Informative genomic microsatellite markers for efficient genotyping applications in sugarcane

Abstract

Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

Genetic Fidelity Testing Using SSR Marker Assay Confirms Trueness to Type of Micropropagated Coconut (Cocos nucifera L.) Plantlets Derived from Unfertilized Ovaries

“…Microsatellite or SSR markers are particularly suitable for detecting somaclonal variations in micropropagated plants as repeated DNA sequences are known to show increased levels of instability in tissue culture (Parida et al, 2009) [19]. The thirteen primers used in the present study were all informative and generated amplicons for the detection of the genetic fidelity of the progeny.…”

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).…”

Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model

“…The characteristics of microsatellite sequences have made them the molecular marker of choice for many types of studies because of their high polymorphism and ability to identify both alleles in diploid organisms and given that they are co-dominant. They are very useful in identifying individuals propagated sexually or vegetatively since it is very improbable that two randomly selected individuals will have exactly the same alleles if several markers are used (Parida et al, 2009;Kalia et al, 2011). These markers have been widely used for the molecular characterization of scion cultivars of Prunus species (Cantini et al, 2001;Dirlewanger et al, 2002;Aranzana et al, 2003a;Struss et al, 2003;Pedersen, 2006;Rojas et al, 2008;Akpinar et al, 2010;Maghuly and Laimer, 2011) and rootstock cultivars (Serrano et al, 2002;Struss et al, 2002;Liu et al, 2007;Turkoglu et al, 2010;Arismendi et al, 2012).…”