A sweet story: modern sugarcanes originate from three ancestral genomes

Sugarcane is a tropical crop, contributing 60-80% of raw sucrose produced worldwide. Two wild sugarcane species are known in the Saccharum genus, S. spontaneum and S. robustum. The sweet domesticated cane, S. officinarum, is thought to have been domesticated from S. robustum in New Guinea about 8,000 years ago. Sugarcanes are all polyploid (have more than two paired sets of chromosomes) and modern cultivars have around 120 chromosomes, making any genomic work with sugarcanes complicated. In comparison, humans have 23 pairs, 46 chromosomes in total.  

Nicolas Pompidor, PhD student, and Dr Angélique D’Hont from CIRAD and colleagues from University of California, Berkeley and University of Illinois analysed hundreds of sequences of sugarcanes and found that the genus originates from three founding genomes. Modern cultivars were found to all derive from a few interspecific hybridisations made by breeders a century ago between a few S. officinarum and S. spontaneum. Dr Angélique D’Hont has contributed to assembling the first sugarcane reference genome and has been working on banana genomics. 

Pompidor, D’Hont and colleagues sequenced 12 haplotypes of the R570 cultivar, focusing on two distinct genomic regions (Adh1 and Rpa1). The researchers additionally collocated 95 whole genome sequences and 304 targeted sequences to capture the genetic diversity of Saccharum (S. officinarum, S. robustum, S. spontaneum, S. barberi, S. edule) and related species. Phylogenetic relationships, divergence times and origin of three groups were analysed. 

The researchers found that the 12 haplotypes formed three groups, suggesting that there were three founding genomes (A, B and C) which were involved in the origin of the Saccharum genus and modern sugarcane cultivars. Genomes A and B were contributed by the sweet sugarcane, S. officinarum whilst C was contributed by the wild species, S. spontaneum. These groups were estimated to have diverged from each other some 0.8 to 1.3 million years ago whilst the Saccharum and Miscanthus genera diverged from each other 5.7 million years ago. Within the two genomic regions, 60-188 single nucleotide polymorphisms (SNPs) were identified that can be used in future studies to investigate the contributions of the three founding genomes in other cultivars.

The first man-made sugarcane hybrids between S. officinarum and S. spontaneum were made due to disease outbreaks but the hybrids had no or low levels of sugar content. 

High sugar content was restored through repeated backcrosses with S. officinarum. 

“The three groups of SNPs [single nucleotide polymorphisms] were also found in all modern cultivars tested which are all derived from a few interspecific hybridizations made by breeders a century ago between a few S. officinarum and S. spontaneum and S. barberi clones. These interspecific hybridizations were followed by backcrosses with S. officinarum to recover good agronomic performance,” Pompidor, D’Hont and colleagues wrote.

“Our results suggested that, after its divergence from the Miscanthus lineage, the Saccharum lineage differentiated in a few sub-lineages (A, B, C and may be others) that further underwent auto- and/or allopolyploid events leading to the present day higher-order polyploids (>4x).”

This study has answered many questions about the origins of the Saccharum genus and overcame the challenges of working with the genomics of a very complicated group of plants. 
Sugarcane cultivation has a great negative impact on the environment as they are the thirstiest crop in the world but it is an important bioenergy. Global demand for them continues to increase. When you are next mixing a spoonful of sugar into your drink, keep in mind that 213 gallons of water is required to produce a pound of refined cane sugar!