AFLP Analysis of the Phenetic Organization and Genetic Diversity in the Sugarcane Complex, Saccharum and Erianthus

Abstract

Amplified fragment length polymorphism (AFLP) markers were evaluated for determining the phylogenetic relationships, and the diversity in the Saccharum complex using 30 clones belonging to S. officinarum, S. robustum, S. spontaneum, S. barberi, S. sinense and the related genus Erianthus. The phenetic tree of the species clones based on AFLP data was consistent with the known taxonomical relationships. AFLP gave higher resolution of closely related species into discrete groups than that by RAPD and RFLP markers, reported earlier. The levels of diversity within the various Saccharum species were also found to be higher than those obtained previously with the same set of clones using RAPD markers. The intraspecies similarity in S. barberi and S. sinense was much higher than interspecies similarity suggesting a clear separation of the two, which are considered 'horticultural species'. The genetic similarity matrix derived from a single primer combination highly correlated (r = 0.980) with that obtained from all the 12 primer combination used in the study, thus highlighting the efficiency of a single primer combination in delineating species relationships. All the primer combinations could identify markers that are specific to each of the species and the genus Erianthus. Among the species, specific markers were highest in S. spontaneum followed by S. robustum, S. barberi, S. officinarum and S. sinense. Erianthus had a distinct profile with 30% of the total amplified fragments being specific to it. This offers great scope for identifying intergeneric hybrids, which has been very difficult using morphological traits and RAPD markers. High degree of correspondence between the results from the cluster analysis based on Jaccard's similarity index, Neighbour Joining tree based on Sokal and Michener distance matrix and AFTD (Analyses Factorielle on Table of Distances) analysis clearly demonstrated that AFLP markers would be an appropriate tool in providing better information about the relationships among the species, estimation of diversity, and in revealing species and genus specific markers that could be directly applied in sugarcane breeding programmes.

Genome size variation in three Saccharum species

“…In contrast, the genome size of S. spontaneum varies between accessions, reflecting the wide range of chromosome The chromosomes numbers analysis were furnished by Rao (1983) * The chromosome numbers were corrected based on the estimated genome sizes number variations in this species (Irvine 1999). The variation of genome sizes among S. spontanum can be explained by distinctively greater diversity within S. spontaneum compared to other Saccharum species, which was demonstrated by RFLP (Burnquist et al 1992;Lu et al 1994;Nair et al 1999), AFLP (Selvi et al 2006), randomly amplified polymorphic DNA (RAPD) (Nair et al 1999;Pan et al 2004), and simple sequence repeat (SSR) markers (Selvi et al 2003). S. robustum is thought to be the ancestral species of S. officinarum (Brandes 1956;Sreenivasan et al 1987;Daniels and Roach 1987;Grivet et al 2006).…”

Genetic variability among sugarcane genotypes based on polymorphisms in sucrose metabolism and drought tolerance genes

“…The very few first hybrids obtained were extensively intercrossed, generating hundreds of sugarcane varieties that in turn determined a very narrow genetic base for the sugarcane crop (Selvi et al 2006). Despite the breakthrough in sugarcane improvement, an apparent plateau has been reached in terms of sugar concentration, and selection for new higher yielding varieties has proven to be difficult (Ming et al 2002).…”

“…In terms of sugarcane germplasm, the genetic variability has been estimated using different molecular markers, such as random fragment length polymorphism (RFLP;D'Hont et al 1994;Janoo et al 1999;Coto et al 2002;Schenck et al 2004), ribosomal DNA (Glaszmann et al 1990), microsatellites (Piperidis et al 2000;Pan et al 2003;Cordeiro et al 2003;Pinto et al 2006;), amplified fragment length polymorphism (AFLP; Hoarau et al 2002;Lima et al 2002;Aitken et al 2006;Selvi et al 2006). Most of these markers reflect the genetic variability in noncoding or repetitive DNA regions of the genome.…”

Sugarcane Genetics and Genomics

“…Simple sequence repeat (SSR) analysis showed that S. spontaneum clones may have significantly higher variation than S. barberi clones (Singh et al 2010). The distinctively greater diversity within S. spontaneum than that of the other five species was additionally supported by RFLP Lu, D'Hont, Walker, et al 1994;Nair et al 1999), amplified fragment length polymorphism (AFLP) (Selvi et al 2006), randomly amplified polymorphic DNA (RAPD) (Nair et al 1999), and SSR markers (Selvi et al 2003).…”