| The genus Gossypium is one of the most economically important crops in the world.The seedling stage of cotton is crucial for entire growth process.Normal growth and resistance of cotton seedlings are the foundation for high and stable cotton yield.For a long time,it is a problem for cotton that genetic germplasm resources is narrow.Although the yield and quality of G.arboreum are less than Upland cotton,the traits of early maturity,stress resistance,disease resistance,and wide stability and adaptability provide the research basis for cotton improvement.It is important to promote the stability and breadth of cotton production.In this study,multi-omics integration analysis of eQTL and GWAS is used to identified candidate genes and expression regulatory networks related to cotton salt resistance and growth.The main results are as follows:1.We use eQTL for gene expression of G.arboreum seedlings association.A total of 30,089 eQTL in10,485 genes are identified.We find target genes for eQTL are enriched in genes highly associated with plant resistance and growth.Using luciferase assays,we confirm that different cis-eQTL haplotypes could affect promoter activity and variate gene expression.we performe a TWAS analysis to integrate the results of eQTL and the results of GWAS about the 15 traits.This allow us to identify 19 candidate genes about seedling growth and resistance.2.trans-eQTL accounted for more than 90% of eQTL.We identified 1,298 hot spots by trans-eQTL.We then calculate the correlation between Hotspots and associated genes.And the results showed positive correlation for most of the genes.We find Hotspot309 regulated 325 e Genes that are involved in cell wall biosynthesis and salt stress response as shown by functional enrichment analysis.We identify that 29 genes have known functions in cell wall biosynthesis and 14 genes in salt stress response.The candidate gene of Hotspot309 encode a basic leucine zipper(b ZIP)transcription factor gene(Ga05G2977).We find Hotspot309 is related with the expression of regulated genes and traits of fresh weight,stem length and germination rate by differential haplotypes and correlation analysis.3.G.arboreum accessions divided into 3 groups(South China,the Yangtze River Region and the Yellow River Region).We analyze the differentially expressed genes,and find difference between the Yangtze River and the Yellow River is less than the difference between South China and the two other groups.Our results suggeste that G.arboreum was initially cultivated in South China before being cultivated in the Yangtze River region and Yellow River region.By comparing and analyzing the eQTL results of five repetitive genes,we identify than 10% of the gene pairs with same eQTL which be regarded as conserved gene pairs.We find correlation of gene expression for these gene pairs and correlation is higher than non-conserved gene paris.By the analysis of transcriptional regulation with repetitive genes,we construct evolutionary regulation model.We found tandem repeat genes associated with plant resistanc.In summary,in this study we contain eQTL and regulated hot spots about traits of G.arboreum seedling and identify candidate genes related with traits by TWAS.we confirm that promoter activity is affected by different haplotypes.We gain Hotspots and regulated network related with seedling traits.An evolutionary regulation model of repetitive genes is speculated.In this study,we provide candidate genes for seedling growth and resistance and a theoretical basis for expression regulatory network.The research basis and genetic resources are provided for people to use cotton growth stress resistance genes to cultivate cotton varieties with excellent stress resistance traits. |
