QTL Mapping And Genetic Basis Study Of Pericarp Thickness In Sweet Corn

Sweet corn is a maize-derived crop developed through one or several recessive endosperm mutations that reduce the synthesis of starch and increase the accumulation of sugars.In recent years,the planting area of sweet corn in China has expanded rapidly.Some new varieties with high yields and good adaptabilities have emerged.However,there is still a big gap with developed countries in edible quality traits especially the varieties with thin pericarp thickness.Pericarp thickness is a complex trait which is the key factor determining the edible quality of sweet corn.To date,there are still few studies on the pericarp thickness of sweet corn.The expression network and regulation mechanism of related genes in the formation of pericarp thickness difference have not been clarified.Hence,148 BC₄F₄inbred lines constructed by two sweet corn inbred lines with distant genetic relationship and different pericarp thickness were used as materials to mining major effect genes based on a high-density linkage genetic map of sweet corn though simplified genome sequencing.Then combined with transcriptome,mi RNA and metabonomics analysis revealed the regulatory networks and molecular mechanisms of genes,mi RNA and metabolites involved in the formation of pericarp thickness differences.The main results obtained in this study are as follows:1.DNA of the 148 BC₄F₄population and two parents were sequenced based on SLAF-seq,a total of 163,961 SLAF tags were obtained,31,486 markers were identified as polymorphic with a polymorphism rate of 19.20%.3,876 SNPs were obtained to construct the high-density genetic linkage map after filtering the original SLAF tags.The length of the genetic map was 2413.25 c M with a mean inter-marker distance of 0.62 c M.Based on the constructed genetic linkage map,the phenotype of the pericarp thickness of the BC₄F₄population collected from three seasons were analyzed by QTL mapping.A total 24 QTLs for pericarp thickness were mapped in the BC₄F₄populations across three seasons.A stable q PT10-5 which was located in a 901.2 Kb region was identified in all three seasons,and could explain 7.78%to 13.84%of phenotypic variations that indicated the q PT10-5 was the stable major locus interval controlling sweet corn pericarp thickness.2.Forty-two candidate genes in the qpt10-5 region were compared with the DEGs identified by transcriptome sequencing.Among the 42 genes,18 were found in the transcriptome sequencing,only five genes were differentially expressed between the M03and M08 lines.Gene annotation indicated that GRMZM2G143352,GRMZM2G143402,and GRMZM2G143389 may be the candidate genes that controlling pericarp thickness.GRMZM2G143352 and GRMZM2G143402 have been annotated as AUX/IAA transcription factor and ZIM transcription factor,respectively,while GRMZM2G143389 is a FATTY ACID EXPORT 2 chloroplastic.3.RNA-seq was used to analyze the gene expression of M03 and M08 pericarp at15DAP,19DAP and 23DAP.A total of 8,951 differentially expressed genes were identified in the three stages of M03 and M08 pericarp.6,168,4,734 and 5,602 DEGs were identified in the individually stage respectively,and 2746 genes were differentially co-expressed in the three stages.The enrichment analysis of KEGG showed that those DEGs in each stage were commonly enriched in“plant hormone signal transduction”,“amino acid biosynthesis”,“starch and sucrose metabolism”,“cysteine and methionine metabolism and fatty acid metabolism”,and only“plant hormone signal transduction”was significantly（p<0.05）.4.Based on the Illumina technology,mi RNA-seq of two inbred lines pericarp were carried out at 15DAP,19DAP and 23DAP.A total of 279 mi RNAs were identified in 18samples,including 155 known mi RNAs and 124 novel mi RNAs,Among them,109mi RNAs were differential expressed in all of three stages,42 mi RNAs were differential co-expressed in those stages.Combined with the results of m RNA sequencing 171mi RNA-m RNA pairs were found,according to the target genes annotation,zma-mir164c,zma-mir166a,zma-mir167g,zma-mir827 and zma-mir171b may regulated pericarp thickness of sweet corn by mediating the plant hormones signal transduction.5.Based on UPLC-MS,metabonomics analyze of two inbred lines pericarp were carried out at 19DAP.In this study,a total of 471 metabolites were identified with 113differential expressed metabolites between the M03 and M08 lines.Among them,64metabolites were down regulated and 49 metabolites were up regulated in the M08 line.KEGG enrichment analysis revealed those metabolites were significantly enriched in“zeatin biosynthesis”,“phenylalanine biosynthesis”,“arginine and proline metabolism”pathways.6.The multic-omics integrative analysis of genes,mi RNAs and metabolites with significant differences between the pericarp of two sweet corn inbred lines was carried out to constructed the network map.The results showed that there were 4213 genes,67mi RNAs and 162 metabolites with significant differences collectively affected“Metabolic pathways”,“Benzoxazinoid biosynthesis”,“plant hormone signal transduction”,“Biotin metabolism Purine metabolism”,“Biosynthesis of secondary metabolites”,“Stilbenoid,diarylheptanoid and gingerol biosynthesis”,“Phenylpropanoid biosynthesis”,“Alanine,aspartate and glutamate metabolism”,“Pyrimidine metabolism”.In summary,the results of this study lay the foundation for the pericarp thickness candidate gene cloning,and also provide theoretical support and gene resources for the improvement of thin pericarp in sweet corn.