Agronomy, Vol. 15, Pages 2638: Sugarcane Genetic Diversity Study of Germplasm Bank and Assessment of a Core Collection

Agronomy doi: 10.3390/agronomy15112638

Authors:
Maria Francisca Perera
Andrea Natalia Peña Malavera
Diego Daniel Henriquez
Aldo Sergio Noguera
Josefina Racedo
Santiago Ostengo

Understanding the genetic diversity and population structure of sugarcane germplasm banks is essential for generating progenies with maximum variability. In this study, 350 accessions from the EEAOC germplasm bank were genotyped using DArT-seq markers. Genetic diversity, population structure, and variability were assessed through Bayesian analysis, principal coordinate analysis (PCoA), and analysis of molecular variance (AMOVA). Additionally, different sizes of core collections were evaluated. After filtering, 74,969 high-quality SNPs were retained, and two outlier genotypes were excluded. The mean observed heterozygosity (HO) was 0.28, while the mean expected heterozygosity (HE) was 0.3. Polymorphic information content (PIC) values ranged from 0 to 0.38 (mean 0.22), and the mean discrimination power (Dj) was 0.28. Structure and PCoA analyses consistently revealed three genetic clusters. AMOVA indicated that most of the genetic variation was found within subpopulations, while 10.25% was attributable to differences among them (p < 0.0001), where ΦFST suggested moderate genetic differentiation. Core collection analysis showed that a subset of 35 genotypes (10%) captured nearly 96% of the total genetic diversity, while a 30% core captured over 98%. These results provide valuable information for the effective management and utilization of sugarcane genetic resources and support the design of breeding strategies to develop superior cultivars.

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Maria Francisca Perera www.mdpi.com