The Genetic Diversity Of Sweet Orange Germplasm Resources And The Related Genes Of Important Agronomic Traits Were Studied Based On SLAF-seq Technology

At present,my sweet orange varieties are in the period of structural adjustment and variety renewal.Therefore,this study screened genes related to excellent traits to deepen the understanding of sweet oranges and directional improvement of some important traits of sweet oranges.It is of great significance to improve the quality of sweet oranges.In this study,the phenotypic data of 240 sweet orange accessions were recorded for two consecutive years.The sweet orange resources were comprehensively evaluated by principal component analysis,correlation analysis and regression analysis combined with 18 phenotypic traits.Based on SLAF-seq sequencing technology,a total of 1,467,968 SNPs were screened out.Genome-wide association analysis and genes annotation were performed on eight traits including transverse diameter,titratable acid content,soluble solids content,anther color,fruit shape index,pulp color,seed number,capsule number,fruit navel etc.F_st and XP-CLR analysis were performed on fruit navel,titratable acid content and single fruit weight,and the candidate genes of titratable acid content were preliminarily verified.The results were as follows:1、Statistical analysis of 18 phenotypic traits of 240 sweet oranges accessions showed that sweet oranges had high phenotypic diversity.The principal component analysis of 240 sweet orange accessions were carried out,and 13 traits such as peel thickness,flesh color,longitudinal diameter,single fruit weight,number of capsule petals,anther color,titratable acid content,soluble solids content,solid acid ratio,petiole length,leaf length,leaf width and seed number could be selected as important evaluation indexes of sweet orange accessions.2、Using SLAF-seq technology to identify SNP loci for 240 sweet orange accessions,a total of 497.82 Mb reads and 1,467,968 population SNPs were obtained.Based on the obtained SNPs,PCA cluster analysis and population genetic structure analysis of 240 sweet oranges were carried out.It was found that the genome of sweet orange accessions was relatively mixtured,and the genetic relationship between varieties were relatively closed.Using genomic SNPs data,navel oranges,blood oranges and common sweet oranges in horticulture could not be accurately discriminated.3、A total of 1,467,968 SNPs were selected to performed GWAS analysis.At the-log₁₀（P）>6 significant level and mixed linear model,one SNP was associated with fruit longitudinal diameter,and 10 candidate genes were annotated,and these genes located on scaffold00010.A SNP locus related to titratable acid content was identified,7 candidate genes located on scaffold00012 were annotated.A SNP locus related to soluble solids was identified,8 candidate genes located on scaffold00003were annotated.Two SNPs loci related to anther color were found on scaffold00005and scaffold00007,respectively.Among them,14 candidate genes were annotated in the region with the highest p value(-log₁₀（P）=28.64),and 17 genes were annotated on scaffold00007.A total of 6 SNP loci related to fruit shape index were found,two on scaffold00004,two on scaffold00009,and two on scaffold00014.Among them,7 candidate genes were annotated in the region with the highest p value(-log₁₀（P）=9.5).One SNP site related to pulp color was identified and 15 candidate genes located on scaffold00014 were annotated;SNP loci related to seed number were annotated to 10 candidate genes on scaffold00005.One SNP locus related to the number of sac valves was annotated to five candidate genes,which were located on scaffold00012.A total of 2 SNP loci related to the navel were found,which were located on scaffold00005 and scaffold00007,respectively.A total of 10candidate genes were annotated in the region with the highest P value(-log₁₀（P）=29.19).4、The F_st and XP-CLR indices were used to screen out candidate genes related to three traits including fruit navel occurrence,fruit weight and titratable acid content.Those genes adjacent to the selected SNPs were called.The result showed that Orange1.1g044639m and orange1.1g023641m which annotated auxin efflux vector were related to the formation of navel in sweet orange.SNP in Orange1.1g023641m which encoded E3 ubiquitin ligase had the highest F_st score between two different single-fruit weight population,and Orange1.1g046891m may affect fruit weight by regulating carbohydrate formation;Orange1.1g011684m encoding dihydrolipoamide transacetylase of PDH,and the SNP cause a nonsynonymous mutation in its CDS region,which might determine the citric acid content in fruit.