Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice

Abstract

The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis. We studied the synteny between each of the four major sorghum staygreen quantitative trait loci (QTL) regions with that in the rice genome and attempted to increase marker density around the QTL with genic-microsatellites from the sorghum transcriptomic resource using the rice genome as template. For each of the sorghum QTL regions, the reported RFLP markers were compiled, used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL, on chromosome 9 for Stg3 QTL, and on chromosome 11 for Stg4 QTL. Using the Gramene genome browsing tool, 869 non-redundant sorghum expressed sequence tags (ESTs) were selected and 50 genic-microsatellites (18, 12, 15, and 5, for Stg1, Stg2, Stg3, and Stg4 QTL, respectively) could be developed. We could experimentally establish synteny of the Stg1, Stg2, Stg3, and Stg4 QTL regions with that of the rice genome by mapping ten polymorphic genic-microsatellite markers (20%) to the positions of the staygreen QTL. The simple strategy demonstrated in the present study could readily be extrapolated to other cereals of the Poaceae family. The markers developed in this study provide a basis for the isolation of genes underling these QTL using an association study or map-based gene isolation approach, and create an additional option for MAS of the staygreen trait in sorghum.

Identification of quantitative trait loci associated with resistance to foliar diseases in sorghum [Sorghum bicolor (L.) Moench]

“…net), and the genomic sequence was downloaded. The parameters set for marker development and PCR amplification conditions were similar to those described in our previous studies (Srinivas et al 2008) except that in this study we used a minimum of ten repeats as the cut-off for the identification of microsatellite motifs for the development of primer pairs. The amplicons were separated on 6% denaturing polyacrylamide gel electrophoresis and visualized by silver staining (Fritz et al 1995).…”

Quantitative trait loci associated to agronomic traits and yield components in a <i>Sorghum bicolor</i> L. Moench RIL population cultivated under pre-flowering drought and well-watered conditions

“…QTL associated with post-flowering drought resistance have been identified in sorghum using restricted fragment length polymorphism (RFLP) markers [3,6,[10][11][12][13][14] and random amplified polymorphic DNA (RAPD) markers [10,13]. EST-derived microsatellite markers, which may improve marker-assisted selection possibilities, were developed [15] and drought stress EST-derived microsatellite loci were mapped by [16]. DArT markers, which were used in the present study, are array based and analyses can be carried out on a minimal DNA sample requirement without prior DNA sequence information.…”

DNA Markers in Diversity Analysis

“…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).…”