| Citation: |
ZHANG Xiaohong, YU Ke, AN Miao, OU Pingyong, WANG Bangping, YANG Shengtong, LI Li, LI Maonian, QIN Kesi. Population structure and diversity of Duyun "Red Carp"[J]. South China Fisheries Science, 2024, 20(4): 154-163. DOI: 10.12131/20240037
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The "Red Carp" from Duyun, Guizhou Province is a product of the traditional rice farming model, with relatively rich genetic diversity, making it an ideal material for breed selection. To enrich the genetic background data of rice field carps in Guizhou Province and provide a theoretical basis for the rational development, utilization, and protection of rice field carp germplasm resources, we used mitochondrial DNA Cyt b gene sequencing technology to explore the population structure and diversity of the "Red Carp" from Duyun and adjacent areas. The results show that a total of 45 variable sites were detected in 253 Cyt b genes, defining 23 haplotypes. The 'Red Carp' from Duyun exhibited 9 haplotypes, 5 of which shared with the control rice field carp, accounting for 76.19% of the total sample size. Phylogenetic and neural network results indicate that the Duyun "Red Carp" is a hybrid population composed of two highly differentiated sub-species groups with minor genetic differences, namely Cyprinus carpio haematopterus Temminck and C. carpio rubrofuscus Lacépède. These sub-species shared the same maternal origin with domestic carp varieties and the control paddy field carp. For the Duyun "Red Carp", Hap22 was shared among individuals belonging to C. carpio haematopterus sub-species, while four unique haplotypes were exclusive to this sub-species, Additionally, four shared haplotypes were present in C. carpio rubrofuscus sub-species. Genetic diversity and differentiation analysis reveal that the two subspecies populations of Duyun "Red Carp" had a low level of genetic variation, both exhibiting characteristics such as high Hd and low π. The C. c. haematopterus subspecies was moderately differentiated from the control paddy field carp; while the sub-species of C. carpio rubrofuscus showed a high degree of differentiation from the Jinping Carp, but a relatively low level of differentiation from the other three control paddy field carp populations. However, due to geographical isolation and selective pressure during domestication, founder effects and genetic drift, their genetic diversity had decreased, resulting in genetic differentiation from the control populations. The study indicates that there is limited genetic exchange among the rice field carp populations in Duyun and its adjacent areas, with different genetic structures within and between populations.
| [1] |
HU W J, GAO Y, HE X M, et al. Origin of domesticated Qingtian paddy-field carp and its genetic differentiation from wild common carp populations[J]. Aquaculture, 2023, 565: 739117. doi: 10.1016/j.aquaculture.2022.739117
|
| [2] |
纪达, 许劲松, 姚俊杰, 等. 贵州省5 个金背鲤(Cyprinus carpio var. Jinbei)地理群体的遗传多样性与遗传结构分析[J]. 水产学杂志, 2022, 35(5): 8-17. doi: 10.3969/j.issn.1005-3832.2022.05.002
|
| [3] |
甘宝江, 张盛, 韦玲静, 等. 广西稻田养殖金边鲤群体遗传多样性分析[J]. 水产科学, 2019, 38(5): 636-646.
|
| [4] |
纪达, 杨玉梅, 姚俊杰, 等. 贵州7 个鲤养殖群体遗传多样性与遗传结构分析[J]. 海洋渔业, 2023, 345(3): 257-266. doi: 10.3969/j.issn.1004-2490.2023.03.001
|
| [5] |
潘贤辉, 周康奇, 陈忠, 等. 基于线粒体D-loop 区和COI 基因序列研究2 个禾花鲤群体和野生鲤群体的遗传多样性与系统进化关系[J]. 淡水渔业, 2019, 49(6): 33-40. doi: 10.3969/j.issn.1000-6907.2019.06.006
|
| [6] |
程磊, 何苹萍, 韦嫔媛, 等. 基于线粒体D-loop 区和 Cyt b 基因分析广西禾花鲤三个群体遗传结构[J]. 水生生物学报, 2021, 45(1): 54-59. doi: 10.7541/2021.2020.041
|
| [7] |
余科, 麻智芳, 安苗, 等. 从江及周边地区稻田鲤的遗传结构及系统发育关系[J]. 水生生物学报, 2022, 46(7): 939-950. doi: 10.7541/2022.2021.0163
|
| [8] |
LIANG Z Q, ZOU L, TIAN L, et al. Genetic origin and differentiation of ten paddy field-farmed Cyprinus carpio strains in China[J]. Aquaculture, 2022, 561: 738573. doi: 10.1016/j.aquaculture.2022.738573
|
| [9] |
杨昌雄. 稻田养鱼-贵州苗族区稻田养鱼调查记[J]. 贵州农业科学, 1984(6): 62-65, 57.
|
| [10] |
杨昌雄. 概述苗族稻田养鱼史及其发展趋势[J]. 古今农业, 1989(1): 124-127.
|
| [11] |
贵州省都匀市史志编纂委员会. 都匀市志[M]. 贵阳: 贵州人民出版社, 1999: 803-807.
|
| [12] |
韩荣培. “饭稻羹鱼”-水族传统农耕文化的主题[J]. 贵州民族研究, 2004, 24(2): 47-51. doi: 10.3969/j.issn.1002-6959.2004.02.009
|
| [13] |
龚良超. 黔南州稻渔综合种养产业发展情况及对策[J]. 农技服务, 2022, 39(11): 99-102. doi: 10.3969/j.issn.1004-8421.2022.11.njfw202211028
|
| [14] |
XIAO W H, ZHANG Y P, LIU H Z. Molecular systematics of Xenocyprinae (Teleoatei: Cyprinidae): taxonomy, biogengraphy, and coevolutionof a special group restricted in East Asia[J]. Mol Phylogente Evol, 2001, 18(2): 163-173. doi: 10.1006/mpev.2000.0879
|
| [15] |
HIGGINS D G, JEANMOUGIN F, GIBSON T J, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucl Acids Res, 1997, 25(24): 4876-4882. doi: 10.1093/nar/25.24.4876
|
| [16] |
LIBRADO, ROZAS. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics (Oxford, England), 2009, 25(11): 1451-1452.
|
| [17] |
TAMURA K, STECHE G, PETERSON D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30: 2725-2729. doi: 10.1093/molbev/mst197
|
| [18] |
KIMURA M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences[J]. J Mol Evol, 1980, 16: 111-120. doi: 10.1007/BF01731581
|
| [19] |
BANDELT H J, FORSTER P, ROUL A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol, 1999, 16(1): 37-48. doi: 10.1093/oxfordjournals.molbev.a026036
|
| [20] |
EXCOFFIER L, LISCHERH E L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows[J]. Mol Ecol Resour, 2010, 10(3): 564-567. doi: 10.1111/j.1755-0998.2010.02847.x
|
| [21] |
DIBATTISTA J D, RANDALL J E, NEWMAN S J, et al. Round herring (genus Etrumeus) contain distinct evolutionary lineages coincident with a biogeographic barrier along Australia's southern temperate coastline[J]. Mar Biol, 2014, 161(11): 2465-2477. doi: 10.1007/s00227-014-2516-5
|
| [22] |
胡玉婷, 胡王, 凌俊, 等. 滁州鲫线粒体细胞色素b基因和控制区序列比较及其系统进化分析[J]. 南方水产科学, 2015, 11(2): 101-108. doi: 10.3969/j.issn.2095-0780.2015.02.015
|
| [23] |
PWENA N T, KOCHER T D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes[J]. J Mol Evol, 1995, 41(3): 353-358. doi: 10.1007/BF01215182
|
| [24] |
PERDICES A, CUNHA C, COELHO M M. Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (Yangtze) drainage inferred from cytochrome b sequences[J]. Mol Phylogenet Evol, 2004, 31(1): 192-203. doi: 10.1016/j.ympev.2003.07.001
|
| [25] |
陈欣, 唐建军, 胡亮亮, 等. 青田稻鱼共生系统生态学基础及保护与利用[M]. 北京: 科学出版社, 2021: 214.
|
| [26] |
WRIGHT S. The interpretation of population structure by F-statistics with special regard to systems of mating[J]. Evol, 1965, 19(3): 395-420. doi: 10.2307/2406450
|
| [27] |
叶玉珍. 丰鲤的应用推广及其经济效益[J]. 水利渔业, 1988, 9(1): 22-24.
|
| [28] |
ZHOU J F, WANG Z W, YE Y Z, et al. PCR-RFLP analysis of mitochondrial DNA ND5/6 region among 3 subspecies of common carp (Cyprinus carpio L.) and its application to genetic discrimination of subspecies[J]. Sci Bull, 2003, 48(5): 465-468. doi: 10.1007/BF03183252
|
| [29] |
ZHOU J F, WU Q J, WANG Z W, et al. Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA[J]. J Zool Syst Evol Res, 2004, 42(4): 266-269. doi: 10.1111/j.1439-0469.2004.00266.x
|
| [30] |
XU P, ZHANG X F, WANG X M, et al. Genome sequence and genetic diversity of the common carp, Cyprinus carpio[J]. Nat Genet, 2014, 46(11): 1212-1219. doi: 10.1038/ng.3098
|
| [31] |
郭梁, 任伟征, 胡亮亮, 等. 传统稻鱼系统中“田鲤鱼”的形态特征[J]. 应用生态学报, 2017, 28(2): 665-672.
|
| [32] |
HOUKI S, YAMADA M, HONDA T, et al. Origin and possible role of males in hermaphroditic androgenetic Corbicula clams[J]. Zool Sci, 2011, 28(7): 526-531. doi: 10.2108/zsj.28.526
|
| [33] |
ZHANG J X, JIAO T, ZHAO S G. Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations[J]. Biochem Bioph Res Co, 2016, 473(4): 814-820. doi: 10.1016/j.bbrc.2016.03.125
|
| [34] |
ICHIKAWA S M, TOKASHIK M, OPARA M N, et al. Molecular characterization and phylogenetic analysis of Fasciola gigantica from Nigeria[J]. Parasitol Int, 2017, 66(1): 893-897. doi: 10.1016/j.parint.2016.10.010
|
| [35] |
WANG C H, LI S F, NAGY Z T, et al. Molecular genetic structure and relationship of Chinese and Hungarian common carp (Cyprinus carpio L.) strains based on mitochondrial sequence[J]. Aquac Res, 2010, 41: 1339-1347. doi: 10.1111/j.1365-2109.2009.02422.x
|
| [36] |
RODRIGUEZ R S T, GARCIA C L A. Artificial selection with traditional or genomic relationships: consequences in coancestry and genetic diversity[J]. Front Genet, 2015, 6: 127-137.
|
| [37] |
REN W Z, HU L L, GUO L, et al. Preservation of the genetic diversity of a local common carp in the agricultural heritage rice fish system[J]. PNAS, 2018, 115(3): 546-554.
|
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