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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Cool Season Food Legumes

Location: Grain Legume Genetics Physiology Research

Title: A validated source panel of SSR markers for effective discrimination of lentil species

item Sen Gupta, Debjyoti -
item Cheng, Peng -
item Sablok, Gaurav -
item Thavarajah, Dil -
item Thavarajah, Pushparajah -
item McGee, Rebecca
item Coyne, Clarice
item Main, Dorrie -
item Kumar, Shiv -

Submitted to: Food Legume Research International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: June 2, 2014
Publication Date: N/A

Technical Abstract: Lentil (Lens culinaris Medic) is an important cool season food legume grown extensively in the world. This crop species has 14 chromosomes (2n=14), is a diploid and has a genome size of more than 4000 Mbp. Development of highly polymorphic molecular markers is a lentil research priority. In this study, 9,513 expressed sequence tags (EST) were systematically downloaded from the National Center for Biotechnology Information database to develop unigene-based simple sequence repeat (SSR) markers. The ESTs were assembled into 4,053 unigenes, and then analyzed to detect 374 SSRs using microsatellite identification tool, MISA. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 v1.14. To classify the functional annotation of ESTs, and EST-SSRs, BLASTx searches (E-value, 1x10-5) were performed against the publicly available UniProt ( and NCBI ( databases. Further functional annotation was performed using the PLAZA comparative genomics and GO annotation was slimmed using the Plant GO Slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of twenty four Lens genotypes consisting of L. culinaris advanced breeding lines, parents of mapping populations, wild types and genotypes of L. nigricans, L. culinaris ssp. orientalis, L. lamottei were tested to identify polymorphic markers. A highly polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with the functional annotation data could be used as molecular tools to lentil breeding.

Last Modified: 7/23/2016
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