Genetic diversity of yam germplasm revealed by chloroplast DNA sequences atpI-rsp2 and psbC-trnS

【Objective】The genetic diversity of 64 yam germplasm was analyzed based on the chloroplast DNA（cpDNA）sequences atpI-rsp2 and psbC-trnS to provide a theoretical basis for the selection，innovative utilization and breeding of yam germplasm resources.【Method】The atpI-rsp2 and psbC-trnS sequences of 64 yam germplasm collected from 14 provinces（regions）were amplified and sequenced for polymorphism. After mosaic and comparison，the genetic distance between germplasms was calculated by MEGA 7.0 and a phylogenetic tree was constructed. The nucleotide polymorphisms were analyzed by DNAsp 5.0 and NET Framework 4.6.1 was used to draw the intermediate adjacency network structure between haplotypes.【Result】The combined sequence length of atpI-rsp2 and psbC-trnS was 1938 bp，with con-tained 117 insert/missing sites（I_S）and 14 variable sites（V_s）. The conversion frequency（S_i） was 49.1%，and the overall transition/transversion bias（R）value was 0.928，resulting in 30 haplotypes. Of these，21 haplotypes were exclusive and 9 haplotypes were shared，corresponding to a haplotype diversity index value（H_d）of 0.92063 and nucleotide diversity value （π）of 0.00139. The Tajima’s D values，Fu and Li’s D * and F * of the atpI-rsp2 sequence and the psbC-trnS sequence and the merged sequences were all negative，and the difference was not significant（P>0.10），suggesting the sequences in yams fitted the neutral evolutionary model. The genetic distance of 64 yam germplasm ranged from 0 to 0.003865 with an average of 0.001400. The results of the structure analysis of the intermediate adjacency network showed that the 30 haplotypes could be divided into three types，H5 was the primitive haplotype.【Conclusion】The 64 yam germplasm resources have close genetic distance and similar genetic background，which may be caused by long-term interregional introduction. It is not entirely correlated with geographical distance. atpI-rsp2 and psbC-trnS sequences can be used for species identification and the phylogenetic analysis of yam.