Genetic Diversity Analysis of 4 Common Carp (Cyprinus carpio) Populations Farmed in Paddy Field Based on COⅠ-D-loop-ITS1 Sequence
LIU Zhi-Gang, LU Mai-Xin*, CAO Jian-Meng, YI Meng-Meng, WANG Miao, GAO Feng-Ying, KE Xiao-Li, WANG Guang-Jun
Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou 510380, China
Abstract：The genetic diversity of fish is closely correlated with its environmental adaptability and genetic evolution potential. In order to reveal the genetic background of different geographical populations of common carp (Cyprinus carpio) raised in paddy field, the genetic diversity and genetic structure of four populations of carp (Guangdong Liannan population (LN), Guangdong Ruyuan population (RY), Guangxi C. carpio var. Jinbian population (JB), Guangxi Sanjiang population (SJ)) were analyzed based on PCR amplification and sequence alignment of COⅠ(cytochrome oxidase subunit Ⅰ)-D-loop (displacement loop region)-ITS1 (internal transcribed spacer 1) sequences. The results showed that there were 71 polymorphic sites in the 1 842 bp COⅠ-D-loop-ITS1 sequences of four populations of carp, including 28 singleton variable sites and 43 parsimony informative sites, a total of 33 haplotypes were found in four populations of carp and 11 haplotypes were found in both JB and RY population. There were no shared haplotypes among the four popultions of carp. The haplotype diversity of LN population (Hd=0.824) and the nucleotide diversity of JB population (Pi=0.002 78) were the highest in the four populations. The haplotype diversity and nucleotide diversity of SJ population (Hd=0.662; Pi=0.000 56) were the lowest in the four populations. The results of genetic difference analysis showed that the genetic distance between SJ and JB populations was the smallest (0.004 6), while it was the largest between LN and RY populations (0.008 7). The genetic differentiation among these four populations were significant (FST>0.25, P<0.01). Molecular variance (AMOVA) analysis results indicated that a high proportion of the total genetic variance was attributable to variations among populations (70.65%). Individual phylogenetic tree constructed based on COⅠ-D-loop-ITS1 sequences could completely separate all the individuals of four populations, which had a better clustering effect than the individual phylogenetic tree constructed based on single gene (COⅠ, D-loop or ITS1). In the phylogenetic tree of four populations, SJ and JB populations firstly clustered into a small branch, and then clustered with RY population into a large branch, while LN population independently clustered into a branch. In conclusion, the haplotype diversity of the four populations of carp raised in paddy field were high, while the nucleotide diversity of them were quite low. The genetic differentiation among these four populations were significant, which indicated that the germplasm resources of these populations of carp should be protected and utilized as “evolutionarily significant units”. This study reveals the genetic structure and genetic relationship of four populations of common carp (Cyprinus carpio) raised in paddy field and enriches the basic information of the germplasm resources of carp in rice-fish system, which would lay a theoretical foundation for the preservation, development and utilization of the germplasm of common carp raised in paddy field.
刘志刚, 卢迈新, 曹建萌, 衣萌萌, 王淼, 高风英, 可小丽, 王广军. 基于COⅠ-D-loop-ITS1序列的4个稻田养殖鲤群体遗传多样性研究[J]. 农业生物技术学报, 2021, 29(7): 1322-1331.
LIU Zhi-Gang, LU Mai-Xin, CAO Jian-Meng, YI Meng-Meng, WANG Miao, GAO Feng-Ying, KE Xiao-Li, WANG Guang-Jun. Genetic Diversity Analysis of 4 Common Carp (Cyprinus carpio) Populations Farmed in Paddy Field Based on COⅠ-D-loop-ITS1 Sequence. 农业生物技术学报, 2021, 29(7): 1322-1331.
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