Study clarifies process of sugarcane genome evolution

After they differentiated, the parent species of modern sugarcane underwent spontaneous chromosome self-duplications before being crossed by humans not much more than a century ago.

By José Tadeu Arantes  |  Agência FAPESP – Brazil is the world’s largest producer of sugarcane, with more than 7 million hectares planted and an annual crop of 480 million metric tons, as well as being the leader in bioethanol technology, according to information published by the Brazilian Agricultural Research Corporation (EMBRAPA). 

Despite the importance of sugarcane to the Brazilian economy and enormous research effort relating to sugarcane, genomic studies have been lacking. This gap in knowledge has now been narrowed by a significant new contribution, “Analysis of three sugarcane homo/homologous regions suggests independent polyploidization events of Saccharum officinarum and Saccharum spontaneum”, published in Genome Biology and Evolution.

The study was supported by FAPESP through the research projects “Allelic variation in sugarcane: quantification of sequence polymorphism” and “Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function”.

Although it appears to be a simple plant, modern sugarcane has an extremely complex genome. “The aim of the study was to understand how this genome came about and how it works,” said Mariane de Mendonça Vilela, first author of the article, in an interview with Agência FAPESP.

One of the reasons for this genomic complexity is sugarcane’s tendency toward polyploidy, i.e., multiplication of homologous chromosomes. “Most organisms, including humans, have a diploid genome, carrying two complete sets of chromosomes, one from each parent,” Vilela said. “However, the genus Saccharum, to which modern sugarcane and its predecessor species belong, is polyploid, carrying more than two copies of each chromosome. In modern sugarcane, the number of homologous chromosomes ranges from eight to 14. Moreover, the number isn’t the same for all chromosomes, which further complicates the study of this genome.”

The other reason has to do with the history of sugarcane’s development. “Modern sugarcane is a product of human action, obtained by crossing S. officinarum with S. spontaneum not much more than a century ago. The point of the cross was to produce a variety with the strengths of both species – the high sugar content of S. officinarum and the hardiness of S. spontaneum,” said Luiz Eduardo Vieira Del Bem, second author of the article.

After this first cross, the plant’s sugar content was increased by more crossings of the hybrid with S. officinarum, so that with each generation, the frequency of the latter’s genome increased compared to that the genome of S. spontaneum. The current proportion is 80:20, according to Del Bem. “As a side-effect of these successive crossings, some chromosomes from the parent species were lost, and others recombined with each other during this process, resulting in even greater genomic complexity,” he said.

As a result, different numbers of chromosomes, ranging from 80 to 120, are found in different contemporary sugarcane varieties. Different varieties are often planted close to each other on opposite sides of the roads that run through sugarcane plantations. 

Within the grass family, the closest cultivated relative of sugarcane is sorghum. The two genera separated between 7 million and 9 million years ago, more or less at the same time as the genus Homo, to which modern humans belong, was separating from the genus Pan, to which the chimpanzee belongs. Like humans, sorghum is diploid, whereas the genus Saccharum has developed a propensity for polyploidy, which can occur in crossings both between and within species.

“Our study discovered that at least two rounds of chromosome self-duplication have occurred in S. officinarum since it differentiated from S. spontaneum between 2.5 million and 3.5 million years ago but before the two species were crossed by humans not much more than a century ago,” Del Bem said. “In the case of S. spontaneum, it’s more complicated because the number of chromosomes is highly variable, but we also discovered that self-duplication occurred during the same period.”

One of the lines of investigation developed in the study set out to understand how the genome organizes itself to accommodate and coordinate these multiplications of homologous chromosomes. “When the number of chromosomes increases, the number of genes increases proportionally,” Vilela said. “What mechanisms does the plant develop to integrate and stabilize this large number of genes? This question guided this specific line of inquiry.”

“Some genes, especially regulatory genes that control flowering time, for example, or the plant’s response to environmental stress, need very fine, well-defined expression, in order not to cause more damage than benefits,” she continued. “Our study confirmed this. We observed that although sugarcane has at least eight copies of each chromosome, not all of them are active at the same time. This information might possibly be used in some future technological application.”

The datings obtained by the study, showing that chromosome self-duplications in the parent species occurred after they differentiated between 2.5 million and 3.5 million years ago, were based on the so-called “molecular clock” hypothesis. Del Bem explained the procedure in general terms.

“In the genetic code, there are several nucleotide triplets that encode amino acids,” he said. “Sixty-four triplets are possible, but [there are] only 20 amino acids. The conclusion must be that there are mutations that don’t affect the function. The base changes, but the encoded amino acid is the same, because different triplets produce identical amino acids. These mutations are called synonymous substitutions. Natural selection is unable to ‘see’ these mutations because their occurrence doesn’t alter the protein, so natural selection neither increases them because they’re beneficial nor discards them because they’re harmful. These substitutions, which occur with variable frequencies in populations, are the ticking of the molecular clock. Based on the rate of mutation in grasses, which had already been determined experimentally, and on a comparison of sequences for the homologous genome regions we analyzed, we were able to calculate the number of generations in which they duplicated and hence the time intervals for chromosome duplications.”

“Our findings were based on an analysis of three genes which we’re almost sure are single-copy genes in the genomes of grasses generally. One is the kinase TOR, which controls growth in response to nutrition. Another is the gene LEAFY, which controls flowering. The third is phytochrome C, which controls light reception. These three genes are crucial to plant development. Precisely for this reason, they must be very finely regulated in the genome,” said Michel Vincentz, a professor at the University of Campinas’s Biology Institute (IB-UNICAMP), principal investigator for the study and last author of the article.

“The real surprise was our discovery that owing to the complex process of autopolyploidization of precursor species, homologous genes are expressed differently,” Vincentz said. “This is a novel finding in the literature, showing that the complexity of the sugarcane genome is much greater than previously thought. Apparently, at some time during the evolution of this genome, there was an invasion of chromosome loci by transposons [DNA sequences that can change position within a genome]. When a transposon inserts itself into a locus, it alters gene expression in that locus.”