Erianthus germplasm collection in Thailand: genetic structure and phylogenetic aspects of tetraploid and hexaploid accessions

Abstract

Background: The genus Erianthus, which belongs to the "Saccharum complex", includes C₄ warm-season grasses. Erianthus species are widely distributed throughout Southeast Asia, East Asia and South Asia. Erianthus arundinaceus (Retz.) Jeswiet is highly adaptable to the environment, has a high percentage of dry matter, and is highly productive. Recently, this species has attracted attention as a novel bioenergy crop and as a breeding material for sugarcane improvement. Such interest in E. arundinaceus has accelerated the collection and conservation of its genetic resources, mainly in Asian countries, and also evaluation of morphological, agricultural, and cytogenetic features in germplasm collections. In Thailand, genetic resources of E. arundinaceus have been collected over the past 20 years and their phenotypic traits have been evaluated. However, the genetic differences and relatedness of the germplasms are not fully understood.

Results: A set of 41 primer pairs for nuclear simple sequence repeats (SSRs) developed from E. arundinaceus were used to assess the genetic diversity of 121 Erianthus germplasms collected in Thailand; of these primer pairs, 28 detected a total of 316 alleles. A Bayesian clustering approach with these alleles classified the accessions into four main groups, generally corresponding to the previous classification based on phenotypic analysis. The results of principal coordinate analysis and phylogenetic analysis of the 121 accessions on the basis of the SSR markers showed the same trend as Bayesian clustering, whereas sequence variations of three non-coding regions of chloroplast DNA revealed eight haplotypes among the accessions. The analysis of genetic structure and phylogenetic relationships, however, found some accessions whose classification contradicted the results of previous phenotypic classification.

Conclusions: The molecular approach used in this study characterized the genetic diversity and relatedness of Erianthus germplasms collected across Thailand. This knowledge would allow efficient maintenance and conservation of the genetic resources of this grass and would help to use Erianthus species as breeding materials for development of novel bioenergy crops and sugarcane improvement.

Keywords: Bioenergy; Chloroplast DNA; Erianthus arundinaceus; Genetic diversity; Germplasm; SSR; Saccharum.

Fig. 1

Genetic assignment of 121 Erianthus accessions using data from genotyping with 28 SSR primer pairs. a Estimation of the most likely number of groups using structure analysis: the mean values of log-likelihood for 10 independent runs for each value of K (left) and ΔK statistics for different K values based on the second-order rate of change in the log-likelihood function (right). b Bar plots of ancestry proportions for the ΔK values at K = 2, K = 3, and K = 4. Accessions identified as the admixture group are marked with asterisks. Ea-TI: E. arundinaceus Type I; Ea-TII: E. arundinaceus Type II; Ea-TIII: E. arundinaceus Type III; Ep: E. procerus

Fig. 2

Principal coordinate analysis of 121 Erianthus accessions based on the Bruvo distance between individuals calculated in Polysat software. Colors indicate four groups corresponding to those in Fig. 1 at K = 4. The admixture group is indicated by grey circles. Map numbers of seven accessions assigned to the admixture group are shown next to the circles. Two accessions with ambiguous phenotypic clustering are marked with asterisks next to the map numbers. Dashed circles indicate grouping (G1–G4). Numbers on each axis indicate the proportion of variance explained by each principal coordinate

Fig. 3

Unrooted neighbor-joining tree of 121 Erianthus accessions based on Nei’s minimum distance. The color of each accession corresponds to that in Fig. 1 at K = 4. Two accessions with ambiguous phenotypic clustering are marked with asterisks

Fig. 4

Correlations between genetic diversity parameters (A_R, H_e, and F_i) and latitude. The analysis was performed for hexaploid E. arundinaceus (orange), tetraploid E. arundinaceus (blue), and E. procerus (yellow). Latitudes were rounded to integers. Significant correlations are indicated (*p < 0.01 and ***p < 0.0001)

Fig. 5

Median-joining network of eight haplotypes (H1–H8) based on sequence variations in three non-coding regions of E. arundinaceus cpDNA. a Locations of the three regions (rps16–trnQ, atpA–rps14, and rpl16–rps3). The position (bp) of each region in full-length cpDNA of E. arundinaceus accession ‘JW630’ is given in parentheses. LSC, large single-copy region; IR, inverted repeat; SSC, small single-copy region. b Circle sizes are proportional to haplotype frequency, and their colors correspond to those in Fig. 1 at K = 4. Positions of mutational steps in concatenated sequences between haplotypes are shown next to the branches. Positions of mutational steps in each cpDNA region are shown in parentheses. Haplotype of each accession is indicated in Table S2