A Transcript-Based Linkage Map in Apios americana ("Potato Bean") and Synteny Analysis with Other Warm-Season Legumes

Current sequencing techniques are capable of generating a good representation of the sequence of an organism’s genome or transcriptome inexpensively. Such sequencing facilitates the genetic characterization of various “orphan” plant species, including some that may have a promising future as new crops. We used transcriptome sequencing to identify polymorphic markers for building a high-density linkage map of a tuberous legume, Apios americana (2n=2x=11). A pseudo-testcross strategy was implemented to perform the linkage analysis in a F1 mapping population (73 individuals), derived from a cross between a known maternal parent (AA-2155) and unknown pollen source. A robust Apios reference transcriptome was de novo assembled and refined for aligning reads from the mapping population genotypes and identifying genetic markers. In total, 2,624 high quality single nucleotide polymorphic (SNP) markers were used to calculate pairwise recombination and linkage distances. The final Apios map consisted of 13 linkage groups with 957 recombinationally distinct loci covering ~1171 cM of genetic distance. Comparative analyses using the sequences of mapped loci revealed distinct regions syntenic to those of related warm-season legumes. More Apios marker sequences showed matches with Phaseolus vulgaris and Glycine max than Vigna angularis and Vigna radiata. However, the co-linearity of the Apios linkage groups was comparatively higher with the Vigna species than with P. vulgaris and G. max, which displayed more interrupted synteny patterns. This study presents the first linkage map for A. americana, and a general protocol for sequencing-based construction of high-density linkage maps in less characterized species.