Characterization of leaf transcriptome, development and utilization of unigenes-derived microsatellite markers in sugarcane (Saccharum sp. hybrid)

Abstract

Sugarcane ( species hybrid) is the major source of sugar (> 80% sugar) in the world and is cultivated in more than 115 countries. It has recently gained attention as a source of biofuel (ethanol). Due to genomic complexity, the development of new genomic resources is imperative in understanding the gene regulation and function, and to fine tune the genetic improvement of sugarcane. In this study, a cDNA library was constructed from mature leaves so as to develop ESTs resources which were further compared with nucleotide and protein databases to explore the functional identity of sugarcane genes. The non-redundant ESTs (unigenes) were categorized into 18 metabolic functions. The major categories were bioenergetics and photosynthesis (4%), cell metabolism (5%), development related protein (3%), membrane-related, mobile genetic elements (5%), signal transduction (2%), DNA (1%), RNA (1%) and protein (2%) metabolism, other metabolic processes (3%), transcription factors (1%), transport (4%) and proteins related to stress/defense (4%). From 540 unique ESTs, 212 simple sequence repeats were identified, of which 206 were from 463 singlets and six were mined from 77 contig sequences. A total of 540 unique EST sequences were used for SSR search of which 97 (17.9%) contained specified SSR motifs, generating 212 unique SSRs. The genes characterized in this study and the EST-derived microsatellite markers identified from the cDNA library will enrich genomic resources for association- and linkage-mapping studies in sugarcane.

Agro-morphological description, genetic diversity and population structure of sugarcane varieties from sub-tropical India

“…Sugarcane varieties have previously been characterized on the basis of distinctness, uniformity and stability (DUS) descriptors as per the guidelines of Protection of Plant Varieties and Farmer's Right Act (Anonymous 2009). Genetic diversity has been analysed in sugarcane varieties using RAPD (Silva et al 2008;Nawaz et al 2010;Ramakrishnan et al 2015), RFLP (Creste et al 2010), AFLP (Aitken et al 2006;Besse et al 1998), SRAP (Alwala et al 2008;Chang et al 2012), SCoT (Que et al 2014), CISP (Khan et al 2011), and EST-SSR (Silva et al 2012;Singh et al 2013.;Khan et al 2018). In this study, an attempt was made to assess the efficiency of SSR markers in genetic diversity analysis, population stratification in 92 sugarcane varieties and exploit them as an additional tool for determining the distinctiveness of sugarcane varieties.…”