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

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 <i>PAP</i> gene family was performed for four cotton species (<i>G. hirsutum</i>, <i>G. barbadense</i>, <i>G. raimondii</i>, and <i>G. arboreum</i>) to explore its potential role in improving fiber quality. A total of 193 <i>PAP</i> genes were identified in these species, revealing several conserved domains that contribute to their functional diversity. Phylogenetic analysis showed that the cotton <i>PAP2</i> genes exhibited high homology with <i>NtPAP12</i>, 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 <i>GhPAP2.2</i>, <i>GhPAP2.6</i>, <i>GhPAP2.8</i>, and <i>GhPAP2.9</i> in EZ60 fibers during 20-25 DPA compared to CCRI127. These results highlight the potential influence of <i>PAP</i> genes on cotton fiber development and provide valuable insights for improving fiber quality in cotton breeding.