Exploiting rice–sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map

Abstract

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred population derived from cross N13 x E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all 10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice-sorghum synteny. The ESTs from which these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not available.

Identification of SSR markers associated with height using pool-based genome-wide association mapping in sorghum

“…Compared to SNP marker system, SSR markers requires just the primer sequences which are usually available once published. This is the primary reason why so much effort has been devoted to developing SSR markers (Kong et al 2000;Li et al 2009;Ramu et al 2009;Srinivas et al 2009;Yonemaru et al 2009) and to using SSR markers in genetic mapping (Bhattramakki et al 2000;Haussmann et al 2002;Wu and Huang 2006), diversity studies (Abu Assar et al 2005;Agrama and Tuinstra 2003;Ali et al 2008;Anas and Yoshida 2004;Barnaud et al 2007;Caniato et al 2007;Casa et al 2005;Deu et al 2008;Dillon et al 2005;Folkertsma et al 2005;Ghebru et al 2002;Menz et al 2004;Pei et al 2010;Shehzad et al 2009b;Smith et al 2000;Wang et al 2009b) and molecular breeding (Knoll and Ejeta 2008) in sorghum. The objective of this study was to identify SSR markers associated with sorghum stem height using the aforementioned poolbased genome-wide association mapping technique.…”

Análise de associação quanto à produtividade e seus caracteres componentes em linhagens e cultivares de arroz de terras altas

“…A avaliação individual dos componentes de produtividade visou diminuir a complexidade da análise, uma vez que esses caracteres têm controle genético quantitativo, e alguns apresentam baixa herdabilidade (Sürek & Beşer, 2005 (Varshney et al, 2005;Castillo et al, 2008;Ramu et al, 2009). Além disso, outra grande vantagem de se utilizar marcadores derivados do genoma transcrito é a de que a variabilidade encontrada entre dois genótipos pode estar associada a diferenças no fenótipo, o que resulta em marcadores passíveis de utilização direta na seleção assistida.…”

DNA Markers in Diversity Analysis

“…This marker system has been employed effectively in studying diversity in rice (Chao et al 2000), wheat (Leigh et al 2003;Gupta et al 2003), and barley (Varshney et al 2008). About 55 SSRs were developed and mapped through data mining of sorghum EST sequence by Ramu et al (2009). Recently, Ramu et al (2013) effectively used 40 reported EST-SSRs to study the functional diversity across the reference set developed by Billot et al (2013).…”

“…Identification of SSRs from ESTs (EST-SSR), referred to as genetic microsatellites, can be directly linked to the genes having agronomic significance (Varshney et al 2002;Gupta et al 2003). ESTSSRs have been successfully developed through data mining in various crop plants, including sorghum (Ramu et al 2009;Srinivas et al 2008Srinivas et al , 2009). This marker system has been employed effectively in studying diversity in rice (Chao et al 2000), wheat (Leigh et al 2003;Gupta et al 2003), and barley (Varshney et al 2008).…”