中国核桃品种的遗传多样性研究
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摘要
核桃是重要的经济树种，中国已经拥有了一批优良品种，但是对核桃品种遗传背景的认识尚待深入。本研究结合形态学标记、AFLP分子标记和SSR标记等技术，分析了核桃品种的遗传多样性，构建了供试核桃品种核心种质，可为进一步选育优良品种奠定基础。本研究所取得的主要结果如下：
（1）利用形态学标记进行分析发现，中国核桃的形态学性状变异比较丰富，供试核桃品种间的欧氏距离最小为0.4946，最大达到了25.2002，平均为6.4246。同时也有一定数量的品种在形态学性状上难以区分；
（2）以核桃一年生枝条的新鲜韧皮部为试材，采用改良的CTAB法获得了高质量的基因组DNA，进一步筛选出了17对多态性高、电泳谱带清晰、谱带分离状态好的荧光引物组合，应用这些引物组合对供试核桃和泡核桃品种进行扩增，取得了良好的扩增效果，建立的荧光AFLP指纹图谱清晰有效、信息量大，为该法在核桃品种分子遗传研究中的应用奠定了良好基础；
（3）应用荧光AFLP体系，对中国136个核桃和泡核桃品种进行分析，构建了136个品种的荧光AFLP指纹图谱，检测到了75个品种的314条特有带和1个品种的1条特无带，通过这些特征带能够快速地将相应品种从全部136个供试品种中辨别出来，其余材料可通过差异带进行区分；
（4）供试核桃品种的AFLP扩增得到了3100条可统计的条带，其中3008条呈多态性，平均多态性带百分率为96.97%。所有供试核桃品种的遗传相似系数范围为0.1397~0.8587，平均为0.5341；等位基因频率平均为0.8358、有效等位基因数平均为1.3091、基因多样度平均为0.2867、Shannon信息指数平均为0.1956，显示中国核桃品种的遗传多样性处于中等水平。基于DICE遗传相似系数构建了136个核桃品种的聚类图，从分子水平上分析了它们的遗传多样性和亲缘关系，揭示了我国核桃品种遗传背景的复杂性，在实际应用中不仅可根据指纹图谱和聚类结果进行亲本选配，还可为核桃品种的鉴定、已知品种的保护、品种间的比较提供依据；
（5）采用AFLP分子标记与形态学标记偶合的方法构建了供试核桃品种的核心种质，抽样比例为18%，保留了95%以上的遗传多样性，能够较好地代表初始种质；
（6）利用AFLP数据对核桃和泡核桃种间分类关系进行分析，发现核桃的遗传多样性主要存在于群体内，群体内的变异大于群体间的变异。FCA分析和UPGMA聚类结果与遗传变异分析结果相一致，研究结果支持核桃与泡核桃可能为同一个种；
（7）采用SSR反应体系对33个核桃及泡核桃品种进行分析，共检测到了117个等位基因，多态位点百分率达到了100%，平均观察杂合度（Ho）与期望杂合度（He）分别为0.3977和0.6152，与AFLP的结果相结合进行分析发现：首先，研究结果支持核桃与泡核桃为同一个种下的不同生态地理型的结论；其次，早实类型与晚实类型的差异未能从基因组DNA酶切片段和SSR上体现出来；第三，大部分川核系列品种与泡核桃品种聚在一起，显示其亲缘关系较为密切；最后，‘北京861’、‘新光’等品种具有优异的经济性状且与其它品种间的遗传距离较远，有利于遗传变异的产生，善加利用将有可能成为优秀的育种材料；
（8）细胞核核糖体IGS区的DNA序列为典型的双亲遗传，在奇异杂种基因组的细胞核核糖体DNAIGS8-ETS1区中检测到了双亲本的遗传成分（约87.50%~88.89%）和子代特有的新的遗传成分（约11.11%~12.50%）。奇异杂种的遗传形成涉及到了核桃J．regia（核桃组）以及如下6种黑核桃（黑核桃组），即：北加州（函兹）黑核桃Juglans hindssiL.、南加州黑核桃J. californica、亚里桑纳黑核桃J. major、美国东部黑核桃J. nigra、小果黑核桃J. microcarpa以及J. hirsuta。细胞核核糖体DNA IGS8-ETS1区的序列有助于理解杂种形成的遗传基础，进而为选育优良砧木品种、提高核桃优良品种的繁育质量提供理论参考。
Walnut is an important non-timber forest tree species. A great amount of excellent walnutcultivars were selected till now. However, there is still a far way to go for walnut geneticdiversity studies. In this research, genetic diversity analysis was carried out on the basis ofmorphology markers, AFLP, and SSR. An advanced AFLP system was established and appliedto analyse the relationships of differenent walnut cultivars. AFLP fingerprintings of136walnutcultivars were conducted. Genetic structures and distances between the tested cultivars weredetermined both at the morphological level and the molecular level. The research has animportant significance in the enrichment of the walnut variety database, the blindness decreaseof walnut breeding and the effective protection of known walnut cultivars. Meanwhile it canimprove the authorization efficiency and accuracy of new walnut cultivars and lay a goodfoundation for walnut germplasm conservation and molecular marker-assisted breeding. Themain results are as follows:
1. Morphological variation was found to be giant among different walnut cultivars. Allassessed cultivars generated genetic distance averaged6.4246. Some cultivars were hard todistinguish according to their morphology.
2. High quality genomic DNA was isolated from fresh phloem of one-year old branchusing an advanced CTAB protocol.17pairs of primer combinations were screened out in theuse of f-AFLP fingerprints conduction. Fingerprints conducted in the study were robust andrepeatable.
3. The f-AFLP fingerprintings of136assayed walnut cultivars were constructed.75cultivars had specific bands and the others could be distinguished by their differential bands inAFLP fingerprinting through the dichotomous classification method. All tested walnut cultivarscould be distinguished according to their specific bands.
4. Seventeen EcoR I/Mse I primer combinations selected with clear and good separationbands and high polymorphism were used for the f-AFLP analysis of136walnut cultivars.3008out of3100bands were polymorphic with an average polymorphism of96.97%. The DICEgenetic coefficients among walnut cultivars were ranged from0.5768to0.8587with anaverage of0.5341. The averaged gene frequency was0.8358, Ne averaged1.3091, H averaged0.2867, I averaged0.1956, which impacted a morderate genetic diversity level of walnutCultivars in China. Dendrogram of assayed walnut cultivars based on f-AFLP data wasconstructed by UPGMA method. The relationships and genetic diversity between them werecarried out at the molecular level. The results revealed the complicated genetic background ofthe walnut cultivars in China which could provide the theoretic basis for the parent selection,cultivar identification and property right protection, and the comparison between cultivars.
5. Twenty out of136walnut cultivars were selected as core collection using a methodcombining f-AFLP and morphology. T-test showed there was no significant difference betweenthe core collection and initial germplasm on0.01level. The core collection could representinitial germplasm.
6. Clonal cultivars selected from a broad geographic range in China including4types,Juglans regia, Juglans sigillata, Juglans sigillata×Juglans regia, and J. hopeiensis, wereapplied in f-AFLP analysis. Nine EcoR I/Mse I primer combinations produced clear-cut AFLPprofiles. The percentages of polymorphic bands (PPBs), observed number of alleles (Na),effective number of alleles (Ne), Nei's gene diversity (H), and Shannon’s information index (I)were calculated based on AFLP data. As for Juglans regia, Juglans sigillata, and their hybrids,PPBs averaged93.86%,93.94%, and60.46%; Na averaged1.5370,1.6389, and1.2593; Neaveraged1.2582,1.2543, and1.1646; H scored0.1560,0.1556, and0.0951; I averaged0.2402,0.2459, and0.1414, respectively. The overall levels of Na, Ne, H, and I were1.7407,1.2701,0.1667, and0.2640. The total gene diversity (Ht=0.1596) can be distributed into intra-(Hs=0.1356) and inter-(Dst=0.0240) species gene diversity. Proportion of the distributed geneticdiversity among populations (Gst) was0.1505represented that only15%of the total gene diversity was attributed to differences between species. The FCA and the UPGMA analysisbased on cultivar polymorphism AFLP data revealed a really close genetic distance betweenJuglans regia and Juglans sigillata.
7. SSR markers were applied to analysis of genetic diversity of walnut cultivars. Totally,52alleles were detected generated a PPB of100%. The total value of observed heterozygosity(Ho) and expected heterozygosity (He) within species were0.3977and0.6152. A moderatelevel of genetic diversity was observed. Genetic stucture of assayed cultivars was analysedusing a popgene software.
8. Paradox is a famous rootstock in the walnut industry for a number of important features,including fast growth and resistance to some diseases. Paradox commonly refers to blackwalnut-Persian walnut hybrid. Nuclear rDNA IGS region, typically bi-parentally inherited,with rapid evolution and broad existence in all eukaryotic genomes, was found to be ofimportance in revealing genetic background of the walnut hybrids. Both parental geneticcomponents (around87.50%to88.89%) and novel genetic components (around11.11%to12.50%) were detected in the nrDNA IGS8-ETS1region of the Paradox genome. Theinheritance was commonly one-parent-dominated in each hybridization event. Our resultsindicated that genetic formation of Paradox hybrids involved in J. regia (sect. Juglans) and thefollowing6black walnut species (sect. Rhysocaryon), i.e., J. hindsii, J. californica, J. major, J.nigra, J. microcarpa and J. hirsuta. The nrDNA IGS8-ETS1region is helpful in understandingthe genetic basis of hybrids.
（1）利用形态学标记进行分析发现，中国核桃的形态学性状变异比较丰富，供试核桃品种间的欧氏距离最小为0.4946，最大达到了25.2002，平均为6.4246。同时也有一定数量的品种在形态学性状上难以区分；
（2）以核桃一年生枝条的新鲜韧皮部为试材，采用改良的CTAB法获得了高质量的基因组DNA，进一步筛选出了17对多态性高、电泳谱带清晰、谱带分离状态好的荧光引物组合，应用这些引物组合对供试核桃和泡核桃品种进行扩增，取得了良好的扩增效果，建立的荧光AFLP指纹图谱清晰有效、信息量大，为该法在核桃品种分子遗传研究中的应用奠定了良好基础；
（3）应用荧光AFLP体系，对中国136个核桃和泡核桃品种进行分析，构建了136个品种的荧光AFLP指纹图谱，检测到了75个品种的314条特有带和1个品种的1条特无带，通过这些特征带能够快速地将相应品种从全部136个供试品种中辨别出来，其余材料可通过差异带进行区分；
（4）供试核桃品种的AFLP扩增得到了3100条可统计的条带，其中3008条呈多态性，平均多态性带百分率为96.97%。所有供试核桃品种的遗传相似系数范围为0.1397~0.8587，平均为0.5341；等位基因频率平均为0.8358、有效等位基因数平均为1.3091、基因多样度平均为0.2867、Shannon信息指数平均为0.1956，显示中国核桃品种的遗传多样性处于中等水平。基于DICE遗传相似系数构建了136个核桃品种的聚类图，从分子水平上分析了它们的遗传多样性和亲缘关系，揭示了我国核桃品种遗传背景的复杂性，在实际应用中不仅可根据指纹图谱和聚类结果进行亲本选配，还可为核桃品种的鉴定、已知品种的保护、品种间的比较提供依据；
（5）采用AFLP分子标记与形态学标记偶合的方法构建了供试核桃品种的核心种质，抽样比例为18%，保留了95%以上的遗传多样性，能够较好地代表初始种质；
（6）利用AFLP数据对核桃和泡核桃种间分类关系进行分析，发现核桃的遗传多样性主要存在于群体内，群体内的变异大于群体间的变异。FCA分析和UPGMA聚类结果与遗传变异分析结果相一致，研究结果支持核桃与泡核桃可能为同一个种；
（7）采用SSR反应体系对33个核桃及泡核桃品种进行分析，共检测到了117个等位基因，多态位点百分率达到了100%，平均观察杂合度（Ho）与期望杂合度（He）分别为0.3977和0.6152，与AFLP的结果相结合进行分析发现：首先，研究结果支持核桃与泡核桃为同一个种下的不同生态地理型的结论；其次，早实类型与晚实类型的差异未能从基因组DNA酶切片段和SSR上体现出来；第三，大部分川核系列品种与泡核桃品种聚在一起，显示其亲缘关系较为密切；最后，‘北京861’、‘新光’等品种具有优异的经济性状且与其它品种间的遗传距离较远，有利于遗传变异的产生，善加利用将有可能成为优秀的育种材料；
（8）细胞核核糖体IGS区的DNA序列为典型的双亲遗传，在奇异杂种基因组的细胞核核糖体DNAIGS8-ETS1区中检测到了双亲本的遗传成分（约87.50%~88.89%）和子代特有的新的遗传成分（约11.11%~12.50%）。奇异杂种的遗传形成涉及到了核桃J．regia（核桃组）以及如下6种黑核桃（黑核桃组），即：北加州（函兹）黑核桃Juglans hindssiL.、南加州黑核桃J. californica、亚里桑纳黑核桃J. major、美国东部黑核桃J. nigra、小果黑核桃J. microcarpa以及J. hirsuta。细胞核核糖体DNA IGS8-ETS1区的序列有助于理解杂种形成的遗传基础，进而为选育优良砧木品种、提高核桃优良品种的繁育质量提供理论参考。
Walnut is an important non-timber forest tree species. A great amount of excellent walnutcultivars were selected till now. However, there is still a far way to go for walnut geneticdiversity studies. In this research, genetic diversity analysis was carried out on the basis ofmorphology markers, AFLP, and SSR. An advanced AFLP system was established and appliedto analyse the relationships of differenent walnut cultivars. AFLP fingerprintings of136walnutcultivars were conducted. Genetic structures and distances between the tested cultivars weredetermined both at the morphological level and the molecular level. The research has animportant significance in the enrichment of the walnut variety database, the blindness decreaseof walnut breeding and the effective protection of known walnut cultivars. Meanwhile it canimprove the authorization efficiency and accuracy of new walnut cultivars and lay a goodfoundation for walnut germplasm conservation and molecular marker-assisted breeding. Themain results are as follows:
1. Morphological variation was found to be giant among different walnut cultivars. Allassessed cultivars generated genetic distance averaged6.4246. Some cultivars were hard todistinguish according to their morphology.
2. High quality genomic DNA was isolated from fresh phloem of one-year old branchusing an advanced CTAB protocol.17pairs of primer combinations were screened out in theuse of f-AFLP fingerprints conduction. Fingerprints conducted in the study were robust andrepeatable.
3. The f-AFLP fingerprintings of136assayed walnut cultivars were constructed.75cultivars had specific bands and the others could be distinguished by their differential bands inAFLP fingerprinting through the dichotomous classification method. All tested walnut cultivarscould be distinguished according to their specific bands.
4. Seventeen EcoR I/Mse I primer combinations selected with clear and good separationbands and high polymorphism were used for the f-AFLP analysis of136walnut cultivars.3008out of3100bands were polymorphic with an average polymorphism of96.97%. The DICEgenetic coefficients among walnut cultivars were ranged from0.5768to0.8587with anaverage of0.5341. The averaged gene frequency was0.8358, Ne averaged1.3091, H averaged0.2867, I averaged0.1956, which impacted a morderate genetic diversity level of walnutCultivars in China. Dendrogram of assayed walnut cultivars based on f-AFLP data wasconstructed by UPGMA method. The relationships and genetic diversity between them werecarried out at the molecular level. The results revealed the complicated genetic background ofthe walnut cultivars in China which could provide the theoretic basis for the parent selection,cultivar identification and property right protection, and the comparison between cultivars.
5. Twenty out of136walnut cultivars were selected as core collection using a methodcombining f-AFLP and morphology. T-test showed there was no significant difference betweenthe core collection and initial germplasm on0.01level. The core collection could representinitial germplasm.
6. Clonal cultivars selected from a broad geographic range in China including4types,Juglans regia, Juglans sigillata, Juglans sigillata×Juglans regia, and J. hopeiensis, wereapplied in f-AFLP analysis. Nine EcoR I/Mse I primer combinations produced clear-cut AFLPprofiles. The percentages of polymorphic bands (PPBs), observed number of alleles (Na),effective number of alleles (Ne), Nei's gene diversity (H), and Shannon’s information index (I)were calculated based on AFLP data. As for Juglans regia, Juglans sigillata, and their hybrids,PPBs averaged93.86%,93.94%, and60.46%; Na averaged1.5370,1.6389, and1.2593; Neaveraged1.2582,1.2543, and1.1646; H scored0.1560,0.1556, and0.0951; I averaged0.2402,0.2459, and0.1414, respectively. The overall levels of Na, Ne, H, and I were1.7407,1.2701,0.1667, and0.2640. The total gene diversity (Ht=0.1596) can be distributed into intra-(Hs=0.1356) and inter-(Dst=0.0240) species gene diversity. Proportion of the distributed geneticdiversity among populations (Gst) was0.1505represented that only15%of the total gene diversity was attributed to differences between species. The FCA and the UPGMA analysisbased on cultivar polymorphism AFLP data revealed a really close genetic distance betweenJuglans regia and Juglans sigillata.
7. SSR markers were applied to analysis of genetic diversity of walnut cultivars. Totally,52alleles were detected generated a PPB of100%. The total value of observed heterozygosity(Ho) and expected heterozygosity (He) within species were0.3977and0.6152. A moderatelevel of genetic diversity was observed. Genetic stucture of assayed cultivars was analysedusing a popgene software.
8. Paradox is a famous rootstock in the walnut industry for a number of important features,including fast growth and resistance to some diseases. Paradox commonly refers to blackwalnut-Persian walnut hybrid. Nuclear rDNA IGS region, typically bi-parentally inherited,with rapid evolution and broad existence in all eukaryotic genomes, was found to be ofimportance in revealing genetic background of the walnut hybrids. Both parental geneticcomponents (around87.50%to88.89%) and novel genetic components (around11.11%to12.50%) were detected in the nrDNA IGS8-ETS1region of the Paradox genome. Theinheritance was commonly one-parent-dominated in each hybridization event. Our resultsindicated that genetic formation of Paradox hybrids involved in J. regia (sect. Juglans) and thefollowing6black walnut species (sect. Rhysocaryon), i.e., J. hindsii, J. californica, J. major, J.nigra, J. microcarpa and J. hirsuta. The nrDNA IGS8-ETS1region is helpful in understandingthe genetic basis of hybrids.
引文
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