Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds
Abstract Background Shandong’s local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China’s waterfowl germplasm. Understanding the genetic characteristics of these populations, along with monitoring and conserving their genetic divers...
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2025-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11782-9 |
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| author | Pengwei Ren Yongdong Peng Liu Yang Muhammad Zahoor Khan Yadi Jing Chao Qi Zhansheng Liu Shuer Zhang Nenzhu Zheng Meixia Zhang Xiang Liu Zhiming Zhu Mingxia Zhu |
| author_facet | Pengwei Ren Yongdong Peng Liu Yang Muhammad Zahoor Khan Yadi Jing Chao Qi Zhansheng Liu Shuer Zhang Nenzhu Zheng Meixia Zhang Xiang Liu Zhiming Zhu Mingxia Zhu |
| author_sort | Pengwei Ren |
| collection | DOAJ |
| description | Abstract Background Shandong’s local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China’s waterfowl germplasm. Understanding the genetic characteristics of these populations, along with monitoring and conserving their genetic diversity, is of paramount importance. In this study, we analyzed the genetic diversity, population structure, and genetic characteristic of 89 ducks, including the Weishan Partridge (WS, n = 30), Matahu (MT, n = 29), and Wendeng Black (WD, n = 30), using genome resequencing data. We also used a random forest model algorithm to identify specific breed-identification SNPs, ensuring accurate differentiation of the three breeds. Results The findings of this study revealed that WS ducks exhibited higher genetic diversity compared to the other two breeds. This may be related to their larger group size and level of inbreeding. Notice that HO values larger than HE values for all three species are associated with random mating patterns, reduced selection pressure, or recovery from historical bottleneck events. Additionally, the WS and MT breeds were found to be closely related, possibly sharing a common ancestral group, while both breeds were genetically distinct from the WD breed. After comparing with meat duck breeds (BJ, CV, ML), we identified several potential functional genes (notably TP63, BMP3, and ACACA) associated with key economic traits, including growth and development, muscle quality, reproductive performance, and disease resistance. Using top 60 feature selected SNPs, the random forest classification model successfully identified different breeds of ducks under the study with 96.2% accuracy. Conclusions This study, utilizing genome sequencing data and machine learning algorithms, provides a comprehensive evaluation of the genetic resources of Shandong’s local duck breeds. It highlights the distinct genetic characteristics of the three breeds, providing valuable insights and a theoretical foundation for the conservation and sustainable utilization of Shandong’s local duck genetic resources. |
| format | Article |
| id | doaj-art-73183a2be2414c68a7d1629db714494a |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-73183a2be2414c68a7d1629db714494a2025-08-20T03:42:40ZengBMCBMC Genomics1471-21642025-08-0126111510.1186/s12864-025-11782-9Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breedsPengwei Ren0Yongdong Peng1Liu Yang2Muhammad Zahoor Khan3Yadi Jing4Chao Qi5Zhansheng Liu6Shuer Zhang7Nenzhu Zheng8Meixia Zhang9Xiang Liu10Zhiming Zhu11Mingxia Zhu12College of Agricultural and Biology, Liaocheng UniversityCollege of Agricultural and Biology, Liaocheng UniversityCollege of Agricultural and Biology, Liaocheng UniversityCollege of Agricultural and Biology, Liaocheng UniversityCollege of Agricultural and Biology, Liaocheng UniversityShandong Animal Husbandry StationShandong Animal Husbandry StationShandong Animal Husbandry StationFujian Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural SciencesCollege of Agricultural and Biology, Liaocheng UniversityCollege of Agricultural and Biology, Liaocheng UniversityFujian Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural SciencesCollege of Agricultural and Biology, Liaocheng UniversityAbstract Background Shandong’s local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China’s waterfowl germplasm. Understanding the genetic characteristics of these populations, along with monitoring and conserving their genetic diversity, is of paramount importance. In this study, we analyzed the genetic diversity, population structure, and genetic characteristic of 89 ducks, including the Weishan Partridge (WS, n = 30), Matahu (MT, n = 29), and Wendeng Black (WD, n = 30), using genome resequencing data. We also used a random forest model algorithm to identify specific breed-identification SNPs, ensuring accurate differentiation of the three breeds. Results The findings of this study revealed that WS ducks exhibited higher genetic diversity compared to the other two breeds. This may be related to their larger group size and level of inbreeding. Notice that HO values larger than HE values for all three species are associated with random mating patterns, reduced selection pressure, or recovery from historical bottleneck events. Additionally, the WS and MT breeds were found to be closely related, possibly sharing a common ancestral group, while both breeds were genetically distinct from the WD breed. After comparing with meat duck breeds (BJ, CV, ML), we identified several potential functional genes (notably TP63, BMP3, and ACACA) associated with key economic traits, including growth and development, muscle quality, reproductive performance, and disease resistance. Using top 60 feature selected SNPs, the random forest classification model successfully identified different breeds of ducks under the study with 96.2% accuracy. Conclusions This study, utilizing genome sequencing data and machine learning algorithms, provides a comprehensive evaluation of the genetic resources of Shandong’s local duck breeds. It highlights the distinct genetic characteristics of the three breeds, providing valuable insights and a theoretical foundation for the conservation and sustainable utilization of Shandong’s local duck genetic resources.https://doi.org/10.1186/s12864-025-11782-9Breed identificationDuckPopulation genetic structureWhole genome resequencingSelection signals |
| spellingShingle | Pengwei Ren Yongdong Peng Liu Yang Muhammad Zahoor Khan Yadi Jing Chao Qi Zhansheng Liu Shuer Zhang Nenzhu Zheng Meixia Zhang Xiang Liu Zhiming Zhu Mingxia Zhu Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds BMC Genomics Breed identification Duck Population genetic structure Whole genome resequencing Selection signals |
| title | Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds |
| title_full | Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds |
| title_fullStr | Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds |
| title_full_unstemmed | Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds |
| title_short | Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds |
| title_sort | whole genome resequencing reveals genetic diversity population structure and selection signatures in local duck breeds |
| topic | Breed identification Duck Population genetic structure Whole genome resequencing Selection signals |
| url | https://doi.org/10.1186/s12864-025-11782-9 |
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