Genome-wide association study reveals candidate genes critical for skin pigmentation in common carp ( Cyprinus carpio ) strains including koi
文献类型： 外文期刊
作者： Shi, Xiulan 1 ; Zhu, Wenbin 2 ; Guo, Jun 3 ; Lin, Kai 3 ; Fu, Jianjun 2 ; Wang, Lanmei 2 ; Dong, Yalun 2 ; Luo, Mingkun 1 ; Dong, Zaijie 1 ;
作者机构： 1.Nanjing Agr Univ, Wuxi Fisheries Coll, Wuxi 214081, Jiangsu, Peoples R China
2.Freshwater Fisheries Res Ctr, Chinese Acad Fishery Sci, Key Lab Freshwater Fisheries & Germplasm Resources, Minist Agr & Rural Affairs, Wuxi 214081, Jiangsu, Peoples R China
3.Jiangsu Qi Hong Ecol Agr Dev Co Ltd, Suzhou 215000, Jiangsu, Peoples R China
关键词： Common carp strains; Population differentiation; Linkage disequilibrium; Selected sweeping; Genome-wide association studies
期刊名称：AQUACULTURE （ 影响因子：4.5； 五年影响因子：4.6 ）
ISSN： 0044-8486
年卷期： 2024 年 590 卷
页码：
收录情况： SCI
摘要： The differentiation and variation of body color in fish is an important component of biological evolution and phylogenetic research, and is influenced by several factors such as heredity, nutrition, physiological hormones and rearing conditions, with heredity being the most critical factor. An improved comprehension of the genetic regulation in different carp populations will facilitate future applications of precision breeding and pigment cell development-related genes editing. In this study, we used restriction site-associated DNA sequencing (2d-RAD) to determine the distribution characteristics of single nucleotide polymorphisms (SNPs) in eight common carp strains including six koi strains, i.e., Kohaku (Hb), Taisho (Dz), Showa (Zh), Golden (Hj), Matsukawabake (Sch) and Five-color (Ws), and two genetically improved breeding strains, i.e., FFRC No. 2 strain (Fr) and red FFRC strain (Hfr), and then SNP markers to resolve genetic information on the population structure and skin color formation of these strains. We found that most individuals of eight strains were clearly divided into eight clades. Genetic diversity within Fr, Sch and Ws is relatively high, while it is low within Dz, Hb and Hfr. A comparison between the populations revealed that Hfr and Ws have the highest degree of genetic differences, while Hb and Dz have the lowest. The GWAS analysis for two strategies identified several SNPs that are significantly related to skin color variation and affect melanin synthesis ( ephrinb 2 , slc 22 a 23 , herc 2 , ephb 2), carotenoid metabolism ( oca 2 , bcmo 1 , bco 2) and circadian rhythm( cipc ). To summarize, our study provides some information on the genetic structure and diversity of Japanese koi and Chinese FFRC carp. Furthermore, based on the data obtained on relevant genes related to skin color differentiation and pigmentation, it can provide a theoretical basis for the subsequent integration of dominant traits and precision breeding in carps.
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