Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato

Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on similar to 4.4 million single nucleotide polymorphisms obtained from 605 diverse accessions, we performed a comprehensive genome-wide association study for 27 agronomic traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many previously reported and additional genes related to vegetative and reproductive development, were identified, and these loci explained an average of similar to 8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection during tomato domestication and improvement. Furthermore, a candidate gene, SI-ACTIVATED MALATE TRANSPORTER15, that encodes an aluminum-activated malate transporter was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation, thereby affecting photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

Automated summary

Tomato yield is an important agronomic trait, and this study identified key genetic loci associated with yield through comprehensive genome-wide association analysis, revealing some genes related to tomato domestication and improvement. Furthermore, a candidate gene related to leaf stomata formation was functionally characterized, providing valuable information for genetics and breeding of tomato.