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According to the original sequences used for development of SSRs, SSRs were divided in two categories: genomic-SSRs, identified from random genomic sequences, and expressed sequence tag (EST -SSRs, idEST -SSRsfrom transcridentifiedequences.
Overall, our results show that mining ESTs for the development of SSRs is a highly effective strategy to increase the SSR database for cassava.
Deep transcriptome sequencing provides a good resource for the development of SSRs because of the enormous amount of sequence of data that it generates.
The SSR markers of castor bean are, however, very limited to date because the de novo development of SSRs is a costly and time consuming endeavor [ 16, 17].
In silico development of SSRs of organelle genomes has brought them up as potential markers for transferability among the species, ease of development and as key players in genome length variation.
Until recently, only a few microsatellites have been available for Cucurbita, and transferability from other cucurbits, such as cucumber of melon, has been demonstrated to be very low [ 9], then the development of SSRs for this genus is highly desirable.
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Early research focused on the development of SSR markers from BPH genomic DNA.
As another approach, development of SSR markers based on important candidate genes related to a particular trait may greatly expedite marker assisted breeding programme for the trait.
In contrast, the GC-rich motifs have been reported as frequent motifs in studies on development of SSR from expressed sequence tags and genomes with methylation filtration [ 27- 30].
In this paper, we report the development of g-SSR, e-SSR, and SNP markers and present a preliminary genetic map for BPH based on these markers.
Developments of SSR markers from other plant species, including cotton [ 35], barley [ 36] and pine [ 37], have also noted positive relationships between SSR polymorphism and number of repeat units.
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