Identification of growth-related genes based on BSA in Pacific white shrimp Litopenaeus vannamei
文献类型：期刊论文
| 作者 | Bao, Zhenning1,3; Yu, Yang2,3,4 ; Lin, Pengfei1,3; Li, Fuhua2,3,4
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| 刊名 | AQUACULTURE
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| 出版日期 | 2025-02-15 |
| 卷号 | 596页码:11 |
| 关键词 | Litopenaeus vannamei Bulk segregation analysis (BSA) Growth trait Single nucleotide polymorphisms (SNPs) Sliding window algorithm |
| ISSN号 | 0044-8486 |
| DOI | 10.1016/j.aquaculture.2024.741708 |
| 通讯作者 | Yu, Yang(yuyang@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn) |
| 英文摘要 | 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. |
| WOS关键词 | BULKED SEGREGANT ANALYSIS ; DISEASE-RESISTANCE ; MARKERS ; PATHWAY ; RICE ; LOCI |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:001335170500001 |
| 出版者 | ELSEVIER |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/199477]  |
| 专题 | 海洋研究所_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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Qingdao Marine Sci & Technol Ctr, Lab Marine Biol & Biotechnol, Qingdao 266071, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Key Lab Breeding Biotechnol & Sustainable Aquacult, 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. |
入库方式： OAI收割
来源：海洋研究所
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