Research note: A low-density SNP genotyping panel for Chinese native chickens
The efficiency of molecular breeding largely depends on the cost of genotyping, which plays an important role in breeding and population genetic studies. Compared to pig, cattle, and sheep, poultry has a small size genome, and lower individual value. Developing a relatively low-density genotyping pa...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579124011878 |
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| author | Jie Wang Siyuan Xing Yan Zhou Jie Liu Yan Sun Qiuxia Lei Haixia Han Wei Liu Dapeng Li Fuwei Li Dingguo Cao |
| author_facet | Jie Wang Siyuan Xing Yan Zhou Jie Liu Yan Sun Qiuxia Lei Haixia Han Wei Liu Dapeng Li Fuwei Li Dingguo Cao |
| author_sort | Jie Wang |
| collection | DOAJ |
| description | The efficiency of molecular breeding largely depends on the cost of genotyping, which plays an important role in breeding and population genetic studies. Compared to pig, cattle, and sheep, poultry has a small size genome, and lower individual value. Developing a relatively low-density genotyping panel is needed to decrease the genotyping cost for poultries. In the present study, we developed a chicken 11 K single nucleotide polymorphism (SNP) genotyping panel for breeding and genetic analysis using genotyping by targeted sequencing (GBTS). The panel design was based on whole genome sequencing data from 7 local breeds and a commercial breed. In total 11,200 SNPs were included in the final chip. Population analyses of the eight breeds showed high SNP call rates and minor allele frequencies (MAF), enabling clear differentiation between populations. The families within population can also be identified. Additionally, the 11K panel was applied to a genomic prediction of Wenshang Barred chickens, the predictive ability and prediction accuracy between the WGS and chip dataset non-significantly differed. Therefore, the newly developed chicken low-density SNP is efficient, cost-effective, and well-suited for application in local Chinese chickens, which can accelerate chicken breeding improvements and enhance conservation efforts. |
| format | Article |
| id | doaj-art-2c472334971e4d8ab7451550a1fd2b43 |
| institution | Kabale University |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj-art-2c472334971e4d8ab7451550a1fd2b432025-01-22T05:40:41ZengElsevierPoultry Science0032-57912025-01-011041104609Research note: A low-density SNP genotyping panel for Chinese native chickensJie Wang0Siyuan Xing1Yan Zhou2Jie Liu3Yan Sun4Qiuxia Lei5Haixia Han6Wei Liu7Dapeng Li8Fuwei Li9Dingguo Cao10Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaMolBreeding Biotechnology Co., Ltd., Shijiazhuang, 050035, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, ChinaPoultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China; Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, 250023, Shandong, China; Corresponding author.The efficiency of molecular breeding largely depends on the cost of genotyping, which plays an important role in breeding and population genetic studies. Compared to pig, cattle, and sheep, poultry has a small size genome, and lower individual value. Developing a relatively low-density genotyping panel is needed to decrease the genotyping cost for poultries. In the present study, we developed a chicken 11 K single nucleotide polymorphism (SNP) genotyping panel for breeding and genetic analysis using genotyping by targeted sequencing (GBTS). The panel design was based on whole genome sequencing data from 7 local breeds and a commercial breed. In total 11,200 SNPs were included in the final chip. Population analyses of the eight breeds showed high SNP call rates and minor allele frequencies (MAF), enabling clear differentiation between populations. The families within population can also be identified. Additionally, the 11K panel was applied to a genomic prediction of Wenshang Barred chickens, the predictive ability and prediction accuracy between the WGS and chip dataset non-significantly differed. Therefore, the newly developed chicken low-density SNP is efficient, cost-effective, and well-suited for application in local Chinese chickens, which can accelerate chicken breeding improvements and enhance conservation efforts.http://www.sciencedirect.com/science/article/pii/S0032579124011878GBTSBreed conservationGenomic predictionPrediction accuracy |
| spellingShingle | Jie Wang Siyuan Xing Yan Zhou Jie Liu Yan Sun Qiuxia Lei Haixia Han Wei Liu Dapeng Li Fuwei Li Dingguo Cao Research note: A low-density SNP genotyping panel for Chinese native chickens Poultry Science GBTS Breed conservation Genomic prediction Prediction accuracy |
| title | Research note: A low-density SNP genotyping panel for Chinese native chickens |
| title_full | Research note: A low-density SNP genotyping panel for Chinese native chickens |
| title_fullStr | Research note: A low-density SNP genotyping panel for Chinese native chickens |
| title_full_unstemmed | Research note: A low-density SNP genotyping panel for Chinese native chickens |
| title_short | Research note: A low-density SNP genotyping panel for Chinese native chickens |
| title_sort | research note a low density snp genotyping panel for chinese native chickens |
| topic | GBTS Breed conservation Genomic prediction Prediction accuracy |
| url | http://www.sciencedirect.com/science/article/pii/S0032579124011878 |
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