|
|
|
| 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 |
|
|
|
|
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.
|
|
Received: 23 February 2026
|
|
|
| Fund:国家重点研发计划淡水鱼种质资源生态化保存与更新(2022YFD2400102) |
|
Corresponding Authors:
*wangch@shou.edu.cn
|
|
|
|
[1] 蔡完其, 轩兴荣, 王成辉,等. 2003. 红鲤4群体间主要组织相容性复合体的差异[J]. 水产学报, (02): 113-118.
(Cai W Q, Xuan X R, Wang C H, et al. 2003. The variations of major histocompatibility complex in four populations of red common carp[J]. Journal of Fisheries of China, (02): 113-118.)
[2] 丁炜东, 曹丽萍, 曹哲明, 等. 2016.建鲤基因组中一个ty3-gypsy反转录转座子的发现与分析[J]. 中国水产科学, 23(02): 284-296.
(Ding W D, Cao L P, Cao Z M, et al.2016. Isolation and analysis of a ty3-gypsy retrotransposon from the genome of Cyprinus carpio var. jian[J]. Chinese Fisheries Science, 23(02): 284-296.)
[3] 李思发, 王成辉, 程起群. 2005. 红鲤四品系的形态差异和种系关系(英文)[J]. 水产学报, (05): 24-29.
(Li S F, Wang C H, Cheng Q Q. 2005. Morphological variations and phylogenesis of four strains in Cyprinus carpio#[J]. Journal of Fisheries of China, (05): 24-29.)
[4] 李思发, 李晨虹, 李家乐. 1998. 尼罗罗非鱼品系间形态差异分析[J]. 动物学报, (04): 75-82.
(Li S F, Li C H, Li J L.1998. Analysis of morphological variations among strains of Nile tilapia (Oreochromis niloticus)[J]. Acta Zoologica Sinica, (04): 75-82.)
[5] 楼允东, 孙景春. 2001. 江西三种红鲤起源与遗传多样性研究的进展[J]. 水产学报, (06): 570-575.
(Lou Y D, Sun J C. 2001. Progress on studies of origin and genetic diversity of three breeds of red carp in Jiangxi province[J]. Journal of Fisheries of China, (06): 570-575.)
[6] 王成辉. 2002. 中国红鲤遗传多样性研究[D]. 博士学位论文, 上海水产大学, 导师: 李思发, pp. 1-2.
(Wang C H.2002. Study on genetic diversity of red common carps in China[D]. Thesis for Ph.D., Shanghai Fisheries University, Supervisor: Li S F, pp. 1-2.)
[7] 王成辉, 李思发, 邹曙明. 2003. 中国红鲤遗传多样性的RAPD分析[J]. 水生生物学报, (03): 329-330.
(Wang C H, Li S F, Zou S M. 2003. RAPD analysis of genetic diversity of red common carp in China[J]. (03): 329-330.)
[8] 王成辉, 李思发, 赵金良. 2004a. 我国4种红鲤群体的生化遗传差异[J]. 上海水产大学学报, (01): 1-4.
(Wang C H, Li S F, Zhao J L. 2004. Study on biochemical genetic differences among 4 populations of red common carp in China[J]. Journal of Shanghai Fisheries University, (01): 1-4.)
[9] 王成辉, 李思发, 邹曙明. 2004b. 中国红鲤四群体线粒体DNA遗传多样性、起源及分化[J].水产学报, (06): 640-644.
(Wang C H, Li S F, Zou S M. 2004. Mitochondrial DNA genetic diversity origin and evolution of four populations of red common carps in China[J]. Journal of Fisheries of China, (06): 640-644.)
[10] 王莉, 何舜平, 陈宜瑜. 2007. 鲤科鱼类 Angel 相关元件的鉴定及其系统发育意义[J]. 自然科学进展, (04): 542-545.
(Wang L, He S P, Chen Y Y. 2007. Identification of Angel-related elements in cyprinid fishes and their phylogenetic implications[J]. Progress in Natural Science, (04): 542-545.)
[11] 邹小晴. 2022. 鲤异源四倍体基因组转座元件的鉴定及演化分析[D]. 硕士学位论文, 厦门大学, 导师: 徐鹏, pp. 57-59.
(Zou X Q.2022. Identification and evolutionary analysis of transposable elements in allotetraploid common carp[D]. Thesis for M.S., Xiamen University, Supervisor: Xu P, pp. 57-59. )
[12] Baduel P, Quadrana L, Colot V.2021. Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data[M]. Quadrana L, Colot V (eds.). Plant Transposable Elements: Methods and Protocols. Springer US, New York, pp. 157-169.
[13] Bourgeois Y, Boissinot S.2019. On the population dynamics of junk: A review on the population genomics of transposable elements[J]. Genes, 10(6): 419.
[14] Bird K A, VanBuren R, Puzey J R, et al.2018. The causes and consequences of subgenome dominance in hybrids and recent polyploids[J]. New Phytologist, 220(1): 87-93.
[15] Donlin L T, Andresen C, Just S, et al.2012. Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization[J]. Genes & Development, 26(2): 114-119.
[16] Feschotte C, Pritham E J.2007. DNA transposons and the evolution of eukaryotic genomes[J]. Annual Review of Genetics, 41(1): 331-368.
[17] Gao B, Yang Y.2013. Planar cell polarity in vertebrate limb morphogenesis[J]. Current Opinion in Genetics & Development, 23(4): 438-444.
[18] Grimes D T, Boswell C W, Morante N F C, et al.2016. Zebrafish models of idiopathic scoliosis link cerebrospinal fluid flow defects to spine curvature[J]. Science, 352(6291): 1341-1344.
[19] Grzebelus D.2006. Transposon insertion polymorphism as a new source of molecular markers[J]. Journal of Fruit and Ornamental Plant Research, 14: 21-29.
[20] Hagiwara N, Yeh M, Liu A.2007. Sox6 is required for normal fiber type differentiation of fetal skeletal muscle in mice[J]. Developmental Dynamics, 236(8): 2062-2076.
[21] Hamada M, Takasaki N, Reist J D, et al.1998. Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of charr during speciation[J]. Genetics, 150: 301-311.
[22] Jackson H E, Ono Y, Wang X, et al.2015. The role of Sox6 in zebrafish muscle fiber type specification[J]. Skeletal Muscle, 5(1): 2.
[23] Kim Y J, Osborn D P S, Lee J Y, et al.2018. WDR11-mediated Hedgehog signalling defects underlie a new ciliopathy related to Kallmann syndrome[J]. EMBO Reports, 19(2): 269-289.
[24] Koga A, Inagaki H, Bessho Y, et al.1995. Insertion of a novel transposable element in the tyrosinase gene is responsible for an albino mutation in the medaka fish, Oryzias latipes[J]. Molecular and General Genetics (MGG), 249(4): 400-405.
[25] Kratochwil C F, Kautt A F, Nater A, et al.2022. An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes[J]. Nature Communications, 13: 296.
[26] Rebollo R, Romanish M T, Mager D L.2012. Transposable elements: An abundant and natural source of regulatory sequences for host genes[J]. Annual Review of Genetics, 46(1): 21-42.
[27] Wang M, Li X, Wang C, et al.2024. Asymmetric and parallel subgenome selection co-shape common carp domestication[J]. BMC Biology, 22: 4.
[28] Wang L, Sun F, Wan Z Y, et al.2022. Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish[J]. BMC Biology, 20(1): 5.
[29] Wansleeben C, Meijlink F.2011. The planar cell polarity pathway in vertebrate development[J]. Developmental Dynamics, 240(3): 616-626.
[30] Wu C, Ma Z, Zheng G, et al.2022. Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution[J]. BMC Genomics, 23: 271.
[31] Xu P, Xu J, Liu G, et al.2019. The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio[J]. Nature Communications, 10(1): 4625. |
|
|
|
