First Report of the Construction of a Genetic Linkage Map of Pea Using Genotyping By Sequencing

Pea (Pisum sativum L.) is one of the oldest domesticated crops in the world and is an important source of protein for human food and animal feed in many countries. It is rich in a variety of nutritional components, such as mineral nutrients, carbohydrates and several vitamins. However, molecular genetic research of pea has lagged behind other crops because of its large and complex genome. The objectives of this research were to develop single nucleotide polymorphism (SNP) markers using genotyping by sequencing (GBS) and to construct a high-density genetic linkage map. A total of 384,693,176 reads were obtained from GBS and the quality of the raw data was verified by FastQC. Through analysis with the UNEAK SNP-calling pipeline, 2292 SNP loci showed polymorphism between Aragorn and Kiflica, the parents of an F₆-derived recombinant inbred line (RIL) population. A high-density genetic linkage map was constructed by integrating previously published SSR and SNP markers with our newly identified SNP markers. Syntenic relationships between the pea map and a Medicago truncatula map were constructed. This SNP-based genetic linkage map will be the foundation of molecular genetic studies in pea and be particularly helpful for the identification of quantitative trait loci (QTL) for traits of interest relating to mineral nutrients in pea.