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

Machine Learning-Based Tomato Fruit Shape Classification System

Fruit shape significantly impacts the quality and commercial value of tomatoes (Solanum lycopersicum L.). Precise grading is essential to elucidate the genetic basis of fruit shape in breeding programs, cultivar descriptions, and variety registration. Despite this, fruit shape classification is still primarily based on subjective visual inspection, leading to time-consuming and labor-intensive processes prone to human error. This study presents a novel approach incorporating machine learning techniques to establish a robust fruit shape classification system. We trained and evaluated seven supervised machine learning algorithms by leveraging a public dataset derived from the Tomato Analyzer tool and considering the current four classification systems as label variables. Subsequently, based on class-specific metrics, we derived a novel classification framework comprising seven discernible shape classes. The results demonstrate the superiority of the Support Vector Machine model in terms of its accuracy, surpassing human classifiers across all classification systems. The new classification system achieved the highest accuracy, averaging 88%, and maintained a similar performance when validated with an independent dataset. Positioned as a common standard, this system contributes to standardizing tomato fruit shape classification, enhancing accuracy, and promoting consensus among researchers. Its implementation will serve as a valuable tool for overcoming bias in visual classification, thereby fostering a deeper understanding of consumer preferences and facilitating genetic studies on fruit shape morphometry.

Genome editing of DWARF and SELF-PRUNING rapidly confers traits suitable for plant factories while retaining useful traits in tomato

Plant factories with artificial light are less affected than open-air areas to environmental factors in crop cultivation and are attracting attention as one of the solutions to the world's food problems. However, the cost of cultivation in plant factories is higher than open-air cultivation, and currently, profitable factory-grown crop varieties are limited to those that are small or have a short growing period. Tomatoes are one of the main crops consumed around the world, but due to their large plant height and width, they are not yet suitable for mass production in plant factories. In this study, the DWARF (D) and SELF-PRUNING (SP) genes of the GABA hyperaccumulating tomato variety #87-17 were genome-edited by the CRISPR-Cas9 method to produce dwarf tomato plants. The desired traits were obtained in the T1 genome-edited generation, and the fruit traits were almost the same as those of the original variety. On the other hand, the F2 cross between #87-17 and Micro-Tom containing the d and sp mutations was dwarfed, but the fruit phenotype was a mixture of the traits of the two varieties. This indicates that genome editing of these two genes using CRISPR-Cas9 can efficiently impart traits suitable for plant factory cultivation while retaining the useful traits of the original cultivar.

A SUPERMAN-like Gene Controls the Locule Number of Tomato Fruit

Tomato (Solanum lycopersicum) fruits are derived from fertilized ovaries formed during flower development. Thus, fruit morphology is tightly linked to carpel number and identity. The SUPERMAN (SUP) gene is a key transcription repressor to define the stamen-carpel boundary and to control floral meristem determinacy. Despite SUP functions having been characterized in a few plant species, its functions have not yet been explored in tomato. In this study, we identified and characterized a fascinated and multi-locule fruit (fmf) mutant in Solanum pimpinellifolium background harboring a nonsense mutation in the coding sequence of a zinc finger gene orthologous to SUP. The fmf mutant produces supersex flowers containing increased numbers of stamens and carpels and sets malformed seedless fruits with complete flowers frequently formed on the distal end. fmf alleles in cultivated tomato background created by CRISPR-Cas9 showed similar floral and fruit phenotypes. Our results provide insight into the functional conservation and diversification of SUP members in different species. We also speculate the FMF gene may be a potential target for yield improvement in tomato by genetic engineering.

Marker assisted early generation identification of root knot disease resistant orange tomato segregants with multiple desirable alleles

Enhanced bioavailability of cis-isomers of lycopene, accumulated in orange-fruited tangerine mutant has broadened the scope of nutritional enrichment in tomato. At the same time, advancements in the field of marker assisted selection (MAS) have made the stacking of multiple desirable alleles through molecular breeding to develop superior tomato genotypes possible. Here we report seedling stage MAS from 146 F2 plants, to identify 3 superior performing, root knot disease resistant orange-fruited segregants. In the selected segregants, fruit weight ranged from 39.2 to 54.6 g, pericarp thickness ranged from 4.56 to 6.05 mm and total soluble solid content ranged from 3.65 to 4.87° Brix. Presence of parental diversity allowed identification of the other desirable alleles of the genes governing late blight and mosaic disease resistance, growth habit (determinate and indeterminate) as well as fruit elongation and firmness. Resistance to root knot disease of the selected 3 segregants was also validated through a unique method employing in vitro rooted stem cuttings subjected to artificial inoculation, where the resistant parent and the selected segregants developed no galls in comparison to ~ 24 galls developed in the susceptible parent. The selected segregants form the base for development of multiple disease resistant, nutritionally enriched orange-fruited determinate/indeterminate tomato lines with superior fruit quality. The study also highlights the utility of early generation MAS for detailed characterization of segregants, through which multiple desirable alleles can be precisely targeted and fixed to develop superior tomato genotypes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01361-1.

Tetra-Primer Amplification Refractory Mutation System (T-ARMS)

Single-nucleotide polymorphisms (SNPs), the most abundant genetic variation in the population, have become the molecular marker of choice. Generally, the efficient detection of SNPs requires specialized costly equipment. Although there are a few strategies for detecting SNPs through polymerase chain reaction, followed by restriction enzyme digestion and agarose gel electrophoresis, these methods are time-consuming and might be less diagnostic. Interestingly, the tetra primer amplification refractory mutation system (T-ARMS) strategy utilizes a pair of allele-specific primers in a single PCR for the diagnostic detection of SNPs in a codominant manner through standard agarose gel electrophoresis. The simplicity and robustness of the strategy have inspired the researchers to adopt this low-cost method of SNP detection in different crop plants. Here, we have described the principle, methods, and conditions for the T-ARMS strategy. The described methodology starts from the isolation of genomic DNA and ends with the post-PCR analysis of refractory amplicons in standard agarose gel electrophoresis. The limitations and future perspectives are also discussed. Taken together, T-ARMS evolves as a method of choice for low-cost SNP detection in plants.