Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

Abstract

Microsatellites, or simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated by 454 sequencing and representing 70,654 contigs and 52,082 singletons) from soybean globular stage embryos. Among 122,736 unique ESTs, 3,729 contained one or more SSRs. In total, 3,989 SSRs were identified including 304 mono, 1,374 di, 2,208 tri, 70 tetra, 13 penta and 20 hexanucleotide SSRs. Thirty three EST-SSRs were selected for primer design and polymorphism analysis using twenty soybean cultivars and one wild-type soybean. Successful amplification was obtained using 21 of these primer pairs, 11 of which detected polymorphisms in these soybean cultivars. These results demonstrated that 454 high throughput sequencing is a powerful tool for molecular marker development. From the 3,989 identified SSRs we expect to obtain a large number of makers with polymorphism among different soybean cultivars, which would be useful for analysis of genetic diversity and maker assisted selection in the soybean breeding programs.

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)

“…Until the reference genome sequence becomes available, transcriptome sequencing is a fast and efficient means for gene discovery and genetic marker development. The simple sequence repeat (SSRs) markers are important resources for determining functional genetic variation and among the various molecular markers, SSRs are highly polymorphic [ 20 ], and serve as rich resource of diversity. SSRs derived from expressed sequence tags (ESTs) have special advantages such as those might be linked to known genes, having higher transferability among related species, lower cost for development and higher proportion of high-quality markers [ 20 ].…”

“…The simple sequence repeat (SSRs) markers are important resources for determining functional genetic variation and among the various molecular markers, SSRs are highly polymorphic [ 20 ], and serve as rich resource of diversity. SSRs derived from expressed sequence tags (ESTs) have special advantages such as those might be linked to known genes, having higher transferability among related species, lower cost for development and higher proportion of high-quality markers [ 20 ]. Transcriptome resources for reproductive tissues are currently available for other commercially important fishes, including channel catfish ( Ictalurus punctatus ) [ 21 ], common carp ( Cyprinus carpio ) [ 19 ], zebrafish ( Danio rerio ) [ 22 ], rainbow trout ( Oncorhynchus mykiss ) [ 23 , 24 ], coho salmon ( Oncorhynchus kisutch ) [ 25 ], tilapia ( Oreochromis mossambicus ) [ 26 ], Atlantic halibut ( Hippoglossus hippoglossus ) [ 27 ], senegalese sole ( Solea senegalensis ) [ 28 ], Atlantic salmon ( Salmo salar ) [ 29 ], and cod ( Gadus morhua ) [ 30 ] but less information is available for L rohita [ 5 , 6 ].…”

Microsatellite analysis in the genome of Acanthaceae: An in silico approach

“…[ 6 ] These repeats have a wide application in the field of plant genetics and breeding as they have multi-allelic, reproducible and co-dominant inheritance properties. [ 7 ] The microsatellites were identified in the genomes of many medicinal plants such as Humulus lupulus (hop),[ 8 ] Ocimum basilicum (basil)[ 9 ] and also for some economically important plants including Oryza sativa (rice),[ 10 ] Glycine max (soybean),[ 11 ] Hordeum vulgare L. (barley), Triticum aestivum (wheat), Solanum lycopersicum (tomato), Vitis vinifera (grape), and Helianthus annuus (sunflower). [ 9 ] The SSRs also provide basis for the development of SSR-based markers that have a wide range of application in genetic research including studies of genetic variation, linkage mapping, gene tagging, and evolution.…”

Analysis of expressed sequence tags (ESTs) from a normalized cDNA library and isolation of EST simple sequence repeats from the invasive cotton mealybug Phenacoccus solenopsis

“…In this study, seven sets of newly designed primer pairs were successfully used to produce amplicons that revealed polymorphisms in the 24 P. solenopsis individuals. These results suggest that the EST‐based SSR markers developed in this study can be used to investigate the genetic structure of P. solenopsis populations, in addition to providing a valuable resource for developing SSR markers, as demonstrated in prior studies (Yu & Li, ; Li et al ., ).…”