Kulaeva Olga A, Zhernakov Aleksandr I, Afonin Alexey M, Boikov Sergei S, Sulima Anton S, Tikhonovich Igor A, Zhukov Vladimir A
All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia.
Saint-Petersburg State University, Universitetskaya embankment, Saint-Petersburg, Russia.
PLoS One. 2017 Oct 26;12(10):e0186713. doi: 10.1371/journal.pone.0186713. eCollection 2017.
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.）是植物遗传学中最古老的模式生物，也是世界上农业上最重要的豆类之一。由于豌豆基因组尚未测序，通常通过遗传作图，随后进行候选基因搜索来鉴定导致突变表型或理想农业性状的基因。这种作图最好使用基于基因的分子标记来进行，因为这为利用豌豆与其近缘种蒺藜苜蓿（Medicago truncatula Gaertn.）之间的基因组共线性提供了可能性，蒺藜苜蓿拥有已测序和注释的基因组。在过去5年中，由于“下一代测序”技术的快速发展，已经设计并定位了大量基于豌豆基因的分子标记。然而，获取全球设计的完整标记集受到限制，因为数据不统一，因此难以使用。豌豆标记数据库旨在以用户友好且实用的在线工具形式整合有关豌豆标记的信息。版本1（PMD1）包含2484个基因标记的信息，包括它们在连锁群中的位置、相应豌豆转录本的序列以及蒺藜苜蓿中相关基因的名称。版本2（PMD2）是一个更新版本，包含15944个格式相同且具有若干高级功能的豌豆标记。为了测试PMD的性能，分别对连锁群VII和V中的豌豆共生基因Sym13和Sym27进行了精细定位。定位结果使我们能够提出Sen1基因（日本百脉根（Regel）K. Larsen的SEN1基因的同源物）作为Sym13的最佳候选基因，并将Sym27可能的候选基因列表缩小到十个，从而证明PMD可用于豌豆基因定位和克隆。PMD1和PMD2中包含的所有信息可在www.peamarker.arriam.ru上获取。
