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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #427395
Research Project: Characterization and Utilization of Genetic Diversity in Soybean and Common Bean and Management and Utilization of the National Rhizobium Genetic Resource Collection

Location: Soybean Genomics & Improvement Laboratory

Title: Lf2 is a knotted homeobox regulator that modulates leaflet number in soybean

Author
item CLARK, CHANCELOR - Purdue University
item CALKWELL, DENISE - Purdue University
item ZHU, QIANG - Purdue University
item PROVANCAL, DOMINIC - Purdue University
item EDWADS, AUSTIN - Purdue University
item Song, Qijian
item Quigley, Charles
item IYER-PASCUZZI, ANJALI - Purdue University
item MA, JIANXIN - Purdue University
item WANG, JINBIN - Purdue University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2025
Publication Date: 1/12/2026
Citation: Clark, C.B., Calkwell, D., Zhu, Q., Provancal, D., Edwads, A.C., Song, Q., Quigley, C.V., Iyer-Pascuzzi, A.S., Ma, J., Wang, J. 2026. Lf2 is a knotted homeobox regulator that modulates leaflet number in soybean. Plant Journal. 125: Article e70658. https://doi.org/10.1101/2025.06.20.660812.
DOI: https://doi.org/10.1101/2025.06.20.660812

Interpretive Summary: Leaves are the primary organ for capturing light energy in photosynthesis. The number of soybean leaflets typically ranges from three to seven, however, the biology and mechanisms of this variation are unknown. Through genetic mapping and genomic analysis, researchers from Purdue University and the USDA-ARS, Beltsville, MD identified a 2-base pair DNA sequence deletion in a gene that disrupts its DNA function, resulting in the seven-leaflet phenotype. This discovery not only deepens the understanding of the compound leaf structure of soybean but also provides a blueprint for using such mutations to improve soybean photosynthetic efficiency and yield.

Technical Abstract: Variation in leaf complexity modulates light capture and is a target for crop enhancement. Soybean typically has compound leaves with three leaflets each, but a spontaneous mutation, designated lf2, possesses seven leaflets, offering a means to dissect the molecular mechanisms specifying leaflet number and assess its potential for soybean improvement. However, the developmental and genetic bases of the lf2 mutation remain unknown. Here, we characterize the seven-leaflet phenotype and identify the mutation responsible for the phenotypic changes. Microscopic examination of leaf emergence sites revealed that the seven-leaflet phenotype arises in a two-step process: five leaflets form initially followed by secondary leaflet initiation at the margins of the central leaflet. Genetic mapping delineated lf2 to a ~2.5 Mb region at the start of chromosome 11. Fortuitously, integration of pedigree analysis with comparative analysis of genomic sequences from the region pinpointed a 2-bp deletion in the coding sequence of a gene, which is homologous to the Arabidopsis KNAT7 encoding a KNOTTED1-LIKE HOMEOBOX 2 transcription factor, as the sole candidate for Lf2. The deletion is predicted to result in disruption of the putative DNA-binding homeodomain. Expression of the wild-type allele of the candidate gene in the seven-leaflet lf2 mutant restored the three-leaflet phenotype, while disruption of the wild-type allele through CRISPR-Cas9 editing induced extra leaflet formation. This study advances our understanding of leaflet formation in legumes and provides a template for utilizing compound leaf architecture to optimize photosynthetic efficiency and yield in soybean.