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

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.豌豆（*Pisum sativum* L.）是植物遗传学领域最古老的模式研究对象，同时也是全球农业生产中极具重要性的豆科植物之一。由于豌豆基因组至今尚未完成测序，针对突变表型或优良农艺性状相关基因的鉴定，通常需先通过遗传定位，再开展候选基因筛选。此类遗传定位最优依托基于基因的分子标记开展，借此可利用豌豆与其近缘物种蒺藜苜蓿（*Medicago truncatula* Gaertn.，已完成基因组测序与注释）之间的基因组共线性优势。近五年来，得益于“下一代测序”技术的快速发展，全球已设计并定位了大量基于基因的豌豆分子标记。然而，全球范围内已开发的全部标记数据集的获取仍受限于数据格式不统一，故实际应用难度较大。本研究开发了豌豆标记数据库（Pea Marker Database, PMD），旨在以用户友好且实用的在线工具形式，整合所有豌豆标记相关信息。版本1（PMD1）收录了2484个基因标记的相关信息，包括其在连锁群上的位置、对应豌豆转录本序列，以及蒺藜苜蓿中的同源基因名称。版本2（PMD2）为更新版本，以相同格式收录了15944个豌豆标记，并新增多项高级功能。为验证PMD的性能，本研究分别对连锁群VII和V上的豌豆共生基因Sym13与Sym27开展了精细定位。定位结果显示，我们可将Sym13的最佳候选基因锁定为Sen1基因（百脉根*Lotus japonicus* (Regel) K. Larsen的SEN1基因的同源基因），并将Sym27的候选基因范围缩小至10个，由此证实PMD可有效应用于豌豆基因定位与克隆研究。PMD1与PMD2的全部数据均可通过www.peamarker.arriam.ru访问获取。