Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network
Background: Oyster is rich in glycogen and free amino acids and is called "the milk of sea". To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the wor...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/162755 2023-05-15T15:58:51+02:00 Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network Meng, Jie Song, Kai Li, Chunyan Liu, Sheng Shi, Ruihui Li, Busu Wang, Ting Li, Ao Que, Huayong Li, Li Zhang, Guofan 2019-07-31 http://ir.qdio.ac.cn/handle/337002/162755 https://doi.org/10.1186/s12864-019-5971-z 英语 eng BMC BMC GENOMICS http://ir.qdio.ac.cn/handle/337002/162755 doi:10.1186/s12864-019-5971-z Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology & Applied Microbiology Genetics & Heredity AGRONOMIC TRAITS COMPLEX TRAITS FAT-CONTENT LOCI SELECTION YIELD DOMESTICATION FRAMEWORK LINKAGE PROTEIN 期刊论文 2019 ftchinacasciocas https://doi.org/10.1186/s12864-019-5971-z 2022-06-27T05:41:09Z Background: Oyster is rich in glycogen and free amino acids and is called "the milk of sea". To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale. Results: After association analysis, 168 clustered significant single nucleotide polymorphism (SNP) loci were identified for glycogen content and 17 SNPs were verified with 288 oyster individuals in another wide populations. These were the most important candidate loci for oyster breeding. Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. This might enhance the gluconeogenesis process by the transcriptionally regulating the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose 6-phosphatase (G6Pase). Also, for amino acids content 417 clustered significant SNPs were identified. After genetic network analysis, three node SNP regions were identified to be associated with glycogen, protein, and Asp content, which might explain their significant correlation. Conclusion: Overall, this study provides insights into the genetic correlation among complex traits, which will facilitate future oyster functional studies and breeding through molecular design. Report Crassostrea gigas Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR BMC Genomics 20 1 |
institution |
Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
topic |
Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology & Applied Microbiology Genetics & Heredity AGRONOMIC TRAITS COMPLEX TRAITS FAT-CONTENT LOCI SELECTION YIELD DOMESTICATION FRAMEWORK LINKAGE PROTEIN |
spellingShingle |
Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology & Applied Microbiology Genetics & Heredity AGRONOMIC TRAITS COMPLEX TRAITS FAT-CONTENT LOCI SELECTION YIELD DOMESTICATION FRAMEWORK LINKAGE PROTEIN Meng, Jie Song, Kai Li, Chunyan Liu, Sheng Shi, Ruihui Li, Busu Wang, Ting Li, Ao Que, Huayong Li, Li Zhang, Guofan Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network |
topic_facet |
Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology & Applied Microbiology Genetics & Heredity AGRONOMIC TRAITS COMPLEX TRAITS FAT-CONTENT LOCI SELECTION YIELD DOMESTICATION FRAMEWORK LINKAGE PROTEIN |
description |
Background: Oyster is rich in glycogen and free amino acids and is called "the milk of sea". To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale. Results: After association analysis, 168 clustered significant single nucleotide polymorphism (SNP) loci were identified for glycogen content and 17 SNPs were verified with 288 oyster individuals in another wide populations. These were the most important candidate loci for oyster breeding. Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. This might enhance the gluconeogenesis process by the transcriptionally regulating the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose 6-phosphatase (G6Pase). Also, for amino acids content 417 clustered significant SNPs were identified. After genetic network analysis, three node SNP regions were identified to be associated with glycogen, protein, and Asp content, which might explain their significant correlation. Conclusion: Overall, this study provides insights into the genetic correlation among complex traits, which will facilitate future oyster functional studies and breeding through molecular design. |
format |
Report |
author |
Meng, Jie Song, Kai Li, Chunyan Liu, Sheng Shi, Ruihui Li, Busu Wang, Ting Li, Ao Que, Huayong Li, Li Zhang, Guofan |
author_facet |
Meng, Jie Song, Kai Li, Chunyan Liu, Sheng Shi, Ruihui Li, Busu Wang, Ting Li, Ao Que, Huayong Li, Li Zhang, Guofan |
author_sort |
Meng, Jie |
title |
Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network |
title_short |
Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network |
title_full |
Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network |
title_fullStr |
Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network |
title_full_unstemmed |
Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network |
title_sort |
genome-wide association analysis of nutrient traits in the oyster crassostrea gigas: genetic effect and interaction network |
publisher |
BMC |
publishDate |
2019 |
url |
http://ir.qdio.ac.cn/handle/337002/162755 https://doi.org/10.1186/s12864-019-5971-z |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
BMC GENOMICS http://ir.qdio.ac.cn/handle/337002/162755 doi:10.1186/s12864-019-5971-z |
op_doi |
https://doi.org/10.1186/s12864-019-5971-z |
container_title |
BMC Genomics |
container_volume |
20 |
container_issue |
1 |
_version_ |
1766394624137494528 |