Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats

Abstract

Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43,141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map.

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.…”

Use of differential levels of mean observed heterozygosity in microsatellite loci of commercial varieties of sugarcane (Saccharum spp)

“…The marker systems that are used in studies of sugarcane include microsatellites or simple sequence repeats (SSR) (Cordeiro et al, 2000Cordeiro and Henry, 2001;Pan et al, 2003;Pinto et al, 2004). Considerable advances have been made in the area of sugarcane genetics through the use of microsatellite markers.…”