Development of the first molecular karyotype of a Brazilian sugarcane cultivar using specific chromosome probes

• Grant number: 25/03974-3
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: June 09, 2025
• End date: June 08, 2026
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Maria Lúcia Carneiro Vieira
• Grantee: Nina Reis Soares
• Supervisor: Nathalie Raymonde Josephe Piperidis
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Institution abroad: Sugar Research Australia, Indooroopilly, Australia
• Associated to the scholarship: 23/16470-8 - Unveiling the chromosome pairing in Saccharum, BP.PD

Abstract

Sugarcane (Saccharum spp.) has an extremely complex genome. Modern cultivars are highly polyploid and aneuploid due to their history of domestication, genetic improvement, and interspecific hybrid origin involving the domesticated species Saccharum officinarum (2n = 8x = 80, x = 10) ('noble cane') and the wild S. spontaneum (2n = 8x = 40 - 128, x = 8, 9, or 10). The first hybrids were backcrossed with S. officinarum, and progeny selection in subsequent generations established the genetic basis of modern cultivars. The complexity of the Saccharum genome has inspired several molecular studies that have shed light on the genome constitution, genetic architecture and cytogenetics of sugarcane. Interestingly, in the case of the French cultivar R570, chromosomes have different numbers of copies, e.g., chromosomes 1 and 2, have 12 copies, though chromosome 9 has 9 copies. In the present study, specific chromosome probes will be made and used in combination with in situ genomic hybridization to define the genome architecture of the modern Brazilian cultivar SP80-3280. From this study, it will be possible to determine the chromosomal constitution of this Brazilian cultivar, SP80-3280, which is considered a model in genetic studies, including the construction of linkage maps and quantitative loci mapping. We aim to provide: (i) the number of chromosome copies originating from each of the parental species, considering each chromosome in particular, if originating from S. officinarum, S. spontaneum or S. barberi, which have distinct basic numbers, x = 10, x = 8 and x = ?, respectively; (ii) the number of divergent chromosome copies due to aneuploidies; (iii) the origin of interspecific recombinant chromosomes. This work has implications for genetic studies of sugarcane since the loci exist in distinct doses depending on the chromosome, duplications and karyotypic rearrangements that characterize each cultivar, whose genealogies diverge considerably.