Whole-genome resequencing identifies a novel SNP associated with lumbar vertebrae number in Dezhou donkeys
- 1College of Agriculture and Biology, Liaocheng University, Liaocheng, China
Abstract
Background: The number of vertebrae is an economically significant trait in livestock, with variations in this trait directly influencing meat and hide production performance. Within the Dezhou donkey population, five distinct thoracolumbar vertebrae combinations have been identified (T17L5, T17L6, T18L5, T18L6, and T19L5).
Methods: This study employed whole-genome resequencing and selective sweep analysis to identify genomic regions under selection pressure associated with thoracic and lumbar vertebrae number variation. Whole-genome resequencing was performed on 87 samples, followed by selective sweep analysis to identify candidate regions and genes. Furthermore, PCR amplification combined with Sanger sequencing was performed to validate this potentially functional SNP locus in an independent cohort of 183 Dezhou donkeys.
Results: In this study, 87 Dezhou donkeys were subjected to whole-genome resequencing, yielding 6,929,687 high-quality SNPs. Selective sweep analysis using the Fst method identified candidate genes enriched in signaling pathways related to skeletal development and vertebral morphogenesis, including the Notch, TGF-beta, Wnt signaling pathways, and retinol metabolism. PCR amplification and Sanger sequencing validation in 183 Dezhou donkeys confirmed that the SNP g.80,827,321 A > G in the LOC106828038 gene was associated with fewer lumbar vertebrae (P < 0.05). Population genetic analysis revealed moderate polymorphism (PIC = 0.3515) with Hardy-Weinberg equilibrium maintained at this locus. Furthermore, in mature donkeys (≥ 2-year-old), this locus was significantly associated with body length, chest girth, cannon circumference, and hip height. In < 2-year-old group, this locus was also significantly associated with cannon circumference.
Conclusion: These findings identify LOC106828038 as a potential regulatory factor associated with the number of lumbar vertebrae in Dezhou donkeys through the retinol metabolism pathway. This could be used for marker-assisted selection to breed superior Dezhou donkey strains with improved body conformation and production traits.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12864-026-13216-6.
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BibTeX
@article{liu2026wholegenome,
title = {{Whole-genome resequencing identifies a novel SNP associated with lumbar vertebrae number in Dezhou donkeys}},
author = {Xiaotong Liu and Anqi Liu and Yunfan Zheng and Wenting Chen and Manna Dou and Bingbing Cai and Zhiyu Yan and Muhammad Zahoor Khan and Yongdong Peng and Changfa Wang},
journal = {BMC Genomics},
year = {2026},
month = aug,
doi = {10.1186/s12864-026-13216-6},
url = {https://doi.org/10.1186/s12864-026-13216-6},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Whole-genome resequencing identifies a novel SNP associated with lumbar vertebrae number in Dezhou donkeys
AU - Xiaotong Liu
AU - Anqi Liu
AU - Yunfan Zheng
AU - Wenting Chen
AU - Manna Dou
AU - Bingbing Cai
AU - Zhiyu Yan
AU - Muhammad Zahoor Khan
AU - Yongdong Peng
AU - Changfa Wang
PY - 2026
DA - 2026/08/10
JO - BMC Genomics
DO - 10.1186/s12864-026-13216-6
UR - https://doi.org/10.1186/s12864-026-13216-6
AB - Background: The number of vertebrae is an economically significant trait in livestock, with variations in this trait directly influencing meat and hide production performance. Within the Dezhou donkey population, five distinct thoracolumbar vertebrae combinations have been identified (T17L5, T17L6, T18L5, T18L6, and T19L5). Methods: This study employed whole-genome resequencing and selective sweep analysis to identify genomic regions under selection pressure associated with thoracic and lumbar vertebrae number variation. Whole-genome resequencing was performed on 87 samples, followed by selective sweep analysis to identify candidate regions and genes. Furthermore, PCR amplification combined with Sanger sequencing was performed to validate this potentially functional SNP locus in an independent cohort of 183 Dezhou donkeys. Results: In this study, 87 Dezhou donkeys were subjected to whole-genome resequencing, yielding 6,929,687 high-quality SNPs. Selective sweep analysis using the Fst method identified candidate genes enriched in signaling pathways related to skeletal development and vertebral morphogenesis, including the Notch, TGF-beta, Wnt signaling pathways, and retinol metabolism. PCR amplification and Sanger sequencing validation in 183 Dezhou donkeys confirmed that the SNP g.80,827,321 A > G in the LOC106828038 gene was associated with fewer lumbar vertebrae (P < 0.05). Population genetic analysis revealed moderate polymorphism (PIC = 0.3515) with Hardy-Weinberg equilibrium maintained at this locus. Furthermore, in mature donkeys (≥ 2-year-old), this locus was significantly associated with body length, chest girth, cannon circumference, and hip height. In < 2-year-old group, this locus was also significantly associated with cannon circumference. Conclusion: These findings identify LOC106828038 as a potential regulatory factor associated with the number of lumbar vertebrae in Dezhou donkeys through the retinol metabolism pathway. This could be used for marker-assisted selection to breed superior Dezhou donkey strains with improved body conformation and production traits. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12864-026-13216-6.
SN - 1471-2164
ER -