Genome Wide Analysis Of Genetic Basis Of Stem Hardness And Cell Wall Related Traits In G.hirsutum

Cotton is a natural fiber crop known as "white gold" and has been used as a vigorous oil seed crop in the world for a long time.Cotton is a widely distributed plant that grows in tropical and subtropical climates around the world.In addition to its economic importance,cotton is an admirable system for studying polyploidazation,cell elongation,and cell wall biosynthesis.On the other hand,fiber yield and quality are critically constrained by numerous stresses.Salinity,lodging,and drought are the main factors causing extensive and massive yield reductions at the crop harvest stage all over the world.Among the various stresses,drought,salinity,and lodging are the major factors causing extensive and massive yield reduction near the crop harvest stage worldwide.As a result,one of the most significant projects during cotton breeding is improving stem strength and lodging resistance in cotton cultivars.In this study,we collected 383 cotton accessions of G.hirsutum from different cotton growing countries.The correlation association studies were suggest that almost all traits of both years of two location(Anyang and Xinjiang)have positive correlation with each other and this trait are the suitable for further GWAS analysis and breeding programs.EMMAX were used for the association analysis of genotyping and phenotyping of 383 accession.A total of 7568 SNPs with the P-value greater than 5were found in the current study.149 SNPs were found to be significantly associated with stem hardness related traits such as Bending stem strength of lower and upper stem(BSS-L,BSS-U),Acupuncture stem strength of lower and upper part(ASS-L,ASS-U),Compression stem strength(CSS-L,CSSU),Stem diameter index(SDI-L,SDI-U),cellulose and lignin.In the current study,total 26 highly associated SNPs were found with different traits of stem hardness,which have greater R2 value in LD block.The different screening methods were used for final selection of candidate genes.In this study,we found 37 SNPs for BSS trait.Among these,we focused on highly significant SNP At10?112879830,which was located in At10 chromosome.For BSS?U,Dt09?2134501 was the candidate SNPs,which was located in Gh?D09G009100.1.Sixty SNPs was found for ASS traits.At05?29636573 and Dt13?56178606 SNPs to be significantly associated with ASS-L and ASS-U respectively.We identified 19 SNPs for trait CSS,which is highly associated.The significant peak was found in Dt02 for CSS-L,and At11?114343593 SNPs was the significant SNPs for CSS-U.Stem diameter index(SDI)is one of the important trait for lodging,stem hardness and cell wall of upland cotton.We also found some significant peak for SDI trait.Cellulose and lignin is a major component of cell wall and a key determinant of mechanical strength of all tissue.In the present study,total 14 and 3 associated SNPs were found for cellulose and lignin traits respectively.These significant SNPs and the underlying genes should be further investigated by using molecular biology techniques to identify as a key gene for stem hardness and cell wall of upland cotton.Furthermore,we identify the function of UGT71K2 and F-Box gene for stem hardness of upland cotton.These two gene select through GWAS analysis.Virus induced gene silencing techniques(VIGS)was used to silence two genes UGT71K2 and F-Box with genotypes(CCRI16 and FQ)and(CCRI16and CCRI36)of upland cotton respectively.We found that in mutant plants cellulose content was decreased,the xylem cells in the transvers section of stem were collapsed,and cell wall thickness was decreased.Transcriptomic analysis showed that cell wall related differential expressed genes(DEGs),including carbohydrate,sucrose and sugar DEGs were down regulated in both mutant varieties.We can say that UGT71K2 may be role in stem hardness of upland cotton.In F-Box,protein we found that in mutant plant had thin stem diameter and the vascular bundles cells were disturb,moreover the contents of cellulose and lignin were decreased.Transcriptomic results showed that mostly DEGs were involved in oxidationreduction reaction,DNA-template,and protein phosphorylation.A huge population of germplasm valuation for stem hardness will be helpful to select some favorable accession for breeding.The identification of natural variations and related candidate genes will help to better understanding the complex mechanism of stem hardness,lodging and cell wall related traits.