Genetic Diversity Of Chinese Pcna Persimmon Based On Whole Genome Resequencing

Diospyros Linn.is the genus with the broadest distribution range,the richest species and the highest economic value of persimmon.China is the origin and distribution center of persimmon plants,with the special Chinese non-astringent persimmon germplasm and richest persimmon germplasm resources.Diospyros kaki Thunb.is a representative germplasm widely cultivated in persimmon species.It can be divided into five types: CPCNA(Chinese pollination constant & non-astringent),J-PCNA(Japanese pollination constant & non-astringent),PCA(Pollination constant & astringent),PVA(Pollination variant & astringent)and PVNA(Pollination variant & non-astringent)types.Now nonastringent persimmon(C-PCNA and J-PCNA)is the main type and the breeding direction in the future.The persimmon varieties in Chinese traditional production areas are mainly full astringent,while Chinese PCNA persimmon is only concentrated in the Dabieshan Mountains at the junction of Anhui,Henan and Hubei provinces.At present,the origin of Chinese PCNA persimmon and their genetic relationship with other germplasm are only limited at the molecular marker level,and there are few reports at the genomic level.In this study,the phylogenetic relationship and genome-specific region of Chinese PCNA persimmon,Chinese PCA persimmon and persimmon germplasm originating in Japan were studied by whole genome resequencing for the first time,in order to provide a scientific basis for genetic diversity of cultivated persimmon germplasm and the origin and evolution of non-astringent persimmon in China.The main results are as following:1.36 persimmon varieties in Dabie Mountain area,were resequenced,and the original data of 1.68 tb were obtained,The sequencing data Q20 > 94.56% and the content of GC ranged from 36.32% to 37.49%.36 resequencing data of persimmon varieties in Dabie Mountains and 50 resequencing data of other persimmon native to China,persimmon native to Japan and persimmon related species,were used for sequence alignment and population variation detection,the average sequencing depth of all samples was 11.77×(2.28-37.45×),the average genome coverage of all samples compared to the reference genome was 78.23%,268812711 SNPs,14210910 In Dels,351794 SVs and 72443 CNVs were obtained detected.2.All samples were divided into four categories by structure analysis,phylogenetic tree and principal component analysis,namely Chinese PCNA persimmon,Chinese PCA persimmon,Japanese original persimmon and related species persimmon.Chinese PCA persimmon is closely related to Chinese PCNA persimmon and the astringent persimmon types in Japanese original persimmon.The germplasm background of PCNA persimmon in Dabieshan Mountain area is single,while the background of the rest of Chinese PCNA persimmon is mixed,and there is gene infiltration of astringent persimmon germplasm.‘Male 1’ and ‘Male 3’ are closely related to ‘Sifang-tianshi’,indicating that they have the genetic background of PCNA in Dabie Mountains.3.Through population genetic analysis,results showed that Chinese PCA persimmon population exhibited high genetic diversity,Chinese PCNA persimmon population had the lowest genetic diversity,while Japanese original persimmon population had the lowest genetic diversity,reflecting the effect of domestication on the genetic diversity of cultivated population.4.The specific gene regions between Chinese PCNA persimmon and Chinese PCA persimmon,between Chinese PCNA persimmon and Japanese original persimmon,between Chinese PCA persimmon and Japanese original persimmon were identified,and the functional enrichment of genes in the region was analyzed.It was found that the selected genes between Chinese PCNA persimmon and Chinese PCA persimmon were significantly enriched in flavonoid biosynthesis,monoterpene biosynthesis,diterpenoid biosynthesis,caffeine metabolism and carbon metabolism.