基于SSILP、InDel和SSR标记的杂草稻籼粳分类

 采用40对SSILP、30对InDel和43对SSR标记对来自斯里兰卡的28份杂草稻和14栽培稻,来自国内外的9份籼型栽培稻、7份粳型栽培稻和4份代表性杂草稻进行遗传多样性分析。SSILP、InDel和SSR标记分别检测到84、61和213个等位基因,其平均多态性信息含量(PIC)分别为0.257、0.255和0.543。聚类分析显示供试的42份斯里兰卡杂草稻和栽培稻均为籼型。SSILP与InDel标记的相关性很高（r=0.989）,而它们与SSR标记相关性较低（0.812和0.808）。结果表明,SSILP和InDel标记可高效鉴别各类稻种资源的籼粳属性,而SSR标记更适用于亚种内的分类。     

A Comparative Study of SSR Diversity in Chinese Major Rice Varieties Planted in 1950s and in the Recent Ten Years （1995-2004）

Forty pairs of SSR markers were used to compare the genetic diversity changes in 151 Chinese major rice varieties planted in 1950s and in the recent ten years. Of 40 SSR loci, 39 were found to be polymorphic while one locus (RM479) monomorphic. A total of 213 alleles were identified from the 39 polymorphic loci. The average number of alleles per locus (Na) was of 5.5, ranging from 2 to 11. Nei’s gene diversity index (He) varied drastically among loci from 0.309 at RM174 to 0.869 at RM418, with an average value of 0.649. There existed significant difference in SSR allelic diversity between indica and japonica subspecies, and indica had more variation than japonica both in Na and He. By comparison with the genetic changes in Na and He, it was revealed that the varieties planted in 1950s had more alleles and higher He than those in the recent ten years both for indica and japonica rices. The difference between two subspecies for Na was significant in a tendency over time (indica: z = 2.677, P = 0.007; japonica: z = 3.441, P = 0.001), but not significant for He (indica: z = 1.471, P = 0.141; japonica: z = 1.932, P = 0.053). Analysis of molecular variance (AMOVA) indicated that there existed significant difference (P < 0.05) in genetic variation between the two periods, of which more genetic variation was contributed by indica (Fst = 0.050) and japonica (Fst = 0.082) subsets. Using locus-by-locus AMOVA procedure, significant genetic differentiations were observed in 13 loci (RM21, RM128, RM147, RM169, RM190, RM221, RM231, RM251, RM253, RM317, RM341, RM418, and RM478) for indica varieties and 11 loci (RM101, RM135, RM152, RM159, RM169, RM190, RM251, RM253, RM311, RM418, and RM478) for japonica ones between the two periods. It was found some alleles had been lost in current major rice varieties as comparing with those in 1950s. Therefore, it should be necessary to exploit more alien elite genetic resources for extension of genetic background in current rice breeding program.     

Genetic Diversity of Rice Landraces from Lowland and Upland Accessions of China

Genetic diversity of rice landraces from lowland and upland accessions of China was investigated using 66 polymorphic simple sequence repeat (SSR) markers.The total number of alleles detected from all 324 tested accessions was 555 with an average allele number (Na) of 8.409 per locus,the average effective number of alleles (Ne) of 3.574 and the average Shannon’s information index (I) of 1.378.The genetic diversity was higher for the indica landraces compared to the japonica landraces,and the upland landraces were more genetically diverse than the lowland landraces.The SSR markers,RM72,RM232,RM219,RM241,RM224 and RM3 showed the highest rates of polymorphism and these SSR markers were suitable to assess the genetic diversity of rice germplasm resources.A dendrogram of 324 accessions of lowland and upland landraces showed that all rice accessions were mainly subdivided into two groups,japonica and indica,with some being intermediate.The distribution of lowland and upland landraces among the japonica and indica rice groups was distinct,with obvious differentiation between the lowland and upland landraces in japonica rice,but no such clear distinction in indica rice.     

Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

A collection of 167 Thai and exotic rice accessions was subjected for evaluation of genetic diversity and assessment of relationship by simple sequence repeat(SSR) markers. Among a total of 49 SSR markers, 13 markers distributing over 12 rice chromosomes showed clear polymorphic band patterns, and they were selected for genetic assessment. A total of 110 alleles were detected with an average of 8.46 alleles per locus. The averages of gene diversity, heterozygosity and polymorphic information content were 0.59, 0.02 and 0.56, respectively. The unweighted-pair group method with arithmetic averages(UPGMA) clustering analysis was performed for genetic distance, and phylogenetic tree was constructed. The result showed that this rice collection was divided into two major groups, classified as japonica and indica subspecies. Within the japonica group, temperate japonica and tropical japonica subgroups can be clearly separated. Three-dimensional principal component analysis projection and model-based population structure analysis showed consistent clustering results with two major groups of UPGMA analysis, supporting the classification of japonica and indica subspecies. The indica allelic frequency was also investigated to provide an indicative guide for breeders to overcome the practical problems on sterility of inter-subspecies hybrid offspring. This rice collection and information obtained in this study will be useful for rice breeding programs.     

Genetic diversity and association mapping for salinity tolerance in Bangladeshi rice landraces

Breeding for salinity tolerance using Bangladeshi rice landraces and understand genetic diversity has been limited by the complex and polygenic nature of salt tolerance in rice genotypes. A genetic diversity and association mapping analysis was conducted using 96 germplasm accessions with variable response to salt stress at the seedling stage. These included86 landraces and 10 indica varieties and lines including Nona Bokra, from southern Bangladesh. A total of 220 alleles were detected at 58 Simple Sequence Repeat(SSR) marker loci randomly distributed on all 12 rice chromosomes and 8 Sequence Tagged Site(STS) markers developed for genes SKC1, DST, and SalT. The average gene diversity was 0.5075 and polymorphism information content value was 0.4426, respectively. Cluster analysis revealed that 68 and 21 accessions were clustered into 2 distinct groups, possibly corresponding to indica and japonica groups, respectively and the remaining 7 landraces were classified as an admixed group. In addition to Wn11463, the STS marker for SKC1, RM22418 on Chr. 8 was significantly associated with salinity tolerance, at the location of a QTL detected in previous studies. Our findings of favorable alleles associated with salinity tolerance in Bangladeshi rice landraces, as well as the development of STS markers for salt tolerance genes, will be helpful in future efforts to breed salinity tolerance in rice.     

我国常规稻主栽品种的遗传变异分析

 采用40个SSR标记,分析了329份我国近50年来常规稻主栽品种的遗传变异。结果显示,39个SSR标记具有多态性,在多态性位点共检测到223个等位基因,每个位点2～11个,平均57个;平均Nei基因多样性指数（He）为0632。籼粳亚种间的SSR变异差异明显,籼稻平均等位基因数（Na）和Nei基因多样性指数（Na = 54,He = 0440）均高于粳稻品种（Na = 44,He = 0397）。Nei遗传相似系数表明总体样本具有较小的遗传相似度（I = 0366）,而骨干亲本具有较高的遗传相似度（籼:I = 0590;粳:I = 0590）。这导致了籼粳亚种内较高的遗传一致性（籼:I = 0558;粳:I = 0600）。早、中、晚稻各类型遗传相似度差异明显,晚籼和早粳类型具有较高的遗传变异。籼粳稻品种尤其是粳稻的聚类结果显示出较强的季节型和地域特征。这些均提示育种家应选择更广泛的亲本源以拓宽选育品种的遗传基础。     

我国水稻主栽品种SSR多样性的比较分析

采用40个SSR标记,比较分析了151份20世纪50年代(78份）和近10年（73份）我国常规稻主栽品种的遗传差异,发现有39个标记具有多态性,多态性位点共检测到213个等位基因,每个位点2～11个,平均5.5个;平均Nei基因多样性指数(He)为0.649,范围在0.309（RM174）～0.869（RM418）。籼粳亚种间SSR多样性差异明显,籼稻平均等位基因数（Na）和Nei基因多样性指数（Na = 4.4,He = 0.458）均高于粳稻品种（Na = 4.0,He = 0.395）。比较了78份20世纪50年代与73份近10年水稻主栽品种的遗传多样性,籼、粳亚种表现出相近的变化趋势,即Nei多样性指数和等位基因数20世纪50年代主栽品种高于近10年的。虽然Nei基因多样性指数的变化并不显著（籼稻：z= 1.471,P=0.141;粳稻：z= 1.932,P=0.053）,但等位基因数目的变化达到显著水平（籼稻：z= 2.677,P=0.007;粳稻：z= 3.441,P=0.001）。分子方差分析(AMOVA)表明,遗传变异绝大部分存在于两时期内,尽管时期间平均贡献的遗传变异仅占1.9％,但仍然达到5％的显著水平;籼、粳亚种两时期间平均贡献的遗传变异高于整个分析样本,分别为5.0％和8.2％;籼、粳亚种不同位点的遗传分化程度也各不相同,籼稻和粳稻品种分别有13个（占33.3％）和11个（占28.2％）SSR位点的等位基因在两时期间差异显著,而其余位点的遗传变异则是因时期内品种间的差异引起的。研究表明近10年我国常规稻主栽品种丢失了一部分等位基因,水稻育种仍应加强更广泛的种质亲本的选择。     

Genetic Diversity of Main Inbred Indica Rice Varieties Applied in Guangdong Province as Revealed by Molecular Marker

Genetic diversity of 299 inbred indica rice varieties, including 33 introduced varieties, applied in Guangdong Province of China were assessed using 20 ILP(intron length polymorphism) and 34 SSR(simple sequence repeat) markers. Totally, 154 loci were screened for the 299 varieties, with the average number of alleles(Na), rare alleles(Nr), and polymorphism information content(PIC) scored at 3.4, 0.7and 0.32, respectively. The Nei’s genetic distance(GD) was estimated ranging from 0 to 0.7529 with an average of 0.4797. There was no significant difference of Na, Nr, PIC or GDs between the introduced and local varieties. Neighbor-joining(NJ) analysis showed that the 299 varieties failed into three main distinct groups, and the 33 introduced varieties were distributed over all the groups or subgroups. Model-based cluster analysis demonstrated that only 73(24.4%) of the 299 varieties and 7(21.2%) of the 33 introduced varieties could be distinctly classified into the three groups. Analysis of molecular variance showed that within the groups divided by NJ analysis, the genetic variations revealed by ILP, SSR and these two combined were 7.7%, 5.6% and 6.6%, and within the groups divided by region(Guangdong local and the introduced varieties), the genetic variables were 2.1%, 4.6%, 5.4%, respectively. These results suggested that the genetic diversity of the 299 inbred rice varieties in Guangdong Province was low, simultaneously relationship among varieties was poor and close in all kind of groups. Hence, it is very necessary to extend the genetic diversity during the breeding and selection practical procedure.     

利用微卫星标记比较云南元阳哈尼梯田两个不同时期种植的水稻地方品种的遗传多样性

 为了揭示云南元阳哈尼梯田两个不同时期种植的水稻地方品种的遗传多样性,以元阳哈尼梯田过去种植（20世纪70年代收集于元阳县,现保存于种质库）的72个和当前种植的76个品种为材料,采用48个SSR分子标记进行多态性、遗传相似性和聚类分析。平均每个标记检测到的等位基因数、有效等位基因数、位点多态信息含量和基因型多样性指标在过去与当前的品种间,差异均未达显著水平。共有24个SSR标记的52个等位基因位点在过去与当前种植的品种中存在差异,其中,有18个SSR标记的32个等位基因位点在当前的品种中未检测到,同样,有16个SSR标记的20个等位基因位点在过去的品种中未检测到。基于48个SSR分子标记的平均遗传相似性系数,当前种植的品种为03340,过去为03313,过去与当前的品种分别在遗传相似性系数0203和0174处分为籼、粳两个亚种群。表明元阳哈尼梯田水稻地方品种经过30多年的自然与人工选择,虽有部分等位基因位点发生了变异,但仍保留了原有的遗传多样性;元阳哈尼梯田水稻地方品种存在明显的籼、粳分化。元阳哈尼梯田及其水稻地方品种是研究稻作籼粳演化的理想基地和材料。     

采用表型和分子标记聚类研究杂交籼稻亲本的遗传多样性

以41份杂交籼稻骨干亲本和部分新育成的亲本为试验材料,采用表型性状和SSR分子标记2种聚类分析方法对杂交籼稻亲本的类群划分进行了比较研究,表型聚类以15个表型性状为依据,将供试材料划分为早、中熟和中、晚熟两大类群、6个亚群。早、中熟类群包含15个保持系、4个早熟恢复系和2个温敏核雄性不育系;中、晚熟类群包括16个恢复系和4个中、晚熟保持系。利用SSR分子标记将供试材料划分为保持系和恢复系两大类群、7个亚群。保持系群包括全部19个保持系、2个温敏核雄性不育系,恢复系群则包含全部20个恢复系,分类结果和系谱分析基本吻合。结合杂交籼稻育种实践,判断分子标记可能是研究亲本遗传多样性的一种较好方法。     

Comparison of Cheng’s Index-and SSR Marker-based Classification of Asian Cultivated Rice

A total of 100 cultivated rice accessions,with a clear isozyme-based classification,were analyzed based on Cheng’s index and simple sequence repeat (SSR) marker.The results showed that the isozyme-based classification was in high accordance with that based on Cheng’s index and SSR markers.Mantel-test revealed that the Euclidean distance of Cheng’s index was significantly correlated with Nei’s unbiased genetic distance of SSR markers (r=0.466,P ≤ 0.01).According to the model-based group and cluster analysis,the Cheng’s index-and SSR-based classification coincided with each other,with the goodness of fit of 82.1% and 84.7% in indica,97.4% and 95.1% in japonica,respectively,showing higher accordance than that within subspecies.Therefore,Cheng’s index could be used to classify subspecies,while SSR marker could be more efficient to analyze the subgroups within subspecies.     

Genetic Diversity among Parents of Hybrid Rice Based on Cluster Analysis of Morphological Traits and Simple Sequence Repeat Markers

Heterosis has been successfully exploited on a large scale in rice (Oryza sativa L.), which is a self-pollinated crop. The selection of parental lines plays a vital role in developing ideal combinations. Therefore, it is essential to study the relationshi…     

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.     

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。     

亚洲栽培稻遗传变异分析最少SSR引物数的研究

以69份类型明确的亚洲栽培稻品种为材料,选用120对SSR引物,通过评估遗传多样性和群体结构,研究分析其遗传变异对SSR引物数的要求。结果表明:1)120对引物在69份试验材料中共检测到1256个等位变异,每个位点的等位基因数差异较大,变化范围为2~27,平均为10.5;平均Nei基因多样性指数变化范围为0.4058~0.9452,平均为0.7616;2)分析亚洲栽培稻遗传多样性时,至少需要72对SSR引物;3)分析亚洲栽培稻群体结构时所需最少引物数可降低至60对。     

中国常规稻主栽品种的遗传结构及籼粳组分变化

 采用SSR标记分析了304份我国20世纪50-90年代生产上广泛应用的常规稻主栽品种的遗传结构及不同时期籼粳组分的变化。结果显示,我国常规稻主栽品种可明显分为籼、粳两类,籼稻的亚遗传结构比粳稻更为复杂,但晚籼和早粳类型的遗传背景略为单一。早、中、晚各季节类型与遗传结构的分型结果符合度较低。利用12个籼粳分化特异的SSR位点分析各品种的籼粳组分,发现20世纪90年代晚籼类型的粳型组分明显增加,而其他类型不同时期间籼粳组分的差异较小。研究结果对了解我国常规稻品种的遗传结构以及籼粳交育种具有一定的意义。     

栽培稻与普通野生稻BC2F2群体产量相关性状的QTL分析

以广陆矮4号(Oryza sativa ssp. indica)为母本及轮回亲本,普通野生稻（Oryza rufipogon）为父本,分单株连续回交2次,构建BC2F2群体。首先用241对具有双亲多态性的SSR标记对BC2F1单株进行代换片段分析,在此基础上,根据BC2F1的表型选产量较优的单株自交获得BC2F2群体,用代换片段上具有双亲杂合型基因型的24对SSR标记进行QTL定位。在所选的BC2F1单株上,共检测到分布于7条染色体上的20个野生稻的代换片段,平均每条染色体上有2.86个;代换片段长度最小为0.55 cM,最大为33.00 cM,平均长度为12.36 cM,总覆盖长度为247.20 cM,覆盖率为16.21%。利用BC2F2群体对14个产量相关性状进行QTL定位,共检测到控制8个性状的20个QTL。对性状表型值起增效作用的有11个,占总检出数的55%。控制产量相关性状的QTL存在簇状分布现象,这与表型相关分析结果相符合。     

Fine Mapping of C（Chromogen for Anthocyanin） Gene in Rice

Seven residual heterozygous lines (RHLs) displaying different genotypic compositions in the genomic region covering probable locations of C (Chromogen for anthocyanin) gene on the short arm of rice chromosome 6 were selected from the progenies of the indica cross Zhenshan 97B/Milyang 46. Seeds were harvested from each of the seven plants, and the resultant F_2:3 populations were used for fine mapping of C gene. It was shown in the populations that the apiculus coloration matched to basal leaf sheath coloration in each plant. By relating the coloration performances of the populations with the genotypic compositions of the RHLs, the C locus was located between rice SSR markers RM314 and RM253. By using a total of 1279 F_2:3 individuals from two populations showing coloration segregation, the C locus was then located between RM111 and RM253, with genetic distances of 0.7 cM to RM111 and 0.4 cM to RM253. Twenty-two recombinants found in the two populations were assayed with seven more markers located between RM111 and RM253, including six SSR markers and one marker for the C gene candidate, OsC1. The C locus was delimited to a 59.3-kb region in which OsC1 was located.     

Seed Length Controlled by Same Locus in Four Different AA GenomeSpecies of Genus Oryza简

To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploitation and utilization of favorable alleles from rice species with the AA genome has become important and urgent in modern breeding programs. Four different interspecific populations were used to detect quantitative trait locus (QTL) for seed length, including a BC₄F₂ population derived from Oryza glumaepatula crossed with Dianjingyou 1 (a japonica cultivar), a BC₄F₂ population derived from O. nivara crossed with Dianjingyou 1, a BC₇F₁ population derived from a cross between O. longistaminata and RD23 (an indica cultivar), and a BC₈F₁ population derived from a cross between O. glaberrima and Dianjingyou 1. The QTLs for seed length in four different populations were termed as SL-3a, SL-3b, SL-3c and SL-3d, respectively. They had good collinearity and accounted for 49% to 60% of the phenotypic variations. Sequencing data indicated that four QTLs were different alleles of GS3 which were responsible for the seed length variation between O. sativa and its four AA genome relatives. These results will be valuable for confirming the evolution of GS3 and also be helpful for rice breeding.     

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。