Natural variations in GhNF-YB3 contribute to seed cotton yield by modulating source-to-sink sucrose allocation

Abstract Cotton is one of the most important textile and oil crops in the world. The fibers derived from the seed coat epidermis are crucial raw materials for the textile industry, and the seeds are also valuable sources of plant protein and oil for human consumption and animal feed. The seed cotton yield is a complex quantitative trait, but few causal genes have been characterized, and the underlying mechanisms remain largely unknown. Here, we characterize a nuclear factor YB subunit coding gene GhNF-YB3 as a key regulator of seed cotton yield, with variations in the promoter and 3’ untranslated region (3’UTR) present in upland cotton cultivars significantly associated with seed cotton yield. Functional investigations reveal that the GhNF-YB3-YC2-YA1 complex directly targets the trehalose-6-phosphate synthase (TPS) genes GhTPS9 and GhTPS11 to activate the trehalose-6-phosphate (T6P)-mediated signaling pathway, thereby promoting sucrose allocation and utilization in developing seeds. Besides, overexpression of GhNF-YB3 activates the expression of most sucrose transport genes in the ovule, which could facilitate phloem unloading and post-phloem transport of sucrose. An increased influx of sucrose into the ovule results in the expansion of the inner integument cells during development. These findings provide insights into the key role of T6P-mediated source-sink carbon allocation in regulating crop yield and offer a strategy for improving seed cotton yield through the selection of ideal genotypes.