Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip

Abstract The domestication of tomato has led to striking variations in fruit morphology. Here, we show a genome-wide association study (GWAS) to understand the development of the fruit tip and describe a POINTED TIP ( PT ) gene that encodes a C2H2-type zinc finger transcription factor. A single nucleotide polymorphism is found to change a histidine (H) to an arginine (R) in the C2H2 domain of PT and the two alleles are referred to as PT H and PT R . Knocking out PT H leads to development of pointed tip fruit. PT H functions to suppress pointed tip formation by downregulating the transcription of FRUTFULL 2 ( FUL2 ), which alters the auxin transport. Our evolutionary analysis and previous studies by others suggest that the PT R allele likely hitch-hiked along with other selected loci during the domestication process. This study uncovers variation in PT and molecular mechanism underlying fruit tip development in tomato.