Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection

Hassanine, Nada N. A. M.; Saleh, Ahmed A.; Essa, Mohamed Osman Abdalrahem; Adam, Saber Y.; Mohai Ud Din, Raza; Rehman, Shahab Ur; Ali, Rahmat; Husien, Hosameldeen Mohamed; Wang, Mengzhi

doi:10.3390/ijms26167688

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Open AccessReview

Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection

by

Nada N. A. M. Hassanine

^†

,

Ahmed A. Saleh

^†

,

Mohamed Osman Abdalrahem Essa

,

Saber Y. Adam

,

Raza Mohai Ud Din

,

Shahab Ur Rehman

,

Rahmat Ali

,

Hosameldeen Mohamed Husien

^*

and

Mengzhi Wang

^*

College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to the current work.

Int. J. Mol. Sci. 2025, 26(16), 7688; https://doi.org/10.3390/ijms26167688

Submission received: 19 June 2025 / Revised: 5 August 2025 / Accepted: 6 August 2025 / Published: 8 August 2025

(This article belongs to the Section Molecular Genetics and Genomics)

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Abstract

This review synthesizes advances in livestock genomics by examining the interplay between candidate genes, molecular markers (MMs), signatures of selection (SSs), and quantitative trait loci (QTLs) in shaping economically vital traits across livestock species. By integrating advances in genomics, bioinformatics, and precision breeding, the study elucidates genetic mechanisms underlying productivity, reproduction, meat quality, milk yield, fibre characteristics, disease resistance, and climate resilience traits pivotal to meeting the projected 70% surge in global animal product demand by 2050. A critical synthesis of 1455 peer-reviewed studies reveals that targeted genetic markers (e.g., SNPs, Indels) and QTL regions (e.g., IGF2 for muscle development, DGAT1 for milk composition) enable precise selection for superior phenotypes. SSs, identified through genome-wide scans and haplotype-based analyses, provide insights into domestication history, adaptive evolution, and breed-specific traits, such as heat tolerance in tropical cattle or parasite resistance in sheep. Functional candidate genes, including leptin (LEP) for feed efficiency and myostatin (MSTN) for double-muscling, are highlighted as drivers of genetic gain in breeding programs. The review underscores the transformative role of high-throughput sequencing, genome-wide association studies (GWASs), and CRISPR-based editing in accelerating trait discovery and validation. However, challenges persist, such as gene interactions, genotype–environment interactions, and ethical concerns over genetic diversity loss. By advocating for a multidisciplinary framework that merges genomic data with phenomics, metabolomics, and advanced biostatistics, this work serves as a guide for researchers, breeders, and policymakers. For example, incorporating DGAT1 markers into dairy cattle programs could elevate milk fat content by 15-20%, directly improving farm profitability. The current analysis underscores the need to harmonize high-yield breeding with ethical practices, such as conserving heat-tolerant cattle breeds, like Sahiwal.

Keywords: livestock genomics; QTL mapping; selection signatures; precision breeding; sustainable agriculture; genetic markers

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MDPI and ACS Style

Hassanine, N.N.A.M.; Saleh, A.A.; Essa, M.O.A.; Adam, S.Y.; Mohai Ud Din, R.; Rehman, S.U.; Ali, R.; Husien, H.M.; Wang, M. Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection. Int. J. Mol. Sci. 2025, 26, 7688. https://doi.org/10.3390/ijms26167688

AMA Style

Hassanine NNAM, Saleh AA, Essa MOA, Adam SY, Mohai Ud Din R, Rehman SU, Ali R, Husien HM, Wang M. Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection. International Journal of Molecular Sciences. 2025; 26(16):7688. https://doi.org/10.3390/ijms26167688

Chicago/Turabian Style

Hassanine, Nada N. A. M., Ahmed A. Saleh, Mohamed Osman Abdalrahem Essa, Saber Y. Adam, Raza Mohai Ud Din, Shahab Ur Rehman, Rahmat Ali, Hosameldeen Mohamed Husien, and Mengzhi Wang. 2025. "Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection" International Journal of Molecular Sciences 26, no. 16: 7688. https://doi.org/10.3390/ijms26167688

APA Style

Hassanine, N. N. A. M., Saleh, A. A., Essa, M. O. A., Adam, S. Y., Mohai Ud Din, R., Rehman, S. U., Ali, R., Husien, H. M., & Wang, M. (2025). Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection. International Journal of Molecular Sciences, 26(16), 7688. https://doi.org/10.3390/ijms26167688

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Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection

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