymorphisms.

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Conflict of interest statement

CONFLICT OF INTEREST

We certify that there is no conflict of interest with any organization regarding the materials discussed in the manuscript.

Figures

Figure 1
Figure 1
Linkage disequilibrium among the nine single nucleotide polymorphisms of the MTNR1A gene in Thin Tailed Indonesian sheep is evident. The color of the squares corresponds to the degree of linkage, where darker shades indicate higher levels of linkage; The numerical values within the squares represent the strength of the correlation between locations, expressed as a percentage. Haplotype blocks are indicated by dark lines.
Figure 2
Figure 2
The in-silico analysis of the deleterious effects of the observed missense p.127Val>Ile variant in the MTNR1A. The 3D structure is shown as cartoons encrypted within a transparent surface.
Figure 3
Figure 3
Docking between MTNR1A with melatonin. (A) Normal MTNR1-melatonin complex, (B) Altered (p.127Val>Ile) MTNR1-melatonin complex. Melatonin is shown as a red stick, while Val127 and Ile127 are shown as green sticks.
See this image and copyright information in PMC

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