细叶桉群体的遗传多样性和受选择位点

Genetic Diversity and Selective Loci in Eucalyptus tereticornis Populations

【目的】分析细叶桉天然群体的多样性水平和遗传结构,为种质资源管理和育种利用提供有用信息;检测细叶桉与原产地气候因子显著关联的基因组位点,探索气候适应过程中趋异选择的分子证据。【方法】以细叶桉9个群体的77株样品为材料,基于覆盖巨桉全基因组的108个SSR位点（包括44个基因组SSRs和64个ESTSSRs）,利用不偏离哈-温平衡、FST值非异常的25个中性的基因组SSRs进行群体多样性水平和遗传结构分析,利用所有位点进行FST异常值检测、再利用空间分析法查找与原产地气候因子关联的适应性位点,注释适应性位点的功能,并通过等位片段在各群体的频率与气候因子的一元线性回归进一步验证关联的显著性。【结果】25个中性的基因组SSR位点对细叶桉9个群体扩增,共检测到556个等位片段、平均每个位点22.2个等位片段,位点多态性较高;群体多样性水平都较高,期望杂合度为0.711-0.847（平均0.800）、基因丰富度为3.054-3.386（平均3.246）,各群体特有等位片段数为6-26（平均14.4）;群体间分化水平较低,25个中性位点平均FST仅0.012,分子方差分析中群体间方差分量仅占1.2%,表明细叶桉遗传变异主要存在于群体内;聚类分析也表明群体分化水平较低。所有108个位点中,共检测到78个FST值异常的位点,与年均气温、年均降水、最热月最高温度和季节性降水变异系数相关的FST值异常的位点数分别为27,10,51和42个,即为受选择位点;其中,4个FST值异常的位点各有1个等位片段在空间分析法中与1个或者2个气候因子显著关联,EUCe SSR485与季节性降水变异系数相关、为富含羟脯氨酸的蛋白家族基因,EUCe SSR0497与年均气温和年均降水均相关、与跨膜内切1,4-β-葡聚糖酶基因同源,而另外2个没有明确的功能注释;线性回归分析验证了1个等位片段（EUCe SSR485-140 bp）与季节性降水变异系数的回归显著性（P≤0.05）。【结论】细叶桉群体的遗传多样性高,育种利用的潜力大,种质资源管理应重视多样性较高和特有等位片段较多的群体;细叶桉群体的遗传分化较低,其适于关联遗传分析;受选择位点的鉴定有助于理解林木适应环境的分子机制和探索林木环境适应性的潜力。

【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 putativelyneutral genomic SSR loci that neither departed from Hardy-Weinberg equilibrium nor showed FSToutlying values. FST 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 FST= 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 FSToutliers 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,EUCe SSR485 associated with precipitation seasonality climatic factors was functionally annotated as a member of hydroxylproline-rich glycoprotein gene family,and EUCe SSR0497 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 EUCe SSR485-140 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.