Uncovering tomato candidate genes for seed germination performance and seedling vigour using the Solanum pennellii introgression line population

•S. pennellii introgressions enhance seed germination and vigour of some IL’s.•Seven candidate genes for seed germination were identified using the IL’s population.•Six candidate genes for seed vigour were identified using the IL’s population. Both fast seed germination and seedling vigour are important for proper crop establishment and higher yields. These traits seem to be controlled by several QTL’s and are highly influenced by environmental conditions. In this work, we aimed to evaluate seed germination performance and vigour traits of several Solanum pennellii introgression lines (IL’s) to select ideotypes for germination and vigour; and then investigate the selected IL’s to uncover candidate genes for these traits. We performed a germination test followed by the analysis of seedling growth in a collection of 46 different homozygous tomato IL’s and their genitors' accession LA716 and cv M82, grown in the field in two consecutive growing seasons. From these tests, several traits were calculated. Then, we used a multi-trait index based on factor analysis and genotype-ideotype distance (FAI-BLUP index) to properly rank the genotypes according to their seed germination performance and seedling vigour. Following the ranking, introgressed segments of interest were identified for further analysis of candidate gene identification using the map of the tomato IL population as provided by the SOL Genomics Network. The IL 6−1, IL 4−1−1, IL 4−4, IL 11−4−1, IL 1−1−2, and IL 10−1 were selected through the FAI-BLUP index as the closest to the ideotype for seed germination performance and vigour. The genes At1g75350, At2g26350, At2g28490, At3g10920, At5g13200, At5g41480, and At4g21800 were identified as candidate genes for seed germination. The genes At5g53000, At1g46480, At1g30755, At5g47390, At2g29630, and At4g03400 were identified as candidate genes for seed vigour. Fine mapping, validation, and further investigation of these genes will provide valuable insights into the genetics of seed quality.