Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens
With the development of molecular genetics and high-throughput sequencing technology, genotyping arrays consisting of large numbers of SNP have raised great interest in animal and plant research. However, the application of commercial chicken 600K SNP arrays has varied in different populations of eg...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-05-01
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| Series: | Poultry Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S003257912100078X |
| _version_ | 1819290969552453632 |
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| author | Zhuang Liu Congjiao Sun Yiyuan Yan Guangqi Li Xiao Chang Li Guiqin Wu Ning Yang |
| author_facet | Zhuang Liu Congjiao Sun Yiyuan Yan Guangqi Li Xiao Chang Li Guiqin Wu Ning Yang |
| author_sort | Zhuang Liu |
| collection | DOAJ |
| description | With the development of molecular genetics and high-throughput sequencing technology, genotyping arrays consisting of large numbers of SNP have raised great interest in animal and plant research. However, the application of commercial chicken 600K SNP arrays has varied in different populations of egg-type chickens. Moreover, their genotyping cost is too high for large-scale population applications. Herein, we independently developed a custom Illumina 50K BeadChip, named PhenoixChip-I, for egg-type chickens based on SNP from 479 sequenced individuals in 7 lines. We filtered and selected SNP with stringent criteria, such as high polymorphism, genome coverage, design score, and priorities. Finally, a total of 43,681 effective SNP successfully genotyped were included on our custom array. Approximately 14K SNP were previously reported to be associated with important economic traits in egg-type chickens. Subsequently, we verified the applicability and efficiency of the PhenoixChip-I SNP array from many aspects, including evaluating its use scientific research (population structure analysis and genome-wide association study) and the poultry breeding industry (genomic selection). The findings in our study will play a crucial role in accelerating the genetic improvement of egg-type chickens. |
| first_indexed | 2024-12-24T03:31:11Z |
| format | Article |
| id | doaj.art-4aa49d5a6b9c4ec1b1742fab0d52ebe3 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-12-24T03:31:11Z |
| publishDate | 2021-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-4aa49d5a6b9c4ec1b1742fab0d52ebe32022-12-21T17:17:11ZengElsevierPoultry Science0032-57912021-05-011005101044Design and evaluation of a custom 50K Infinium SNP array for egg-type chickensZhuang Liu0Congjiao Sun1Yiyuan Yan2Guangqi Li3Xiao Chang Li4Guiqin Wu5Ning Yang6National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Beijing Engineering Research Centre of Layer, Beijing 101206, ChinaBeijing Engineering Research Centre of Layer, Beijing 101206, ChinaNational Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaBeijing Engineering Research Centre of Layer, Beijing 101206, ChinaNational Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Corresponding author:With the development of molecular genetics and high-throughput sequencing technology, genotyping arrays consisting of large numbers of SNP have raised great interest in animal and plant research. However, the application of commercial chicken 600K SNP arrays has varied in different populations of egg-type chickens. Moreover, their genotyping cost is too high for large-scale population applications. Herein, we independently developed a custom Illumina 50K BeadChip, named PhenoixChip-I, for egg-type chickens based on SNP from 479 sequenced individuals in 7 lines. We filtered and selected SNP with stringent criteria, such as high polymorphism, genome coverage, design score, and priorities. Finally, a total of 43,681 effective SNP successfully genotyped were included on our custom array. Approximately 14K SNP were previously reported to be associated with important economic traits in egg-type chickens. Subsequently, we verified the applicability and efficiency of the PhenoixChip-I SNP array from many aspects, including evaluating its use scientific research (population structure analysis and genome-wide association study) and the poultry breeding industry (genomic selection). The findings in our study will play a crucial role in accelerating the genetic improvement of egg-type chickens.http://www.sciencedirect.com/science/article/pii/S003257912100078Xgenomic analysisgenotyping arrayegg-type chickenSNP |
| spellingShingle | Zhuang Liu Congjiao Sun Yiyuan Yan Guangqi Li Xiao Chang Li Guiqin Wu Ning Yang Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens Poultry Science genomic analysis genotyping array egg-type chicken SNP |
| title | Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens |
| title_full | Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens |
| title_fullStr | Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens |
| title_full_unstemmed | Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens |
| title_short | Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens |
| title_sort | design and evaluation of a custom 50k infinium snp array for egg type chickens |
| topic | genomic analysis genotyping array egg-type chicken SNP |
| url | http://www.sciencedirect.com/science/article/pii/S003257912100078X |
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