| Wheat lodging closely related to stem characteristics is one of the main factors affecting yield,and breeding lodging-resistant varieties is the key to solve this problem.Analysis of genetic mechanism of stem characteristics is helpful to breed new wheat varieties with high and stable yield.In this study,a set of 192 wheat varieties(lines)from southern Huanghuai region of China was used to evaluate stem characteristics in 6 environments including Zhengzhou,Yuanyang and Luyi in2019-2020,and Yuanyang(Nitrogen topdressing and no nitrogen topdressing in spring)and Luohe in 2020-2021.The genetic differences of different varieties and correlations between stem traits were analyzed,and the whole genome association analysis(GWAS)was carried out by using wheat 660 k SNP Array.The varieties with extreme length of second internode at base were selected for transcriptome(RNA-Seq)analysis.The conjoint analysis of the integrated transcriptomics data and GWAS were carried out to detect the related genes that correlated with the stem characteristics.The main results and conclusions are as follows:1.Joint analysis of variance showed that the differences among varieties for all traits were very significant.There was no significant difference in interaction between environment and variety in lodging level,significant in plant height and very significant in other traits.Broad-sense heritabilities ranged from 55.32% to 88.87%.The broad-sense heritabilities of internode filling and lodging level was lower,while those of equilibrium point and plant height were higher.The variation coefficients of plant height,equilibrium point and the diameter of the first 3 internodes at base were smaller,followed by the length of each internode,and that of lodging level was the highest.The variation coefficients of internode breaking force,filling and lodging level in the grouting medium stage and internode length and diameter in the mature stage in environment with topdressing were significantly higher than those without topdressing.2.Highly significant correlations were found between stem characters in the environments of nitrogen topdressing and no nitrogen topdressing.Nitrogen topdressing reduced the filling of second and third internodes at base,increased the length of the first 3 internodes at base,decreased the diameter of the first 3 internodes at base,and increased the lodging level.From grouting medium stage to maturity stage,breaking force of the first 3 internodes at base,and filling of second and third internodes at base all decreased,but the lodging level increased.3.Plant height was closely related to length and breaking force of second and third internodes at base.There was a very significant negative correlation between length of the first three internodes at base and breaking force of the first three internodes,filling of second and third internodes at base,while the diameter of the first three internodes at base was very significantly positive correlation with them.The breaking force of the first three internodes at base was very significantly positive correlation with filling of second and third internodes at base.4.A total of 1733 SNP loci related to wheat stem traits were detected,including1212 markers related to length,280 markers related to diameter and 241 markers related to breaking force.A total of 132 SNPs associated with 2 or more stem traits were detected,of which 43 SNPs that were associated with 3 or more stem traits.AX-111032457 located on chromosome 5B was associated with five stem traits,AX-109419774,AX-108910198,AX-109004798,AX-110084749 and AX-94610974 were all associated with four stem traits,and 37 SNP loci were associated with 3 stem traits.5.GWAS analysis found that 49 stable chromosomal regions significantly associated with stem traits were detected in at least 2 environments,including 36 stable regions for internode length,12 stable regions for internode diameter and 1stable region for internode breaking force.Sixty-five stable SNPs associated with stem traits were found on chromosomes 1B,1D,2D,4A,5B,6B and 6D,of which 61 were favorable alleles.The percentage of favorable alleles of SNPs in length of third internode,length of fourth internode and diameter of first internode at base were higher in the 192 wheat varieties,while those in length of first internode,length of second internode,length of fifth internode,diameter of second internode and diameter of third internode at base were lower.The extended sequence of 65 SNP stable markers were found in TGACv1.0 database and NCBI Blast.A total of 33 candidate genes were found,of which 31 had gene or protein annotation function,mainly encoding ubiquitin-conjugating enzyme,casein kinase substrate phosphoprotein,glycosyltransferase and eukaryotic translation initiation factor.Among them,Traes CS5B02G005100 was an important candidate gene for length of first internode,third internode and fourth internode at base,and encoded ubiquitin binding enzyme.6.Nine candidate regions associated with length of second internode at base were detected by GWAS,which were mainly distributed on chromosomes 1A,1B,2A,2B,2D,3A,4A and 6B.Single SNP in the regions could explain 8.46%-15.09% of the phenotypic variation.Transcriptome analysis showed that the related sites controlling the length of the second internode at base were mainly regulated by molecular functions,and the related metabolic pathways were involved in starch and sucrose metabolism.In the GWAS candidate regions,5 genes were found to be differentially expressed,and mainly involved in polysaccharide biosynthesis,hypothetical proteins and plant proteins encoding DNA binding domains... |
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