Multi-Omics analysis reveals the important role of indole-3-acetic acid homeostasis in male fertility of cotton

Auxin (Indole-3-acetic acid, IAA) is essential for anther development and male fertility, but little is known about its homeostasis in developing anthers due to its complex and diverse synthesis pathways. Here, we employed transcriptomic, targeted metabolomic, and amino acid analyses on a wild type (WT) cotton ( Gossypium hirsutum ) line SD98–6 and its nearly-isogenic male sterile (MS) line SD98–6A, to delve into the relationship between IAA and anther fertility. In WT anthers, IAA homeostasis was achieved mainly through self-synthesis, conjugate hydrolysis, and polar transport, and accumulation of IAA exhibited an inverted "U" pattern with the highest content observed at the tetrad stage. In MS anthers, no IAA accumulation was observed after the meiosis stage and the IAA content remained constantly low, mainly due to reduction of the substrates (phenylalanine and tryptophan) for IAA synthesis, and significantly decreased expression of the genes involved in IAA synthesis. Meanwhile, carbohydrate metabolism pathways directly contributing to IAA synthesis and synthesis of amino acids were malfunctional in MS anthers based on the expression profile of the metabolic genes and content measurement. These results provide valuable insights into the IAA homeostasis in cotton anthers and imply that genes related to IAA homeostasis are potential targets for development of IAA-sensitive male sterile cotton lines.