Genetic Basis and Identification of Candidate Genes for Alkalinity Tolerance Trait in Spotted Sea Bass (Lateolabrax maculatus) by Genome-Wide Association Study (GWAS)

IF 2.6 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Yonghang Zhang, Chong Zhang, Haishen Wen, Xin Qi, Qing Wang, Kaiqiang Zhang, Lingyu Wang, Donglei Sun, Yani Dong, Pengyu Li, Yun Li
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引用次数: 0

Abstract

Given the challenges of overcrowded coastal aquaculture spaces and insufficient production, utilizing saline-alkaline water areas represents a vital strategy to alleviate these bottlenecks. Spotted sea bass (Lateolabrax maculatus), with its formidable osmoregulatory capabilities, is an ideal candidate to develop a saline-alkaline tolerant strain. In our study, genotypic and phenotypic data from 287 L. maculatus individuals exposed to carbonate alkaline conditions were collected, and a genome-wide association study (GWAS) conducted to elucidate genetic basis related to carbonate alkalinity tolerance trait. Results showed that 14 SNPs and 8 InDels were markedly related to carbonate alkalinity tolerance trait, and 404 candidate genes were pinpointed within a ± 300-kb region surrounding these variants. Notably, the most significant SNP (SNP_05_17240108), along with two adjacent SNPs (SNP_05_17240102 and SNP_05_17240340) and two InDels (InDel_05_17240228 and InDel_05_17240231), was situated in the intron region of trio gene that could play vital roles in cell remodeling, and cell junction and activity of aquaporins to deal with carbonate alkalinity stress. Furthermore, candidate genes were significantly involved in pathways associated with carbohydrate metabolism, cell remodeling, ion transport, and RNA degradation, which were consistent with RNA-Seq analysis results of gills and kidneys in response to alkalinity stress. Our study will contribute to elucidate the genetic basis of alkalinity tolerance and the identified SNPs and InDels could be used for marker-assisted selection (MAS) and genomic selection (GS) for alkalinity tolerance trait in the breeding programs of spotted sea bass.

斑点黑鲈耐碱性性状遗传基础及候选基因的全基因组关联研究(GWAS)
鉴于沿海水产养殖空间过度拥挤和产量不足的挑战,利用咸碱水域是缓解这些瓶颈的重要战略。斑点海鲈(Lateolabrax maculatus)具有强大的渗透调节能力,是培养耐盐碱品系的理想候选者。本研究收集了287份暴露于碳酸盐碱性条件下的斑马鱼个体的基因型和表型数据,并进行了全基因组关联研究(GWAS),以阐明与碳酸盐碱性耐受性状相关的遗传基础。结果表明,14个snp和8个indel与耐碳酸盐碱性性状显著相关,在这些变异周围±300 kb的区域内确定了404个候选基因。值得注意的是,最重要的SNP (SNP_05_17240108)以及相邻的两个SNP (SNP_05_17240102和SNP_05_17240340)和两个InDel_05_17240228和InDel_05_17240231)位于trio基因的内含子区域,这些基因在细胞重塑、细胞连接和水通道蛋白活性中发挥重要作用,以应对碳酸盐碱胁迫。此外,候选基因显著参与与碳水化合物代谢、细胞重塑、离子转运和RNA降解相关的途径,这与鳃和肾脏在碱度胁迫下的RNA- seq分析结果一致。本研究将有助于阐明耐碱性性状的遗传基础,所鉴定的snp和indel可用于斑点黑鲈耐碱性性状的标记辅助选择(MAS)和基因组选择(GS)。
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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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