Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo and is unique to SiFT and not introgressed from other tomato genomes. These results provide new insights into the natural variation in phenotypic traits introduced into crops during improvement processes after domestication and establish homeobox genes as evolutionary hotspots.

驯化的植物表现出不同的表型特征。然而，育种努力对这种表型多样性的影响仍然未知。在这里，我们证明了BEL-LIKE HOMEODOMAIN基因BIPINNATA的同源框基序中的单核苷酸缺失导致传家宝番茄（Solanum lycopersicum）银杉树（SiFT）中的高度复杂的叶子表型，它被用作一种景观和观赏植物。比较基因网络分析显示，抑制SOLANIFOLIA是WUSCHEL RELATED HOMEOBOX 1的直系同源物，导致在 SiFT 中看到的窄小叶表型。比较基因组学表明SiFT中的bip突变可能是从头产生的并且是 SiFT 独有的，并且没有从其他番茄基因组中渗入。这些结果为驯化后改良过程中引入作物的表型性状的自然变异提供了新的见解，并将同源盒基因确立为进化热点。