Development of gene-based markers for black fruit color traits based on GBS-GWAS analysis of tomato germplasms

Black tomatoes (Solanum lycopersicum) are characterized by high anthocyanin levels, offering numerous health benefits. This study aimed to develop molecular markers for accurate identification of black tomatoes to enhance breeding efficiency in two populations consisting of 96 tomato lines each. Genotyping-by-sequencing (GBS) and genome-wide association study (GWAS) analyses of the first population revealed 10 significant single nucleotide polymorphisms (SNPs) associated with black tomatoes on chromosomes 7 and 10. The 10 SNPs distinguished black tomatoes with 98.82–98.96% accuracy in the first population. Further investigation into the SNP-containing region found three candidate genes of MYB-like transcription factor ETC1 (Solyc07g052490) and R2R3-MYB transcription factors (Solyc10g086250 and Solyc10g086260). A comparative analysis of allelic sequences revealed two SNPs on Solyc07g052490 and five on Solyc10g086260 distinguishing black tomatoes. Three gene-based markers (B07_2490-2, B10_6260-1, and B10_6260-3) derived from Solyc07g052490 and Solyc10g086260 achieved 100% accuracy in identifying black tomatoes. These markers have the potential to significantly reduce development time and enhance efficiency in black tomato breeding programs, providing valuable tools for tomato breeders and researchers.