| [Objective] Cotton Verticillium wilt,known as "cotton cancer",is a vascular disease with strong pathogenicity,rapid variation and complex pathogenic mechanism,which seriously affects cotton production in China.It was found that after Verticillium dahliae invaded cotton plants,the tissue structure of cotton plants was induced by pathogens,lignin accumulation increased and cell walls thickened,resulting in changes in cell morphology and structure.The vascular tissue of cotton stalk was strengthened,which could effectively limit the invasion and spread of Verticillium dahliae and reduce the subsequent systematic occurrence of Verticillium wilt.However,the genetic basis of the response of lignin to Verticillium wilt is not clear.Therefore,mining and identifying the QTL/ gene of lignin response to Verticillium wilt not only provides genetic resources for the genetic improvement of cotton Verticillium wilt resistance,but also opens a new field of vision for revealing the genetic basis of cotton Verticillium wilt resistance.[Methods] In this study,an upland cotton MAGIC population with 280 inbred lines was used as experimental material,which was constructed from 8 upland cotton varieties / lines with different resistance to Verticillium wilt.MAGIC population was planted in artificial disease nursery(ADN: Artificial disease nursery)and rotation nursery(RN: Rotation nursery)in Shihezi City and Manas County in Xinjiang in 2019 and 2020 respectively.During the maturity stage of cotton,10 plants with uniform growth were selected,and the total lignin content of 10 cm cotton stalks above cotyledon nodes was determined by mercaptoacetic acid method.The ratio of total lignin content of ADN to RN was taken as phenotypic value,which was named lignin response value(LRVW: The lignin response to Verticillium Wilt).Phenotypic analysis of LRVW was performed using SPSS,R language and QTL Icimapping.9323 high quality SNPs obtained from 63 k chip were used to analyze the genotype of MAGIC population.Combined with 63 K chip data and LRVW,Genome-wide association analysis was carried out,and significant SNP sites were mined within the whole genome.Then,according to the population LD,candidate intervals were determined within 500 kb upstream and downstream of significant SNP,and all candidate genes were listed according to the reference genome.Combined with sequence variation,functional annotation and expression pattern analysis,candidate genes were screened.[Results] The lignin content of cotton stalk in ADN experimental field was significantly higher than that in RN in all four environments.Phenotypic analysis showed that the standard deviation and coefficient of variation of LRVW in the population were larger than those in the parents,showing abundant variation.There was a significant positive correlation between years and environment(P < 0.001),and the heritability was about 70.36%.The results of genotypic data analysis showed that 9323 high quality SNPs were distributed in the whole genome,ranging from 1.14SNP/Mb(Chr A06)to 10.08SNP/Mb(Chr D08),and the average density was 4.78SNP/Mb.Three QTLs were identified by association analysis.According to the reference genome annotation,there were 179 genes in the three QTL candidate intervals.Combined with sequence variation,functional annotation and expression pattern analysis,two key candidate genes,Ghi＿D05G01046 and Ghi＿D05G01221 were identified.[Conclusion] In this study,a MAGIC population containing 280 inbred lines was constructed using 8upland cotton materials as parents.The genotypes of the populations were analyzed by Cotton-SNP63 K chip,and a new phenotypic LRVW associated with Verticillium wilt resistance was used for genome-wide association analysis.Three stable QTL,namely q LRVW-A04,q LRVW-A10 and q LRVW-D05,were identified in more than 2 environments.In addition,combined with gene sequence variation analysis,functional annotation and induced expression pattern analysis,two key candidate genes,Ghi＿D05G01046and Ghi＿D05G01221,were identified,which may be involved in Verticillium wilt resistance response by regulating lignin metabolism.The results not only provide valuable genetic resources for cotton breeding for Verticillium wilt resistance,but also open up a new perspective for revealing the genetic basis of cotton Verticillium wilt resistance. |
