Molecular diversity and genetic structure of Saccharum complex accessions

Abstract

Sugarcane is an important crop for food and energy security, providing sucrose and bioethanol from sugar content and bioelectricity from lignocellulosic bagasse. In order to evaluate the diversity and genetic structure of the Brazilian Panel of Sugarcane Genotypes (BPSG), a core collection composed by 254 accessions of the Saccharum complex, eight TRAP markers anchored in sucrose and lignin metabolism genes were evaluated. A total of 584 polymorphic fragments were identified and used to investigate the genetic structure of BPSG through analysis of molecular variance (AMOVA), principal components analysis (PCA), a Bayesian method using STRUCTURE software, genetic dissimilarity and phylogenetic tree. AMOVA showed a moderate genetic differentiation between ancestors and improved accessions, 0.14, and the molecular variance was higher within populations than among populations, with values of 86%, 95% and 97% when constrasting improved with ancestors, foreign with ancestors and improved with foreign, respectively. The PCA approach suggests clustering in according with evolutionary and Brazilian breeding sugarcane history, since improved accessions from older generations were positioned closer to ancestors than improved accessions from recent generations. This result was also confirmed by STRUCTURE analysis and phylogenetic tree. The Bayesian method was able to separate ancestors of the improved accessions while the phylogenetic tree showed clusters considering the family relatedness within three major clades; the first being composed mainly by ancestors and the other two mainly by improved accessions. This work can contribute to better management of the crosses considering functional regions of the sugarcane genome.

Fig 1. Principal Components Analysis (PCA) of the Brazilian Panel of Sugarcane Genotypes (BPSG) based on TRAP markers.

(a) PCA performed with all 254 accessions of the BPSG. (b) PCA performed with 248 accessions of the BPSG, i.e., without accessions representatives of the genus Erianthus. The different colors indicates the predefined groups: ancestors accessions (A) in orange; accessions of Saccharum spp. hybrids from Brazilian breeding programs (BB) in black; accessions of Saccharum spp. hybrids from foreign breeding programs (FH) in blue. The A group in the Fig 1A was composite by ancestors accessions of the genus Saccharum and Erianthus, while in the Fig 1B, the A group was composite only by accessions of the genus Saccharum.

Fig 2. Phylogenetic tree estimated through neighbor-joining method for 248 accessions of the Brazilian Panel of Sugarcane Genotypes (BPSG).

The names of the accessions belonging to predefined groups were write with different colors: ancestors accessions (A) in orange; accessions of Saccharum spp. hybrids from Brazilian breeding programs (BB) in black; and accessions of Saccharum spp. hybrids from foreign breeding programs (FH) in blue. The A group was composite by ancestors accessions of the genus Saccharum. The circumference around the phylogenetic tree represents the two subpopulations estimated by the STRUCTURE analysis and the green and yellow colors indicate accessions of the P1 and P2 subpopulations, respectively. The three major clades C1, C2 and C3 were indicated within the phylogenetic tree with square, triangle and circle in black.