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Whole-Genome Sequencing Reveals the Role of Cis-Regulatory Elements and eQTL/sQTL in the Adaptive Selection of Hubei Indigenous Cattle
by
, ,
Liangyu Shi
1,†
,
Pu Zhang
1,†,
Bo Yu
1,
Qing Liu
1,
Chenhui Liu
2,
Wei Lu
3,
Lei Cheng
2,* and
Hongbo Chen
1,*
1
Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
2
Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan 430208, China
3
Hubei Cereals, Oils and Foodstuffs lmport and Export Group Co., Ltd., Wuhan 430015, China
*
Authors to whom correspondence should be addressed.
†
These authors contribute equally to the work.
Animals 2025, 15(9), 1301; https://doi.org/10.3390/ani15091301
Submission received: 25 March 2025
/
Revised: 22 April 2025
/
Accepted: 29 April 2025
/
Published: 30 April 2025
(This article belongs to the Section Animal Genetics and Genomics)
Simple Summary
Hubei indigenous cattle exhibit unique adaptations to their local environments. This study investigates the genetic footprints underlying these adaptations by analyzing whole-genome sequences from five local cattle breeds in Hubei. The analysis identified genomic regions under adaptive selection, highlighting genes associated with sensory perception, fat deposition, reproduction, and immune responses. Further examination of cis-regulatory elements revealed their critical role in controlling gene expression related to lipid metabolism, meat quality, and fertility. The findings reveal breed-specific adaptations and support breeding strategies to enhance resilience and meat traits in Hubei indigenous cattle.
Abstract
Hubei indigenous cattle have adapted to diverse environmental conditions, exhibiting unique genetic traits associated with both economic and adaptive characteristics. Understanding their adaptive selection offers insight into their evolutionary history and genetic enhancements. In this study, we analyzed whole-genome sequencing (WGS) data from five Hubei indigenous cattle breeds to identify selection signals. Selective sweep analysis revealed the candidate genes (USH2A, TMTC2, ABCC12, and SUGT1) associated with sensory perception, backfat thickness, reproduction, and immune function. The further integration of cis-regulatory elements (CREs) and expression quantitative trait loci (eQTL) highlighted regulatory variants, influencing adaptive traits. Notably, positively selected genes such as RPS6KA2, CRLS1, MGST3, GPCPD1, and LDLRAP1 were associated with lipid metabolism, meat quality, and reproductive traits, influencing aldehyde volatile organic compounds (VOCs) and fat deposition. These findings highlight the understanding of the genetic basis of adaptation and production traits in Hubei indigenous cattle and provide valuable insights for their conservation and potential breeding strategies.
Keywords:
indigenous cattle; adaptive selection; cis-regulatory elements; eQTL; immune; meat quality
