Drought is one of the main abiotic stresses that seriously influences cotton production. Many indicators can be used to evaluate cotton drought tolerance, but the key indicators remain to be determined. The objective of this study was to identify effective cotton drought tolerance indicators from 19 indices, including morphology, photosynthesis, physiology, and yield-related indices, and to evaluate the yield potential of 104 cotton varieties under both normal and drought-stress field conditions. Combined with principal component analysis (PCA) and a regression analysis method, the results showed that the top five PCs among the 19, with eigenvalues > 1, contributed 65.52, 63.59, and 65.90% of the total variability during 2016 to 2018, respectively, which included plant height (PH), effective fruit branch number (EFBN), single boll weight (SBW), transpiration rate (Tr) and chlorophyll (Chl). Therefore, the indicator dimension decreased from 19 to 5. A comparison of the 19 indicators with the 5 identified indicators through PCA and a combined regression analysis found that the results of the final cluster of drought tolerance on 104 cotton varieties were basically consistent. The results indicated that these five traits could be used in combination to screen cotton varieties or lines for drought tolerance in cotton breeding programs, and Zhong R2016 and Xin lu zao 45 exhibited high drought tolerance and can be selected as superior parents for good yield performance under drought stress.

Background: Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. Results: Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. Conclusions: This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.

Background: Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. Results: Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. Conclusions: This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing Upland cotton varieties with high yields and salt stress tolerance.

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Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for G. barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a G. barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0-35 days post-anthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using weighted gene co-expression network analysis. In total, 55 genes were identified as differentially expressed from four specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670 and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. qRT-PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.

Cotton fibre yield and quality are markedly influenced by drought and high-temperature stress. We examined the traits of the leaf stomata in 39 cotton genotypes subjected to exogenous phytohormone abscisic acid (ABA) signalling, electrolyte leakage under 40°C thermal stress, and relative GhHsfA, GhbZIP and GhHSP70 expression levels under two treatments. Stomatal density and area ranged from 66 to 182/mm2 and 663 to 1305 μm2, respectively. Under exogenous ABA signalling, the changes in stomatal aperture (ΔSAp) were in the range of 2.5–31.2%; ΔSAp and relative GhHsfA, GhbZIP and GhHSP70 expression levels were significantly correlated, respectively. Electrolyte leakage increased unequally among cotton genotypes after heat stress. The changes in electrolyte leakage (ΔEL) and relative GhHsfA, GhbZIP and GhHSP70 expression levels were very strongly correlated, respectively. Their relative expression levels could be used as references for the rapid identification of stress-tolerant cotton strains. Cluster analysis of the 39 cotton genotypes indicated that Xinluzao36, Shiyang1, shinong98-7 and Zhongmiansuo293 are heat- and drought-resistant. We integrated both analysis of physiological parameters and molecular methods to identify cotton varieties with the drought and heat tolerance, in order to provide a reference for the selection of materials and methods for the research and production of cotton.

Background Cotton is an economically important crop in China, and drought has seriously affected cotton production. Understanding genetic variation, genotype ×environment interactions, and the associations between these traits is critical for developing improved cotton varieties with high drought tolerance. Methods To screen ideal drought-resistant cotton germplasm lines and excellent genotypes, the yield traits of 103 cotton germplasm lines were analyzed. Cotton resource material was planted under normal watering and water deficit conditions for three consecutive years. The yield traits under normal irrigation and water stress conditions were measured, and then five screening indicators were calculated based on the cotton yield per plant under the two water treatments to determine the ideal genotype and most accurate identification indicators. Results The results of correlation analysis and principal component analysis showed that the geometric mean productivity (GMP), mean productivity (MP), and stress tolerance index (STI) were significantly positively correlated with yield under water stress and could be used to distinguish genotypes with high drought tolerance. Among the experimental germplasm lines, some had higher STI and GMP values, indicating their higher drought tolerance. This result indicates that best linear unbiased prediction (BLUP) analysis of the STI and GMP under drought stress can effectively improve screening for drought tolerance in cotton germplasm lines. The results from the screening index, three-dimensional map, and genotype ×environment (GGE) biplots were consistent with the above results. We determined that CQJ-5, Xin lu zao 45, Bellsno, Zhong R 2016 and ND 359-5 are drought-tolerant genotypes that can be used to breed drought-tolerant germplasm lines that produce high and stable yields.

The 2OG-Fe(II) oxygenase (RF) family of enzyme proteins can affect bulliform cells and cause leaf curling. However, there are few studies related to this family in cotton, and there has been no systematic analysis of RF genes. Here, we determined 25 RF genes in the complete genome sequence of upland cotton (Gossypium hirsutum L.) and 11 RF genes in the complete genome sequence of Arabidopsis thaliana. Cotton RF proteins can be divided into three categories. Whole genome/fragment and scattered replication events played an important role in the expansion of the RF gene family. qRT-PCR analysis results showed that RF genes respond to drought stress Pairwise comparison results showed that the expression of RF genes in Shi yuan 321 was higher than that in Kui 85–174. Overall, genome-wide identification approach was used to further analyze the related functions of the RF gene family, which may include the response to drought stress, in cotton.