Integrating selective signature analysis and genome-wide association study to identify candidate genes associated with litter size in Leizhou goat
- 1College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
Abstract
Objective: Litter size is a key trait for evaluating goat reproductive performance, since it has a direct influence on the breeding efficiency and production cycle profitability. However, a comprehensive understanding of its genetic architecture, including the causative mutations and their functional impacts, remains scarce, hindering its application in precision breeding.
Methods: A total of 92 female Leizhou goats were genotyped through whole-genome sequencing, and their litter sizes were measured over three consecutive births. Following genotype and phenotype data collection, population genetic structure analysis, selection signature analysis, and genome-wide association study (GWAS) were performed.
Results: We identified 20,802,514 SNPs in the 92 Leizhou goats. Analysis of genetic structure revealed that the high-litter-size group exhibited greater genetic diversity than the low-litter-size group, although no significant genetic differentiation was found between them. We identified 340 putative selective regions and 346 candidate genes across the genome. A total of 37 candidate genes were identified as being closely associated with reproductive traits, including BMP6, MAPK8, RPTOR, etc. The GWAS revealed 63 quantitative trait loci (QTLs) at suggestive significance, 52 of which were associated with litter size. After that, 207 candidate genes were annotated, and four of them were highlighted that have been previously reported to be associated with reproductive processes (e.g., TMEM100, PDGFD, NLRP9, and ARHGAP22). By integrating the results from both approaches, we identified MAPK8 as a potential candidate gene associated with litter size. Furthermore, our findings from motif recognition, transcription factor prediction, and previous studies lead us to propose that the BMP6-GATA4-MAPK8 signaling pathway may play a key role in regulating litter size in goats.
Conclusion: Our findings identify several candidate genes and putative associated variants for litter size, providing valuable insights into the genetic basis of reproductive traits in goats.
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BibTeX
@article{feng2026integrating,
title = {{Integrating selective signature analysis and genome-wide association study to identify candidate genes associated with litter size in Leizhou goat}},
author = {Da Feng and Siyi Hu and Jian Ma and Chunmei Du and Guangxian Zhou and Chen Wei and Shangquan Gan},
journal = {Animal Bioscience},
year = {2026},
month = jul,
doi = {10.5713/ab.260280},
url = {https://doi.org/10.5713/ab.260280},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrating selective signature analysis and genome-wide association study to identify candidate genes associated with litter size in Leizhou goat
AU - Da Feng
AU - Siyi Hu
AU - Jian Ma
AU - Chunmei Du
AU - Guangxian Zhou
AU - Chen Wei
AU - Shangquan Gan
PY - 2026
DA - 2026/07/27
JO - Animal Bioscience
DO - 10.5713/ab.260280
UR - https://doi.org/10.5713/ab.260280
AB - Objective: Litter size is a key trait for evaluating goat reproductive performance, since it has a direct influence on the breeding efficiency and production cycle profitability. However, a comprehensive understanding of its genetic architecture, including the causative mutations and their functional impacts, remains scarce, hindering its application in precision breeding. Methods: A total of 92 female Leizhou goats were genotyped through whole-genome sequencing, and their litter sizes were measured over three consecutive births. Following genotype and phenotype data collection, population genetic structure analysis, selection signature analysis, and genome-wide association study (GWAS) were performed. Results: We identified 20,802,514 SNPs in the 92 Leizhou goats. Analysis of genetic structure revealed that the high-litter-size group exhibited greater genetic diversity than the low-litter-size group, although no significant genetic differentiation was found between them. We identified 340 putative selective regions and 346 candidate genes across the genome. A total of 37 candidate genes were identified as being closely associated with reproductive traits, including BMP6, MAPK8, RPTOR, etc. The GWAS revealed 63 quantitative trait loci (QTLs) at suggestive significance, 52 of which were associated with litter size. After that, 207 candidate genes were annotated, and four of them were highlighted that have been previously reported to be associated with reproductive processes (e.g., TMEM100, PDGFD, NLRP9, and ARHGAP22). By integrating the results from both approaches, we identified MAPK8 as a potential candidate gene associated with litter size. Furthermore, our findings from motif recognition, transcription factor prediction, and previous studies lead us to propose that the BMP6-GATA4-MAPK8 signaling pathway may play a key role in regulating litter size in goats. Conclusion: Our findings identify several candidate genes and putative associated variants for litter size, providing valuable insights into the genetic basis of reproductive traits in goats.
SN - 2765-0189
SN - 2765-0235
ER -