Resequencing data of Litopenaeus vannamei
Description
Litopenaeus vannamei, a key species in global aquaculture, shows excellent growth and adaptability, making it central to shrimp farming. As genetic improvement progresses, genomic characteristics of L. vannamei populations continue to evolve. To clarify their genetic status, we analyzed selection signals using resequencing data and environmental factors, identifying adaptive genomic regions. In this study, a large-scale family was constructed by hybridizing six L. vannamei populations (two breeding and four introduced) to produce offspring. The offspring were subjected to ammonia nitrogen and low pH stress experiments, and extreme difference groups were established based on survival time under stress. Whole-genome resequencing was performed on the six original populations and stress groups (320 individuals). After quality control, 17,104,219 high-quality SNPs were obtained. Using the multi-reference population rotation method, we identified population-specific selection regions in six L. vannamei populations through Fst and θπ ratio analyses. Functional enrichment revealed multiple cross-functional modules and conserved genes across populations. This distribution indicates that L. vannamei adaptive evolution features both population differentiation and conservation of core pathways. Further multi-method joint analysis using Fst, θπ ratio, and XP-CLR identified 356 (ammonia nitrogen) and 370 (low pH) candidate genes in the stressed populations. After GO/KEGG annotation and selection signal screening determined nine core stress response genes, including Aldh-Ⅲ, Vang, and Aralar1. Notably, Vang showed a significant selection signal in the XH-K breeding population, and may regulate the Wnt/β-catenin signaling pathway. Genome-wide selection signal analysis in L. vannamei populations revealed key functional genes, thereby enriching genetic resources and facilitating the breeding of new varieties. This data consists of genotype data (in VCF format) obtained through whole-genome resequencing, genotyping and quality control.
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Source of experimental materials: In this study, the breeding population with significant growth (from the foundation population with faster growth rate) was named XH-F and the breeding population with strong stress resistance was named XH-K (each generation has a high survival rate in the stress resistance experiment, and the breeding value ranked high in all experimental families). Four introduced populations were from different commercial companies, namely Charoen Pokphand Group (CP), Shrimp Improvement Systems (SIS), SyAqua, and Top Aquaculture Technology (Top). Sampling and DNA extraction: 200 shrimps from six populations (four introduced populations and two breeding populations) and 120 shrimps from stress experiment. Muscle samples of each individual were collected for DNA extraction. Genomic DNA was extracted using the MolPure Call/TIANamp Marine Animal DNA Kits (Yeasen Biotech Co., Ltd. Shanghai, China). SNP sequencing and genotyping: An insert size of 300 to 500 bp small DNA fragment library was constructed (Supplementary material), and then DNB (DNA nanoball) was loaded into the sequencing chip using the loading device MGIDL-T7 (The key auxiliary equipment of the design of the ultra-high throughput gene sequencer DNBSEQ-T7), and sequenced by the joint probe anchoring polymerization technology (Huazhi Rice Bio-Tech Co., Ltd., Changsha, China). Original image data files obtained by high-throughput sequencing were transformed into sequencing sequences (reads) by base recognition analysis (base calling). Low-quality bases and reads were trimmed by FASTP (v0.23.4). Sentieon was used to align the data and detect variants. The reference genome was provided by our own sequencing assembly (GCF_042767895.1). To keep the most reliable SNPs for subsequent analysis, Sentieon was used to perform a preliminary hard screening of the SNPs obtained after the joint analysis, and the screening criteria were as follows: low quality by depth score (QD <5.0), high Fisher strand score (FS > 60.0); low mapping quality (MQ < 40.0); high strand odds ratio (SOR > 3.0); low mapping quality rank-sum score (MQRankSum < -12.5); and low read Position Rank Sum (ReadPosRankSum < -8.0). Delete anchored SNP sites and perform secondary filtering. SNP loci with multiple alleles (max-alleles < 2), low minor allele frequency (MAF < 0.05), and missing genotypes (max-missing < 0.9) were also removed using the VCFtools (v0.1.16) .
Institutions
- Guangdong Ocean University
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Funders
- The National Key Research and Development Program of ChinaGrant ID: 2022YFD2400204
- The Key Special Program on Science and Technology Innovation in Marine Agriculture and Freshwater FisheriesGrant ID: 2023YFD2401705