S. spontaneum is a founding Saccharum species that contributes stress resistance to the genetic background of modern sugarcane cultivars. Here, we have assembled the autopolyploid S. spontaneum Np-X genome with ancestral form into 40 pseudo-chromosomes in 10 homologous groups, revealing the recent chromosome reduction and polyploidization that occurred in Saccharum. The paleo-duplicated chromosomal pairs exhibit functional redundancy in Saccharum and underwent ssion followed by fusion accompanied by centromeric spreading around 0.80 million years ago (Mya) before evolving into their current forms with basic chromosome numbers x = 9 and x = 8 in S. spontaneum, likely in a stepwise manner. WGDs occurred independently in Saccharum species around 1.5 Mya. Highly diverse chromatin structures exist among homologous chromosomes despite their high collinearity, and the re-structuring of NpChr5 and NpChr8 might have suppressed switching of chromatin structure from inactive to active. Resequencing of 116 sugarcane accessions elucidated that the S. spontaneum originated from North India and that the basic chromosome numbers x = 8, x = 9, and x = 10 originated independently, indicating that recent chromosome reduction rather than polyploidization has driven the adaptive evolution of Saccharum. Our study provides genomic resources and suggests new directions for accelerating sugarcane improvement and advances our knowledge of the evolution of auto-polyploids.
Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the chromosome numbers of sugarcane and its wild relatives, the chromosome composition and evolution among the species in the Saccharum complex have been elusive owing to the complex polyploidy and the large numbers of chromosomes of these species.Oligonucleotide-based chromosome painting has become a powerful tool of cytogenetic studies especially for plant species with large numbers of chromosomes. We developed oligobased chromosome painting probes for all 10 chromosomes in Saccharum officinarum (2n = 8x = 80). The 10 painting probes generated robust fluorescence in situ hybridization signals in all plant species within the Saccharum complex, including species in the genera Saccharum, Miscanthus, Narenga and Erianthus.We conducted comparative chromosome analysis using the same set of probes among species from four different genera within the Saccharum complex. Excitingly, we discovered several novel cytotypes and chromosome rearrangements in these species.We discovered that fusion from two different chromosomes is a common type of chromosome rearrangement associated with the species in the Saccharum complex. Such fusion events changed the basic chromosome number and resulted in distinct allopolyploids in the Saccharum complex.
Identification of hybrids derived from crosses between cultivated sugarcane (Saccharum spp.) and its wild relatives, including Erianthus fulvus Nees ex Hack., is important for the development of new sugarcane cultivars. The aim of the present study was to identify true hybrids in 73 F1 progeny obtained from five crosses with cultivated sugarcane as female parents and E. fulvus as male parents. Three random 10mers were used as primers in random amplified polymorphic DNA (RAPD) reactions. A total of 10 E. fulvus–specific RAPD markers were cloned and sequenced, of which four were successfully applied as sequence‐characterized amplified region (SCAR) markers. Based on the four RAPD marker sequences, five SCAR primer pairs were designed for polymerase chain reaction amplifications. Of the 73 progeny examined, 58 produced E. fulvus–specific SCAR bands, thus representing true hybrids of cultivated sugarcane and E. fulvus These results demonstrate the first use of SCAR marker analysis as an effective tool for the identification of intergeneric sugarcane hybrids.
Background Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane varieties. Results A hypoploid clone 12–23 (2n = 54) and hyperploid clone 15–28 (2n = 92) of S. spontaneum were analysed under cold stress from morphological, physiological, and transcriptomic perspectives. Compared with clone 15–28, clone 12–23 plants had lower plant height, leaf length, internode length, stem diameter, and leaf width; depressed stomata and prominent bristles and papillae; and thick leaves with higher bulliform cell groups and thicker adaxial epidermis. Compared with clone 15–28, clone 12–23 showed significantly lower electrical conductivity, significantly higher water content, soluble protein content, and superoxide dismutase activity, and significantly higher soluble sugar content and peroxidase activity. Under cold stress, the number of upregulated genes and downregulated genes of clone 12–23 was higher than clone 15–28, and many stress response genes and pathways were affected and enriched to varying degrees, particularly sugar and starch metabolic pathways and plant hormone signalling pathways. Under cold stress, the activity of 6-phosphate glucose trehalose synthase, trehalose phosphate phosphatase, and brassinosteroid-signalling kinase and the content of trehalose and brassinosteroids of clone 12–23 increased. Conclusions Compared with hyperploid clone 15–28, hypoploid clone 12–23 maintained a more robust osmotic adjustment system through sugar accumulation and hormonal regulation, which resulted in stronger cold tolerance.
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