Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communisL.)

Abstract

BackgroundThe castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers.ResultsIn total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean.ConclusionCastor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure analysis, facilitating breeding and crop improvement of castor bean.

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

“…The proportion of polymorphic primers was 41.1 % when null allele primers and those that harbor introns were excluded resulting in 2.97 alleles per marker. This revealed that the polymorphic ratio of EST-SSR primers to be at medium level in castor (Qiu et al 2010). PIC values for the tested primers varied from a low of 0.27 (Rc DES 596) to a high of 0.49 (Rc DES 592) with an average value of 0.332.…”

“…Fig. 1 Total number of amino acid distribution, total repeats and number of loci identified whereas Qiu et al (2010) reported 96.9 %. Hence, from both the studies it can be concluded that in castor genome MNR, A/T are the richest repeat.…”

“…Bajay et al (2009) developed 12 genomic SSR markers with an average of 0.416 gene diversity (He) and 3.3 alleles per locus. Qiu et al (2010) reported 118 polymorphic SSR loci, 0.36 PIC and 2.97 alleles per locus which suggested that EST-SSR markers developed had moderate level of polymorphism. Seo et al (2011) developed 28 polymorphic SSR loci with PIC value of 0.26 and an average of 3.18 alleles per locus.…”

“…The interspecific transferability of ESTSSRs and genomic SSRs has been well proved (Wen et al 2010). EST-SSR markers have been widely applied in gene tagging, linkage map construction and QTL mapping (Qiu et al 2010). Hence, for various crops, EST-SSRs have been developed and widely used in crop improvement (Qiu et al 2010).…”

“…EST-SSR markers have been widely applied in gene tagging, linkage map construction and QTL mapping (Qiu et al 2010). Hence, for various crops, EST-SSRs have been developed and widely used in crop improvement (Qiu et al 2010). In Castor the availability of EST-SSR markers are limited when compared with other crops viz., wheat, rice, maize, chickpea, pigeon pea, groundnut, sunflower and rapeseed mustard.…”