# The PAP Gene Family in Cotton: Impact of Genome-Wide Identification on Fiber Secondary Wall Synthesis

## TL;DR

This study identifies PAP genes in cotton and links them to fiber quality, offering insights for improving cotton fiber traits.

## Contribution

The study provides a genome-wide analysis of PAP genes in cotton and links specific PAP genes to fiber secondary wall synthesis.

## Key findings

- 193 PAP genes were identified across four cotton species with conserved functional domains.
- GhPAP2.2, GhPAP2.6, GhPAP2.8, and GhPAP2.9 showed higher expression in fibers of a cotton variety with thicker fibers.
- PAP2 genes in cotton are closely related to a known cell wall synthesis gene, NtPAP12.

## Abstract

Cotton is a crucial cash crop widely valued for its fiber. It is an important source of natural fiber and has diverse applications. Improving fiber quality is of significant economic and agricultural importance. Purple acid phosphatases (PAPs) are multifunctional enzymes critical for plant cell wall biosynthesis, root architecture modulation, low-phosphorus stress adaptation, and salt/ROS stress tolerance. In this study, a comprehensive genome-wide analysis of the PAP gene family was performed for four cotton species (G. hirsutum, G. barbadense, G. raimondii, and G. arboreum) to explore its potential role in improving fiber quality. A total of 193 PAP genes were identified in these species, revealing several conserved domains that contribute to their functional diversity. Phylogenetic analysis showed that the cotton PAP2 genes exhibited high homology with NtPAP12, a cell wall synthesis-related gene. Using cotton varieties with contrasting fiber thickness (EZ60, micronaire 4.5 vs. CCRI127, micronaire 3.5), qRT-PCR analysis demonstrated significantly higher expression levels of GhPAP2.2, GhPAP2.6, GhPAP2.8, and GhPAP2.9 in EZ60 fibers during 20–25 DPA compared to CCRI127. These results highlight the potential influence of PAP genes on cotton fiber development and provide valuable insights for improving fiber quality in cotton breeding.