基于RAD-seq的大口黑鲈选育群体快长SNP挖掘及其与生长性状的关联分析
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华吉祥(1998-),男,硕士,研究方向为水产生物技术.E-mail:huajixiang@ffrc.cn

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S917

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国家重点研发计划项目(2022YFE0139600); 科技创新2030-重大项目(2023ZD04065); 苏州市科技计划项目(SNG2021009);江苏省种业振兴“揭榜挂帅”项目(JBGS[2021]130); 加州鲈产业重大技术协同推广计划项目(2022-ZYXT-07); 中国水产科学研究院淡水渔业研究中心基本科研业务费项目(2023JBFR02)


Development of fast-growth SNP screening and association analysis with growth traits based on RAD-seq for largemouth bass (Micropterussalmoides) breeding populations
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    摘要:

    大口黑鲈(Micropterus salmoides)生长性状是衡量品质与产量的重要标准, 开发快长SNP 标记与挖掘优势基因型及生长主效基因, 有助于进一步解析其生长发育遗传机制, 为选育优质高产新品系奠定基础。基于简化基因组测序技术(restriction-site associated DNA sequencing, RAD-seq), 在大口黑鲈美国北方亚种F0 生长性状极端群体(体重极大前1%和极小后1%)中, 筛选了与生长性状存在潜在关联的SNP 位点, 利用一般线性模型(generalized linearmodel, GLM)将SNP 位点基因型与230 尾F0 个体的体重、体长、体高和体厚进行相关性分析, 此外通过基因注释信息预测生长候选基因, 并结合优势基因型加性效应分析优势基因型聚合效果。在大口黑鲈23 条染色体上发现了4196486 个高质量SNPs, 基于种群特异基因型频率阈值0.7, 初步筛选出100 个与生长性状潜在相关的SNP 位点。关联性分析显示, 有12 个SNP 标记存在显著关联, 包括5 个标记与体重显著关联, 10 个与体长显著关联, 4 个与体高显著关联, 5 个与体厚显著关联。其中标记SNP19140160、SNP24406191、SNP3355498 和SNP9244620 分别定位至生长候选基因fam174bdiaph2kiaa1549lbppip5k1b 上。富集6~10 个优势基因型的群体较富集0~5 个优势基因型的群体在平均体重、体长、体高和体厚上分别提高了32.07%、9.63%、9.96%和10.58%。本研究所鉴定的12 个快长SNP 标记和4 个生长候选基因可助力大口黑鲈生长性状改良。

    Abstract:

    Growth traits in largemouth bass (Micropterus salmoides) are crucial indicators of quality and yield. Thedevelopment of growth single nucleotide polymorphism (SNP) markers and exploration of dominant genotypesand growth genes will enhance our understanding of the genetic mechanisms underlying growth and development.Moreover, this research will facilitate the selection and breeding of new populations with exceptional growth traits.Using restriction site-associated DNA sequencing (RAD-seq), we conducted SNP screening in the F0 generation ofthe northern subspecies of largemouth bass, focusing on extreme groups with very high body weights (top 1%) andvery low body weights (bottom 1%). A general linear model (GLM) was applied to establish correlations betweenthe SNP genotypes and four growth traits (body weight, body length, body height, and body thickness) in a cohortof 230 F0 individuals. Additionally, candidate genes associated with growth were predicted using gene annotationinformation, and the combined additive effects of the dominant genotypes were analyzed through examination oftheir aggregation. A total of 4196486 high-quality SNPs were identified across 23 chromosomes of the largemouthbass. Using a population-specific genotype frequency threshold of 0.7, we initially screened 100 potential SNPloci related to growth and identified 12 that were significantly associated with growth. Specifically, five SNPswere significantly associated with body weight, 10 SNPs were significantly associated with body length, fourSNPs were significantly associated with body height, and five SNPs were significantly associated with bodythickness. Notably, the candidate growth genes fam174b, diaph2, kiaa1549lb, and ppip5k1b were linked to specificSNP markers including SNP19140160, SNP24406191, SNP3355498, and SNP9244620, respectively. Theenrichment of 6−10 dominant genotypes resulted in an average increase of 32.07% in body weight, 9.63% in bodylength, 9.96% in body height, and 10.58% in body thickness compared to the enrichment of 0–5 dominant genotypes,significantly improving the effect of genotype enrichment. The 12 fast-growth SNP markers and four candidategrowth genes identified in this study could assist in the improvement of growth traits in largemouth bass.

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华吉祥,陶易凡,李岩,王庆春,陈文华,诸葛燕,张茂友,董亚伦,路思琪,姜冰洁,强俊.基于RAD-seq的大口黑鲈选育群体快长SNP挖掘及其与生长性状的关联分析[J].中国水产科学,2024,31(3):241-256
HUA Jixiang, TAO Yifan, LI Yan, WANG Qingchun, CHEN Wenhua, ZHUGE Yan, ZHANG Maoyou, DONG Yalun, LU Siqi, JIANG Bingjie, QIANG Jun. Development of fast-growth SNP screening and association analysis with growth traits based on RAD-seq for largemouth bass (Micropterussalmoides) breeding populations[J]. Journal of Fishery Sciences of China,2024,31(3):241-256

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  • 收稿日期:2023-12-19
  • 最后修改日期:2024-02-18
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  • 在线发布日期: 2024-06-11
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