Sugarcane genome architecture decrypted with chromosome‐specific oligo probes

Abstract

SUMMARY Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n = 100–120) are highly polyploids and aneuploids derived from interspecific hybridization between Saccharum officinarum (2n = 80) and Saccharum spontaneum (2n = 40–128). Chromosome‐specific oligonucleotide probes were used in combination with genomic in situ hybridization to analyze the genome architecture of modern cultivars and representatives of their parental species. The results validated a basic chromosome number of x = 10 for S. officinarum. In S. spontaneum, rearrangements occurred from a basic chromosome of x = 10, probably in the Northern part of India, in two steps leading to x = 9 and then x = 8. Each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical extension of clones with x = 8. We showed that the S. spontaneum contribution to modern cultivars originated from cytotypes with x = 8 and varied in proportion between cultivars (13–20%). Modern cultivars had mainly 12 copies for each of the first four basic chromosomes, and a more variable number for those basic chromosomes whose structure differs between the two parental species. One−four of these copies corresponded to entire S. spontaneum chromosomes or interspecific recombinant chromosomes. In addition, a few inter‐chromosome translocations were revealed. The new information and cytogenetic tools described in this study substantially improve our understanding of the extreme level of complexity of modern sugarcane cultivar genomes.

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning

“…Although cytogenetic information is limited for sugarcane genotypes, we do expect differences in chromosome numbers and ploidy level among them. Most hybrids, with the exception of US85-1008, have a larger number of S. officinarum chromosomes and a minor and variable contribution of S. spontaneum, likely with a basic chromosome number of x = 10 [22]. The basic chromosome number of S. officinarum is also x = 10, but different numbers have been verified in S. spontaneum [22].…”

“…Most hybrids, with the exception of US85-1008, have a larger number of S. officinarum chromosomes and a minor and variable contribution of S. spontaneum, likely with a basic chromosome number of x = 10 [22]. The basic chromosome number of S. officinarum is also x = 10, but different numbers have been verified in S. spontaneum [22]. Ploidy levels and interspecific hybridization have the potential to affect gene expression patterns, in addition to mechanisms of transcriptional control and epigenetic factors [23,24].…”

Differential Expression in Leaves of Saccharum Genotypes Contrasting in Biomass Production Provides Evidence of Genes Involved in Carbon Partitioning

“…Most hybrids, with the exception of US85-1008, have a larger number of S. o cinarum chromosomes and a minor and variable contribution of S. spontaneum, likely with a basic chromosome number of x = 10 (22). The basic chromosome number of S. o cinarum is also x = 10, but different numbers have been veri ed in S. spontaneum (22). Ploidy levels and interspeci c hybridization have the potential to affect gene expression patterns, in addition to mechanisms of transcriptional control and epigenetic factors (23,24).…”

Temporal changes in the expression of genes involved in carbon partitioning in apical culms of contrasting sugarcane genotypes

“…The former was used because of its higher sugar content in its culms, and the latter for its robustness, resistance to diseases (Campos and Caligari, 2017) and abiotic stress tolerance (Zhang et al, 2018). Following hybridization, successive backcrossing with S. officinarum was used to increase sugar content yield, a process called "nobilization" (Piperidis and D'Hont, 2020).…”

“…These noble canes exhibit lower fiber content, thicker culms and recalcitrant flowering when compared to S. spontaneum (Kaffka and Grantz, 2014). Also, modern sugarcane cultivars (Saccharum X officinarum) are aneuploid and autopolyploid, with a basic ploidy level of 10x to 12x (Piperidis and D'Hont, 2020), resulting in a total genome size of roughly 10 Gbp (D'Hont, 2005). Interspecific crossing has led to genotypes with chromosome numbers varying from 100 to 120, of which 80% come from S. officinarum, 10% from S. spontaneum and 10% from interspecific rearrangements (Piperidis et al, 2010).…”