Construction of a SNP-based high-density genetic map for pummelo using RAD sequencing

Abstract

Pummelo (Citrus grandis) is one of the most important gene pools for citrus breeding programmes. A high-density linkage map is a valuable tool for functional genomics and genetic breeding studies. A newly developed genome sequence-based marker technology, restriction site-associated DNA (RAD) sequencing, has proven to be powerful for the rapid discovery and genotyping of genome-wide SNP markers and for the high-density genetic map construction. We present the construction of a high-density genetic map of pummelo using RAD sequencing. An F1 population of 124 individuals and its parents (‘Pingshan’ pummelo and ‘Guanxi’ pummelo) were applied to the map construction. One thousand five hundred forty three high-quality single nucleotide polymorphism (SNP) markers were developed and mapped to nine linkage groups. In addition, 20 simple sequence repeat (SSR) markers were included and showed general consistency with the SNP markers. These 1563 markers constituted a total genetic length of 976.58 cM and an average of 0.62 cM between adjacent loci. The number of markers within each linkage group (LG) ranged from 81 (for LG4) to 285 (for LG2). A comparison of the genetic maps to the published sweet orange (Citrus sinensis) genome revealed both conservation and variations. The alignment of the LGs from this map was also shown in comparison with a previously genetic linkage map from pummelo. This study showed that the RAD sequencing allowed the rapid discovery of a large number of SNPs in the pummelo. The SNP-based high-density genetic map for pummelo was successfully generated by using these designed SNP markers. The completed genetic map is a valuable resource for further pummelo genetic studies and provides useful information for gene positional cloning, MAS breeding and C. grandis genome assembly.