云南栽培稻种SSR遗传多样性比较

采用64个SSR标记对96份云南水稻（Oryza sativa）地方品种和选育品种的遗传多样性进行比较分析。结果发现64个标记都具有多态性,共检测到741个等位基因,每个多态性位点检测到的等位基因数为2—29个,平均11．57个：Nei基因多样性指数（He）范围在0．345（RM321）-0．932（RM1）之间,平均为0．56。水稻品种的遗传多样性并非按地理位置均匀分布,而是在相似系数为0．17的水平上明显分为2个不同类群,即籼稻类群和粳稻类群,且籼粳亚种间的SSR多样性差异不明显,籼稻平均等位基因数（Ap）和Nei基因多样性指数（Ap=10．6,He=0．46）与粳稻品种（Ap=10．7,He=0．48）十分接近,可能与这些品种间存在一定频率的基因交流有关。糯稻和非糯稻在籼稻群和粳稻群中都有表现,没有特别的分布规律。云南栽培稻选育品种与地方稻亲缘关系较近,其遗传基础可能来源于云南水稻地方品种。本研究结果表明,SSR标记能较好地区分云南栽培稻品种,且云南水稻地方品种遗传多样性丰富,存在大量的优质性状可供育种实践选择。     

香稻资源遗传多样性的比较

利用60个水稻SSR标记, 对来自国内外的370份香稻材料的遗传多样性进行了比较分析。结果共检测到361个等位基因, 每个位点的等位基因变幅为2~10个, 平均Nei基因多样性指数(He)为0.663, 变幅为0.104(RM308)~0.885(RM2634)。籼粳亚种间的遗传多样性具有明显差异, 籼稻的等位基因数和Nei基因多样性指数均高于粳稻。地方品种的遗传多样性高于选育品种, 选育品种等位基因数仅为地方品种的86.5%。分子方差分析表明, 香稻材料中总变异的43.08%是由于亚种间的遗传差异引起的。不同稻区的遗传分化程度总体介于1.69%~14.40%之间。其中, 华南与西南、华中与西南地方品种间遗传差异的分化程度达显著水平。聚类分析将参试材料明显分为籼粳两大类, 同时地域相同(稻区)、相邻省份的香稻材料基本归为同一类群。     

中国水稻地方品种与选育品种遗传多样性的比较分析

利用98对SSR标记对202份中国水稻地方品种和选育品种的遗传多样性进行比较分析.结果显示供试品种具有较丰富的遗传多样性,共检测到等位基因1350个,每个位点的等位基因数(Na)变化范围为3～ 39,平均14个;Nei基因多样性指数变化范围(He)为0.125 ～0.955,平均0.733;多态信息量(PIC)变化范围为0.122 ～0.953,平均0.680;稀有等位基因数(Nr)913个;等位基因丰度(Rs)8.33.栽培稻地方品种和选育品种遗传多样性差异明显,地方品种等位基因数、Nei基因多样性指数、多态信息量、稀有等位基因数和等位基因丰度(Na=1219,He=0.747,PIC=0.710,Nr=756,Rs =8.50)均高于选育品种(Na =919,He =0.704,PIC =0.650,Nr=529,Rs =7.01).各染色体组水平的遗传多样性分析表明,选育品种仅在1号染色体上的遗传多样性高于地方品种,进一步分析显示选育品种的遗传改良在基因组水平上具有区间特异性.     

中国水稻地方品种与选育品种的遗传多样性比较分析

利用98对SSR标记对202份中国水稻地方品种和选育品种的遗传多样性进行比较分析。结果显示供试品种具有较丰富的遗传多样性,共检测到等位基因1350个,每个位点的等位基因数(Na)变化范围为3~39,平均14个;Nei基因多样性指数变化范围(He)为0.125~0.955,平均0.733;多态信息量(PIC)变化范围为0.122~0.953,平均0.680;稀有等位基因数(Nr)913个;等位基因丰度(Rs)8.33。栽培稻地方品种和选育品种遗传多样性差异明显,地方品种等位基因数、Nei基因多样性指数、多态信息量、稀有等位基因数和等位基因丰度(Na=1219,He=0.747,PIC=0.710,Nr=756,Rs=8.50)均高于选育品种(Na=919,He=0.704,PIC=0.650,Nr=529,Rs=7.01)。各染色体组水平的遗传多样性分析表明,选育品种仅在1号染色体上的遗传多样性高于地方品种,进一步分析显示选育品种的遗传改良在基因组水平上具有区间特异性。     

宁夏不同年代水稻品种的遗传多样性比较

对宁夏不同阶段主栽水稻品种(系)的主要农艺性状比较表明,第1阶段(1950-1962年)宁夏地方品种与第2阶段(1978-1989年)、第3阶段(1990-1999年)、第4阶段(2000-2005年)、第5阶段(2006-2012年)、第6阶段(2010-2013年)育成品种(系)的农艺性状差异显著,说明通过育种手段宁夏水稻品种的主要农艺性状得到了改良;从第2阶段到第6阶段的变化趋势为生育天数变长,有效穗数减少,穗长、穗粒数、单株粒重、单穗粒重、产量等增加,说明产量性状的育种改良从穗数型向穗粒兼顾型或穗重型发展。利用48对SSR引物对76份宁夏不同年代水稻品种(系)进行遗传多样性分析表明,共检测出290个等位基因,每个位点等位基因变幅为3~15个,平均6.04个;稀有等位基因有109个,占等位基因总数的37.59%;多态信息含量(PIC)变异范围为0.1423~0.8783,平均为0.5512;Nei’s基因多样性指数(He)的变幅为0.1492~0.8945,平均为0.6032。RM333、RM297、RM249、RM501和RM206引物表现为较高的等位基因数和稀有等位基因数,认为较适合应用于宁夏水稻品种的遗传多样性检测。分子方差分析(AMOVA)结果表明,6个不同阶段间遗传变异占总体变异的19.27%,各阶段内品种间的遗传变异占总体变异的80.73%。参试水稻UPGMA聚类分析表明,在遗传相似系数(GS)为0.805处可将其划分为5大类群,12个地方品种都被聚为第Ⅰ类群,具有外来引进血缘的8个常规粳稻品种被聚为第Ⅱ类群,5个优质常规粳稻被聚为第Ⅲ类群,第Ⅴ类群包括2个大穗高产品种,49个宁夏常规粳稻选育品种被聚为第Ⅳ类,说明大多数宁夏水稻品种的亲缘关系较近。6个不同阶段品种聚类分析,第1阶段(地方品种)独聚一类,第2、第3、第4阶段与第5、第6阶段育成品种亲缘关系相对较远;表明不同年代宁夏水稻遗传多样性有较大差异,2005年后宁夏水稻品种的遗传多样性趋于变小。宁夏水稻育种中应加强国内外种质资源的引进和利用,深入挖掘宁夏稻区地方品种和杂草稻资源的有利基因,拓宽宁夏水稻品种的遗传基础,以促进宁夏水稻育种的快速发展。     

广西地方稻种资源核心种质构建和遗传多样性分析

以丁颖分类体系分组原则与组内逐层聚类取样方法,对8609份广西地方栽培稻资源表型数据信息进行分析,通过对表型保留比例等评价指标的多重比较确定核心种质总体取样比例,构建出占总体样本5%(414份)的广西地方栽培稻资源初级核心种质。初级核心种质能代表总体遗传变异的89%。用34对SSR分子标记对初级核心种质进行遗传多样性分析,结果表明:广西地方栽培稻资源有较高的遗传多样性(等位基因数A为4.91,Nei’s多样性指数为0.574)。就Nei’s遗传多样性指数而言,粳稻高于籼稻,晚稻高于早稻,水稻高于陆稻,糯稻高于粘稻;来自桂中的稻种资源具有最高的遗传多样性。研究最终利用SSR数据,把414份初级核心种质压缩50%后形成209份核心种质,核心种质基因保留比例达到98%以上,有效代表了广西地方栽培稻资源多样性水平。     

SSR标记揭示的云南地方稻品种遗传多样性及其保育意义

为了探索水稻(Oryza sativa L.)地方品种的遗传多样性及其有效保育方法,对采自云南省17个村寨的82个水稻地方品种和3个国际常用的典型籼稻和粳稻品种进行了微卫星(SSR)分子标记的分析.利用19对SSR引物在85个水稻品种中共扩增出了83个基因型,其分子量变异在100～500 bp之间.基于各品种SSR基因型遗传相似系数聚类分析而获得的UPGMA树状图表明各水稻品种之间存在较大的遗传多样性,其相似系数变异在0.15～0.90之间.但这些地方品种的遗传多样性并非呈均等的地理分布.这85个水稻品种在相似系数为0.52之处分为二组,其中一组包括几乎所有的籼稻品种,而另一组包括全部的粳稻品种,表明SSR标记能很好揭示水稻籼-粳分化.同时,有些来自不同采集地的同名品种表现出一定的遗传差异,说明同名异物的现象存在.云南水稻地方品种具有丰富的遗传多样性,对其有效保育十分重要和迫切,但只有根据遗传多样性的水平和分布特点,采用正确的保育对策和取样方法才能确保对云南水稻地方品种的有效保育.结果进一步表明,选用适当的微卫星引物,可以为准确鉴定籼稻和粳稻品种及研究其进化规律提供有效的分子标记方法,并有利于有目标的水稻遗传资源保育和育种创新.     

SSR标记揭示的云南地方稻品种遗传多样性及其保育意义

为了探索水稻(Oryza　sativa　L.)地方品种的遗传多样性及其有效保育方法,对采自云南省17个村寨的82个水稻地方品种和3个国际常用的典型籼稻和粳稻品种进行了微卫星(SSR)分子标记的分析。利用19对SSR引物在85个水稻品种中共扩增出了83个基因型,其分子量变异在100～500　bp之间。基于各品种SSR基因型遗传相似系数聚类分析而获得的UPGMA树状图表明各水稻品种之间存在较大的遗传多样性,其相似系数变异在0.15～0.90之间。但这些地方品种的遗传多样性并非呈均等的地理分布。这85个水稻品种在相似系数为0.52之处分为二组,其中一组包括几乎所有的籼稻品种,而另一组包括全部的粳稻品种,表明SSR标记能很好揭示水稻籼-粳分化。同时,有些来自不同采集地的同名品种表现出一定的遗传差异,说明同名异物的现象存在。云南水稻地方品种具有丰富的遗传多样性,对其有效保育十分重要和迫切,　但只有根据遗传多样性的水平和分布特点,采用正确的保育对策和取样方法才能确保对云南水稻地方品种的有效保育。结果进一步表明,选用适当的微卫星引物,可以为准确鉴定籼稻和粳稻品种及研究其进化规律提供有效的分子标记方法,并有利于有目标的水稻遗传资源保育和育种创新。     

东南亚国家引进水稻种质的遗传多样性和遗传结构分析

用72对SSR引物对316份东南亚不同地理来源的水稻种质资源进行遗传多样性和遗传结构分析。结果表明,共检测到387个等位基因,平均每对引物检测到5.375个,变幅在2~12之间;其中频率5%的稀有等位基因有293个,占全部等位基因数的75.7%。Nei基因多样性指数(He)变化幅度在0.055~0.855之间,平均为0.623。He以菲律宾的种质资源最为丰富(He=0.619),其余国家的He大小依次是越南(He=0.515)老挝(He=0.467)柬埔寨(He=0.455);聚类分析显示分为籼粳稻两大群体,地理分组不是特别清晰。AMOVA分析表明,遗传变异主要来源于不同地理类群间,且遗传分化极显著。遗传结构分析结果显示K=2时,有相对明显的遗传结构。其次是K=5时,显示菲律宾群体分为了3个比较明显的小类群,存在较为明显的遗传分化结构。东南亚引进水稻种质资源丰富的遗传多样性和遗传结构为后期水稻育种的亲本选择提供依据。     

贵州地方水稻种质资源籼-粳遗传分化的InDel分子标记研究

本研究利用36对InDel分子标记引物对贵州地方水稻种质的籼-粳遗传分化和亲缘关系进行分析,结果表明,82份贵州地方栽培稻中49份为粳稻,33份为籼稻,贵州地方栽培稻“禾”品种主要属于粳稻,而“谷”品种主要为籼稻。基于Nei氏遗传距离的亲缘关系分析表明在粳稻群体和籼稻群体中均存在与野生稻亲缘关系近的品种,其中的粳稻品种与野生稻的遗传关系比之籼稻品种近。而基于MCMC算法的遗传结构分析揭示了贵州地方籼稻品种中存在较为复杂的遗传结构。分子变异分析显示,粳稻和籼稻品种的遗传变异主要来自亚种内,遗传多样性分析表明其亚种内籼稻品种的遗传多样性略高于粳稻品种。研究结果揭示了贵州省黔东南地区栽培稻种质资源的籼-粳分化程度、遗传关系及其遗传多样性。     

Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR.

Yunnan Province is one of the largest centers of genetic diversity of Oryza sativa L. in China, and in the world. Using a genetically representative core collection of 692 rice landraces from Yunnan, the genetic structure, differentiation, and geographic diversity of this rice germplasm were analyzed. The accessions were classified into different populations, according to the model-based structure analysis. Model-based populations were characterized through the reconstruction of a neighbor-joining tree, principal coordinate analysis, and the estimation of morphologic and SSR variations. Finally, the distribution of genetic diversity and differentiation among districts were studied. Seven model-based populations were identified on the basis of the structure analysis. This classification was partly consistent with Ting's 5-level taxonomic system. Differentiation between 2 rice subspecies is the most apparent, with a clearer differentiation between soil-watery ecotypes in japonica than in indica; however, differentiation among seasonal ecotypes in indica is clearer than in japonica. Cropping system and man-made restricted-growth environments could be considered to be the main forces driving the intraspecific differentiation of cultivated rice. It has been suggested that, because it possesses the highest genetic diversity and all the necessary conditions as a center of genetic diversity, the southwest region of Yunnan, encompassing Simao, Lincang, and Xishuangbanna districts, is the center of genetic diversity of Yunnan rice landraces.     

Temporal changes in SSR allelic diversity of major rice cultivars in China

Forty simple sequence repeats （SSRs） were used to assess the changes of diversity in 310 major Chinese rice cultivars grown during the 1950s-1990s. Of the 40 SSR loci, 39 were polymorphic. A total of 221 alleles were detected with an average of 5.7 alleles per locus （Na）. The Nei＇s genetic diversity index （He） varied drastically among the loci （0.207 to 0.874, mean 0.625）. Comparing the temporal changes in Na and He, the cultivars from the 1950s had more alleles and higher He scores than the cultivars from the other four decades. Analysis of molecular variance （AMOVA） indicated that the genetic differentiation among the five decades was not significant in the whole set, but significant within indica and japonica. More changes among the decades were revealed in indica cultivars than in japonica cultivars. Some alleles had been lost in current rice cultivars in the 1990s, occurring more frequently in indica. These results suggest that more elite alien genetic resources should be explored to widen the genetic backgrounds of rice cultivars currently grown in China.     

Microsatellite diversity within Oryza sativa with emphasis on indica-japonica divergence

The molecular evolution of cultivated rice Oryza sativa L. has long been a subject of rice evolutionists. To investigate genetic diversity within and differentiation between the indica and japonica subspecies, 22 accessions of indica and 35 of japonica rice were examined by five microsatellite loci from each chromosome totalling 60 loci. Mean gene diversity value in the indica rice (H=0.678) was 1.18 times larger than in the japonica rice (H=0.574). Taking the sampling effect into consideration, average allele number in the indica rice was 1.40 times higher than that in the japonica rice (14.6 vs 10.4 per variety). Chromosome-based comparisons revealed that nine chromosomes (1, 2, 3, 4, 5, 8, 9, 10 and 11) harboured higher levels of genetic diversity within the indica rice than the japonica rice. An overall estimate of F(ST) was 0.084-0.158, indicating that the differentiation is moderate and 8.4-15.8% of the total genetic variation resided between the indica and japonica groups. Our chromosome-based comparisons further suggested that the extent of the indica-japonica differentiation varied substantially, ranging from 7.62% in chromosome 3 to 28.72% in chromosome 1. Cluster analyses found that most varieties formed merely two clusters for the indica and japonica varieties, in which two japonica varieties and five indica varieties were included in the counterpart clusters, respectively. The 12 chromosome-based trees further showed that 57 rice varieties cannot be clearly clustered together into either the indica or japonica groups, but displayed relatively different clustering patterns. The results suggest that the process of indica japonica differentiation may have proceeded through an extensive contribution by the alleles of the majority in the rice genome.     

Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markets including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei,s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties.     

Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers

The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a Fst of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.     

水稻长日抑制基因PhyB的多样性及区域适应性初探

Phy 是在长日照条件下抑制水稻开花的关键基因,但目前对水稻PhyB基因的遗传基础还不清楚,研究其分子遗传机制,对于培育光周期适应性广的品种以及扩大水稻种植区域具有重要意义。本研究选择78份亚洲栽培稻(34份籼稻和44份粳稻)及47份野生稻进行测序,对Phy B基因的核苷酸多态性、单倍型进行分析,计算籼稻、粳稻和野生稻的遗传多样性。结果表明,Phy B基因共有28个单倍型,其中有2个高频率的单倍型分别存在于2个栽培稻亚种中。从Network图可以看出栽培稻分为2组(A组和B组),A组栽培稻包括全部的籼稻和4个粳稻个体,B组栽培稻全是粳稻品种。亲缘地理学分析发现,A、B两组栽培稻具有明显不同的地理分布格局,且A组和B组开花时间差异显著,说明Phy B基因的2个高频率单倍型在2个栽培稻亚种中具有区域适应性,Phy B基因在栽培稻中具有明显的驯化信号,随着水稻种植区域的扩大,进化出适应不同地域特有的等位基因,导致开花时间对不同地区的区域适应性及多样性。