Abstract: [Objective] Genetic diversity and population structure were analyzed in an important tree species Eucalyptus tereticornis to provide useful information for germplasm management and breeding. Genomic loci significantly associated with habitat climatic variables were identified to explore the molecular signature of divergent selection during climatic adaptation. [Method] A total of 77 individuals sampled from nine E. tereticornis populations were analyzed using 108 simple sequence repeats (SSR) markers spanning the E. grandis genome, including 44 genomic SSRs and 64 expressed sequence tag (EST) derived SSRs. The genetic diversity and population structure were assessed using 25 putatively neutral genomic SSR loci that neither departed from Hardy-Weinberg equilibrium nor showed F_ST outlying values. F_ST outlying loci and their significant associations with habitat climatic variables were investigated for all the 108 SSRs, with further functional annotation of the significantly associated loci. The significance of associations was also tested through univariate linear regression analysis between the allelic frequency and the climatic factor. [Results] A total of 556 alleles were detected, averaging at 22.2 alleles per locus and indicating high levels of locus polymorphism. Population diversity was high, with expected heterozygosity 0.711-0.847 (mean 0.800), allelic richness 3.054-3.386 (mean 3.246) and number of private alleles 6-26 (mean 14.4). Population differentiation was extremely low, with mean F_ST=0.012 at 25 putative neutral genomic SSRs as well as among-population variation percentage of 1.2% in analysis of molecular variance (AMOVA), indicating within-population accounting for the majority of genetic variations. The clustering analysis indicated also a low level of population differentiation. A total of 78 F_ST outliers were identified as selective loci form all the 108 SSR loci, and the numbers of outliers related with mean annual temperature, mean annual precipitation, maximum temperature of the warmest month and precipitation seasonality were 27, 10, 51 and 42, respectively. Four alleles from independent outlier loci were revealed with spatial analysis methods (SAM), each associated with one or two climatic factors. Of the four selective loci, EUCeSSR485 associated with precipitation seasonality climatic factors was functionally annotated as a member of hydroxylproline-rich glycoprotein gene family, and EUCeSSR0497 with mean annual temperature and mean annual precipitation was homologous to membrane-anchored endo-1,4-beta-glucanase gene, while the rest two loci were of unknown function. One significant association between frequency of EUCeSSR485-140 bp and precipitation seasonality was validated with univariate linear regression (P≤0.05). [Conclusion] The high levels of genetic diversity in E. tereticornis may suggest that great potential can be expected in breeding and attention should be paid to those populations with higher diversity and more private alleles in germplasm management. The low genetic differentiation may indicate that E. tereticornis populations are suitable for further association genetics analysis. The selective loci indentified herein may help in understanding the molecular mechanism of adaptation to environments and exploring the adaptation potential in forest trees.

Key words: Eucalyptus tereticornis, SSR marker, genetic diversity, population structure, adaptation