Study on Morphological Traits and Transposable Element Variation Among Four Red Carp (Cyprinus carpio) Populations
GE Yue1,2, KE Jing1,2, YU Yang-Le-Fu1,2, XU Bo-Wen1,2, CHEN Xiao-Wen1,2, WANG Jun1,2, WANG Cheng-Hui1,2,*
1 Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; 2 National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University,Shanghai 201306, China
摘要体型是鲤(Cyprinus carpio)重要的种质评估和经济性状,不同红鲤群体在长期驯化与选育过程中形成了明显的形态分化,但其遗传基础尚未得到充分解析。转座子插入多态性(transposable element insertion polymorphism, TIP)是基因组结构变异的重要形式,可能通过影响邻近基因的结构与表达参与表型分化。为探究4种红鲤群体间体型差异相关的潜在遗传基础,评估转座子插入多态性在群体鉴别与形态性状关联研究中的应用潜力,本研究以兴国红鲤(C. carpio var. xingguonensis)、荷包红鲤(C. carpio var. wuyuanensis)、玻璃红鲤(C. carpio var. wananensis)和“全红”体色瓯江彩鲤(C. carpio var. color)为对象,开展形态性状多元分析和全基因组TIP比较研究。基于24项形态比例性状的分析表明,荷包红鲤在体高性状上显著高于其他3个群体(P<0.05),且在聚类分析和主成分分析中形成稳定独立分支,表现出显著的形态“特化”特征。全基因组TIP分析显示,4种红鲤基因组中转座子(transposable elements, TEs)家族组成高度一致,均以hAT、Gypsy和CACTA为主要类型,且在染色体尺度上呈现相似的分布特征。基于TIP位点的主成分分析、系统发育分析及STRUCTURE聚类结果均表明,不同群体在转座子插入模式上存在稳定遗传分化;核苷酸多样性(π)和群体间分化指数(FST)分析进一步支持群体间存在显著的遗传差异。群体特异转座子插入位点分析发现,玻璃红鲤最多,而兴国红鲤最少。基于荷包红鲤特异性TIP位点定位与选择信号分析,鉴定出wdr11、rsph14、sox6和smyd2b等可能与荷包红鲤体高差异存在潜在关联的候选基因。本研究为鲤体型相关性状的遗传关联研究及后续候选基因验证提供参考。
Abstract：Body shape is an important economical trait for germplasm evaluation and aquaculture in common carp (Cyprinus carpio). Different populations of red common carp have developed distinct morphological differentiation during long-term domestication and selective breeding, yet the underlying genetic basis remains insufficiently understood. Transposable element insertion polymorphism (TIP), an important form of genomic structural variation, may contribute to phenotypic differentiation by affecting the structure and expression of adjacent genes. In this study, 4 populations of red common carp, namely Xingguo red common carp (C. carpio var. xingguonensis), Hebao red common carp (C. carpio var. wuyuanensis), Wanan glass red common carp (C. carpio var. wananensis) and 'whole-red' strain of Oujiang color common carp (C. carpio var. color), were used to investigate potential genetic factors associated with body-shape differences and to evaluate the potential application of TIP in population discrimination and trait association studies, by using multivariate analyses of morphological traits and genome-wide comparisons of TIP. The results based on the 24 morphometric ratio traits showed that Hebao red common carp exhibited significantly higher body depth than the other 3 carps (P<0.05) and consistently formed a stable and independent cluster in both hierarchical clustering and principal component analyses, displaying obvious morphological 'specialization' characteristics. Genome-wide analysis of TIP demonstrated a highly conserved transposable element (TE) family composition among the 4 populations of red common carp, which were dominated by the hAT, Gypsy, and CACTA superfamilies. Meanwhile, the similar chromosomal distribution patterns of TIP were found among these carps. Principal component analysis, phylogenetic reconstruction, and STRUCTURE clustering based on TIP loci consistently revealed stable genetic differentiation among populations in TE insertion patterns, which was further corroborated by analyses of nucleotide diversity (π) and population differentiation (FST). Population-specific TIP analysis showed that the highest number of unique TE insertion loci was found in Wanan glass red common carp, but the lowest in Xingguo red common carp. By integrating morphology-associated TIP screening with selective sweep analysis, several candidate genes potentially associated with body-depth variation were detected in Hebao red common carp, including wdr11, rsph14, sox6, and smyd2b. This study provides a reference for genetic association studies on body shape-related traits in common carp and candidate gene verification in the future.
葛悦, 柯景, 喻杨乐夫, 徐博文, 陈晓雯, 王军, 王成辉. 四种红鲤群体的形态性状和转座子差异性研究[J]. 农业生物技术学报, 2026, 34(11): 2420-2429.
GE Yue, KE Jing, YU Yang-Le-Fu, XU Bo-Wen, CHEN Xiao-Wen, WANG Jun, WANG Cheng-Hui. Study on Morphological Traits and Transposable Element Variation Among Four Red Carp (Cyprinus carpio) Populations. 农业生物技术学报, 2026, 34(11): 2420-2429.
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