Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information

Lentil(Lens culinaris Medik.), a diploid(2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information(ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information(NCBI) database to develop unigene-based simple sequence repeat(SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed.Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches(using E-value 1 × 10-5) against the public UniP rot(http://www.uniprot.org/) and NCBI(http://www.ncbi.nlh.nih.gov/) databases were performed. Further functional annotation was performed using PLAZA(version3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.

A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection

Globally,pea(Pisum sativum L.)is an important temperate legume crop for food,feed and fodder,and many breeding programs develop cultivars adapted to these end-uses.In order to assist pea development efforts,we assembled the USDA Pea Single Plant Plus Collection(PSPPC),which contains 431 P.sativum accessions with morphological,geographic and taxonomic diversity.The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding.To that end,we used genotyping-by-sequencing—a cost-effective method for de novo single-nucleotide polymorphism(SNP)marker discovery—to generate 66591 high-quality SNPs.These data facilitated the identification of accessions divergent from mainstream breeding germplasm that could serve as sources of novel,favorable alleles.In particular,a group of accessions from Central Asia appear nearly as diverse as a sister species,P.fulvum,and subspecies,P.sativum subsp.elatius.PSPPC genotypes can be paired with new and existing phenotype data for trait mapping;as proof-of-concept,we localized Mendel’s A gene controlling flower color to its known position.We also used SNP data to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire PSPPC,resulting in a smaller germplasm set for research screening and evaluation under limited resources.Taken together,the results presented in this study along with the release of a publicly available SNP data set comprise a valuable resource for supporting worldwide pea genetic improvement efforts.