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Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network
Meng, Jie1,4,5; Song, Kai1,4,5; Li, Chunyan1,4,6; Liu, Sheng1,4,6; Shi, Ruihui1,4,6; Li, Busu1,4,6; Wang, Ting1,4,6; Li, Ao1,4,6; Que, Huayong1,2,4,5; Li, Li1,3,4,5; Zhang, Guofan1,2,4,5
2019-07-31
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume20Issue:1Pages:14
Corresponding AuthorLi, Li(lili@qdio.ac.cn) ; Zhang, Guofan(gfzhang@qdio.ac.cn)
AbstractBackground: 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.
KeywordOyster Nutrient traits Genome resequencing Population structure Genome-wide association study Genetic network
DOI10.1186/s12864-019-5971-z
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31530079] ; Earmarked Fund for Modern Agro-industry Technology Research System[CARS-49] ; Qingdao National Laboratory for Marine Science and Technology[2015ASKJ02-03] ; Qingdao National Laboratory for Marine Science and Technology[2017-2B07] ; Shandong Provincial Natural Science Foundation of China[ZR2016DQ13] ; Laboratory for Marine Fisheries Science and Food Production Processes
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000482318400004
PublisherBMC
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/162757
Collection实验海洋生物学重点实验室
Corresponding AuthorLi, Li; Zhang, Guofan
Affiliation1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Shandong, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266071, Shandong, Peoples R China
3.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao 266071, Shandong, Peoples R China
4.Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Shandong, Peoples R China
5.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao 266071, Shandong, Peoples R China
6.Univ Chinese Acad Sci, Beijing 100039, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Meng, Jie,Song, Kai,Li, Chunyan,et al. Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network[J]. BMC GENOMICS,2019,20(1):14.
APA Meng, Jie.,Song, Kai.,Li, Chunyan.,Liu, Sheng.,Shi, Ruihui.,...&Zhang, Guofan.(2019).Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network.BMC GENOMICS,20(1),14.
MLA Meng, Jie,et al."Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network".BMC GENOMICS 20.1(2019):14.
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