Screening Of Extreme Materials And Mapping Of QTLs For Pigment-Related Traits In Pepper Fruit

[Objective]Pepper(Capsicum spp.)commonly known as chili peppers,is an important vegetable crop globally.However,in China,there are issues such as limited genetic background of pepper germplasm resources,difficulty in germplasm innovation,and a lack of breakthrough varieties.Therefore,the exploration of core germplasm materials and key genes associated with fruit traits is of significant importance for promoting innovation in pepper germplasm and breeding new varieties.[Methods]In this study,a total of 52 pepper germplasm resources were used as materials.Through investigation and determination of the phenotypic traits and intrinsic quality of pepper fruit,and the use of multiple analytical methods,the diversity of phenotypic genetics and the selection of trait-specific materials were explored.Targeted metabolomic analysis was conducted on the extreme pigment materials screened(high pigment materials GB9 and GB23,low pigment materials GB6 and GB42)to decipher the metabolic mechanisms underlying the differences in accumulation of carotenoids in pepper.Additionally,a genetic linkage map of inter-specific pepper was constructed using the F2 population obtained by crossing the selected "ZL-280(C.chinense)" and "GB-35(C.annuum)" as parents,and the QTLs of the main fruit traits of pepper were detected and analyzed by combining the inter-specific map and genetic population phenotype data.[Results and Conclusion]The results of this study are as follows:1.There is varying degrees of variation in the 13 main fruit traits among the 52 pepper germplasm resources,with a coefficient of variation ranging from 13.15%to 143.15%and a mean coefficient of variation of 58.19%,indicating a relatively rich genetic diversity among these 52 pepper germplasm resources.Among them,the genetic diversity of fruit quality-related traits is the richest,with a mean coefficient of variation of 91.81%.Through cluster analysis,it was found that at a Euclidean distance of 7.5,the shrub pepper,bird pepper,and devil pepper can be distinguished from annual peppers.At a Euclidean distance of 5.0,the 52 pepper germplasm resources can be classified into four categories.Among them,the five horned pepper materials in subgroup IIIB of the third category have the highest color value.There is also a special material GB-35 in the fourth category with high color value and relatively high pungency,which can be used for later pepper fruit quality improvement and genetic research on specific materials.2.In total,18 types of carotenoids were detected in the extreme pigmented materials,with zeaxanthin(25.41%),β-carotene(16.70%),β-cryptoxanthin(18.89%),and capsanthin(13.11%)being the major carotenoids.Differential analysis was conducted on the carotenoids at the color transition and red ripening stages,resulting in the identification of 12 upregulated metabolites.At the red ripening stage,zeaxanthin,β-cryptoxanthin,lycopene,capsanthin,and capsorubin increased by 4286.55,3256.10,1888.96,1277.50,and 482.77 μg/g,respectively.Differential analysis of carotenoids in materials with extremely high and low carotenoid contents identified 6 different metabolites at the red ripening stage.Capsanthin,zeaxanthin,β-cryptoxanthin,and β-carotene had the highest content and the most significant differences among the carotenoids.Further research revealed that the upregulated expression of upstream and β,β-branching genes involved in carotenoid synthesis in high carotenoid materials resulted in the accumulation of upstream and β,β-branching carotenoids,leading to a significant increase in total carotenoid content compared to that in materials with low carotenoid content.3.A total of 223 F2 generation offspring were obtained by crossing the selected parents "ZL-280(C.chinense)" and "GB-35(C.annuum)" and 940,447 SLAF markers were developed using the SLAF-seq technology,of which 413,903 were identified as polymorphic,accounting for 44.01%of the total.The polymorphic SLAF markers were genotyped and filtered,resulting in 2,430 SLAF tags that were suitable for mapping.Finally,a pepper inter-species genetic map was constructed,which included 2,086 SLAF markers,12 linkage groups,a total length of 1233.87 cM,and an average genetic distance of 0.59 cM between markers,with a complete mapping rate of 85.84%.4.A total of 16 QTLs related to eight major fruit traits of pepper were detected,located on chromosomes 1,2,4,5,6,7,8,and 11,with a contribution rate ranging from 1.64%to 18.95%.Among them,three QTL loci associated with color value were detected,named cv.2.1,cv.4.1,and cv.5.1,located on chromosomes 2,4,and 5,respectively,with contribution rates of 8.58%,10.66%,and 12.44%.Two QTL loci associated with capsaicin were detected,named c.2.1 and c.5.1,located on chromosomes 2 and 5,respectively,with contribution rates of 7.14%and 11.40%.Three QTL loci associated with fruit length were detected,named fl.2.1,fl.2.2,and fl.4.1,located on chromosomes 2 and 4,with contribution rates of 6.18%,4.71%,and 4.01%.One QTL locus associated with fruit diameter was detected,named fd.6.1,located on chromosome 6,with a contribution rate of 10.07%.Two QTL loci associated with placenta size were detected,named ps.2.1 and ps.7.1,located on chromosomes 2 and 7,respectively,with contribution rates of 4.55%and 5.35%.One QTL locus associated with fruit flesh thickness was detected,named pt.11.1,located on chromosome 11,with a contribution rate of 1.64%.Finally,one QTL locus associated with single fruit weight was detected,named sfw.7.1,located on chromosome 7,with a contribution rate of 4.33%.