Genetic diversity and population structure of common walnut (Juglans regia) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (PAL)

Common walnut (Juglans regia L.) is an economically important temperate tree species valued for both its nut and wood. We investigated the genetic diversity and population structure of J. regia germplasm from 13 locations in China using 10 markers derived from expressed sequences (EST-SSR) and sequence polymorphisms within the phenylalanine ammonia-lyase (PAL) gene. Analysis of the population genetic structure based on EST-SSRs showed distinct populations in northern versus southern China that were not reflected in the spatial distribution of PAL haplotypes. High levels of population differentiation were probably the result of reproductive isolation and in southern China, hybridization with Juglans sigillata. The results indicate the possible presence of distinct evolutionary lineages of J. regia in the Qinling and Daba Mountains of China and in Yunnan province that may require ecological management if they are to be retained as in situ resources.