PT  - JOURNAL ARTICLE
AU  - Hokuto Nakayama
AU  - Steven D. Rowland
AU  - Zizhang Cheng
AU  - Kristina Zumstein
AU  - Julie Kang
AU  - Yohei Kondo
AU  - Neelima R. Sinha
TI  - Leaf form diversification in an heirloom tomato results from alterations in two different <em>HOMEOBOX</em> genes
AID  - 10.1101/2020.09.08.287011
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.09.08.287011
4099  - http://biorxiv.org/content/early/2020/09/09/2020.09.08.287011.short
4100  - http://biorxiv.org/content/early/2020/09/09/2020.09.08.287011.full
AB  - Domesticated plants and animals display tremendous diversity in various phenotypic traits and often this diversity is seen within the same species. Tomato (Solanum lycopersicum; Solanaceae) cultivars show wide variation in leaf morphology, but the influence of breeding efforts in sculpting this diversity is not known. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, which is a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato, Silvery Fir Tree (SiFT). Additionally, a comparative gene network analysis revealed that reduced expression of the ortholog of WUSCHEL RELATED HOMEOBOX 1 is also important for the narrow leaflet phenotype seen in SiFT. Phylogenetic and comparative genome analysis using whole-genome sequencing data suggests that the bip mutation in SiFT is likely a de novo mutation, instead of standing genetic variation. These results provide new insights into natural variation in phenotypic traits introduced into crops during improvement processes after domestication.Competing Interest StatementThe authors have declared no competing interest.