Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network
Abstract 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...
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ftdoajarticles:oai:doaj.org/article:d7cba96f7d594bfca37efba623e0dcb0 2023-05-15T15:58:46+02:00 Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network Jie Meng Kai Song Chunyan Li Sheng Liu Ruihui Shi Busu Li Ting Wang Ao Li Huayong Que Li Li Guofan Zhang 2019-07-01T00:00:00Z https://doi.org/10.1186/s12864-019-5971-z https://doaj.org/article/d7cba96f7d594bfca37efba623e0dcb0 EN eng BMC http://link.springer.com/article/10.1186/s12864-019-5971-z https://doaj.org/toc/1471-2164 doi:10.1186/s12864-019-5971-z 1471-2164 https://doaj.org/article/d7cba96f7d594bfca37efba623e0dcb0 BMC Genomics, Vol 20, Iss 1, Pp 1-14 (2019) Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology TP248.13-248.65 Genetics QH426-470 article 2019 ftdoajarticles https://doi.org/10.1186/s12864-019-5971-z 2022-12-31T08:44:21Z Abstract 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. Article in Journal/Newspaper Crassostrea gigas Directory of Open Access Journals: DOAJ Articles BMC Genomics 20 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Oyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network Biotechnology TP248.13-248.65 Genetics QH426-470 Jie Meng Kai Song Chunyan Li Sheng Liu Ruihui Shi Busu Li Ting Wang Ao Li Huayong Que Li Li Guofan Zhang 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 TP248.13-248.65 Genetics QH426-470 |
description |
Abstract 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 |
Article in Journal/Newspaper |
author |
Jie Meng Kai Song Chunyan Li Sheng Liu Ruihui Shi Busu Li Ting Wang Ao Li Huayong Que Li Li Guofan Zhang |
author_facet |
Jie Meng Kai Song Chunyan Li Sheng Liu Ruihui Shi Busu Li Ting Wang Ao Li Huayong Que Li Li Guofan Zhang |
author_sort |
Jie Meng |
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 |
https://doi.org/10.1186/s12864-019-5971-z https://doaj.org/article/d7cba96f7d594bfca37efba623e0dcb0 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
BMC Genomics, Vol 20, Iss 1, Pp 1-14 (2019) |
op_relation |
http://link.springer.com/article/10.1186/s12864-019-5971-z https://doaj.org/toc/1471-2164 doi:10.1186/s12864-019-5971-z 1471-2164 https://doaj.org/article/d7cba96f7d594bfca37efba623e0dcb0 |
op_doi |
https://doi.org/10.1186/s12864-019-5971-z |
container_title |
BMC Genomics |
container_volume |
20 |
container_issue |
1 |
_version_ |
1766394536244805632 |