Genetic diversity and inferred ancestry of Asian lotus (Nelumbo nucifera) germplasms in Thailand and Vietnam

doi:10.1016/j.pld.2022.05.004

Abstract

Abstract: Tropical lotus (Nelumbo) is an important and unique ecological type of lotus germplasm. Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization. Using 42 EST-SSR (expressed sequence tag-simple sequence repeats) and 30 SRAP (sequence-related amplified polymorphism) markers, we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam. In total, 164 and 41 polymorphic bands were detected in 69 accessions by 36 EST-SSR and seven SRAP makers, respectively. Higher genetic diversity was revealed in Thai lotus than in Vietnamese lotus. A Neighbor-Joining tree of five main clusters was constructed using combined EST-SSR and SRAP markers. Cluster I included 17 accessions of Thai lotus; cluster II contained three Thai accessions and 11 accessions from southern Vietnam; and cluster III was constituted by 13 accessions of seed lotus. Consistent with the results from the Neighbor-Joining tree, the genetic structure analysis showed that the genetic background of most Thai and Vietnamese lotus was pure, as artificial breeding has been rare in both countries. Furthermore, these analyses indicate that Thai and Vietnamese lotus germplasms belong to two different gene pools or populations. Most lotus accessions are genetically related to geographical distribution patterns in Thailand or Vietnam. Our findings showed that the origin or genetic relationships of some unidentified lotus sources can be evaluated by comparing morphological characteristics and the data of molecular markers. In addition, these findings provide reliable information for the targeted conservation of tropical lotus and parent selection in breeding novel cultivars of lotus.

Key words: Aquatic plant, Asian lotus, EST-SSR, Nelumbo, Southeast Asia, Tropical lotus

Feng-Luan Liu, Ya-Lan Dai, Thi Nga Hoang, Vichai Puripunyavanich, Primlarp Wasuwat Chukiatman, Mi Qin, Yan-Rong Fu, Yu-Chu Chen, Dai-Ke Tian. Genetic diversity and inferred ancestry of Asian lotus (Nelumbo nucifera) germplasms in Thailand and Vietnam[J]. Plant Diversity, 2023, 45(01): 69-79.

References

[1] Chaveerach, A., Sudmoon, R., Tanee, T., et al., 2007. Genetic relationships in a population of Nelumbo nucifera Gaertn. (Nelumbonaceae). J. Biol. Sci. 7, 5-13. https://dx.doi.org/10.3923/jbs.2007.1388.1393
[2] Chen, G.L., Zhu, M.Z., Guo, M.Q., 2019. Research advances in traditional and modern use of Nelumbo nucifera:phytochemicals, health promoting activities and beyond. Crit. Rev. Food Sci. Nutr. 59, S189-S209. https://doi.org/10.1080/10408398.2018.1553846
[3] Chen, Y.Y., Zhou, R.C., Lin, X.D., et al., 2008. ISSR analysis of genetic diversity in sacred lotus cultivars. Aquat. Bot. 89, 311-316. https://doi.org/10.1016/j.aquabot.2008.03.006
[4] Doyle, J.J., Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15
[5] Earl, D.A., vonHoldt, B.M., 2011. STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359-361. https://doi.org/10.1007/s12686-011-9548-7
[6] Evanno, G., Regnaut, S., Goudet, J., 2005. Detecting the number of clusters of individuals using the software structure:a simulation study. Mol. Ecol. 14, 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
[7] Godwin, H., Willis, EH., 1964. The viability of lotus seeds (Nelumbium nucifera, Gaertn.). New Phytol. 63, 410-412. https://doi.org/10.1111/j.1469-8137.1964.tb07391.x
[8] Guo, H.B., 2009. Cultivation of lotus (Nelumbo nucifera Gaertn. ssp. nucifera) and its utilization in China. Genet. Resour. Crop Evol. 56, 323-330. https://doi.org/10.1007/s10722-008-9366-2
[9] Hall, T.F., Penfound, W.T., 1944. The biology of the American lotus, Nelumbo lutea (Willd.) Pers. Am. Midl. Nat. 31, 744-758. https://doi.org/10.2307/2421417
[10] Han, Y.C., Teng, C.Z., Wahiti, G.R., et al., 2007. Genetic variation and clonal diversity in populations of Nelumbo nucifera (Nelumbonaceae) in central China detected by ISSR markers. Aquat. Bot. 86, 69-75. https://doi.org/10.1016/j.aquabot.2006.09.007
[11] Han, Y.C., Teng, C.Z., Wahiti, G.R., et al., 2009. Mating system and genetic diversity in natural populations of Nelumbo nucifera (Nelumbonaceae) detected by ISSR markers. Plant Syst. Evol. 277, 13-20. https://doi.org/10.1007/s00606-008-0096-x
[12] Hu, J.H., Pan, L., Liu, H.G., et al., 2012. Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers. Mol. Biol. Rep. 39, 3637-3647. https://doi.org/10.1007/s11033-011-1138-y
[13] Islam, M.R., Zhang, Y., Li, Z.Z., et al., 2020. Genetic diversity, population structure, and historical gene flow of Nelumbo lutea in USA using microsatellite markers. Aquat. Bot. 160, 103162. https://doi.org/10.1016/j.aquabot.2019.103162
[14] Kalinowski, S.T., Taper, M.L., Marshall, T.C., 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099-1106. https://doi.org/10.1111/j.1365-294x.2007.03089.x
[15] Kim, H., Song, M.J., Kim, K.J., et al., 1998. Genetic variation analysis of Korean lotus (Nelumbo nucifera) using randomly amplified polymorphic DNA (RAPD) markers. Kor. J. Plant Tax. 28, 343-355
[16] Kubo, N., Hirai, M., Kaneko, A., et al., 2009. Classification and diversity of sacred and American Nelumbo species:the genetic relationships of flowering lotus cultivars in Japan using SSR markers. Plant Genet. Resour. 7, 260-270. https://doi.org/10.1017/S1479262109356580
[17] Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870-1874. https://doi.org/10.1093/molbev/msw054
[18] Li, C., Mo, H.B., Tian, D.K., et al., 2015. Genetic diversity and structure of American lotus (Nelumbo lutea Willd.) in North America revealed from microsatellite markers. Sci. Hortic. 189, 17-21. https://doi.org/10.1016/j.scienta.2015.03.026
[19] Li, G., Quiros, C.F., 2001. Sequence-related amplified polymorphism(SRAP), a new marker system based on a simple PCR reaction its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103, 455-461. https://doi.org/10.1007/s001220100570
[20] Lin, Z.Y., Zhang, C., Cao, D.D., et al., 2019. The latest studies on lotus (Nelumbo nucifera)-an emerging horticultural model plant. Int. J. Mol. Sci. 20, 3680. https://doi.org/10.3390/ijms20153680
[21] Liu, F.L., Qin, M., Liu, Q.Q., et al., 2020a. Detection of genetic variation between broad and narrow-tepalled American lotus (Nelumbo lutea Willd.) by EST-SSR markers. Acta Agric. Boreali-Occident. Sin. 29, 306-314 (in Chinese with English abstract). https://doi.org/10.7606/j.issn.1004-1389.2020.02.017
[22] Liu, F.L., Qin, M., Zhang, D.S., et al., 2018. Comparison and analysis of the difference of variegated-petalled cultivars of sacred lotus (Nelumbo nucifera) based on morphological traits and EST-SSR marker. Mol. Plant Breed. 16, 1607-1618 (in Chinese with English abstract). https://doi.org/10.13271/j.mpb.016.001607
[23] Liu, Z.W., Zhu, H.L., Zhou, J.H., et al., 2020b. Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history. Plant J. 104, 1673-1684. https://doi.org/10.1111/tpj.15029
[24] Li, Y., Svetlana, P., Yao, J.X., et al., 2014. A review on the taxonomic, evolutionary and phytogeographic studies of the lotus plant (Nelumbonaceae:Nelumbo). Acta Geol. Sin. (Engl Ed) 88, 1252-1261. https://doi.org/10.1111/1755-6724.12287
[25] Li, Z., Liu, X.Q., Gituru, R.W., et al., 2010. Genetic diversity and classi?cation of Nelumbo germplasm of different origins by RAPD and ISSR analysis. Sci. Hortic. 125, 724-732. https://doi.org/10.1016/j.scienta.2010.05.005
[26] Mekbib, Y., Huang, S.X., Ngarega, B.K., et al., 2020. The level of genetic diversity and differentiation of tropical lotus, Nelumbo nucifera Gaertn. (Nelumbonaceae) from Australia, India, and Thailand. Bot. Stud. 61, 15. https://doi.org/10.1186/s40529-020-00293-3
[27] Pan, L., Quan, Z.W., Hu, J.H., et al., 2011. Genetic diversity and differentiation of lotus (Nelumbo nucifera) accessions assessed by simple sequence repeats. Ann. Appl. Biol. 159, 428-441. https://doi.org/10.1111/j.1744-7348.2011.00509.x
[28] Pritchard, J.K., Stephens, M., Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945-959. https://doi.org/10.1093/genetics/155.2.945
[29] Roldan-Ruiz, I., Dendauw, J., Van-Bockstaele, E., et al., 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol. Breed. 6, 125-134. https://doi.org/10.1023/A:1009680614564
[30] Serrote, C.M.L., Reiniger, L.R.S., Silva, K.B., et al., 2020. Determining the polymorphism information content of a molecular marker. Gene 726, 144175. https://doi.org/10.1016/j.gene.2019.144175
[31] Sharma, B.R., Gautam, L.N.S, Adhikari, D., et al., 2016. A comprehensive review on chemical profiling of Nelumbo nucifera:potential for drug development. Phytother. Res. 31, 3-26. https://doi.org/10.1002/ptr.5732
[32] Shen-Miller, J., 2002. Sacred lotus, the long-living fruits of China Antique. Seed Sci. Res. 12, 131-143. https://doi.org/10.1079/SSR2002112
[33] Tian, D.K., Chen, Y.C., Hoang, T.N., 2019. Understanding current status of germplasm, research and industry of lotus (Nelumbo) in Vietnam through a survey. J. Changjiang Veg. 6, 40-45 (in Chinese with English abstract). https://doi.org/10.3865/j.issn.1001-3547.2019.06.014
[34] Tian, H.L., Xue, J.H., Wen, J., et al., 2008. Genetic diversity and relationships of lotus (Nelumbo) cultivars based on allozyme and ISSR markers. Sci. Hortic. 116, 421-429. https://doi.org/10.1016/j.scienta.2008.02.011
[35] Wang, Q.C., Zhang, X.Y., 2004. Lotus Flower Cultivars in China. Bao MZ trans. China Forestry Publishing House, Beijing, China. pp 59
[36] Xue, J.H., Zhuo, L.H., Zhou, S.L., 2006. Genetic diversity and geographic pattern of wild lotus (Nelumbo nucifera) in Heilongjiang Province. Chinese Sci. Bull. 51, 421-432. https://doi.org/10.1007/s11434-006-0421-0
[37] Xu, Y.X., Zhang, W.W., Mo, H.B., et al., 2015. Genetic diversity analysis of Nelumbo accessions based on EST-SSR markers. Plant Diver. Resour. 37, 595-604 (in Chinese with English abstract). https://doi.org/10.7677/ynzwyj201515004
[38] Yang, M., Fu, J., Xiang, Q.Y., et al., 2011. The core-collection construction of flower lotus based on AFLP molecular markers. Sci. Agric. Sin. 44, 3193-3205 (in Chinese with English abstract). https://doi.org/10.3864/j.issn.0578-1752.2011.15.015
[39] Yang, M., Liu, F., Han, Y.N., et al., 2013. Genetic diversity and structure in populations of Nelumbo from America, Thailand and China:Implications for conservation and breeding. Aquat. Bot. 107, 1-7. https://doi.org/10.1016/j.aquabot.2013.01.001
[40] Yeh, F.C., Yang, R.C., Boyle, T., 1999. Microsoft window-based freeware for population genetic analysis (Popgene Version 1.31). University of Alberta, Edmonton, Canada
[41] Zhang, W.W., Tian, D.K., Huang, X., et al., 2014. Characterization of flower-bud transcriptome and development of genic SSR markers of in Asian louts. PLoS ONE 9, e112223. https://doi.org/10.1371/journal.pone.0112223
[42] Zhang, X.Y., Chen, L.Q., Wang, Q.C., 2011. New Lotus Flower Cultivars in China. China Forestry Publishing House, Beijing, China. pp 36-41
[43] Zhang, X.Y., Wang, Q.C., 2004. Research of winter lotus varieties' selection, cultivation, and planting-Sanshui Lotus World as a base. Chinese Landsc. Archit. 10, 62-65 (in Chinese with English abstract). https://doi.org/10.3969/j.issn.1000-6664.2004.10.015
[44] Zhang, X.Y., Wang, Q.C., 2006. Preliminary study of the eco-types of genetic resources of tropical lotus. Chinese Landsc. Archit. 7, 82-85 (in Chinese with English abstract). https://doi.org/10.3969/j.issn.1000-6664.2006.07.018
[45] Zheng, X.W., Cheng, T., Yang, L.B., et al., 2019. Genetic diversity and DNA fingerprints of three important aquatic vegetables by EST-SSR markers. Sci. Rep. 9, 14074. https://doi.org/10.1038/s41598-019-50569-3