Development and validation of the OVATE gene-based functional marker to assist fruit shape selection in tomato.

Fruit size, shape and colour are important determinants of fruit quality in tomato. Among the different genetic factors, the OVATE gene is a key regulator of fruit elongation in tomato. The loss-of-function recessive ovate allele results from a functional single nucleotide polymorphism (SNP) in the second exon of the gene to produce fruit elongation and variable fruit shapes in different genetic backgrounds. The mutation has also been associated with increased fruit firmness, a desirable trait for processing purpose of tomato. However, the recessive nature of this important mutant allele makes its identification and utilization in breeding programme difficult. Hence, we developed the OVATE gene-based functional marker using the tetra-primer amplification refractory mutation system (T-ARMS) strategy. The developed functional marker was capable of identifying the allelic status at OVATE locus in a co-dominant manner, using routine polymerase chain reaction (PCR) followed by standard agarose gel electrophoresis. Trait-marker association of the developed functional marker was validated in the F2 segregants bearing elongated and non-elongated fruits. Thus, the functional marker developed and validated in this study will assist the tomato breeders in identification and introgression of the desired allelic version of the OVATE gene in a time-, labour- and cost-effective manner. Moreover, identification of the allelic status at the OVATE locus will help in exploring its interacting partners and modifiers for detailed understanding of the fascinating genetics behind fruit shape variation in tomato. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03029-7. © King Abdulaziz City for Science and Technology 2021.