Abstract
Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.
Highlights
Cultivated sugarcanes (Saccharum spp., Poaceae) are unusual among leading crops in that they are polyploid interspecific hybrids, with singularly complex genomes
The identification of 80% of disease resistance genes on rearranged chromosomes suggests that reduction of basic chromosome number might have contributed to the retention of disease-resistance genes
It is likely an unintended consequence that these rearranged chromosome arms are enriched with NBSencoding genes, resulting in more disease-resistance genes being retained in S. spontaneum, which leads to higher resistance to disease and abiotic stresses in S. spontaneum than in other Saccharum species and makes S. spontaneum the source of disease and stress tolerance in sugarcane breeding program
Summary
Cultivated sugarcanes (Saccharum spp., Poaceae) are unusual among leading crops in that they are polyploid interspecific hybrids, with singularly complex genomes. While the high sugar content of modern sugarcane cultivars derives from cultivated ‘noble’ forms of Saccharum officinarum, their hardiness, disease resistance and ratooning capacity were obtained during ‘nobilization’, backcrossing into S. officinarum selected traits from a sugar-poor relative, Saccharum spontaneum. Dutch breeders in Java made interspecific crosses between S. officinarum and a wild relative, S. spontaneum, to obtain disease resistance and stress tolerance traits of S. spontaneum while backcrossing to S. officinarum to recover high biomass and high sugar content[4]. Modern sugarcane cultivars are interspecific hybrids with approximately 80% chromosomes from S. officinarum, 10–15% chromosomes from S. spontaneum, and 5–10% recombinant chromosomes[5]. This study illuminates the hereditary blueprint and evolutionary history of one of our most important, and most complex, crop genomes
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