水稻品种DUS测试标准品种多样性和测试性状稳定性分析
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摘要
利用水稻DUS测试指南中选定的49个标准品种和59个测试形态性状进行表型多样性和性状稳定性及重要性进行分析；采用农业行业标准(NY/1433-2077)推荐的24对水稻SSR引物对49个标准品种和949份申请保护水稻测试材料进行DNA指纹图谱多样性研究；利用表型和基因型多样性参数对标准品种和测试品种进行聚类分析。旨在评价当前水稻DUS测试中标准品种、形态测试性状及SSR标记选择的合理性,为DUS测试指南(标准)的改进提供参考依据。主要结论如下：
(1)以DUS测试指南中选定的49个水稻标准品种为材料,根据2008年在杭州田间试验对59个形态性状的调查数据,利用PopGen32软件计算了等位变异数、有效等位变异数和Shannon's多样性信息指数,对标准品种的形态性状多样性进行了评价；并根据其多样性参数采用NTSYS软件对标准品种进行了聚类分析。结果表明,59个形态性状在19份籼稻和30份粳稻品种中分别检测到201和262个等位变异,平均每个性状可以检测到3.4068(籼稻)和4.4407(粳稻)个等位变异,籼、粳稻类群中59个性状的平均Shannon's多样性指数分别为0.8318(0-1.7674)和0.9828(0-1.8547)。聚类分析结果表明,籼、粳稻群体内品种间的形态性状相似系数分别介于0.45-0.81和0.36-0.76,取相似系数0.70为阈值,可将19份籼稻和30份粳稻品种分别分为16和27类。多样性分析表明本研究的49个品种形态性状多样性丰富,具有性状描述的示例和校正作用。
(2)以DUS测试指南中选定的49个水稻标准品种为材料,采用农业行业标准(NY/1433-2077)中推荐的24对水稻SSR引物进行DNA指纹图谱构建和遗传多样性分析。结果表明,24对SSR引物在19份籼稻和30份粳稻品种中分别检测到141和156个等位变异,平均每对引物可以检测到5.88(籼稻)和6.50(粳稻)个等位变异,籼、粳稻类群中24对SSR引物的平均Shannon's多样性指数分别为1.5141(1.0460-1.9959)和1.4389(0.4677-2.4503)。聚类分析结果表明,籼、粳稻群体内品种间的形态性状相似系数分别介于0.13-0.80和0.15-0.75,取相似系数0.65为阈值,可将19份籼稻和30份粳稻品种分别分为17和27类。分析表明,本研究的49个品种形态性状和DNA指纹图谱多样性丰富,结合形态性状和基因型聚类分析结果,可将现有的49个水稻DUS测试标准品种减少到46个
(3)对水稻测试品种进行DNA指纹图谱多样性研究结果表明,24对SSR引物在949份水稻测试材料中共检测到227个等位变异,平均每对引物可以检测到9.46个等位变异；949份水稻材料中24对SSR引物的平均Shannon's多样性指数为1.4783,变幅介于0.8872-2.084。大部分标记都适合应用于DUS测试,极少部分标记如RM274和RM85的多样性相对较差,建议开发新的多样性好的SSR标记。聚类分析结果表明,相似系数在0.3处可大体将949份测试品种分为籼稻和粳稻两个大的类群,且这一分类结果与品种来源信息基本吻合。测试品种间大部分遗传相似系数都大于0.7,表明多数品种显示出较近的遗传距离,共有126组测试品种的基因型相似系数在0.8以上,部分品种间的相似系数高达0.95以上,说明当前水稻育种主要采用少数骨干亲本,遗传基础较狭窄。测试中4组的基因型相似系数为100%,且其DUS测试的形态性状也未表现出明显差异,可视为同一品种。
(4)应用AMMI模型对DUS测试指南中列出的49份水稻品种DUS测试性状进行稳定性分析,并采用随机森林算法对测试性状的重要性进行评价。结果显示35个目测性状的稳定性相对较高,但性状间也有一定变化,Di值介于0.028-0.886。其中,护颖长度、剑叶卷曲等15个性状稳定性很高,Di值都在0.1以下,而叶茸毛和茎节包露二性状的稳定性相对较低,在不同的环境中表现出较大的变异性。量测性状的稳定性总体上较目测性状差,其中结实率、茎杆长度、抽穗期、每穗粒数和成熟期等性状的稳定性相对较低,稳定性参数Di都在0.5以上。测试性状的重要性分析表明,以量测方式观测的性状的重要性参数较大,而以目测方式观测的性状重要性参数相对较小
(5)对不同施氮水平51个测试性状表达状态的研究结果表明,氮素施用量对目测性状和量测性状均有不同程度影响。其中,38个目测性状中,抽穗期、叶片绿色深浅与茎节花青甙显色对氮素的反应较明显,其他性状稳定性相对较好；13个量测性状中,最长芒长度稳定性较好,其他性状在不同氮素施用水平下均发生显著变化。
In this study,59morphological characteristics'phenotypic diversity of49example varieties which listed as example varieties in the DUS testing guidelines was studied; genetic diversity based on DNA fingerprint of the49example varieties and949rice test materials was analyzed by using24rice SSR primers recommended by testing guidelines; The clustering analysis for the example varieties and test varieties was conducted according to their phenotypic and genotypic diversity parameters; the stability and the importance of morphological characteristics for the example varieties in rice DUS testing was also analyzed. It aims to evaluate the current DUS test example varieties, the morphological test characteristics and SSR markers in the DUS testing guidelines, and to provide a criterion for selection and optimization of example varieties, morphological test characteristics and SSR markers in rice DUS testing system; it could also give a reference for developing DUS testing guidelines for other plant species. The main results are as follows:
(1) Diversity analysis, including observed number of alleles, effective number of alleles and Shannon's information index, were conducted with49rice varieties which listed as example varieties in the DUS testing guidelines as materials, combining with the59morphological characteristics investigated at Hanzhou in2008. The clustering analysis for the example varieties was also conducted according to their species diversity parameters. The results showed that total of201and262alleles for59morphological characteristics were observed in the indica and japonica rice group, respectively, with an average of3.4068and4.4407alleles for each characteristic in the two subspecies. The Shannon's diversity index averaged from59morphological characteristics was0.8318with a range of0-1.7674and0.9828with a range of0-1.8547in the indica and japonica rice group, respectively. Several groups, with each includes2-3rice varieties with similarity over0.7, were found in both indica and japonica rice group, based on the clustering results. The results indicated that the49example varieties, which with rich diversity in morphological characteristics, could be used for demonstration and adjusting for characteristics' describing in DUS testing.
(2) DNA fingerprinting and genetic diversity were conducted with49rice varieties which listed as example varieties in the DUS testing guidelines as materials, combining with24SSR markers. The clustering analysis for the example varieties was also conducted according to their species diversity parameters. The results showed that the total of141and156alleles for24SSR markers were observed in the indica and japonica rice group, respectively, with an average of5.88and6.50alleles for each marker in the two subspecies. The Shannon's diversity index averaged for24SSR markers were1.5141with a range of1.0460-1.9959and1.4389with a range of1.4389in the indica and japonica rice group, respectively. Several groups, with each includes2-3rice varieties with similarity over0.65, were found in both indica and japonica rice group, based on the clustering results. The results indicated that the49example varieties, which with rich diversity based on DNA fingerprint, could be used for demonstration and adjusting for SSR markers in DUS testing. The49rice example varieties could be reduced to46combined with the results of morphological characteristics and genotypic cluster analysis.
(3) DNA fingerprinting and genetic diversity were conducted with949rice test varieties as materials, combining with the24SSR markers. The clustering analysis for the example varieties was also conducted according to their species diversity parameters. The results showed that a total of227alleles for24SSR markers were observed in the949rice varieties, with an average of9.46alleles for each marker. The Shannon's diversity index averaged for24SSR markers were1.4783with a range of0.8872-2.0841. Most of the markers are suitable for DUS test, a very small part of the SSR markers'diversity was relatively poor, such as RM274and RM85, it is recommended to develop new SSR markers. The cluster analysis showed that the949test rice varieties can be roughly divided into two large groups of indica and japonica according the threshold with similarity of0.3, and this classification was consistent with the varieties'sources information. Most of the test varieties'genetic similarity coefficient was greater than0.7; and a total of126test varieties'genetic similarity coefficient was above0.8, which indicated these varieties showed close genetic distance. Some test varieties'genetic coefficient was above0.95, which indicated the narrow genetic basis of current rice breeding. Among them, the genetic similarity coefficient of4rice groups was100%and their morphological characteristics also didn't show significant differences, field phenotypic identification was needed to decide whether they are the same rice varieties.
(4) The stability analysis of DUS testing characteristics were conducted with49rice varieties which listed as example varieties in the DUS testing guidelines as materials, combining with AMMI model. The results showed that the stability of the35visual characteristics are relatively high, but there are some differences between different characteristics, the Di values ranged from0.028to0.886. The15morphological characteristics, such as glum length, leaf roll degree have high stability; the Di values were all below0.1. While the leaf hairs and phimosis degree have relatively low stability, they showed large variability in different environments. In a whole, the stability of measured characteristics was worse than the visual characteristics. Some of the measured characteristics'stability was relatively low, such as seed setting rate, stem length, heading date, grains per panicle and maturity date, the stability parameter Di was more than0.5. The importance parameters of the characteristics by measurement observation were greater than the characteristics by visual observation.
(5) The51morphological characteristics of44rice varieties which listed as example varieties in the DUS testing guidelines were investigated by different nitrogen treatment. The results showed that application amount of nitrogen had varying degrees affects on visual characteristics and measured characteristics. Among them,38visual characteristics, such as heading date, leaf green degree and internodes anthocyanin coloration had obvious response to nitrogen, other visual characteristics had relatively better stability. The length of the longest awn had better stability among the13measurement indexes; other characteristics all had significant change in different nitrogen fertilizer levels.
(1)以DUS测试指南中选定的49个水稻标准品种为材料,根据2008年在杭州田间试验对59个形态性状的调查数据,利用PopGen32软件计算了等位变异数、有效等位变异数和Shannon's多样性信息指数,对标准品种的形态性状多样性进行了评价；并根据其多样性参数采用NTSYS软件对标准品种进行了聚类分析。结果表明,59个形态性状在19份籼稻和30份粳稻品种中分别检测到201和262个等位变异,平均每个性状可以检测到3.4068(籼稻)和4.4407(粳稻)个等位变异,籼、粳稻类群中59个性状的平均Shannon's多样性指数分别为0.8318(0-1.7674)和0.9828(0-1.8547)。聚类分析结果表明,籼、粳稻群体内品种间的形态性状相似系数分别介于0.45-0.81和0.36-0.76,取相似系数0.70为阈值,可将19份籼稻和30份粳稻品种分别分为16和27类。多样性分析表明本研究的49个品种形态性状多样性丰富,具有性状描述的示例和校正作用。
(2)以DUS测试指南中选定的49个水稻标准品种为材料,采用农业行业标准(NY/1433-2077)中推荐的24对水稻SSR引物进行DNA指纹图谱构建和遗传多样性分析。结果表明,24对SSR引物在19份籼稻和30份粳稻品种中分别检测到141和156个等位变异,平均每对引物可以检测到5.88(籼稻)和6.50(粳稻)个等位变异,籼、粳稻类群中24对SSR引物的平均Shannon's多样性指数分别为1.5141(1.0460-1.9959)和1.4389(0.4677-2.4503)。聚类分析结果表明,籼、粳稻群体内品种间的形态性状相似系数分别介于0.13-0.80和0.15-0.75,取相似系数0.65为阈值,可将19份籼稻和30份粳稻品种分别分为17和27类。分析表明,本研究的49个品种形态性状和DNA指纹图谱多样性丰富,结合形态性状和基因型聚类分析结果,可将现有的49个水稻DUS测试标准品种减少到46个
(3)对水稻测试品种进行DNA指纹图谱多样性研究结果表明,24对SSR引物在949份水稻测试材料中共检测到227个等位变异,平均每对引物可以检测到9.46个等位变异；949份水稻材料中24对SSR引物的平均Shannon's多样性指数为1.4783,变幅介于0.8872-2.084。大部分标记都适合应用于DUS测试,极少部分标记如RM274和RM85的多样性相对较差,建议开发新的多样性好的SSR标记。聚类分析结果表明,相似系数在0.3处可大体将949份测试品种分为籼稻和粳稻两个大的类群,且这一分类结果与品种来源信息基本吻合。测试品种间大部分遗传相似系数都大于0.7,表明多数品种显示出较近的遗传距离,共有126组测试品种的基因型相似系数在0.8以上,部分品种间的相似系数高达0.95以上,说明当前水稻育种主要采用少数骨干亲本,遗传基础较狭窄。测试中4组的基因型相似系数为100%,且其DUS测试的形态性状也未表现出明显差异,可视为同一品种。
(4)应用AMMI模型对DUS测试指南中列出的49份水稻品种DUS测试性状进行稳定性分析,并采用随机森林算法对测试性状的重要性进行评价。结果显示35个目测性状的稳定性相对较高,但性状间也有一定变化,Di值介于0.028-0.886。其中,护颖长度、剑叶卷曲等15个性状稳定性很高,Di值都在0.1以下,而叶茸毛和茎节包露二性状的稳定性相对较低,在不同的环境中表现出较大的变异性。量测性状的稳定性总体上较目测性状差,其中结实率、茎杆长度、抽穗期、每穗粒数和成熟期等性状的稳定性相对较低,稳定性参数Di都在0.5以上。测试性状的重要性分析表明,以量测方式观测的性状的重要性参数较大,而以目测方式观测的性状重要性参数相对较小
(5)对不同施氮水平51个测试性状表达状态的研究结果表明,氮素施用量对目测性状和量测性状均有不同程度影响。其中,38个目测性状中,抽穗期、叶片绿色深浅与茎节花青甙显色对氮素的反应较明显,其他性状稳定性相对较好；13个量测性状中,最长芒长度稳定性较好,其他性状在不同氮素施用水平下均发生显著变化。
In this study,59morphological characteristics'phenotypic diversity of49example varieties which listed as example varieties in the DUS testing guidelines was studied; genetic diversity based on DNA fingerprint of the49example varieties and949rice test materials was analyzed by using24rice SSR primers recommended by testing guidelines; The clustering analysis for the example varieties and test varieties was conducted according to their phenotypic and genotypic diversity parameters; the stability and the importance of morphological characteristics for the example varieties in rice DUS testing was also analyzed. It aims to evaluate the current DUS test example varieties, the morphological test characteristics and SSR markers in the DUS testing guidelines, and to provide a criterion for selection and optimization of example varieties, morphological test characteristics and SSR markers in rice DUS testing system; it could also give a reference for developing DUS testing guidelines for other plant species. The main results are as follows:
(1) Diversity analysis, including observed number of alleles, effective number of alleles and Shannon's information index, were conducted with49rice varieties which listed as example varieties in the DUS testing guidelines as materials, combining with the59morphological characteristics investigated at Hanzhou in2008. The clustering analysis for the example varieties was also conducted according to their species diversity parameters. The results showed that total of201and262alleles for59morphological characteristics were observed in the indica and japonica rice group, respectively, with an average of3.4068and4.4407alleles for each characteristic in the two subspecies. The Shannon's diversity index averaged from59morphological characteristics was0.8318with a range of0-1.7674and0.9828with a range of0-1.8547in the indica and japonica rice group, respectively. Several groups, with each includes2-3rice varieties with similarity over0.7, were found in both indica and japonica rice group, based on the clustering results. The results indicated that the49example varieties, which with rich diversity in morphological characteristics, could be used for demonstration and adjusting for characteristics' describing in DUS testing.
(2) DNA fingerprinting and genetic diversity were conducted with49rice varieties which listed as example varieties in the DUS testing guidelines as materials, combining with24SSR markers. The clustering analysis for the example varieties was also conducted according to their species diversity parameters. The results showed that the total of141and156alleles for24SSR markers were observed in the indica and japonica rice group, respectively, with an average of5.88and6.50alleles for each marker in the two subspecies. The Shannon's diversity index averaged for24SSR markers were1.5141with a range of1.0460-1.9959and1.4389with a range of1.4389in the indica and japonica rice group, respectively. Several groups, with each includes2-3rice varieties with similarity over0.65, were found in both indica and japonica rice group, based on the clustering results. The results indicated that the49example varieties, which with rich diversity based on DNA fingerprint, could be used for demonstration and adjusting for SSR markers in DUS testing. The49rice example varieties could be reduced to46combined with the results of morphological characteristics and genotypic cluster analysis.
(3) DNA fingerprinting and genetic diversity were conducted with949rice test varieties as materials, combining with the24SSR markers. The clustering analysis for the example varieties was also conducted according to their species diversity parameters. The results showed that a total of227alleles for24SSR markers were observed in the949rice varieties, with an average of9.46alleles for each marker. The Shannon's diversity index averaged for24SSR markers were1.4783with a range of0.8872-2.0841. Most of the markers are suitable for DUS test, a very small part of the SSR markers'diversity was relatively poor, such as RM274and RM85, it is recommended to develop new SSR markers. The cluster analysis showed that the949test rice varieties can be roughly divided into two large groups of indica and japonica according the threshold with similarity of0.3, and this classification was consistent with the varieties'sources information. Most of the test varieties'genetic similarity coefficient was greater than0.7; and a total of126test varieties'genetic similarity coefficient was above0.8, which indicated these varieties showed close genetic distance. Some test varieties'genetic coefficient was above0.95, which indicated the narrow genetic basis of current rice breeding. Among them, the genetic similarity coefficient of4rice groups was100%and their morphological characteristics also didn't show significant differences, field phenotypic identification was needed to decide whether they are the same rice varieties.
(4) The stability analysis of DUS testing characteristics were conducted with49rice varieties which listed as example varieties in the DUS testing guidelines as materials, combining with AMMI model. The results showed that the stability of the35visual characteristics are relatively high, but there are some differences between different characteristics, the Di values ranged from0.028to0.886. The15morphological characteristics, such as glum length, leaf roll degree have high stability; the Di values were all below0.1. While the leaf hairs and phimosis degree have relatively low stability, they showed large variability in different environments. In a whole, the stability of measured characteristics was worse than the visual characteristics. Some of the measured characteristics'stability was relatively low, such as seed setting rate, stem length, heading date, grains per panicle and maturity date, the stability parameter Di was more than0.5. The importance parameters of the characteristics by measurement observation were greater than the characteristics by visual observation.
(5) The51morphological characteristics of44rice varieties which listed as example varieties in the DUS testing guidelines were investigated by different nitrogen treatment. The results showed that application amount of nitrogen had varying degrees affects on visual characteristics and measured characteristics. Among them,38visual characteristics, such as heading date, leaf green degree and internodes anthocyanin coloration had obvious response to nitrogen, other visual characteristics had relatively better stability. The length of the longest awn had better stability among the13measurement indexes; other characteristics all had significant change in different nitrogen fertilizer levels.
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