Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India

A set of 50 rice genotypes comprising landraces, local selections, and improved varieties were characterized using simple sequence repeat(SSR) and inter simple sequence repeat(ISSR) markers to study genetic diversity and population structure. Following unweighted pair group method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 5 clusters and 11 sub-clusters, whereas population structure analysis separated 50 rice genotypes into 5 sub-populations. Grouping of rice genotypes showed better resemblance with the pedigree information of the genotypes. Both genetic diversity and population structure analysis separated majority of the improved varieties from landraces and local selections. Some of the SSR markers amplified unique alleles which were specific to a particular genotype and could distinguish them from the rest. The results indicate that these rice genotypes exhibit a higher genetic diversity and can be very useful in rice improvement program.     

利用SSR分子标记分析云南陆稻品种遗传多样性

 利用24对SSR引物对云南131个陆稻品种进行遗传多样性分析。共检测到195个等位基因。每个位点的等位基因数平均为8.125个,范围在5(RM55)～13(RM218、RM241)之间;平均表观杂合度为0.0014,平均期望杂合度为0.6545;平均Shannon Weaver指数(I)为1.381;Nei基因多样性指数(H)平均为0.6543,变幅为0.2073(RM235)～0.8689(RM218)。不同地区间陆稻种质资源遗传多样性比较分析表明,滇西南和滇南地区存在丰富的遗传变异,是云南陆稻品种遗传多样性的分布中心。藏缅语族和孟 高棉语族所种植的陆稻品种遗传多样性最丰富。AMOVA分析表明陆稻的遗传变异主要存在于地区内品种间(82%),只有3%遗传变异存在于地区间,品种内的遗传变异占15%。聚类分析显示Nei遗传相似系数为0.22时,云南陆稻品种分为籼粳两个类群,主坐标分析与UPGMA聚类结果基本吻合,并将类群Ⅳ的4个偏籼品种从粳稻类群中重新划归到籼稻类群中,校正了UPGMA聚类的误差,但是不能区分地理组。     

贵州地方水稻品种的SSR遗传多样性分析

利用21对SSR引物对74份贵州"禾"水稻品种及6份国际上常用的典型籼稻和粳稻品种进行遗传多样性研究。共检测到92个等位基因,每个位点的等位基因数变幅为2~9个,平均4.381个;平均Shannon信息指数为0.935,变幅为0·2793~1.8732;期望杂合度为0.5145,范围在0.0988~0.8313;品种间遗传相似系数为0.64~0.98。UPGMA聚类分析表明,在相似系数为0.682处可将"禾"品种分为4大类,大部分材料被聚类到典型粳稻的附近,品种间的亲缘关系与地理来源关系不大;主坐标分析结果与UPGMA聚类结果基本吻合。SSR检测结果表明,贵州省水稻地方品种——"禾"的多样性程度较低,且大多数属于粳稻。     

布朗族当前种植稻作地方品种的SSR位点多样性分析

 调查收集了80份布朗族当前仍在种植的稻作地方品种,利用分布于水稻12条染色体上的72对SSR引物,进行了遗传多样性分析。共检测出271个等位基因,平均每对引物3.764个;197个有效等位基因,平均每对引物2.739个;多态性信息含量变幅为0.163~0.827,平均为0.582;稀有等位基因数20个。云南省内3个不同地区布朗族种植的地方品种遗传多样性有差异,表现为勐海县>双江县>墨江县。地方品种的遗传相似系数变幅为0.111~0.875,平均为0.411;在相似系数0.266处可以将供试品种分为籼粳两大类,但不能再将布朗族同一集居区的地方品种完全聚成同一亚类,暗示着布朗族不同集居区的条件对地方品种进化的影响还比较有限。最后还就布朗族对地方品种多样性的贡献及可能的原因等进行了讨论分析,对如何防止地方品种收集中同名异种和同种异名问题发生提出了建议。     

基于SSR标记的云南地方稻种群体内遗传多样性分析

 用20对SSR引物对原产于云南的16份地方稻种和2份选育品种进行单个品种群体内的遗传多样性分析。结果表明,87.5%的地方品种群体内SSR多态性高于选育品种,而12.5%的地方品种群体内SSR标记多态性与选育品种相近。81.2%的地方稻种群体内的等位基因数(Na)和Nei基因遗传多样性指数(He)高于选育品种,而18.8%的地方品种群体内Na和He与选育品种相同或略小。水稻地方稻种群体内He的差异较大,其变异范围为0.0146～0.5117,其中,黄板所 1（1980年收集）、黄板所 2（2007年收集）、麻线谷 1（1980年收集）、麻线谷 2（2007年收集）的群体内遗传多样性较高,分别为0.2327、0.4214、0.5117和0.4489。87.5%地方品种的杂合度(Ho)明显高于选育品种;地方品种群体间遗传多样性差异很大,其中1/4的遗传差异来源于地方稻种群体内,差异极显著。RM333、RM257和RM180在供试云南地方稻种群体内的多态性、等位基因数、多样性指数和变异百分率均较高,适用于云南地方稻种群体内遗传多样性检测。     

太湖流域粳稻地方品种的微卫星分析

 采用45对SSR引物对224份太湖流域粳稻地方品种进行遗传多样性分析,共检测到162个等位变异,每个位点等位基因数的变幅为2～7,平均为3.6。各位点Nei基因多样性指数变异较大,为0.009（RM169）～0.663（RM444）,平均为0.197。青稻、黄稻、红稻和白稻各传统生态型均具较低的遗传多样性。分子方差分析表明,SSR遗传变异绝大部分存在于传统生态型内。青稻与红稻间、青稻与白稻、红稻与白稻、红稻与黄稻间遗传分化显著。太湖流域粳稻地方品种SSR多样性较低,稀有类型等位基因较多。这对科学制定太湖粳稻地方资源的保护和利用策略具有指导意义。     

Genetic Diversity of Tropical Hybrid Rice Germplasm Measured by Molecular Markers

Investigation of genetic diversity and relationships among breeding lines is of great importance to facilitate parent selection in hybrid rice breeding programs.In this study,we characterized 168 hybrid rice parents from International Rice Research Institute with 207 simple sequence repeat (SSR) and 353 single nucleotide polymorphism (SNP) markers.A total of 1 267 SSR and 706 SNP alleles were detected with the averages of 6.1 (SSR) and 2.0 (SNP) alleles per locus respectively across all lines.Based on the genetic distances estimated from the SSR and SNP markers separately and combined,the unrooted neighbor-joining cluster and STRUCTURE analyses consistently separated the 168 hybrid rice parents into two major groups:B-line and R-line,which is consistent with known parent pedigree information.The genetic distance matrices derived from the SSR and SNP genotyping were highly correlated (r=0.81,P < 0.001),indicating that both of the SSR and SNP markers have distinguishable power to detect polymorphism and are appropriate for genetic diversity analysis among tropical hybrid rice parents.A subset of 60 SSR markers were also chosen by the Core Hunter with 368 alleles,and the cluster analysis based on the total and subset of SSR markers highly corresponded at r=0.91 (P < 0.001),suggesting that fewer SSR markers can be used to classify and evaluate genetic diversity among parental lines.     

80份陆稻晚稻农家种资源的遗传多样性综合分析

为保护和利用陆稻农家种资源,本研究利用SNP标记和表型鉴定对80份陆稻晚稻农家种资源进行遗传多样性综合分析。结果表明：利用水稻1KSNP芯片对80份资源进行检测后共获得739个SNP的基因型数据,基于SNP的群体结构分析、PCA分析和聚类分析,均将80份资源分为云南亚群（63份）、海南亚群（11份）和贵州亚群（6份）共3个亚群,3个亚群间的平均遗传距离分别为0.83、0.63、0.80,其中海南亚群与其他2个亚群的遗传距离较远。贵州的陆稻资源分别属于贵州亚群和云南亚群,表明黔南地区的陆稻资源可能存在不同的来源。云南亚群可进一步分为3个亚群,平均遗传距离分别为0.30、0.28和0.22,表明细分亚群间的遗传距离很近。表型鉴定结果表明,11个表型性状的变异系数在4.09%~38.77%之间,其中有效分蘖数和穗重的变异系数较大,均超过25.00%,株高、种子长、种子宽、种子长宽比和种子圆度均值变异系数较小,均低于10%;遗传多样性指数范围为1.76~2.84,种子长的遗传多样性最丰富。相关分析结果表明,11个表型性状间存在着复杂的相关关系,其中种子长宽比与圆度均值的相关系数最高为0.98。在表型PCA分析中,前5个因子累计贡献率为82.37%,可反映表型性状的绝大部分信息,各成分的贡献率分别为29.08%、23.42%、12.35%、9.77%和7.75%,主要反映了株型和产量相关信息。80份资源的综合得分范围为0.15~0.73,排名前10的种质资源（ZRG36、ZRG101、ZRG58、ZRG31、ZRG1、ZRG102、ZRG104、ZRG63、ZRG29、ZRG11）均来自海拔较高地区,其中2份来源于海南,5份来源于贵州,3份来源于云南,且在穗长、种子长、种子宽、穗重和千粒重表现较好。该研究结果为陆稻农家种资源的保护和利用提供了参考。     

335份旱稻核心样品的构建

通过方差分析和多重比较,评价了36种预选核心样品的遗传多样性,筛选出最适于本研究的核心样品构建方法,即25％总体取样量一多样性取样比例一组内聚类取样。并依据此方案构建了总数为84的旱稻核心样品。经2a重复实验,从多样性指数、质量性状、数量性状和群体结构四个方面所选核心样品的代表性进行评价和补充,最终形成总数为86的旱稻核心样品,该核心样品很好地代表了原始群体的质量性状及数量性状变异。为进一步将旱稻资源应用于水稻抗性改良和抗早稻育种打下良好的基础。     

我国三系杂交稻主要不育系的微卫星标记多样性和遗传结构分析

选取均匀分布在水稻12条染色体上的48对SSR引物,对28份我国杂交水稻主要不育系进行了多样性和遗传结构分析。 在所分析的48个位点中,多态性位点41个,多态性位点百分率（P）为85.4%;每1个位点平均等位基因数（A）为3.5,变幅2～6个;平均基因多样性指数（He）和平均多态性信息含量指数（PIC）分别为0.40和0.36。AMOVA分析表明,不育系遗传变异主要存在于各选育时期内,时期间的遗传变异仅占总变异的3.3%,且未达到显著水平。基于模型的遗传结构分析表明,我国三系杂交稻主要不育系多数含有相近血缘,背景单一。     

用SSR标记评估东北三省水稻推广品种的遗传多样性

 利用53个SSR标记和24个表型性状分析东北三省107个水稻推广品种,探讨东北水稻推广品种群体遗传多样性及不同育成年代、省份间的遗传多样性和互补性。结果表明,表型遗传多样性高于DNA水平,年代间表型与微卫星标记的遗传多样性具有较高的相似性,而地区间无明显相似性。东北水稻推广品种遗传多样性比较狭窄,随着时间推移增加的新等位基因多于消失的旧等位基因数。三省水稻推广品种遗传多样性呈现黑龙江>吉林>辽宁的趋势,但由于地区间频繁引种,东北水稻品种在区域上的遗传分化已不明显,其差异主要来源于品种间的基因型差异。不同省份存在较多的互补等位变异,最多的在黑龙江和辽宁之间。不同省份和不同年代间分别拥有各自特有和特缺的等位变异。参试品种可分为5个类群,每一类群均有两个以上年代（省份）品种分布。     

Genetic Diversity and Relationship of Weedy Rice in Taizhou City, Jiangsu Province, China

Microsatellite markers and morphological charactedstics were used to explore the genetic diversity and possible origin of weedy dce in Taizhou City, Jiangsu Province, China. Fifty-two weedy rice (Oryza sativa L.) accessions were compared with two wild rice, four hybdd rice and five cultivars using 22 simple sequence repeat (SSR) primer pairs. A total of 107 fragments were amplified, averaging 5.6 alleles per primer pair. The polymorphic index content (PIC) values ranged from 0.3077 to 0.7951, averaging at 0.5870. The average genetic distance of all samples ranged from 0.02 to 0.46 with an average of 0.262. The genetic distance among Taizhou weedy rice ranged from 0.03 to 0.44 with an average of 0.224. Cluster analysis showed that all the weedy rice accessions from Taizhou City were indica, and could be subdivided into different genotypes. The majority (86%) of weedy rice was most closely related to hybrid rice. The Taizhou weedy dce accessions were morphologically similar, but still could be delineated into indica or japonica group by some morphological traits. it is suggested that the levels of genetic and morphological diversities of weedy rice in Taizhou City are low and these weedy rice plants originated from the segregating progenies of hybrid rice that had naturally introgressed with cultivated rice.     

24份木薯(Manihot esculenta)种质的遗传多样性研究

采用产量性状和12个表型性状聚类分析以及SSR标记技术,对不同产地来源的24份木薯(Manihot esculenta)种质遗传多样性进行了研究。结果表明,依据12个表型性状在欧氏距离系数为39.353处可将供试的24个木薯种质分为3类,一些品种的表型性状与地理来源之间存在相关性;利用18对SSR引物对24份木薯种质进行多态性分析,共检测到154条带,其中多态性带145条,每一个位点上检测到5～12条,平均8.6条。材料间相似系数在0.510～0.967之间,平均相似系数为0.695。以相似系数0.78为结合点,可以将材料分为三大类。不同国家和地区来源的材料不能明显聚类,不同淀粉含量、干物质量分数的品种却聚在一起,且没有发现与淀粉含量、干物质量分数相关的特异性条带。农艺性状的聚类结果与SSR聚类的结果有很大的差异,说明木薯在长期的演化和自然选择过程中发生了显著的表型变化。     

Evaluation of Population Structure,Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon's diversity index(I) of 0.748 and the heterozygosity(He) of 0.434. In each regional population, I value varied widely. The widest range of I(0.228–0.489) was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea(0.168–0.270). The F-statistics of regional populations(Fis, Fit and Fst) also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea. All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.     

稻属AA染色体组8个种间SSR多样性与亲缘关系

选用平均分布于水稻基因组的30对SSR 引物,对AA染色体组8个野生稻种共42份材料的遗传多样性及遗传关系进行了研究。结果显示,本试验选取的30个SSR标记均具有多态性,多态性位点百分率为100%。30个多态性位点共扩增出的等位基因数为224, 每个位点可扩增出3～10个等位基因,平均7.47个;等位基因有效数(Ae)变幅为1.25～891,平均5.45。多样性指数中,Shannon多样性指数(I)为0.454～2.386,平均1.826;而Nei基因多样性指数变幅为0.199～0.888,平均0.774。系统聚类和带型分析结果表明,亚洲栽培稻(Oryza sativa) 与普通野生稻(O. rufipogon) 的亲缘关系最近,非洲栽培稻(O. glaberrima) 则与巴蒂野生稻(O. barthii) 关系最为密切,杂草稻(O. spontanea) 与普通野生稻 (O. rufipogon)、亚洲栽培稻(O. sativa) 之间有较近的亲缘关系,而展颖野生稻(O. glumaepatula)、长雄蕊野生稻(O. longistaminata)与AA组其他稻种之间的亲缘关系较远。     

云南地方稻种抗稻瘟病基因Pi ta和Pi b的鉴定

 根据抗病等位基因Pi ta、Pi b与pi ta、pi b感病等位基因在DNA序列上的差异,合成Pi ta引物YL155/YL87和YL183/YL87,Pi b基因引物Pi bdomF/Pi bdomR和Lys145F/Lys145R。利用这两套分子标记检测了176份云南地方稻种抗性基因Pi ta和Pi b的分布。结果表明,供试材料中72份含有Pi ta基因,占40.9%,其中99份粳稻中有28份含有Pi ta基因,占28.3%;77份籼稻中有44份含有该基因,占57.1%;抗性基因Pi ta在粳稻和籼稻品种中的分布频率存在明显差异,籼稻高于粳稻;Pi ta基因主要分布于玉溪、保山、临沧、思茅等地区。而176份供试材料中仅有33份含有Pi b基因,占18.8%,其中99份粳稻中有18份含有该基因,占18.2%;77份籼稻中有15份含有该基因,占19.5%;Pi b基因主要分布在滇西部的怒江、保山和昭通等地区。分别选取具有代表性的18及17份材料在温室进行Pi ta和Pi b基因抗性鉴定,结果与分子鉴定结果基本相符。     

水旱稻三交种的应用价值初步研究

 以水稻野败不育系ZZA、旱稻野败不育系保持系沪旱1B和旱稻恢复系旱恢3号配制的一个水旱稻三交种（ZZA/沪旱1B//旱恢3号）和两个相应的单交种（ZZA/旱恢3号和沪旱1A/旱恢3号）为材料,进行田间性状调查,测定产量、抗旱性和稻米品质等指标。结果表明,三交种株高、叶绿素含量、穗长等性状与单交种的变异系数差异不显著,但群体抽穗历期延长;产量明显高于单交种,2006年比两单交种分别增产17.33%和25.63%,2007年比两单交种分别增产357%和11.71%;抗旱性增强,抗旱系数达51.21%,高于两单交种和亲本;主要稻米品质指标与两单交种差异不大。结果表明,水旱稻三交种可以拓展杂交稻的遗传基础,具有一定的应用价值。     

两极交变磁场对水稻和陆稻品种幼苗生长发育的影响

 用两极交变磁场对水稻和陆稻各4个品种的种子进行处理,处理种子的发芽特性优于未处理种子,其秧苗高度、鲜重及根长均比未处理的提高。种子经处理的水稻秧苗叶绿素a和b含量较未处理的高,650和680 nm荧光强度较低,而陆稻则相反。磁场处理对水稻种子浸泡液的电导率无显著影响,而陆稻则处理的较未处理的为低。     

Diversity Analysis in Selected Non-basmati Scented Rice Collection

Diversity analysis among 23 rice varieties including 16 non-basmati scented accessions, 5 basmati accessions and 2 non-scented accessions was performed by random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) marker systems. The varieties analyzed by 11 RAPD and 8 ISSR primers yielded an average of 65% and 80% polymorphism, respectively. The average number of polymorphic bands generated per RAPD primer was 6 and per ISSR primer was 5.87. RAPD and ISSR data analysis individually could not segregate basmati and non-basmati scented rice accessions. However, the analysis using a combined data could group basmati and non-basmati scented rice accessions separately. The bands present specifically among three accessions of non-basmati scented rice were also identified. The study revealed a high genetic diversity among non-basmati scented rice accessions.     

利用微卫星标记分析浙江省近年来主要水稻品种的遗传多样性

 利用12个DNA微卫星标记分析了浙江省近年来主要的44个常规水稻品种和54个杂交水稻组合,共检测到等位基因68个,每个标记2~10个;带型数共127种,每个标记3~18种;平均多态性频率0.752,变幅为0.567~0905。常规品种和杂交组合均表现为亚种间遗传差异明显、亚种内遗传差异较小,籼型遗传多样性高于粳型。平均遗传相似系数,常规品种籼型为0.672,粳型为0.711,籼粳间为0.103,杂交组合籼型为0.636,粳型为0.669,籼粳间为0.343。聚类分析显示,以遗传相似系数0.618为阈值将常规品种分成6类,以0.601为阈值将杂交组合分成7类,且多数同类型品种或组合聚为同一类。