Characterization of new polymorphic functional markers for sugarcane

Abstract

Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST-SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST-SSR markers were used to screen 18 sugarcane (Saccharum spp.) varieties. A high proportion (65.5%) of the above EST-SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST-SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST-SSRs were found to be functional, showing homology to known genes. As the EST-SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST-SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.

Identification of marker-trait associations for morphological descriptors and yield component traits in sugarcane

“…Genotyping was carried out using a set of 174 polymorphic SSR primers (Table S3) comprising of 43 genomic SSRs (Govindaraj et al 2005;Parida et al 2009), and 131 EST-SSRs (Pinto et al 2004;Oliveira et al 2009;Singh et al 2013). DNA amplification was carried out in a 15 lL reaction volume consisting of 1 9 PCR assay buffer, 200 mM of each dNTPs (Fermentas, USA), 12 ng (1.8 pmol) each of forward and reverse primers (Operon Biotechnologies, GmbH, Germany), 0.5 units of Taq DNA polymerase (Fermentas, USA) and 25 ng genomic DNA using a thermal cycler (MyCycler, Biorad, USA).…”

Selfing rate estimation in sugarcane under unfavorable natural conditions of crossing by using microsatellite markers

“…The simple sequence repeat (SSR) primer pairs SCB312, SCB436, SCB381, and SCC01 (Pinto et al, 2004;Oliveira et al, 2009) were screened in the family derived from IACSP95-5000, while SMC31CUQ, SMC2017FL, SMC1047HA (Liu et al, 2011), and SCC01 SCA48 (Pinto et al, 2004) were used for the 24 individuals that were derived from SP89-1115. The best resolution and polymorphic primer pairs were selected for each family.…”

Genetic diversity in sugarcane varieties in Brazil based on the Ward-Modified Location Model clustering strategy

“…In sugarcane, studies evaluating the genetic diversity have been conducted with the use of quantitative and qualitative traits, and/or with molecular markers (Da Silva et al, 2008;Oliveira et al, 2009;Duarte Filho et al, 2010;Dutra Filho et al, 2011;Sindhu et al, 2011;Santos et al, 2012;Santchurn et al, 2012;Perera et al, 2012). In these works, a high degree of genetic similarity between the genotypes has been found, resulting in the formation of few groups.…”