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We recently determined the complete sequence of the sugarcane chloroplast genome. Here, we have used the information for a comprehensive phylogenetic analysis of the genus Saccharum, using all six species (13 accessions). The polymorphisms between sugarcane and maize in 26 chloroplast genome regions were used for the analysis. In 18 of the 26 regions (a total of 5,381 bp), we found 41 mutations involving 17 substitutions, three inversions, six insertion/deletion mutations, and 15 simple sequence repeat length polymorphisms. Based on these results, we calculated a phylogenetic tree of the genus Saccharum, in which all six species are clearly separated. By the analysis, (1) S. sinense and S. barberi, which have identical sequences, belong to the same clade, whereas the other four species, S. officinarum, S. robustum, S. edule, and S. spontaneum, form an independent clade; (2) S. spontaneum has a paraphyletic relationship with the other five species; and (3) no or very low intraspecific variation was observed in S. officinarum, S. robustum, S. sinense, S. barberi, and S. edule, whereas higher intraspecific variation was observed in S. spontaneum. Based on the number of nucleotide substitutions, the divergence time between S. officinarum and S. spontaneum, and between S. officinarum and maize were calculated to be about 730-780 thousand years ago and about 5.9 million years ago, respectively. These results suggest that the cytoplasm of Saccharum species are very closely related.

Erianthus, one of the genus in Saccharum complex, is important genetic resources for sugarcane improvement. The morphology and flowering phenology of 108 accessions belonging to Erianthus procerus and three types of E. arundinaceus collected from throughout Thailand were compared. PCA analysis based on 22 characteristics clearly supported the separation of Type II and Type III of E. arundinaceus from E. procerus and Type I of E. arundinaceus according to their morphological characteristics, particularly their bud size, and the development of root primordia, which greatly affected axis I of the PCA analysis. E. procerus and Type I showed overlapping in many of their characteristics including their flowering periods. Flower characteristics such as rachis joint length, which were used for previous taxonomic classifications, were not available for the classification of the Thai samples because of the wide variation and overlapping among them. Most of these phenotype similarities and differences are considered to have developed convergently as a result of niche adaptation. Type II and III inhabit riverbanks and streambeds where floods occur frequently, while E. procerus and Type I mainly grow in non-flooding areas such as mountainous grassland, the edge of forests, and beside fields. All Thai Erianthus show unique geographic distributions in Thailand. In particular, the biogeographic boundary between Type II and Type III appeared to be located at the Isthmus of Kra. Although some types showed morphological similarities, reproductive isolation among the four groups seemed to be maintained by differentiation in geographic distribution, habitat preference, and flowering timing.

In sugarcane (Saccharum spp. hybrid) breeding, introgression of useful genes via intergeneric hybridization is a powerful strategy for improving the crop productivity. Erianthus arundinaceus shows great potential in terms of useful traits; however, little is known about the cytogenetic and agronomic characteristics of intergeneric hybrids between these two species. Here, we examine the cytogenetic and agronomic characteristics, and relationships between the two in intergeneric F1 hybrids between modern sugarcane cultivar and E. arundinaceus identified by amplification of 5S rDNA markers and morphological characteristics. The nuclear DNA content of the hybrids varied from 6.07 to 8.94 pg/2C, with intra-clonal variation in DNA content and 5S rDNA sites. Genomic in situ hybridization revealed 53 to 82 chromosomes in the hybrids, with 53 to 56 derived from sugarcane and 1 to 29 from E. arundinaceus. There were significant positive correlations between the number of E. arundinaceus chromosomes and dry matter yield, millable stalk weight, single stalk weight, and stalk diameter, but not sucrose content, reducing sugar content, sucrose/reducing sugar ratio or fiber content. This detailed information on intergeneric F1 hybrids between modern sugarcane cultivar and E. arundinaceus will contribute to effective utilization of E. arundinaceus in sugarcane breeding.

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