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.
[1] 郭梁, 任伟征, 胡亮亮, 等.2017.传统稻鱼系统中“田鲤鱼”的形态特征[J].应用生态学报, 28(2): 665-672. (Guo L, Ren W Z, Hu L L, et al.2017.Morphological traits of indigenous field carps maintained in traditional rice-based farming systems[J].Chinese Journal of Applied Ecology, 28(2): 665-672.) [2] 刘念, 傅建军, 董在杰, 等.2017.中国6个鲤群体的mtDNA D-loop序列遗传变异分析[J].水生态学杂志, 38(3): 75-82. (Liu N, Fu J J, Dong Z J, et al.2017.Genetic variation of six Cyprinus carpio populations in China based on mtDNA D-loop sequences[J].Journal of Hydroecology, 38(3): 75-82.) [3] 马冬梅, 黄樟翰, 朱华平, 等.2018.广东粤北地区禾花鱼的形态特征及遗传学分析[J].渔业科学进展, 40(2): 33-42. (Ma D M, Huang Z H, Zhu H P, et al.2018.Morphological characteristics and genetic analysis of the rice flower carp in the northern region of Guangdong province[J].Progress in Fishery Sciences, 40(2): 33-42.) [4] 邵科, 闫书祥, 李伟涛, 等.2018.长江上游长鳍吻鮈群体线粒体控制区遗传多样性分析[J].水生态学杂志, 39(1): 76-82. (Shao K, Yan S X, Li W T, et al.2018.Genetic structure and diversity of Rhinogobio ventralis in the upper Yangze River obtained by analysis of the mitochondrial DNA control region[J].Journal of Hydroecology, 39(1): 76-82.) [5] 王桢璐, 姚东林, 谢少林, 等.2018.基于线粒体Cyt b和COⅠ基因序列的华南鲤群体遗传结构分析[J].江苏农业科学, 46(18): 179-183. (Wang Z L, Yao D L, Xie S L, et al.2018.Analysis of population genetic structure of Cyprinus carpio rubrofuscus based on mitochondrial Cyt b and COⅠ gene sequences[J].Jiangsu Agricultural Sciences, 46(18): 179-183.) [6] 肖同乾, 鲁翠云, 李超, 等.2013.8种鲤养殖品种线粒体Cyt b基因的遗传多样性和系统进化分析[J].水产学报, 37(3): 344-350. (Xiao T Q, Lu C Y, Li C, et al.2013.Genetic diversity and phylogenetic analysis of eight cyprinoid aquaculture breeds based on mitochondrial Cyt b gene[J].Journal of Fisheries of China, 37(3): 344-350.) [7] 袁吉贵, 李爵乾, 刘丽, 等.2017.基于18S-ITS1-5.8S序列的吉富罗非鱼群体遗传多样性分析[J].广东海洋大学学报, 37(6): 7-10. (Yuan J G, Li J Q, Liu L, et al.2017.Genetic diversity of GIFT strains of Oreochromis niloticus based on 18S-ITS1-5.8S sequence[J].Journal of Guangdong Ocean University, 37(6): 7-10.) [8] 乐佩琦.2000.中国动物志-硬骨鱼纲鲤形目(下卷)[M].北京: 科学出版社, pp.391-427. (Yue P Q.2000.Fauna Sinica, Osteichthyes, CypriniformesⅢ[M].Beijing: Science Press, pp.391-427.) [9] 张晓宇, 张富铁, 姚富城, 等.2020.岩原鲤遗传多样性和种群历史动态研究[J].水生生物学报, 44(2): 330-338. (Zhang X Y, Zhang F T, Yao F C, et al.2020.Study on genetic diversity and population historical dynamics of Procypris rabaudi (Tchang) endemic in the upper Yangze River[J].Acta Hydrobiological Sinica, 44(2): 330-338.) [10] 钟立强, 张成锋, 周凯, 等.2011.四个鲤鱼种群ITS-1序列的遗传变异分析[J].湖泊科学, 23(2): 271-276. (Zhong L Q, Zhang C F, Zhou K, et al.2011.Sequence variation of ribosomal DNA intemal transcribed spacer 1 of four common carp populations[J].Journal of Lake Sciences, 23(2): 271-276.) [11] Allwndorf F W.1983.Isolation, gene flow and genetic differentiation among populations.In: Schonewald-Cox CM, Chambers SM, MacBryde B and Thomas WL (Eds) Genetics and conservation: A reference for managing wild animal and plant populations[M].Benjamin Cummings Press, Menlo Park.pp.51-65. [12] Booton G C, Kaufman L, Chandler Mark, et al.1999.Evolution of the ribosomal RNA internal transcribed spacer one (ITS-1) in cichlid fishes of the lake victoria region[J].Molecular Phylogenetics and Evolution, 11(2): 273-282. [13] Dong C J, Xu J, Wang B S, et al.2015.Phylogeny and evolution of multiple common carp (Cyprinus carpio L.) populations clarified by phylogenetic analysis based on complete mitochondrial genomes[J].Marine Biotechnology, 17: 565-575. [14] Frankham R, Ballou J, Briscoe D, et al.2010.Introduction to conservation genetics: Second edition[M].Cambridge University Press, Cambridge.pp.41-65. [15] Grant W, Bowen B W.1998.Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity, 89(5): 415-426. [16] Hebert P D N, Ratnasingham S, de Waard J R.2003.Barcoding animal life: cytochrome c oxidsse subunit 1 divergences among closely related species[J].Proceedings of the Royal Society of London B - Biological Science, 270(Suppl 1): 96-99. [17] Hillis D M, Dixon M T.1991.Ribosomal DNA: Molecular evolution and phylogenetic inference[J].The Quarterly Review of Biology, 66(4): 411-453. [18] Moritz C.1994.Defining "Evolutionarily Significant Units" for conservation[J].Trends in Ecology and Evolution, 9(10): 373-375. [19] Moritz C, Dowling T E, Brown W M.1987.Evolution of animal mitochondrial DNA: Relevance for population biology and systematics[J].Annual Review of Ecology and Systematics, 18: 269-292. [20] Wright S.1978.Variability within and among natural populations[M].The university of Chicago Press, Chicago.pp.79-103.