Abstract: Aims In this study, we analyzed the genetic diversity and structure of Haloxylon ammodendron populations in Turpan-Hami area, Xinjiang. Methods We sampled 154 individuals from 13 natural populations of H. ammodendron. Based on single nucleotide polymorphism(SNP) and chloroplast sequences genome data obtained by population resequencing, nucleotide diversity, haplotype diversity and genetic differentiation coefficient were calculated. The genetic structure was assessed by conducting ADMIXTURE, principal components analysis (PCA), phylogenetic tree and chloroplast haplotype network analyses. Important findings The SNPs variations indicated that population Qitai exhibited higher nucleotide diversity compared to Barikun, Xishan and Qincheng Township in Hami City. Haloxylon ammodendron populations in Turpan-Hami area can be divided into 4 groups. Populations in Barkol County of Hami City has similar genetic composition with populations in the southeast of Junggar Basin and Gansu Province, and unique genetic compositions were retained in Gaochang District and Xishan Township. The chloroplast genome analyses results showed that 39 haplotypes were detected, and Qitai region had the most diverse haplotypes and the highest genetic diversity. The haplotypes from Qitai were found in both Turpan-Hami and Gansu populations. This may suggest that H. ammodendron populations in the Turpan-Hami region originated from the Qitai and dispersed eastward.

Key words: Haloxylon ammodendron, Turpan-Hami area, genome resequencing, population genetic structure