Harnessing genomic and molecular biology resources for genetic improvement of lotus: current achievements and future directions

Heng Sun , Jia Xin , Heyun Song , Lin Chen , Dong Yang , Hui Yang , Xianbao Deng , Juan Liu , Rui Cui , Yanyan Su , Gangqiang Dong , Mei Yang

Horticulture Advances ›› 2025, Vol. 3 ›› Issue (1) : 1

PDF
Horticulture Advances ›› 2025, Vol. 3 ›› Issue (1) : 1 DOI: 10.1007/s44281-024-00055-2
Review

Harnessing genomic and molecular biology resources for genetic improvement of lotus: current achievements and future directions

Author information +
History +
PDF

Abstract

Lotus, an economically significant aquatic crop within the genus Nelumbo (family Nelumbonaceae), includes the two extant species Nelumbo nucifera and Nelumbo lutea. Renowned for its ornamental, culinary, and medicinal value, lotus has seen notable advancements in genomics and molecular biology, particularly in reference genome sequencing and assembly, bioactive compound biosynthetic pathways, and molecular mechanisms underlying key traits. Critical genes linked to horticultural characteristics, edible quality, medicinal properties, and stress resilience have been identified and functionally validated. This review presents a thorough overview of recent molecular developments in lotus research, emphasizing genome sequencing and functional gene analysis. Additionally, it addresses prevailing challenges and future directions, providing valuable insights for foundational research and genetic enhancement of lotus.

Keywords

Nelumbo / Lotus / Genome / Molecular biology / Molecular mechanism / Genetic improvement / Biological Sciences / Genetics

Cite this article

Download citation ▾
Heng Sun, Jia Xin, Heyun Song, Lin Chen, Dong Yang, Hui Yang, Xianbao Deng, Juan Liu, Rui Cui, Yanyan Su, Gangqiang Dong, Mei Yang. Harnessing genomic and molecular biology resources for genetic improvement of lotus: current achievements and future directions. Horticulture Advances, 2025, 3(1): 1 DOI:10.1007/s44281-024-00055-2

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

BayerPE, GoliczAA, SchebenA, BatleyJ, EdwardsD. Plant pan-genomes are the new reference. Nat Plants, 2020, 6: 914-920.

[2]

BaysoyA, BaiZ, SatijaR, FanR. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol, 2023, 24: 695-713.

[3]

Bishayee A, Patel PA, Sharma P, Thoutireddy S, Das N. Lotus (Nelumbo nucifera Gaertn.) and its bioactive phytocompounds: a tribute to cancer prevention and intervention. Cancers (Basel). 2022;14:529. https://doi.org/10.3390/cancers14030529.

[4]

CaoD, LinZ, HuangL, DamarisRN, LiM, YangP. A CONSTANS-LIKE gene of Nelumbo nucifera could promote potato tuberization. Planta, 2021, 253: 65.

[5]

CaoJ, JinQ, KuangJ, WangY, XuY. Regulation of flowering timing by ABA-NnSnRK1 signaling pathway in lotus. Int J Mol Sci, 2021, 22: 3932.

[6]

ChenHH, ChuP, ZhouYL, DingY, LiY, LiuJ, et al. . Ectopic expression of NnPER1, a Nelumbo nucifera 1-cysteine peroxiredoxin antioxidant, enhances seed longevity and stress tolerance in Arabidopsis. Plant J, 2016, 88: 608-619.

[7]

ChenJ, WangZ, TanK, HuangW, ShiJ, LiT, et al. . A complete telomere-to-telomere assembly of the maize genome. Nat Genet, 2023, 55: 1221-1231.

[8]

ChenL, SongH, XinJ, DongG, XuF, SuY, et al. . Comprehensive genome-wide identification and functional characterization of MAPK cascade gene families in Nelumbo. Int J Biol Macromol, 2023, 233. 123543

[9]

ChenL, XinJ, SongH, XuF, YangH, SunH, et al. . Genome-wide study and functional characterization elucidates the potential association of late embryogenesis abundant (LEA) genes with lotus seed development. Int J Biol Macromol, 2023, 226: 1-13.

[10]

ChenL, XinJ, SongH, ChengW, YangM, YangD, et al. . Evolution and seed development responses of Nelumbo SWEET genes. Sci Hortic, 2024, 333. 113281

[11]

ChenW, WangX, SunJ, WangX, ZhuZ, AyhanDH, et al. . Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis. Nat Commun, 2024, 15: 4295.

[12]

Cheng L, Liu X, Yin J, Yang J, Li Y, Hui L, et al. Activity and expression of ADP-glucose pyrophosphorylase during rhizome formation in lotus (Nelumbo nucifera Gaertn.). Bot Stud. 2016;57:26. https://doi.org/10.1186/s40529-016-0140-z.

[13]

ChuP, ChenH, ZhouY, LiY, DingY, JiangL, et al. . Proteomic and functional analyses of Nelumbo nucifera annexins involved in seed thermotolerance and germination vigor. Planta, 2012, 235: 1271-1288.

[14]

DengJ, LiM, HuangL, YangM, YangP. Genome-wide analysis of the R2R3 MYB subfamily genes in lotus (Nelumbo nucifera). Plant Mol Biol Rep, 2016, 34: 1016-1026.

[15]

DengX, ZhuL, FangT, VimolmangkangS, YangD, OgutuC, et al. . Analysis of isoquinoline alkaloid composition and wound-induced variation in Nelumbo using HPLC-MS/MS. J Agric Food Chem, 2016, 64: 1130-1136.

[16]

DengX, ZhaoL, FangT, XiongY, OgutuC, YangD, et al. . Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus. Hortic Res, 2018, 5: 29.

[17]

DengJ, LiJ, SuM, LinZ, ChenL, YangP. A bHLH gene NnTT8 of Nelumbo nucifera regulates anthocyanin biosynthesis. Plant Physiol Biochem, 2021, 158: 518-523.

[18]

Deng X, Yang D, Sun H, Liu J, Song H, Xiong Y, et al. Time-course analysis and transcriptomic identification of key response strategies to complete submergence in Nelumbo nucifera. Hortic Res. 2022;9:uhac001. https://doi.org/10.1093/hr/uhac001.

[19]

DongC, ZhengX, DiaoY, WangY, ZhouM, HuZ. Molecular cloning and expression analysis of a catalase gene (NnCAT) from Nelumbo nucifera. Appl Biochem Biotechnol, 2015, 177: 1216-1228.

[20]

Feng CY, Li SS, Taguchi G, Wu Q, Yin DD, Gu ZY, et al. Enzymatic basis for stepwise C-glycosylation in the formation of flavonoid di-C-glycosides in sacred lotus (Nelumbo nucifera Gaertn.). Plant J. 2021;106:351–65. https://doi.org/10.1111/tpj.15168.

[21]

GaoZ, LiH, YangX, YangP, ChenJ, ShiT. Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera). Plant Mol Biol, 2021, 106: 207-220.

[22]

GaoZ, LiangY, WangY, XiaoY, ChenJ, YangX, et al. . Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. Front Plant Sci, 2022, 13. 973347

[23]

GaoZ, YangX, ChenJ, RausherMD, ShiT. Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation. Plant Physiol, 2023, 19: 1662-1683.

[24]

GuiS, PengJ, WangX, WuZ, CaoR, SalseJ, et al. . Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements. Plant J, 2018, 94: 721-734.

[25]

HanX, ZhangY, ZhangQ, MaN, LiuX, TaoW, et al. . Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol Plant, 2023, 16: 452-470.

[26]

HaoC, YuY, LiuY, LiuA, ChenS. The CYP80A and CYP80G are involved in the biosynthesis of benzylisoquinoline alkaloids in the sacred lotus (Nelumbo nucifera). Int J Mol Sci, 2024, 25: 702.

[27]

HuangW, KhaldunABM, LvH, DuL, ZhangC, WangY. Isolation and functional characterization of a R2R3-MYB regulator of the anthocyanin biosynthetic pathway from Epimedium sagittatum. Plant Cell Rep, 2016, 35: 883-894.

[28]

Huang L, Li M, Cao D, Yang P. Genetic dissection of rhizome yield-related traits in Nelumbo nucifera through genetic linkage map construction and QTL mapping. Plant Physiol Biochem. 2021;160:155–65. https://doi.org/10.1016/j.plaphy.2021.01.020.

[29]

KashiwadaY, AoshimaA, IkeshiroY, ChenYP, FurukawaH, ItoigawaM, et al. . Anti-HIV benzylisoquinoline alkaloids and flavonoids from the leaves of Nelumbo nucifera, and structure-activity correlations with related alkaloids. Bioorg Med Chem, 2005, 13: 443-448.

[30]

KoesR, VerweijW, QuattrocchioF. Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci, 2005, 10: 236-242.

[31]

KuboN, HiraiM, KanekoA, TanakaD, KasumiK. Development and characterization of simple sequence repeat (SSR) markers in the water lotus (Nelumbo nucifera). Aquat Bot, 2009, 90: 191-194.

[32]

LiY, ZhuFL, ZhengXW, HuML, DongC, DiaoY, et al. . Comparative population genomics reveals genetic divergence and selection in lotus. Nelumbo Nucifera BMC Genomics, 2020, 21: 146.

[33]

LiJ, ChenL, SongH, XinJ, LiC, YangM, et al. . Systematic analysis of the expansin gene family in Nelumbo reveals candidate seed development responsive members in lotus (Nelumbo nucifera). Sci Hortic, 2024, 324. 112578

[34]

Li X, Zhang D, Xu J, Jiang J, Jiang H. The protective effect of cold acclimation on the low temperature stress of the lotus (Nelumbo nucifera). Hortic Sci. 2022;49:29–37. https://doi.org/10.17221/62/2020-hortsci.

[35]

LinZ, ZhangC, CaoD, DamarisRN, YangP. The latest studies on lotus (Nelumbo nucifera)-an emerging horticultural model plant. Int J Mol Sci, 2019, 20: 3680.

[36]

LinZ, CaoD, DamarisRN, YangP. Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development. BMC Plant Biol, 2020, 20: 497.

[37]

LinZ, CaoD, DamarisRN, YangP. Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera). PeerJ, 2021, 9. e12322

[38]

LiuZ, ZhuH, ZhouJ, JiangS, WangY, KuangJ, et al. . Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history. Plant J, 2020, 104: 1673-1684.

[39]

LiuY, SongH, ZhangM, YangD, DengX, SunH, et al. . Identification of QTLs and a putative candidate gene involved in rhizome enlargement of Asian lotus (Nelumbo nucifera). Plant Mol Biol, 2022, 110: 23-36.

[40]

LiuJ, WangY, DengX, ZhangM, SunH, GaoL, et al. . Transcription factor NnMYB5 controls petal color by regulating GLUTATHIONE S-TRANSFERASE2 in Nelumbo nucifera. Plant Physiol, 2023, 193: 1213-1226.

[41]

MatthewsPGD, SeymourRS. Stomata actively regulate internal aeration of the sacred lotus Nelumbo nucifera. Plant Cell Environ, 2014, 37: 402-413.

[42]

Menéndez-PerdomoIM, FacchiniPJ. Benzylisoquinoline alkaloids biosynthesis in sacred lotus. Molecules, 2018, 23: 2899.

[43]

Menéndez-PerdomoIM, FacchiniPJ. Elucidation of the (R)-enantiospecific benzylisoquinoline alkaloid biosynthetic pathways in sacred lotus (Nelumbo nucifera). Sci Rep, 2023, 13: 2955.

[44]

Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 2013;14:R41. https://doi.org/10.1186/gb-2013-14-5-r41.

[45]

MuhlemannJK, KlempienA, DudarevaN. Floral volatiles: from biosynthesis to function. Plant Cell Environ, 2014, 37: 1936-1949.

[46]

OgeL, BourdaisG, BoveJ, ColletB, GodinB, GranierF, et al. . Protein repair L-isoaspartyl methyltransferase 1 is involved in both seed longevity and germination vigor in Arabidopsis. Plant Cell, 2008, 20: 3022-3037.

[47]

Qi H, Yu F, Deng J, Zhang L, Yang P. The high-quality genome of lotus reveals tandem duplicate genes involved in stress response and secondary metabolites biosynthesis. Hortic Res. 2023;10:uhad040. https://doi.org/10.1093/hr/uhad040.

[48]

ShangL, HeW, WangT, YangY, XuQ, ZhaoX, et al. . A complete assembly of the rice Nipponbare reference genome. Mol Plant, 2023, 16: 1232-1236.

[49]

Shen-MillerJ, MudgettMB, SchopfJW, ClarkeS, BergerR. Exceptional seed longevity and robust growth: ancient sacred lotus from China. Am J Bot, 1995, 82: 1367-1380.

[50]

Shen-MillerJ, SchopfJW, HarbottleG, CaoRJ, OuyangS, ZhouKS, et al. . Long-living lotus: germination and soil gamma-irradiation of centuries-old fruits, and cultivation, growth, and phenotypic abnormalities of offspring. Am J Bot, 2002, 89: 236-247.

[51]

Shen-MillerJ, LindnerP, XieY, VillaS, WoodingK, ClarkeSG, et al. . Thermal-stable proteins of fruit of long-living sacred lotus Nelumbo nucifera Gaertn var. China Antique Trop Plant Biol, 2013, 6: 69-84.

[52]

ShiT, RahmaniRS, GuggerPF, WangM, LiH, ZhangY, et al. . Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. Mol Biol Evol, 2020, 37: 2394-2413.

[53]

ShiJ, TianZ, LaiJ, HuangX. Plant pan-genomics and its applications. Mol Plant, 2023, 16: 168-186.

[54]

SongH, SunH, XinJ, YangD, DengX, LiuJ, et al. . FLOWERING LOCUS T genes control floral induction in lotus. Plant Physiol Biochem, 2024, 207. 108339

[55]

SongH, SunH, DongG, YangH, XinJ, YangD, et al. . NnSBE1 encodes a starch branching enzyme involved in starch biosynthesis in lotus seeds. Int J Biol Macromol, 2024, 279. 135104

[56]

SongH, XinJ, YangD, DongG, DengX, LiuJ, et al. . NnSUS1 encodes a sucrose synthase involved in sugar accumulation in lotus seed cotyledons. Plant Physiol Biochem, 2024, 210. 108591

[57]

SunH, LiuY, MaJ, WangY, SongH, LiJ, et al. . Transcriptome analysis provides strategies for postharvest lotus seeds preservation. Postharvest Biol Tec, 2021, 179. 111583

[58]

SunH, LiJ, SongH, YangD, DengX, LiuJ, et al. . Comprehensive analysis of AGPase genes uncovers their potential roles in starch biosynthesis in lotus seed. BMC Plant Biol, 2020, 20: 457.

[59]

Sun H, Song H, Deng X, Liu J, Yang D, Zhang M, et al. Transcriptome-wide characterization of alkaloids and chlorophyll biosynthesis in lotus plumule. Front Plant Sci. 2022;13:885503. https://doi.org/10.3389/fpls.2022.885503.

[60]

Sun SS, Gugger PF, Wang QF, Chen JM. Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.). Peer J. 2016;4:e2369. https://doi.org/10.7717/peerj.2369.

[61]

WangL. A critical review on robust self-cleaning properties of lotus leaf. Soft Matter, 2023, 19: 1058-1075.

[62]

WangY, FanG, LiuY, SunF, ShiC, LiuX, et al. . The sacred lotus genome provides insights into the evolution of flowering plants. Plant J, 2013, 76: 557-567.

[63]

WangL, FuJ, LiM, FragnerL, WeckwerthW, YangP. Metabolomic and proteomic profiles reveal the dynamics of primary metabolism during seed development of lotus (Nelumbo nucifera). Front Plant Sci, 2016, 7: 750.

[64]

WangB, JinQ, ZhangX, MattsonNS, RenH, CaoJ, et al. . Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses. Sci Rep, 2018, 8: 9187.

[65]

Wang J, Liao X, Gu C, Xiang K, Wang J, Li S, et al. The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics. Ornamental Plant Research. 2022;2:2. https://doi.org/10.48130/OPR-2022-0002.

[66]

Wei X, Zhang M, Yang M, Ogutu C, Li J, Deng X. Lotus (Nelumbo nucifera) benzylisoquinoline alkaloids: advances in chemical profiling, extraction methods, pharmacological activities, and biosynthetic elucidation. Veg Res. 2024;4:e005. https://doi.org/10.48130/vegres-0024-0004.

[67]

YangM, ZhuL, PanC, XuL, LiuY. Comparative transcriptomic analysis of the regulation of flowering in temperate and tropical lotus (Nelumbo nucifera) by RNA-Seq. Ann Appl Biol, 2014, 165: 73-95.

[68]

YangM, ZhuL, PanC, XuL, LiuY, KeW, et al. . Transcriptomic analysis of the regulation of rhizome formation in temperate and tropical lotus (Nelumbo nucifera). Sci Rep, 2015, 5: 13059.

[69]

Yang M, Zhu L, Xu L, Liu Y. Population structure and association mapping of flower-related traits in lotus (Nelumbo Adans.) accessions. Scientia Horticulturae. 2014;175:214–22. https://doi.org/10.1016/j.scienta.2014.06.017.

[70]

Yu Y, Liu Y, Dong G, Jiang J, Leng L, Liu X, et al. Functional characterization and key residues engineering of a regiopromiscuity O-methyltransferase involved in benzylisoquinoline alkaloid biosynthesis in Nelumbo nucifera. Hortic Res. 2023;10:uhac276. https://doi.org/10.1093/hr/uhac276.

[71]

ZhangD, LiuT, ShengJ, LvS, RenL. TMT-Based quantitative proteomic analysis reveals the physiological regulatory networks of embryo dehydration protection in lotus (Nelumbo nucifera). Front Plant Sci, 2021, 12. 792057

[72]

ZhangL, ZhangF, LiuF, ShenJ, WangJ, JiangM, et al. . The lotus NnFTIP1 and NnFT1 regulate flowering time in Arabidopsis. Plant Sci, 2021, 302. 110677

[73]

ZhaoS, ZhangY, TanM, ZhangC, JiaoJ, WuP, et al. . NnNF-YB1 induced by the potassium fertilizer enhances starch synthesis in rhizomes of Nelumbo nucifera. Ind Crops Prod, 2023, 203. 117197

[74]

ZhengP, SunH, LiuJ, LinJ, ZhangX, QinY, et al. . Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication. Plant J, 2022, 110: 1498-1515.

[75]

Zheng X, Wang T, Cheng T, Zhao L, Zheng X, Zhu F, et al. Genomic variation reveals demographic history and biological adaptation of the ancient relictual, lotus (Nelumbo Adans). Hortic Res. 2022;9:uhac029. https://doi.org/10.1093/hr/uhac029.

[76]

ZhouML, MaJT, ZhaoYM, WeiYH, TangYX, WuYM. Improvement of drought and salt tolerance in Arabidopsis and lotus corniculatus by overexpression of a novel DREB transcription factor from Populus euphratica. Gene, 2012, 506: 10-17.

[77]

ZhouY, ChuP, ChenH, LiY, LiuJ, DingY, et al. . Overexpression of Nelumbo nucifera metallothioneins 2a and 3 enhances seed germination vigor in Arabidopsis. Planta, 2012, 235: 523-537.

[78]

Zhou Y, Chen H, Chu P, Li Y, Tan B, Ding Y, et al. NnHSP17.5, a cytosolic class II small heat shock protein gene from Nelumbo nucifera, contributes to seed germination vigor and seedling thermotolerance in transgenic Arabidopsis. Plant Cell Rep. 2012c;31:379–89. https://doi.org/10.1007/s00299-011-1173-0.

[79]

ZhuF. Structures, properties, and applications of lotus starches. Food Hydrocolloids, 2017, 63: 332-348.

[80]

ZhuHH, YangJX, XiaoCH, MaoTY, ZhangJ, ZhangHY. Differences in flavonoid pathway metabolites and transcripts affect yellow petal colouration in the aquatic plant Nelumbo nucifera. BMC Plant Biol, 2019, 19: 277.

[81]

ZhuF, SunH, WangJ, ZhengX, WangT, DiaoY, et al. . Differential expression involved in starch synthesis pathway genes reveal various starch characteristics of seed and rhizome in lotus (Nelumbo Nucifera). J Food Sci, 2022, 87: 4250-4263.

[82]

Zhu F, Sun H, Diao Y, Zheng X, Xie K, Hu Z. Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.). Peer J. 2019;7:e7750. https://doi.org/10.7717/peerj.7750.

Funding

Biological Resources Programme, Chinese Academy of Sciences(KFJ-BRP-007-009)

Hubei Provincial Natural Science Foundation of China(JCZRJQ202400159)

RIGHTS & PERMISSIONS

The Author(s)

AI Summary AI Mindmap
PDF

207

Accesses

0

Citation

Detail

Sections
Recommended

AI思维导图

/