The level of genetic diversity and differentiation of tropical lotus, Nelumbo nucifera Gaertn. (Nelumbonaceae) from Australia, India, and Thailand

Abstract

Background: Nelumbo nucifera Gaertn., a perennial aquatic macrophyte species, has been cultivated in several Asian countries for its economic importance, and medicinal uses. Two distinct ecotypes of the species are recognized based on the geographical location where the genotypes are adapted, i.e., tropical lotus and temperate lotus. The genetic diversity levels and differentiation of the tropical lotus from poorly studied geographic regions still remain unclear. Here, the population genetic diversity and structure of 15 tropical lotus populations sampled from the previous understudied natural distribution ranges, including India, Thailand, and Australia, were assessed using nine polymorphic SSR markers. Results: The SSR markers used to genotype the 216 individuals yielded 65 alleles. The highest and lowest genetic diversity estimates were found in Thailand and Indian populations, respectively. STRU CTU RE analysis revealed three distinct genetic clusters, with relatively low admixtures, supported by PCoA cluster analysis. Low levels of gene flow (mean N m = 0.346) among the three genetic clusters signified the Mantel test for isolation by distance, revealing the existence of a positive correlation between the genetic and geographic distances (r = 0.448, P = 0.004). Besides, AMOVA analysis revealed a higher variation among populations (59.98%) of the three groups. Overall, the populations used in this study exposed a high level of genetic differentiation (F ST = 0.596). Conclusions: The nine polymorphic microsatellite markers used in our study sufficiently differentiated the fifteen tropical N. nucifera populations based on geography. These populations presented different genetic variability, thereby confirming that populations found in each country are unique. The low genetic diversity (H E = 0.245) could be explained by limited gene flow and clonal propagation. Conserving the available diversity using various conservation approaches is essential to enable the continued utilization of this economically important crop species. We, therefore, propose that complementary conservation approaches ought to be introduced to conserve tropical lotus, depending on the genetic variations and threat levels in populations.

Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus)

“…One novelty of our study on methylation patterns of rhizomes between lotus ecotypes is that we explored transcriptomic data to decipher the role of methylation in mediating adaptive phenotypic divergence through gene regulation. Lotus ecotypes evolve adaptively to different latitudinal environments, and the adaptive‐growth habits and phenotypic features are formed, where thick rhizome and short florescence were found in the high latitude populations (ecotypes) versus whip‐like rhizome and long florescence in the low latitude populations (ecotypes) (Gao et al, 2021; Huang et al, 2018; Li et al, 2020; Mekbib et al, 2020; Yang et al, ,2014, 2015; Zhang & Wang, 2006). Deciphering the molecular mechanisms, underlying their morphological and physiological differentiation based on omic data is important for understanding lotus adaptive evolution, as well as the stolon swelling process (Cao et al, 2019; Yang et al, 2015).…”

“…Temperate and tropical lotus are two ecotypes of N . nucifera that have been recognized in the 1980s (Zhang & Wang, 2006), and they differ in geographic distribution (high vs. low latitudes) (Li et al, 2020; Mekbib et al, 2020; Zhang & Wang, 2006), morphology (thick vs. thin rhizome) (Yang et al, 2015), flowering time (short vs. long florescence) (Yang et al, 2014), genetics (Huang et al, 2018; Li et al, 2010), gene expression patterns (Yang et al, 2015) and cis‐regulations (Gao et al, 2021)—the enlarged and nutritious rhizome of the temperate lotus (ecotype) is a specialized organ adapted to its winter dormancy, which is also harvested as a vegetable in many Asian countries. In contrast, the tropical lotus (ecotype) grown in South East Asia and North Oceania features a whip‐like and thin rhizome, which continues to grow (elongating/branching) for almost the entire year (Zhang & Wang, 2011).…”

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

“…Thus, the ever-flowering tropical lotus is a good material for creating new cultivars with longer flowering lifespan than the temperate lotus. However, little is known about germplasm diversity of either the subtropical or tropical lotus ( Chaveerach et al., 2007 ; Tian et al., 2019 ; Mekbib et al., 2020 ). Field surveys and assessment of genetic background are required to understand the diversity of tropical lotus in Southeast Asia (e.g., Thailand and Vietnam) and provide a reference for its conservation and utilization.…”

Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes

“…Sacred lotus ( Nelumbo nucifera ) or lotus, an aquatic vegetable and gardening flower widely distributed throughout Asia and Oceania with rich nutrients, including starch and anti-oxidants in rhizome [ [10] , [11] ]. Intriguingly, in development, lotus shows adaptive phenotypic divergence according to different latitudinal environments, especially in its rhizomes and flowering time, and therefore it was further defined as two ecotypes: temperate and tropical lotus [ [12] , [13] , [14] , [15] , [16] , [17] ]. The two ecotypes exhibit great distinction in growth behaviors and phenotypes for rhizomes.…”