Screening Of Key Genes Controlling The Main Inflorescence And The Mian Stem Elongation Rate In Brassica Napus L.

Plant height as well as the length of the main inflorescence and the main stem（stem height）are the important factors of ideal plant architecture and high yield of Brassica napus.It is reported that the longer main inflorescence and shorter main stem are the basis of high yield on the premise of certain plant height.In this study,the relationship between the elongation rate and the final length of main inflorescence（MIL）and stem height（SH）at the bud and the flowering stage are focused.The innovation is to decompose plant height into two characters and then detail to different development stage.In this study,following tests were carried out: 1)the SNP data of 588 samples of natural population were obtained by re-sequencing and the highly significant SNPs of the main inflorescence elongation rate（MIER）and the main stem elongation rate（MSER）for two consecutive years were detected using genome-wide association study analysis（GWAS）;2)QTL mapping of the MIER and the MSER for two consecutive years was carried out using our previous constructed high-density linkage map,which consist of 189 lines;3)The hormone content of the extreme materials of the MIER and the MSER;4)RNA-Seq were also used for screening the differentially expressed genes（DEGs）.Combined with the results of GWAS and QTL,candidate genes related to the MIER and MSER were selected.The main results are as follows:1.Phenotypic analysis of MIL,SH,MIER and MSERIn RIL,the average number and coefficient of variation of the main inflorescence length measured in six different periods in 2018 and 2019 were 9.86 cm 52.27 cm and 4.13% 26.94% respectively,the average and coefficient of variation of elongation rate were 0.0146 cm/day 0.0888 cm/day and 20.64% 44.56%.In natural population,the average number and coefficient of variation of 6 different periods were 14.08 cm 68.61 cm and 15.60% 87.62%,respectively,the average number and coefficient of variation of elongation rate were 0.015 cm/day 0.0921 cm/day and 44.30% 101.98%.In RIL,the average number and coefficient of variation of stem height measured in 8 different periods in 2018 and 2019 were 18.14 cm 139.1 cm and 5.49% 32.36%,respectively,the average number and coefficient of variation of the corresponding elongation rate were 0.0102cm/day 0.0799cm/day and 20.70% 67.84%.In natural population,the average number and coefficient of variation of 8 measurements in different periods were 38.93 cm 144.21 cm and 11.65% 54.27%,the average number and coefficient of variation of elongation rate were 0.0097 cm/day 0.0609 cm/day and 26.22% 105.72%.The main inflorescence length,stem height,MIER and MSER were in continuous normal distribution in all environments,which conformed with the characteristics of polygenic quantitative characters controlled by different genes.2.Correlation analysis among traits detected in this studyIt was found that there was a significant positive correlation between the main inflorescence elongation rate at the later stage and the final main inflorescence length,and the main stem elongation rate at the later stage was significantly positively related to the final stem height.The final stem height was significantly negative correlation with the final main inflorescence length,while both the final stem height and the length of the main inflorescence were significant positive correlation with the final plant height in both natural population and RILs for two years.Therefore,it’s feasible to obtain ideal high-yield plant architecture with shorter plants and developed main inflorescences by reducing stem height.3.GWAS of main inflorescence and main stem elongation rateIn total,62 and 8 significant SNPs related to the MIER（P < 1 / 385692）were detected in the best model in 2018 and 2019,respectively.These significant SNPs distributed on A03,A07,A09,C03,C04,C06,C08 and C09 chromosomes,and their phenotype contribution rate were between 9.5% and 27.7%.Among them,S7₁6388885 was repeatedly detected in two years with 10.15% and 20.4% of the phenotype contribution rate.Meanwhile,57 and 89 significant SNPs related to the MSER（P < 1 / 385692）were detected in the best model in 2018 and 2019,respectively.These significant loci were distributed on all chromosomes except chromosome A01,A05,C05 and C07 with7.02% 23.18% of the phenotype contribution rate.S2₅9259 was repeatedly detected in two years,and the phenotype contribution rate was 8.08% and 13.75%.Both the main inflorescence and main stem elongation rate are controlled by multiple genes and are greatly affected by the environment.4.QTL mapping of main inflorescence and main stem elongation rateIn this study,7 QTLs of the MIER were detected on A07,C03,C04,C05 and C06 chromosomes and their phenotypic contribution rate was 5.36% 9.08%.Among them,q-2018MIER-2-C06-1 and q-2018MIER-2-C06-2 overlap with the significant SNP S16₃2025979 of 2018MIER-2,q-2019MIER-2-A07-1 overlap with significant SNP S7₁829865 of 2018MIER-2.For the MSER 14 QTLs were detected in 2018 and 2019.These QTL were located on A01,A02,A03,A05,A06,C03,C04,C05 and C06 chromosomes with 5.65% 12.83% of the phenotypic contribution rate.Among them,q-2018MSER-3-A02-1 overlap with 2018MSER-2 significant SNPs S2₅3178,S2₅9259,S2₅3469,S2₅9202,S2₅3104 and 2019MSER-2 significant SNP S2₂240175,q-2019MSER-2-A03-1 overlap with 2018MSER-2 significant SNPs S3₁8937528 and S3₁9258339,q-2019MSER-3-A03-1 overlap with 2018MSER-1 significant SNP S3₁8202956.5.Transcriptome analysis and hormone content analysis of extreme materialsA total of 4,715 differentially expressed genes（DEGs）were detected in the extreme materials of the MIER.Compared with the lower MIER materials,2,038 genes were significantly up-regulated and 2,677 genes significantly down-regulated in higher MIER materials.Among the 1,333 DEGs detected in the extreme materials of MSER.Compared with the lower MSER materials,688 genes were significantly up-regulated and 645 genes significantly down-regulated in heighter MSER materials.Similar enriched GO terms and KEGG pathways were detected for MIER and MSER.In biological process（BP）,cell process,metabolism process,single biological process and stimulation response were the most involved GO terms.For molecular function（MF）category,binding,catalysis and transportation were the largest terms and cells,cell components and organelles were the most enriched terms in cellular components.Ribosome,followed by carbon metabolism,amino acid biosynthesis and plant hormone signal transduction pathways were the top four enriched pathways in KEGG analysis.In the extreme materials of MSER,the gibberellins（GAs）content was significantly higher in higher elongation rate materials than that of the materials with low elongation rate at the bud stage,while significantly lower than that of the materials with low elongation rate at the flowering stage,and no significant difference at the opening stage were detected.Gibberellins（GAs）promoted stem elongation during the bud stage,but inhibited it at opening stage.6.Screening of candidate genesGenes in the QTL confidence interval and 500 kb regions of significant SNPs detected in GWAS were obtained based on the genome（Darmor-bzh）reference.Combined with RNA-Seq analysis and gene annotations,11 candidate genes related to MSER and 14 candidate genes related to MIER were screened out.The functions of these genes in Arabidopsis participated in plant growth and development affect cell development,cell growth,cell cycle regulation,cell wall formation,participate in gibberellin,auxin signal transduction and other aspects.