Abstract: We studied the genetic diversity and population genetic structure of 265 individuals from different regions of China by using the roles of phenylalanine ammonia-lyase(PAL) nuclear gene JRD5680 DNA sequence of 40 common walnut(Juglans regia) and 5 out group plant species. The length of JRD5680 sequence was 809 bp, the content of G+C was 46.2% with 74 information sites. A total of 30 haplotypes, haplotype diversity variation showed low genetic diversity(H_d=0.370, π=0.005 3). There is a clear geographical structure(N_ST>G_ST), which is a regional distribution pattern. The spatial genetic structure analysis showed that the correlation between geographical isolation and genetic distance was significant(r=0.263 2; P=0.032 4*), and there was obvious geographical isolation effect among different geographic populations. The results of comprehensive mismatch analysis and neutral test can be deduced from the recent history of the different regions of the population expansion event. From the genetic structure, the walnut population can be divided into two groups(southwest and other regions). By AMOVA, the genetic variation among the populations was mainly stored in the populations(56.54%), and the genetic differentiation among the populations was higher(F_ST=0.885). The total of 5 species of Juglandaceae could be a single branch, and the JRD5680 sequence might be with high molecular identification radio in the members of the Juglandaceae.

Key words: Juglans regia, phenylalanine ammonia-lyase(PAL) gene, genetic diversity, genetic structure