Genetic diversity in arabica coffee germplasm determined from specific length amplified fragment sequencing and transcriptome

The genetic relationship of Coffee arabica resources was analyzed by specific length amplified fragment sequencing (SLAF) and transcriptome to provide theoretical basis for the breeding of new variety. Total 20 Coffee arabica accessions were used for genetic relationship analysis based on SNP-variation using SLAF-seq and the gene expression-variation using transcriptome. For SLAF-seq, the total reads ranged from 2 665 424 to 7 210 310, GC percentage varied from 38.49% to 40.91%, and Q30 percentage changed from 94.99% to 96.36% across all 20 C. arabica accessions, two C. canephora accessions, one C. liberica accession, and one C. racemosa accession. Through sequencing data analysis, a total of 3 347 069 SLAF tags were obtained and the average sequencing depth of the tags was 13.90x. In total, 1 048 575 raw SNPs identified from the polymorphic SLAFs were filtered, and the remaining 198 955 SNPs were applied in the phylogenetic tree, principal component analysis, population genetic structure. For transcriptome, the 128.50 Gb of clean reads were generated based on transcriptome sequencing in all 20 C. arabica accessions. The GC percentage was 44.36-51.09% and Q30 percentage varied from 94.55-95.40%. A total of the expression levels of 25 872 genes were used in correlation analysis. The C. arabica Typica type accessions were clearly distinguished from C. arabica Bourban type based on the phylogenetic tree, principal component analysis, population genetic structure by the SNP-variation and correlation analysis by the gene expression-variation. In addition, several C. arabica local selections with unknown genetic background were classified into corresponding types based on all four clustering results.