5 Molecular Linkage Maps in Castor Bean Xuegui Yin, Jiannong Lu, Rukam Singh Tomar, Rajinder Singh Chauhan and Kwadwo Gyapong Agyenim-Boateng Abstract With the development of the global economy, the demand for castor bean and castor oil is increasing rapidly, but its cultivation suffers from a lack of high-yielding varieties due to limited genetic research. In this chapter, we describe novel SSR markers developed from the castor bean genome sequence and the first SSR-based genetic linkage map of castor bean, constructed with three different F 2 populations derived from crosses between the YC2, YF1, and YF2 lines. The SSR density in the castor bean genome is approx- imately 15.81 SSR/Mbp, and the frequency of SSR motifs decreased with the increase of repeat unit size. Dinucleotide and trinucleotide repeats, with (AT)n and (AAT)n are the most common repeat units. The linkage map con- sisted of 331 markers, distributed on ten linkage groups (LGs), encompassing 1164.73 cM, with an average marker interval of 3.63 cM. We will also discuss the first high-density genetic map of castor by using SLAF markers, developed by specific length amplified fragment sequencing (SLAF-seq). This map contains 4300 markers as well as 120 SSR markers with an average marker interval of 0.35 cM, making it the densest castor bean genetic map. These genetic resources are expected to facilitate castor bean research and breeding as well as comparative genomics analyses within the spurge family. 5.1 Introduction Genetic mapping is the process of determining the order of and relative distance between genetic markers (specific DNA sequences or heritable elements that generate a detectable phenotype) on a given species’ chromosomes. The relative location of genetic markers is determined based on their pattern of inheritance and is represented on a genetic or linkage map. The frequencies of recombination between markers due to the crossover of homologous chromosomes during meiosis are used to construct genetic maps. The genetic distance between markers in a genetic map is proportional to the recombination X. Yin (&) Á J. Lu Á K. G. Agyenim-Boateng Agricultural College, Guangdong Ocean University, Zhanjiang, Guangdong, China e-mail: yinxuegui@126.com R. S. Tomar Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India e-mail: rukam@jau.in; rukamsingh@gmail.com R. S. Chauhan Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India © Springer Nature Switzerland AG 2018 C. Kole and P. Rabinowicz (eds.), The Castor Bean Genome, Compendium of Plant Genomes, https://doi.org/10.1007/978-3-319-97280-0_5 77