Combination analysis of genome-wide association and transcriptome sequencing identifies tuberous root development-related homeobox transcription factors and functional analysis of IbHB040 in sweetpotato

Homeobox (HB) transcription factors are a large gene family and function as critical regulators in plant growth and development. Here, 134 sweetpotato HBs (IbHBs) were systematically identified from the sweetpotato genome and designated as IbHB001-IbHB134. These IbHBs were unevenly distributed on 15 chromosomes, and multiple segmental duplications were identified between them. Collinearity analysis between IbHBs and HBs from other species revealed the evolution of the HB gene family. The 134 IbHB proteins were categorized into 13 classes based on phylogenetic analysis and conserved motifs, while no members were found in the LD class. Additionally, transcriptome data showed 77 differentially expressed IbHBs, and six IbHBs (IbHB003, IbHB040, IbHB064, IbHB071, IbHB080 and IbHB117) were selected for further analysis. The qRT-PCR results suggested that the selected IbHBs were variably expressed in different sweetpotato tissues and varied in response to multiple hormone treatments (IAA, indoleacetic acid; ZT, zeatin and ABA, abscisic acid). Moreover, multiple hormone-related and light-responsive cis-elements were detected in IbHB promoters. In addition, multiple complexes between IbHB proteins were predicted and IbHB064, IbHB071, and IbHB080 exhibited transactivation activity in yeasts. The function of IbHB040 in sweetpotato roots was investigated using the sweetpotato root transgenic system, and the results indicated that IbHB040 might regulate tuberous root development by impacting auxin biosynthesis, cell division and SRD1. These findings provide valuable information for further functional investigation of HBs in tuberous root development.