Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences

Abstract

Saccharum spontaneum L. is a crucial wild parent of modern sugarcane cultivars whose ploidy clones have been utilized successfully in improving the stress resistance and yield related traits of sugarcane cultivars. To establish knowledge regarding the genetic variances and evolutional relationships of ploidy clones of Saccharum spontaneum collected in China, the rDNA-ITS sequences of 62 ploidy clones including octaploid clones (2n = 64), nonaploid clones (2n = 72), decaploid clones (2n = 80), and dodecaploid clones (2n = 96), were obtained and analyzed. The rDNA-ITS sequences of four species from Saccharum and Sorghum bicolor selected as controls. The results showed that decaploid clones (2n = 80) possess the most abundant variances with 58 variable sites and 20 parsim-informative sites in ITS sequences, which were then followed by octaploid clones with 43 variable sites and 17 parsim-informative sites. In haplotype diversity, all four population exhibited high diversity, especially nonaploid and decaploid populations. By comparing the genetic distances among four ploidy populations, the dodecaploid population exhibited the closest relationship with the nonaploid population, and then the relationship strength decreased successively for the decaploid population and then for the octaploid population. Population differentiation analysis showed that the phenomena of population differentiation were not found among different ploidy populations, and low coefficient of gene differentiation(Gst) and high gene flow(Nm) occur among these populations possessing close genetic relationship. These results mentioned above will contribute to the understanding of the evolution of different ploidy populations of Saccharum spontaneum and provide vital knowledge for their utilization in sugarcane breeding and innovation.

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers

“…Due to its large ecogeographical distribution, S . spontaneum is considered the most diverse species in the Saccharum genus [ 67 , 68 ]. This species presented the highest number of alleles across the 12 microsatellite loci.…”

A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum

“…Liu et al analyzed differences among nrDNA-ITS sequences from 62 different multiple S . spontaneum materials and showed that 4 species had high variation, especially the nonuploid and decaploid population [ 10 ].…”

“…Based on previous studies on nrDNA-ITS in sugarcane germplasms, the tetra-primer ARMS PCR technique can be used to analyze genetic diversity and phylogenetic relationships in interspecific and intergenus samples [ 9 , 10 , 19 ]. However, studies exploring the identification and use of SNPs as molecular markers in Saccharum breeding have not been performed.…”

Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species

“…officinarum were clustered together based on 45S rDNA-ITS haplotype data in S . spontaneum [ 3 ]. Pan et al found that the two S .…”

“…However, the taxonomy within the genus Saccharum remains controversial. Over the past two decades, molecular cytogenetics and markers have contributed to inference of the phylogenetic relationship of the species within the genus Saccharum [ 3 – 7 ], and therefore the classification of the species within this genus has gradually been elucidated. The currently accepted taxonomy for the genus Saccharum comprises six species, including Saccharum officinarum , Saccharum robustum , Saccharum spontaneum , Saccharum sinense , Saccharum barberi , and Saccharum edule [ 8 ].…”