Genetic diversity and population structure of wild lotus (Nelumbo nucifera Gaertn.) in China
-
摘要: 以我国长江中下游地区和北方地区33个居群的195份野莲（Nelumbo nucifera Gaertn.）为材料，基于SLAF简化基因组测序技术，对不同区域野莲居群的遗传多样性进行研究。结果显示：通过测序共得到742 992个SLAF标签，挖掘高质量SNP位点1 064 789个；供试材料基因型差异明显，主要可分为长江流域和东北区域2个亚群。研究结果支持长江流域野莲和东北区域野莲应分属为亚热带及温带生态型莲。我国野莲居群总多样性较低（π=1.04×10-5），居群间平均分化系数较高（F ST=0.42）。长江中下游地区不同湖泊野莲π值变幅为0.5×10-5~2.2×10-5，梁子湖野莲多样性最为丰富。梁子湖区域内各个小湖π值为3.13×10-6~2.3×10-5，表明小湖内不同居群仍存有较大遗传差异。北部地区不同湖泊野莲π值变幅为3.05×10-6~1.50×10-5，山东梁山古代莲多样性最为丰富。长江中下游地区野莲遗传多样性高于北部地区且两者间分化程度较高（F ST=0.34），表明野莲居群间和区域间均有较高的分化程度，原因可能是野莲居群内主要为克隆繁殖，而居群间基因交流少所致。
-
关键词:
- 莲 /
- 野莲居群 /
- 遗传多样性 /
- SLAF简化基因组测序
Abstract: Lotus (Nelumbo nucifera Gaertn.) is a special aquatic plant in China. However, habitat destruction by both natural factors and human activity have impacted many wild populations. Furthermore, the genetic diversity of these wild populations remains poorly understood. In this study, the genetic diversity and structure of wild lotus in China were evaluated based on 33 populations using 1 064 789 single nucleotide polymorphism (SNP) loci obtained by specific-locus amplified fragment sequencing (SLAF). Cluster, principal coordinate, and STRUCTURE analyses revealed that the northeast China populations were genetically separated from those of the Yangtze River Basin. Thus, wild lotus from these two regions represented two ecotypes of N. nucifera. Low genetic diversity within each population (average π = 1.04×10-5) and a high degree of genetic differentiation among populations (average FST = 0.42) were found. For the Yangtze River Basin populations, π ranged from 0.[KG-*3]5×10-5 to 2.2×10-5 among the various lakes. The Liangzi Lake area exhibited the highest diversity, with π ranging from 3.13×10-6 to 2.3×10-5 among the small lakes, indicating that lotus diversity was not evenly distributed. For populations in North China, π ranged from 3.05×10-6 to 1.50×10-5, with the Liangshan populations showing the highest diversity. Thus, higher genetic diversity was observed in the Yangtze River Basin populations than in the North China populations. The FST value from comparison was 0.34, indicating a high degree of genetic differentiation between the areas. Low genetic diversity within populations and high differentiation among populations could be attributed to clonal reproduction within populations and low genetic exchange among populations. Our results indicate that ex situ conservation should be supplemented with in situ preservation for wild lotus conservation. -
-
[1] Qiu YL, Chase M, Les D, Parks C. Molecular phylogene-tics of the Magnoliidae:cladistic analyses of nucleotide sequences of the plastid gene rbcL[J]. Ann Mo Bot Gard, 1993, 80(3):587-606.
[2] 薛建华, 卓丽环, 周世良. 黑龙江野生莲遗传多样性及其地理式样[J]. 科学通报, 2006, 51(3):299-308. Xue JH, Zhuo LH, Zhou SL.Genetic diversity and geographical pattern of wild lotus in Heilongjiang province[J]. Science Bulletin, 2006, 51(3):299-308.
[3] 郭宏波, 柯卫东, 李双梅, 彭静. 不同类型莲资源的RAPD聚类分析[J]. 植物遗传资源学报, 2004, 5(4):328-332. Guo HB, Ke WD, Li SM, Peng J. RAPD cluster analysis of different types of lotus resources[J]. Journal of Plant Genetic Resources, 2004, 5(4):328-332.
[4] 郭宏波, 柯卫东, 李双梅, 彭静. 野生莲资源的RAPD分析[J]. 植物学报, 2005(s1):64-67. Guo HB, Ke WD, Li SM, Peng J. RAPD analysis of wild lotus resources[J]. Acta Botanica Sinica, 2005(S1):64-67.
[5] An N, Guo HB, Ke WD. Genetic variation in rhizome lotus (Nelumbo nucifera Gaertn.) germplasms from China assessed by RAPD markers[J]. J Integr Agr, 2009, 8(1):31-39.
[6] Li Z, Liu XQ, Gituru RW, Juntawong N, Zhou MQ, Chen LQ. Genetic diversity and classification of Nelumbo germplasm of different origins by RAPD and ISSR analysis[J]. Scientia Horticulturae, 2010, 125(4):724-732.
[7] Chen YY, Zhou RC, Lin XD, Wu KQ, Qian X, Huang SZ. ISSR analysis of genetic diversity in sacred lotus cultivars[J]. Aquat Bot, 2008, 89(3):311-316.
[8] 徐玉仙, 张微微, 莫海波, 李春, 曹建国, 田代科. 基于EST-SSR标记的莲属种质资源遗传多样性分析[J]. 植物分类与资源学报, 2015, 37(5):595-604. Xu YX, Zhang WW, Mo HB, Li C, Cao JG, Tian DK. Genetic diversity analysis of nelumbo accessions based on EST-SSR markers[J]. Journal of Plant Classification and Resources, 2015, 37(5):595-604.
[9] Kubo N, Hirai M, Kaneko A, Tanaka D, Kasumi K. Deve-lopment and characterization of Simple Sequence Repeat (SSR) markers in the water lotus (Nelumbo nucifera)[J]. Aquat Bot, 2009, 90(2):191-194.
[10] Pan L, Xia Q, Quan Z, Liu H, Ke WD, Ding Y. Development of novel EST-SSRs from sacred lotus (Nelumbo nucifera Gaertn.) and their utilization for the genetic diversity analysis of N. nucifera[J]. J Hered, 2010, 101(1):71.
[11] Kubo N, Hirai M, Kaneko A, Tanaka D, Kasumi K. Classification and diversity of sacred and American Nelumbo species:the genetic relationships of flowering lotus cultivars in Japan using SSR markers[J]. Plant Genet Resour, 2009, 7(3):260-270.
[12] Li C, Mo HB, Tian DK, Xu YX, Meng J, Tilt K. Genetic diversity and structure of American lotus (Nelumbo lutea willd.) in north America revealed from microsatellite mar-kers[J]. Scientia Horticulturae, 2015, 189:17-21.
[13] Mekbib Y, Huang S, Ngarega B, Li Z,Shi T,et al. The level of genetic diversity and differentiation of tropical lotus, Nelumbo nucifera Gaertn. (Nelumbonaceae) from Australia, India, and Thailand[J]. Bot Stud, 2020, 61:15.
[14] Li ZZ, Islam MR, Huang SX, Yang D, Yang XY. Genetic diversity comparisons of wild populations of Nelumbo nucifera (Nelumbonaceae) in Russia and China using microsatellite markers[J]. Plant Syst Evol, 2020, 306(5):79.
[15] Hu JH, Pan L, Liu HG, Wang SZ, Wu ZH, et al. Compa-rative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers[J]. Mol Biol Rep, 2012, 39(4):3637-3647.
[16] Fu J, Xiang QY, Zeng XB, Yang M, Wang Y, Liu YL. Assessment of the genetic diversity and population structure of lotus cultivars grown in China by amplified fragment length polymorphism[J]. J Amer Soc Hort Sci, 2011, 136(5):491-496.
[17] 瞿桢, 魏英辉, 李大威, 肖丽舟, 徐金星, 等. 品种资源的SRAP遗传多样性分析[J]. 氨基酸和生物资源, 2008, 30(3):21-25. Qu Z, Wei YH, Li DW, Xiao LZ, Xu JX, et al. Genetic diversity analysis of Nelumbo nucifera based on SRAP mar-kers[J]. Amino Acids and Biotic Resources, 2008, 30(3):21-25.
[18] Yang M, Han YN, Xu LM, Zhao JR, Liu YL. Comparative analysis of genetic diversity of lotus (Nelumbo) using SSR and SRAP markers[J]. Scientia Horticulturae, 2012, 30(3):21-25.
[19] Huang LY, Yang M, Li L, Li H, Yang D, et al. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)[J]. J Integr Plant Biol, 2018, 60(1):4-17.
[20] Liu ZW, Zhu HL, Zhou JH, Jiang SJ, Wang Y, et al. Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history[J]. Plant J, 2020, 104(6):1673-1684.
[21] Li Y, Zhu FL, Zheng XW, Hu ML, Dong C, et al. Compa-rative population genomics reveals genetic divergence and selection in lotus, Nelumbo nucifera[J]. BMC Genomics, 2020, 21(1):146.
[22] Yang M, Liu F, Han YN, Xu LM, Juntawong N, Liu YL. Genetic diversity and structure in populations of Nelumbo from America, Thailand and China:implications for conservation and breeding[J]. Aquat Bot, 2013, 107(107):1-7.
[23] 王其超,张行言. 中国荷花品种图志[M]. 北京:中国林业出版社, 2004. [24] 柯卫东, 李峰, 黄新芳, 刘义满, 彭静. 水生蔬菜种质资源研究及利用进展[C]//中国园艺学会. 第二届全国水生蔬菜学术及产业化研讨会论文集. 武汉:中国农业科学院蔬菜花卉研究所, 2007:72-75. [25] Han YC, Teng CZ, Sheng Z, Zhou MQ, Hu ZL, Song YC. Genetic variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers[J]. Aquat Bot, 2007, 86(1):69-75.
[26] Han YC, Teng CZ, Wahiti GR, Zhou MQ, Hu ZL, Song YC. Mating system and genetic diversity in natural populations of Nelumbo nucifera(Nelumbonaceae) detected by ISSR markers[J]. Plant Syst Evol, 2009, 277(1):13-20.
[27] Islam MR, Zhang Y, Li ZZ, Liu H, Yang XY. Genetic diversity, population structure, and historical gene flow of Nelumbo lutea in USA using microsatellite markers[J]. Aquat Bot, 2019, 160(3):103162.
[28] 张行言, 王其超. 热带型荷花的发现与荷花品种分类系统[J]. 中国园林, 2006(7):82-85. Zhang YX, Wang QC. Preliminary study of the eco-types of genetic resources of tropical lotus[J]. Landscape Plants, 2006(7):82-85.
[29] Liu ZW, Zhu HL, Liu YP, Kuang J, Zhou K, et al. Construction of a high-density, high-quality genetic map of cultivated lotus (Nelumbo nucifera) using next-generation sequencing[J]. BMC Genomics, 2016, 17(1):466.
[30] Sun XW, Liu DY, Zhang XF, Li WB, Liu H, et al. SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013, 8(3):e58700.
[31] Wang Y, Fan GY, Liu YM, Sun FM, Shi CC, et al. The sacred lotus genome provides insights into the evolution of flowering plants[J]. Plant J, 2013, 76(4):557-567.
[32] Zhou ZK, Jiang Y, Wang Z, Gou ZH, Lyu J, et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean[J]. Nat Biotechnol, 2015, 4(33):408-414.
[33] Huang XH, Kurata N, Wei XH, Wang ZX, Wang A, et al. A map of rice genome variation reveals the origin of cultivated rice[J]. Nature, 2012, 490(7421):497-501.
[34] 李效尊,杨百战,尹静静,杜绍印,崔太昌,等. 梁山古莲(Nelumbo nucifera Gaertn.)的种质资源价值研究[J]. 长江蔬菜, 2015,396(22):41-43. -
期刊类型引用(4)
1. 朱凌寒，郑丹妮，南倩茹，周文吉，赵丽娅. 环境因子对一年蓬群落分布及物种多样性的影响. 湖北大学学报(自然科学版). 2025(02): 201-208 . 
百度学术
2. 高旭硕，王震，石兆勇. 菌根类型对森林草本植物群落物种丰富度的影响. 应用生态学报. 2024(05): 1251-1259 . 百度学术
3. 祝存兄，孙树娇，肖建设，乔斌. 青海湖东北沙区植被恢复时空格局演变分析. 干旱区资源与环境. 2023(03): 169-177 . 百度学术
4. 刘俊杰，王娟，袁顺捷，韩亚南，刘超，戎战磊，高云飞，赵传燕. 高寒草甸群落结构对不同氮素添加的响应分析. 华侨大学学报(自然科学版). 2022(06): 790-798 . 百度学术
其他类型引用(8)
计量
- 文章访问数: 565
- HTML全文浏览量: 2
- PDF下载量: 494
- 被引次数: 12
下载:
