(1) Background: Upland cotton (Gossypium hirsutum L.) is the most important natural fiber worldwide, and it is extensively planted and plentifully used in the textile industry. Major cotton planting regions are frequently affected by abiotic stress, especially drought stress. Drought resistance is a complex, quantitative trait. A genome-wide association study (GWAS) constitutes an efficient method for dissecting the genetic architecture of complex traits. In this study, the drought resistance of a population of 316 upland cotton accessions was studied via GWAS. (2) Methods: GWAS methodology was employed to identify relationships between molecular markers or candidate genes and phenotypes of interest. (3) Results: A total of 8, 3, and 6 SNPs were associated with the euphylla wilting score (EWS), cotyledon wilting score (CWS), and leaf temperature (LT), respectively, based on a general linear model and a factored spectrally transformed linear mixed model. For these traits, 7 QTLs were found, of which 2 each were located on chromosomes A05, A11, and D03, and of which 1 was located on chromosome A01. Importantly, in the candidate regions WRKY70, GhCIPK6, SnRK2.6, and NET1A, which are involved in the response to abscisic acid (ABA), the mitogen-activated protein kinase (MAPK) signaling pathway and the calcium transduction pathway were identified in upland cotton at the seedling stage under drought stress according to annotation information and linkage disequilibrium (LD) block analysis. Moreover, RNA sequencing analysis showed that WRKY70, GhCIPK6, SnRK2.6, and NET1A were induced by drought stress, and the expression of these genes was significantly different between normal and drought stress conditions. (4) Conclusions: The present study should provide some genomic resources for drought resistance in upland cotton. Moreover, the germplasm of the different phenotypes, the detected SNPs and, the potential candidate genes will be helpful for molecular marker-assisted breeding studies about increased drought resistance in upland cotton.

Background: Appropriate plant architecture can improve the amount of cotton boll opening and allow increased planting density, thus increasing the level of cotton mechanical harvesting and cotton yields. The internodes of cotton fruiting branches are an important part of cotton plant architecture. Thus, studying the molecular mechanism of internode elongation in cotton fruiting branches is highly important.Results: In this study, we selected internodes of cotton fruiting branches at three different stages from two cultivars whose internode lengths differed significantly. A total of 76,331 genes were detected by transcriptome sequencing. By KEGG pathway analysis, we found that DEGs were significantly enriched in the plant hormone signal transduction pathway. The transcriptional data and qRT-PCR results showed that members of theGH3gene family, which are involved in auxin signal transduction, andCKXenzymes, which can reduce the level of CKs, were highly expressed in the cultivar XLZ77, which has relatively short internodes. Genes related to ethylene synthase (ACS),EIN2/3andERFin the ethylene signal transduction pathway and genes related toJAR1,COI1andMYC2in the JA signal transduction pathway were also highly expressed in XLZ77. Plant hormone determination results showed that the IAA and CK contents significantly decreased in cultivar XLZ77 compared with those in cultivar L28, while the ACC (the precursor of ethylene) and JA contents significantly increased. GO enrichment analysis revealed that the GO categories associated with promoting cell elongation, such as cell division, the cell cycle process and cell wall organization, were significantly enriched, and related genes were highly expressed in L28. However, genes related to the sphingolipid metabolic process and lignin biosynthetic process, whose expression can affect cell elongation, were highly expressed in XLZ77. In addition, 2067 TFs were differentially expressed. TheWRKY,ERFandbHLHTF families were the top three largest families whose members were active in the two varieties, and the expression levels of most of the genes encoding these TFs were upregulated in XLZ77.Conclusions: Auxin and CK are positive regulators of internode elongation in cotton branches. In contrast, ethylene and JA may act as negative regulators of internode elongation in cotton branches. Furthermore, theWRKY,ERFandbHLHTFs were identified as important inhibitors of internode elongation in cotton. In XLZ77(a short-internode variety), the mass synthesis of ethylene and amino acid conjugation of auxin led to the inhibition of plant cell elongation, while an increase in JA content and degradation of CKs led to a slow rate of cell division, which eventually resulted in a phenotype that presented relatively short internodes on the fruiting branches. The results of this study not only provide gene resources for the genetic improvement of cotton plant architecture but also lay a foundation for improved understanding of the molecular mechanism of the internode elongation of cotton branches.

Cotton has a high salt tolerance. However, due to the high salt content and low K⁺/Na⁺ ratio in saline soils, cotton yield and fiber quality are difficult to improve. To investigate the effects of potassium (K) on cotton fiber length under salt stress, a two-year bucket-based field experiment was conducted using two different cultivars (CCRI 79, salt tolerant, and Simian 3, salt sensitive). Three K rates (K0, 0 kg K₂O ha⁻¹; K150, 150 kg K₂O ha⁻¹; and K300, 300 kg K₂O ha⁻¹) were applied at low, middle, and high soil electrical conductivities (S1, 1.7–1.8 dS m⁻¹; S2, 6.4–6.9 dS m⁻¹; and S3, 10.6–11.8 dS m⁻¹) to investigate the absorption, transport, and distribution characteristics of K⁺ and Na⁺ in the boll-leaf system (including the leaf subtending the cotton boll (LSCB), fruiting branch, boll shell, and fiber) of both cotton cultivars, as well as the relationship with fiber length. The results showed that K application (K150 and K300) significantly increased the cotton fiber length under salt stress, with the largest fiber length alleviation coefficients (AC) in the middle fruiting branches. The AC decreased with an increase in salt stress and was greater in CCRI 79 than in Simian 3. The K150 treatment (soil K⁺/Na⁺ = 1/13) completely mitigated the reduction in fiber length caused by S2 salt stress in CCRI 79, whereas the K300 treatment (soil K⁺/Na⁺ = 1/10) completely eased the reduction in fiber length caused by S2 salt stress in Simian 3. An application of K under salt stress increased the K⁺ content and K⁺/Na⁺ ratio in the soil and the organs of the boll-leaf system, regulated the K⁺/Na⁺ homeostasis in the boll-leaf system, enhanced the K⁺-selective transport coefficient (S_K-Na) in the LSCB, maintained a high K⁺/Na⁺ ratio in the fiber, and mitigated the fiber length reduction. In conclusion, the fiber length reduction in salt-tolerant cultivars was completely mitigated by K150 (i.e., soil K⁺/Na⁺ = 1/13) under moderate salt stress; however, it was not completely mitigated by K application under high salt stress.

Plant growth regulators (PGRs) enhance crop stress resistance but their roles in microbial-mediated phosphorus cycling within intercropping systems are unclear. Thus, We conducted a two-year field study using corn (Zea mays L. cv. Denghai 605) and soybean (Glycine max L. cv. Hedou 22) in fluvisols and luvisols soil according to World Reference Base for Soil Resources (WRB) standard. Under a 4-row corn and 6-row soybean strip intercropping system, three treatments were applied: a water control (CK), and two plant growth regulators—T1 (EC: ethephon [300 mg/L] + cycocel [2 g/L]) and T2 (ED: ethephon [300 mg/L] + 2-Diethyl aminoethyl hexanoate [10 mg/L]). Foliar applications were administered at the V7 stage (seventh leaf) of intercropped corn plants to assess how foliar-applied PGRs (T1/T2) modulated the soil phosphorus availability, microbial communities, and functional genes in maize intercropping systems. PGRs increased the soil organic phosphorus and available phosphorus contents, and alkaline phosphatase activity, but not total phosphorus. PGRs declined the α-diversity in fluvisols soil but increased the α-diversity in luvisols soil. The major taxa changed from Actinobacteria (CK) to Proteobacteria (T1) and Saccharibacteria (T2) in fluvisols soil, and from Actinobacteria/Gemmatimonadetes (CK) to Saccharibacteria (T1) and Acidobacteria (T2) in luvisols soil. Functional gene dynamics indicated soil-specific regulation, where fluvisols soil harbored more phoD (organic phosphorus mineralization) and relA (polyphosphate degradation) genes, whereas phnP gene dominated in luvisols soil. T1 stimulated organic phosphorus mineralization and inorganic phosphorus solubilization in fluvisols soil, upregulating regulation genes, and T2 enhanced polyphosphate synthesis and transport gene expression in luvisols soil. Proteobacteria, Nitrospirae, and Chloroflexi were positively correlated with organic phosphorus mineralization and polyphosphate cycling genes, whereas Bacteroidetes and Verrucomicrobia correlated with available potassium (AP), total phosphorus (TP), and alkaline phosphatase (ALP) activity. Thus, PGRs activated soil phosphorus by restructuring soil type-dependent microbial functional networks, connecting PGRs-induced shifts with microbial phosphorus cycling mechanisms. These findings facilitate the targeted use of PGRs to optimize microbial-driven phosphorus efficiency in strategies for sustainable phosphorus management in diverse agricultural soils.