Development and utilisation of conserved-intron scanning marker in sugarcane

Abstract

Genetic dissection of economic traits in sugarcane requires sufficiently informative molecular markers that are currently lacking in this highly valued crop. Through comparative analysis of publicly available expressed-sequence data of sugarcane, sorghum and barley, and the whole rice genome-sequence survey, novel functional markers based on conserved-intron scanning primers (CISP) were developed and evaluated in different accessions across various taxonomic ranks of sugarcane. Polymorphism was moderate (55.2%), whereas 94.7% of the markers developed amplified fragments in selected genotypes. Mean polymorphism information content value was 0.582 (range 0.320–0.715), which was comparable to that with genic microsatellite markers (0.52) but lower than that with EST-SSR (0.73). Genetic-similarity coefficient ranged from 0.39 to 0.95, indicating variable levels of divergence depending on the taxonomic rank assessed. Cluster analysis revealed that the genotypes grouped in accordance with the taxonomical classification of sugarcane, with a relatively good support from a Mantel’s test (r = 0.847) and a moderate bootstrap value (65–89%). The CISP markers reported in the present study have potential utility for genetic-diversity analysis and application in sugarcane-breeding programs.

Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses

“…Following these hypothesis, in total 3425 primer pairs (PPs) were developed and designed (See Additional file 1). Initially, we tested 30 PPs with DNA of sugarcane and related taxa and results indicated reactivity of 29 PPs [31]. In the present study, another group of 337 PPs (CISP_SC-31 to −367) based on their functional significance related to carbohydrate metabolism, photosynthesis-related proteins and many other traits, were tested with 13 sugarcane varieties released from different research stations of the country and tested with four species (namely, S. spontaneum, S. barberi, S. officinarum and S. sinense ) (Table  1).…”

“…Recently, we reported 30 CISP markers in sugarcane, for the first time, showed a moderate level of polymorphism (55.2%). Mean polymorphism information content value was 0.582 and genetic-similarity coefficient ranged from 0.39 to 0.95, indicating variable levels of divergence depending on the taxonomic rank assessed [31]. In the present study, we report a total of 3425 CISP markers which will facilitate understanding of the extent of natural variation at molecular level.…”

Challenges, Opportunities and Recent Advances in Sugarcane Breeding

“…Most functional genomics projects performed in the 1990's focused on sucrose content, disease resistance and stress tolerance, and involved several techniques, such as EST characterization, microarray and SAGE analyses (Vettore et al, 2003;Papini-Terzi et al, 2005;Calsa Jr & Figueira 2007;Rocha et al, 2007;Menossi et al, 2008;Papini-Terzi et al, 2009;Waclawovsky et al, 2010;Iskandar et al, 2011). The post-genomic era comprises the use of this information into breeding programs, with the identified markers that reveal expression profile of genes in different environmental conditions (Moore, 2005;Waclawovsky et al, 2010;Khan et al, 2011). Although still rather incipient in this crop , proteomics is increasing its applicability in sugarcane.…”

Genomics Meets Biodiversity: Advances in Molecular Marker Development and Their Applications in Plant Genetic Diversity Assessment

“…The closer the genetic relationship between the two individuals, the more similar the corresponding band patterns of the amplified PCR products will be (Wang et al, 2009). The technique has been used successfully to identify economically important traits in sugarcane (Khan et al, 2011).…”