Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers

PLoS One. 2017 Oct 26;12(10):e0186713. doi: 10.1371/journal.pone.0186713. eCollection 2017.

Abstract

Pea (Pisum sativum L.) is the oldest model object of plant genetics and one of the most agriculturally important legumes in the world. Since the pea genome has not been sequenced yet, identification of genes responsible for mutant phenotypes or desirable agricultural traits is usually performed via genetic mapping followed by candidate gene search. Such mapping is best carried out using gene-based molecular markers, as it opens the possibility for exploiting genome synteny between pea and its close relative Medicago truncatula Gaertn., possessing sequenced and annotated genome. In the last 5 years, a large number of pea gene-based molecular markers have been designed and mapped owing to the rapid evolution of "next-generation sequencing" technologies. However, the access to the complete set of markers designed worldwide is limited because the data are not uniformed and therefore hard to use. The Pea Marker Database was designed to combine the information about pea markers in a form of user-friendly and practical online tool. Version 1 (PMD1) comprises information about 2484 genic markers, including their locations in linkage groups, the sequences of corresponding pea transcripts and the names of related genes in M. truncatula. Version 2 (PMD2) is an updated version comprising 15944 pea markers in the same format with several advanced features. To test the performance of the PMD, fine mapping of pea symbiotic genes Sym13 and Sym27 in linkage groups VII and V, respectively, was carried out. The results of mapping allowed us to propose the Sen1 gene (a homologue of SEN1 gene of Lotus japonicus (Regel) K. Larsen) as the best candidate gene for Sym13, and to narrow the list of possible candidate genes for Sym27 to ten, thus proving PMD to be useful for pea gene mapping and cloning. All information contained in PMD1 and PMD2 is available at www.peamarker.arriam.ru.

MeSH terms

  • Databases, Genetic*
  • Genetic Linkage
  • Genetic Markers*
  • Genome, Plant*
  • Internet*
  • Lotus / genetics
  • Medicago truncatula / genetics
  • Molecular Sequence Annotation
  • Pisum sativum / genetics*
  • Software*

Substances

  • Genetic Markers

Grants and funding

The work of AMA and IAT on development of PMD1 and localization of the Sym27 gene was supported by the Russian Science Foundation (http://www.rscf.ru/en) (Grant # 14-24-00135). The work of OAK on development of PMD2 was supported by the Russian Foundation for Basic Research (http://www.rfbr.ru/rffi/eng) (Grant # 16-34-60132). The work of AIZ, ASS and VAZ on localization of the Sym13 gene and Sen1 sequencing was supported by the Russian Science Foundation (http://www.rscf.ru/en) (Grant # 16-16-00118). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.