Transcriptome Analysis Reveals Molecular Insights Into The Yield Heterosis Of Upland Cotton

Cotton is a prime fiber crop worldwide.The growing demand for fiber in textile industry has imposed breeding for higher yield.The utilization of F₁ heterosis is one of the main objectives of the breeder and greatly improved crop productivity.However,genetic basis about how hybridization produces superior yield in cotton has not yet clearly identified.In this project,11 upland cotton inbred lines and their respective 30 intraspecific F₁ hybrids were tested in six diverse environments of China.Analysis of variance revealed genotypes,environments,and their interaction had highly significant effects on yield and yield components.Mean comparison among genotypes quantified that most hybrids had higher means than inbred lines.Additionally,the environments were not clustered together for most traits,implying their contrasting interaction with genotypes.Stability measurement specified that hybrid SJ48-1×Z98-15 and SJ48-1×A2-10 had the best performance for yield traits.Based on results of field experimentation,high,medium,and low heterosis hybrids along with their four inbred parents were screened to perform transcriptome analysis.Phenotypically,these hybrids showed biomass growth differences at seedling emergence as well as significant heterosis in yield contributing traits at maturity.The high hybrid produced a mean of 14%more seed cotton yield than its better parent.For genetic perspective,a total of 105 samples comprised of different tissues of hybrids and parents from the seedling and squaring stages were used to perform RNA sequencing.Comparison of differentially expressed genes?DEGs?in each hybrid parent triad revealed higher differences at seedling compared to squaring.Furthermore,expression level dominance analysis measured majority of DEGs with transgressive/overdominant expressions in hybrids at seedling,but parent like expressions were dominant at squaring.Functional annotations identified an array of DEGs involved in chloroplast,plasma membrane,vacuole,and stress-responsive at seedling.While ATP and protein binding,membrane,cell wall,mitochondrion,and protein phosphorylation were the most enriched terms at squaring.Several genes associated with circadian rhythm pathway had differential expression in hybrids at seedling.However,majority of genes linked with sugar metabolic and hormone signaling showed differential expression at both stages.Further,these two pathways had most mapped DEGs on known seed cotton yield QTLs.Integration of transcriptome,QTLs,and weighted gene co-expression network analysis raveled nine genes had complex biological network.A total of 10 putative candidate DEGs from seedling and nine from the squaring stage were selected to validate RNA-Seq data using qRT-PCR.Our results of field experiments revealed hybridization improves yield and adaptability in upland cotton.Comprehensive transcriptomic analysis suggests that accumulation of overdominance expressed genes at seedling and dominance at the reproductive stage are the major determinant of heterosis.Further,LHY,PRR9,and CO-like protein-encoding genes play a critical role in early seedling growth.Genes including BZR1,ASK8,JAZ10,MPK4,PHO1,At3g43860,GBSS1,APL2,and CRR21 have potential role in reproductive growth.Concisely,the current study provides novel insights about phenomics and genomics of cotton heterosis.Our data resources will not only be significant for dissecting the molecular mechanism of yield heterosis but also useful for the cotton yield improvement programs.