By using specific locus amplified fragment sequencing (SLAF-seq) sequencing method and combined with fixation indices analysis on different sweet orange populations, the candidate genes related with some excellent traits in sweet orange were mined, so as to provide some candidate genes for the further molecular breeding in sweet orange.

SLAF-seq technology was used to genotype 240 sweet orange germplasm resources, which represented extensive genetic diversity and from different geographical origins accessions preserved in the National Citrus Germplasm Repository in Beibei of Chongqing. The genomic SNP genotype data were obtained using the sweet orange genome as the reference, and the Fst and XP-CLR values between different subpopulations were calculated.

A total of 497.82 Mb_- reads were obtained by sequencing 240 sweet oranges accessions with SLAF-seq technology, after the sequencing reads were mapped on to the reference genome by BWA software, and a total of 1 467 968 SNPs were identified by GATK and samtools. The Fst 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 Fst score between two different single-fruit weight population, and orange1.1G046891m might affect fruit weight by regulating carbohydrate formation; orange1.1G011684m encoding dihydrolipoamide transacetylase of PDH, and the SNP caused a nonsynonymous mutation in its CDS region, which might determine the citric acid content in fruit; orange1.1G034502m encodes Serine/threonine protein kinase, annotated as phosphorylation dephosphorylation function also related with the citric acid content in fruit.

In this study, the Fst indices were used to screen six candidate genes associated with three fruit traits in sweet orange by using SNPs from SLAF-seq data. Finally, the relevant genes were screened out for three horticultural traits, including navel occurrence, fruit weight and titratable acid content, and the identified candidate genes should be giving further investigation to explore their regulation mechanism in these traits.