Identification of growth-related genes based on BSA in Pacific white shrimp Litopenaeus vannamei

doi:10.1016/j.aquaculture.2024.741708

IOCAS-IR > 实验海洋生物学重点实验室

	Identification of growth-related genes based on BSA in Pacific white shrimp Litopenaeus vannamei
	Bao, Zhenning 1,2; Yu, Yang1,3,4 ; Lin, Pengfei 1,2; Li, Fuhua 1,3,4
	2025-02-15
发表期刊	AQUACULTURE
ISSN	0044-8486
卷号	596 页码:11
通讯作者	Yu, Yang([email protected]) ; Li, Fuhua([email protected])
摘要	The development of SNP genotyping techniques has facilitated the application of genome-wide association studies (GWAS) and genomic selection (GS) in plants and animals. However, the cost of high-throughput SNP genotyping is particularly high in the case of aquaculture animals which can produce a large number of offspring. Consequently, a cost effective method for trait-associated SNP identification and application was urgently needed in aquaculture breeding. In this study, a Bulk Segregation Analysis sequencing (BSA-seq) method was employed to identify growth-related single nucleotide polymorphisms (SNPs) and genes in the Pacific white shrimp Litopenaeus vannamei. Two independent families were used for this analysis to reduce the false positive. The DNA of individuals with the highest and lowest body weights was pooled separately. Two methods including the ED (Euclidean distance) method and the chi-square test were applied to calculate the allele differences between high and low growth rate individuals. A total of 24,325,437 SNPs were identified and consequently 1,299 SNPs and 163 genes were identified to be associated with growth traits. KEGG enrichment analysis showed that these genes were significantly enriched in phosphatidylinositol signaling system and phospholipase D signaling pathway. The diacylglycerol kinase genes, phosphatidylinositol 3-kinase genes, inositol polyphosphate 5-phosphatase genes, mitogen-activated protein kinase genes, myotubularin-related protein genes and epidermal growth factor receptor genes in these pathways were considered as candidate growth genes. This study demonstrated that the BSA-seq based on whole genome resequencing is cost-effective and useful in aquaculture. The results not only provide useful information for understanding the genetic basis of growth traits, but also offer a source of SNPs for marker-assisted selection (MAS) and genomic selection (GS) in shrimp.
关键词	Litopenaeus vannamei Bulk segregation analysis (BSA) Growth trait Single nucleotide polymorphisms (SNPs) Sliding window algorithm
DOI	10.1016/j.aquaculture.2024.741708
收录类别	SCI
语种	英语
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences[XDA24030105]; National Key Research and Development Program of China[2022YFD2400203]; Key Research and Development Program of Shandong[2021LZGC029]; Earmarked fund for CARS-48; Taishan Scholars Program
WOS研究方向	Fisheries ; Marine & Freshwater Biology
WOS类目	Fisheries ; Marine & Freshwater Biology
WOS记录号	WOS:001335170500001
出版者	ELSEVIER
WOS关键词	BULKED SEGREGANT ANALYSIS ; DISEASE-RESISTANCE ; MARKERS ; PATHWAY ; RICE ; LOCI
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/199478
专题	实验海洋生物学重点实验室
通讯作者	Yu, Yang; Li, Fuhua
作者单位	1.Chinese Acad Sci, Inst Oceanol, Key Lab Breeding Biotechnol & Sustainable Aquacult, Qingdao 266071, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Qingdao Marine Sci & Technol Ctr, Lab Marine Biol & Biotechnol, Qingdao 266071, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
推荐引用方式 GB/T 7714	Bao, Zhenning,Yu, Yang,Lin, Pengfei,et al. Identification of growth-related genes based on BSA in Pacific white shrimp Litopenaeus vannamei[J]. AQUACULTURE,2025,596:11.
APA	Bao, Zhenning,Yu, Yang,Lin, Pengfei,&Li, Fuhua.(2025).Identification of growth-related genes based on BSA in Pacific white shrimp Litopenaeus vannamei.AQUACULTURE,596,11.
MLA	Bao, Zhenning,et al."Identification of growth-related genes based on BSA in Pacific white shrimp Litopenaeus vannamei".AQUACULTURE 596(2025):11.