Key messageqLKR4.1, controlling low K+ resistance in tomato, was fine-mapped to an interval of 67.5 kb on chromosome A04, and one gene encoding phospholipase D delta was identified as a candidate gene.In plants, changes in root length are an important morphological response to low K+ (LK) stress; however, the underlying genetics in tomato remain unclear. Here, we combined bulked segregant analysis-based whole-genome sequencing, single-nucleotide polymorphism haplotyping, and fine genetic mapping to identify a candidate gene as a major-effect quantitative trait loci (QTL), i.e., qLKR4.1, which was associated with LK tolerance due to increased root elongation in the tomato line JZ34. Through multiple analyses, we found that Solyc04g082000 is the most likely candidate for qLKR4.1, which encodes phospholipase D delta (PLD delta). Increased root elongation under LK in JZ34 may be attributed to a non-synonymous single-nucleotide polymorphism in the Ca2+-binding domain region of this gene. Solyc04g082000 increases root length through its PLD delta activity. Silencing of Solyc04g082000(Arg) in JZ34 led to a significant decrease in root length compared with silencing of Solyc04g082000(His) allele in JZ18 under LK conditions. Mutation of a Solyc04g082000 homologue in Arabidopsis, pld delta, resulted in decreased primary root lengths under LK conditions, compared to the wild type. Transgenic tomato expressing the qLKR4.1(Arg) allele from JZ34 exhibited a significant increase in root length compared with the wild type expressing the allele from JZ18 under LK conditions. Taken together, our results confirm that the PLD delta gene Solyc04g082000 exerts important functions in increasing tomato root length and LK tolerance.
