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Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090 , GhM_D05G1692 , GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton. • A total of 909 novel fiber and yield loci were detected via WGRS with 10.65× coverage depth in 1,081 cotton accessions. • Three novel stable SNP peaks associated with FL and FS were found. • GhM_D11G2208 can promote cell elongation based up leaf trichome and dark-grown hypocotyls in Arabidopsis. • 14 consistent and stable superior haplotypes were detected based on 915 SNPs in Dt11 region. [ABSTRACT FROM AUTHOR]

Background: Cotton has tremendous economic value worldwide; however, its allopolyploid nature and time-consuming transformation methods have hampered the development of cotton functional genomics. The protoplast system has proven to be an important and versatile tool for functional genomics, tissue-specific marker gene identification, tracking developmental trajectories, and genome editing in plants. Nevertheless, the isolation of abundant viable protoplasts suitable for single-cell RNA sequencing (scRNA-seq) and genome editing remains a challenge in cotton. Results: We established an efficient transient gene expression system using protoplasts isolated from cotton taproots. The system enables the isolation of large numbers of viable protoplasts and uses an optimized PEG-mediated transfection protocol. The highest yield (3.55 × 105/g) and viability (93.3%) of protoplasts were obtained from cotton roots grown in hydroponics for 72 h. The protoplasts isolated were suitable for scRNA-seq. The highest transfection efficiency (80%) was achieved when protoplasts were isolated as described above and transfected with 20 μg of plasmid for 20 min in a solution containing 200 mM Ca2+. Our protoplast-based transient expression system is suitable for various applications, including validation the efficiency of CRISPR vectors, protein subcellular localization analysis, and protein–protein interaction studies. Conclusions: The protoplast isolation and transfection protocol developed in this study is stable, versatile, and time-saving. It will accelerate functional genomics and molecular breeding in cotton. [ABSTRACT FROM AUTHOR]

Cotton is sensitive to waterlogging stress, which usually results in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in cotton remain elusive. Cotton was grown in a rain-shelter and subjected to 0 (control)-, 10-, 15- and 20-d waterlogging at flowering stage. The fourth-leaves on the main-stem from the top were sampled and immediately frozen in liquid nitrogen for physiological measurement. Global gene transcription in the leaves of 15-d waterlogged plants was analyzed by RNA-Seq. Seven hundred and ninety four genes were up-regulated and 1018 genes were down-regulated in waterlogged cotton leaves compared with non-waterlogged control. The differentially expressed genes were mainly related to photosynthesis, nitrogen metabolism, starch and sucrose metabolism, glycolysis and plant hormone signal transduction. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that most genes related to flavonoid biosynthesis, oxidative phosphorylation, amino acid metabolism and biosynthesis as well as circadian rhythm pathways were differently expressed. Waterlogging increased the expression of anaerobic fermentation related genes, such as alcohol dehydrogenase (ADH), but decreased the leaf chlorophyll concentration and photosynthesis by down-regulating the expression of photosynthesis related genes. Many genes related to plant hormones and transcription factors were differently expressed under waterlogging stress. Most of the ethylene related genes and ethylene-responsive factor-type transcription factors were up-regulated under water-logging stress, suggesting that ethylene may play key roles in the survival of cotton under waterlogging stress. [ABSTRACT FROM AUTHOR]

• Foliar spray of exogenous nitric oxide increased its concentration in waterlogged cotton. • Increased nitric oxide concentration triggered a series of physiological and molecular events. • Foliar spray of nitric oxide ultimately reduced yield loss under waterlogging. Waterlogging is a major abiotic stress that reduces crop growth and productivity. Nitric oxide (NO) is an essential signaling molecule involved in abiotic stress responses in many plant species. However, it is unclear if and how NO mitigates waterlogging stress in field-grown cotton. In this study, the NO donor sodium nitroprusside (SNP) or its scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethyl -imidazoline-1-1-oxyl-3-oxide (cPTIO) was foliar-applied to waterlogged and non-waterlogged cotton plants. The NO concentrations in different plant parts, plant growth, yield and yield components, as well as related physiological and molecular events, were examined over three consecutive years under field conditions. Foliar application of SNP increased NO concentration in leaves by 83.6 and roots by 80.2 % under waterlogging, while cPTIO decreased the NO concentration by 18.9 and 5.3 %, respectively. Biomass and lint yield were reduced by 17.2 and 36.0 % under waterlogging without the application of SNP or cPTIO, but the reductions were 8.8 and 28.4 % following SNP application and 29.5 and 43.4 % respectively, following cPTIO application. Foliar applied SNP increased biomass by 10.2 % and lint yield by 12.0 % under waterlogging, whereas cPTIO caused 5.0 and 11.5 % reductions in biomass and lint yield. Quantitative real-time PCR analysis showed that the SNP up-regulated the NO synthesis gene (Gh NIR), but down-regulated the genes involved in glycolysis and fermentation (Gh ADH 2 and Gh PDC), ethylene production (Gh ACO and Gh ACS 8), and abscisic acid (ABA) synthesis (Gh NCED 2). It also reduced hydrogen peroxide (H 2 O 2) production and malonaldehyde (MDA) content in the leaves, but increased the leaf chlorophyll content and photosynthetic rate. The levels of auxin (IAA) and gibberellic acid (GA) were increased by SNP but those of ABA and ethylene contents as well as the activities of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC) in leaves were decreased. The cPTIO showed an opposite effect to SNP in almost all physiological and molecular responses to waterlogging. The overall results indicated that increasing the concentrations of NO in plant tissues via the foliar application of SNP mitigates waterlogging stress through a series of physiological and molecular events, ultimately reducing biological and lint yield loss under waterlogging. Therefore, increasing the concentration of NO in plant tissues by genetic breeding or agronomic measures might be a potential strategy for improving waterlogging tolerance and reducing yield loss in cotton. [ABSTRACT FROM AUTHOR]