Composite selection signal analysis: Uncovering candidate genes and quantitative trait loci in Indian sheep breeds

Sapna Nath, Satish Kumar Illa, Destaw Worku, Sabyasachi Mukherjee, Anupama Mukherjee and Vinod Kumar Yata

PLOS ONE, 2026, vol. 21, issue 3, 1-21

Abstract: Selective pressures, both natural and artificial, have significantly influenced the genomic architecture of domesticated sheep. Understanding their underlying molecular mechanisms is critical for developing efficient breeding programs to conserve and improve economically important traits in native breeds. In this study, we analysed high-density 50K SNP data from three Indigenous sheep breeds: Chanthangi (CHA, n = 29), Garole (GAR, n = 24), and Deccani (IDC, n = 26), each native to diverse climatic regions of India. We implemented a novel SNP-based de-correlated composite of multiple signals (DCMS) statistic, which integrates p-values from five selection metrics viz., FST, H1, H12, Tajima’s D, and nucleotide diversity (π) into a unified measure. The SNP-based DCMS approach offers finer resolution and complements window-based methods by enabling more precise localisation of selection signals and candidate genes. Multiple testing correction was applied at a False Discovery Rate (FDR) threshold of

Date: 2026
References: Add references at CitEc
Citations:

Downloads: (external link)
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0344299 (text/html)
https://journals.plos.org/plosone/article/file?id= ... 44299&type=printable (application/pdf)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0344299

DOI: 10.1371/journal.pone.0344299

Access Statistics for this article

More articles in PLOS ONE from Public Library of Science
Bibliographic data for series maintained by plosone ().