Identification of genomic regions related to lactation persistency and milk production traits in different sheep breeds

Document Type : Research Paper

Authors

1 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Environmental Sciences, Arak University, Arak, Iran.

2 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

Abstract

Objective
Lactation persistence and milk production are among the most economically important traits in the dairy sheep industry. Lactation persistency is defined as the ability of a sheep to maintain milk production at a high level after reaching peak production. Identifying selection signatures can provide valuable insights about the genes or genomic regions that have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. This study aimed to identify genomic regions with positive selection signatures related to lactation persistency and milk production in sheep breeds using the FST method.
 
Materials and Methods
In this study, data from Zandi (96 samples), Chios (317 samples), and Valle del Belìce (481 samples) sheep, genotyped using a 50K BeadChip, were used to identify genomic regions under selection associated with milk traits. After quality control of the initial data using PLINK software, 36,605 SNP markers in 880 sheep were retained for further analysis. To identify the selection signatures, the statistical method of FST was employed using the FST software package. Candidate genes were identified by SNPs located in the top 0.1% of FST values. The GeneCards and UniProtKB databases were also used to interpret the functions of the identified genes.
 
 
Results
Using the FST approach, we identified ten genomic regions on chromosomes 1, 2, 4, 6, 8, 9, 11, 13, 17, and 20 that were in the 99.9th percentile of all FST values. The identified candidate genes associated with milk and lactation persistency traits in these genomic regions included FAIM, CEP70, TLR4, SLC37A3, KDM7A, HERC6, NT5DC1, SPIDR, SMOX, and RNF144B. Genes located in these identified regions under selection were associated with milk production, milk fat synthesis, lactation persistency, inflammatory response, and immune system functions, which can be directly and indirectly related to milk production traits. Additionally, a review of the extracted QTLs showed that these QTLs are involved in economically important traits in sheep, such as milk yield, milk fat composition, milk fat percentage, and milk yield persistence.
 
Conclusions
The genes identified within these regions can be considered candidates under selection based on their functions. However, further association and functional studies are necessary to confirm the implications of the genes obtained from this analysis. The results of this research can be used to understand the genetic mechanisms controlling milk production and persistency traits. These findings could potentially support genetic selection in sheep for improved milk yield and lactation persistence following peak lactation.

Keywords

References

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Agricultural Biotechnology Journal
Volume 17, Issue 1
March 2025
Pages 141-160

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