A New Intra-Specific and High-Resolution Genetic Map of Eggplant based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour

Eggplant is the second most important Solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches have been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross '305E40?, (androgenetic introgressed line carrying the locus Rfo-Sa1 conferring Fusarium resistance) x '67/3? (breeding line whose genome sequence was recently released). 163 RILs were genotyped by a genotype-by-sequencing (GBS) approach, which allowed us to identify 10,361 polymorphic sites. Overall, 267 Gb of sequencing data were generated and ~773M Illumina paired-ends (PE) reads were mapped against the reference sequence. A new linkage map was developed, including 7,249 SNPs assigned to the 12 chromosomes and spanning 2,169.23 cM, with an average distance of 0.4 cM between adjacent markers. This was used to elucidate the genetic bases of seven traits related to anthocyanin content in different organs recorded in three locations as well as seed vigor. Overall, from 7 to 17 QTLs (at least one major QTL) were identified for each trait. These results demonstrate that our newly developed map supplies valuable information for QTLs fine mapping, candidate gene identification, and the development of molecular markers for marker assisted selection (MAS) of favorable alleles.