Identification and Validation of New Alleles of FALSIFLORA and COMPOUND INFLORESCENCE Genes Controlling the Number of Branches in Tomato Inflorescence

The architecture of inflorescences shows extensive diversity in both branching frequency and flower number, which eventually, determines agricultural productivity. In this study, F(2) (second filial) populations derived from a cross between Solanum lycopersicum 10AS111A (highly-branched inflorescence) and the S. pimpinellifolium PI124039 (inflorescence having a single branch) were used to decipher the genetic control of branch number (BN) of inflorescence in plants bearing small-sized tomato fruits. The segregation ratio of single- and moderately-branched types to the highly-branched type was significantly different from 3:1 but not different from 15:1 at p < 0.05, suggesting that more than one gene controls the branch number of the inflorescences. Through genome-wide comparison of single-nucleotide polymorphism (SNP) profiles between the highly-branched type bulk and the single-branch type bulk constructed using the F(2) plants, we identified a major quantitative trait locus (QTL) on chromosome 3 (58.75–61.4 Mb) and a minor QTL on chromosome 2 (32.95–37.1 Mb), which explained 15.7% and 6.1% of the BN variation, respectively. FALSIFLORA (FA) and COMPOUND INFLORESCENCE (S) genes, located in the QTL peak regions, caught our attention. Sequence comparison of the FA and S genes and their promoter regions from the two parental lines revealed that both contain missense mutations in the coding regions. Segregation analysis of FA and S alleles by high-resolution melting (HRM) method confirmed that alleles for both genes from 10AS111A significantly increased the BN and the size of inflorescence. In conclusion, we propose that SNPs in coding sequences might cause changes in the function of FA and S genes, which might be important determinants of BN.