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Genome-wide identification of bHLH gene family and screening of genes related to prickle development in Zanthoxylum armatum

Yuwei Yi, Hualin Zou, Nuo Wang, Yansheng Xue, Weiwei Zhang , Feng Xu, Jiabao Ye, Yongling Liao

Abstract

Zanthoxylum armatum has edible and medicinal value but its prickles make harvesting hard. The bHLH gene family is vital in regulating physiological and developmental processes. 195 ZabHLH genes from its genome were grouped into 11 subgroups and 23 subfamilies. Members of the bHLH IIIf subfamily play an important role in trichome development, and ZabHLH22, ZabHLH110, ZabHLH161, and ZabHLH194, which belong to this subfamily, were selected as candidate genes. Chromosomal localization analysis showed that 165 of 195 ZabHLHs were unevenly distributed on 31 chromosomes, and 30 ZabHLHs were localized to unanchored scaffolds. The expansion of ZabHLHs mainly includes dispersed replication and WGD or Segmental replication. 47 cis-acting elements were predicted in the promoters of ZabHLHs, with hormone-responsive elements being the most abundant. Expression profiles of 4 candidate genes were mapped in two Z. armatum cultivars. Trichome development is regulated by hormones such as MeJA, SA, and IAA. The qRT-PCR results indicate that 4 candidate genes respond to the stress induced by these three hormones. We predict that ZabHLH110, ZabHLH161 and ZabHLH194 are most likely involved in prickle development. The results are helpful to further explore the potential roles and mechanism of ZabHLHs in the development of Z. armatum prickle.

FP24345  Accepted 26 June 2025

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