Assessing indica-japonica differentiation of improved rice varieties using microsatellite markers

To assess the indica-japonica differentiation of improved rice varieties, a total of 512 modem varieties including 301 indica and 211 japonica accessions were analyzed using 36 microsatellites. The Fst coefficients ranged from 0.002 to 0.730 among the loci with an average of 0.315. Significant differentiation was detected at 94.4% of the loci studied （P 〈 0.05, pairwise Fst tests）, indicating that there was a high level of indica-japonica differentiation within the improved varieties. At 18 loci, about 74%-98% of the alleles of indica and japonica accessions were distributed in two ranges of amplicon length. Linkage disequilibrium analysis showed that the distribution trends were significantly nonrandomly associated. Using the differentiation trends at the 18 loci, microsatellite index （MI） was proposed for discrimination of the two subspecies. When rice accessions with MI value greater than zero were classified as indica, and those with MI value smaller than zero were classified as japonica, about 96.1% of the accessions could be classified. This result agrees with the classification based on morphological-physiological characters, indicating that this method is feasible and effective.     

几个水稻株系的亲和性测定及微卫星标记分析

利用典型的籼稻南京11号、典型的粳稻秋光对16个水稻株系的亲和性进行了测定,测交结果表明,NLl73、NL15、NL61、NL67、NL82和NL279表现亲籼性,NL208表现亲粳性,NL78表现一定广亲和性,其余株系与籼、粳测验种杂交育性都不高。根据测交结果选择不同育性的株系用分布于12条染色体上的前人证明籼粳稻间有多态性的56个微卫星标记进行分析,在微卫星标记聚类分析基础上计算梗型性判别值Dj,并据此把NL173、NLl5、NL78、NL58判别为偏籼型,而NL208为偏粳型。综合亲和性测交结果和分子标记分析结果发现,在亲和性测交中表现亲籼的2个株系NL173、NL15分子标记判别为偏籼类型,杂交亲和性表现亲粳的株系NL208分子标记判断为偏粳类型,表现广亲和特性的株系NL78被分子标记判别为偏籼类型,与测验种杂交育性均不高的NL58分子标记判别为偏籼型。     

水稻染色体G—带的研究

用改良的ASG法首次在籼稻(O.sativa subsp.indica)品种珍汕97和粳稻(O.subsp.iaponica)品种秀岭的有丝分裂染色体上显示了G-带,并作了相应的G-带核型分析。就同一材料来说,随着有丝分裂时期的推进,染色体上带纹数目逐渐减少。籼、粳亚种间相对应的同源染色体上G-带带纹特征彼此相似。讨论了水稻G-带带型与染色体不同区域分化的关系;G-带带型与籼、粳稻分歧的关系;以及G-显带的方法。     

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。     

水稻籼粳杂种生殖障碍的基因定位分析

籼稻(Oryza sativa L.ssp.indica)与粳稻(O.sativa ssp.japonica)杂交优势明显但存在生殖隔离。生殖障碍主要表现为胚囊败育、花粉败育、开花时花药不开裂和雌雄异熟。应用具有137个标记位点的籼、粳杂交(“窄叶青8号”/“京系17”)F_1花药培养获得的127个双单倍体(DH)群体构建的RFLP图谱,对控制籼、粳杂种小穗败育的基因座位进行了定位研究。结果在第1、3、4、5、6、7、8、12染色体上检测到10个基因座位,其中第3、12染色体上的2个不育基因位点stj-3和stj-12与同一杂交组合F_2分离群体中发现的异常分离热点处于相同的染色体区段。Ssj-6的基因加性效应为负值,有增加籼、粳亲和性的作用;其余的不育基因座位皆有增加籼、粳杂种不育性的作用。     

水稻品种SSR与PFLP及其与杂条优势的关系比较研究

用48对SSR引物和50个RFLP探针对来自6个生态型的57份水稻材料之间的遗传差异进行了比较分析,从单个位点的等位基历数和平均基因多样性看,SSR的多态性要高于RFLP,从遗传距离看,在总计1596对材料的遗传距离中,只有144对（占9％）用RFLP标记估计的遗传距离（简称GDRFLP,下同）高于用SSR标记估计的遗传距离（简称GDSSR,下同）,平均高出的幅度为0．0371,而有1452对（占91％）材料间的GDSSR高于GDRFLP,平均高出幅度为0．2492,无论是籼,粳亚种内还是灿粳亚种间,SSR标记比RFLP估计的遗传离高,如用SSR标记估计的籼稻亚种内材料之间平均遗传距离为0．5483,而RFLP标记估计的只有0．2776,粳稻亚种内SSR平均遗传距离为0．5777,RFLP的只有0．2405,用SSR和RFLP估计的亚种间的平均遗传距离分别为0．8047和0．731,成对材料的SSR遗传距离与RFLP遗传距离之间的相关分析表明,对于典型的籼粳品种,这两种标记估计的遗传距离相关系数较高,而中间型材料或偏籼偏粳材料的相关程序较低,通过分析4个两系不育系与48恢复系之间的遗传距离与F1的产量表现及杂种优势之间的相关关系得知,这两种标记估计的遗传距离与杂种表现间的相关均没有达到显著水平,而与杂种优势的相关系数中,除108s与恢复系的GDRFLP和LS2S与恢复系的GDSSR与超亲优势没有达到显著水平外,其他均达到极显著的水平。     

水稻零等位RFLP标记的遗传学研究

采用8种限制性内切酶与247个已定位到水稻12条染色体上的分子探针组合,对典型籼稻(Oryza sativa L.ssp.indica)“南京11”和粳稻(O.sativa L.ssp.japonica)“金南凤M”以及中间型品种“Bellemont”之间存在的零等位位点进行了分析,9个探针揭示出零等位位点的存在。其中,RG573、G122、G93、G402和G1318特异揭示了“南京11”的零等位,G261特异揭示了“金南凤M”的零等位,RG229特异揭示了“Bellemont”的零等位,C397揭示了“南京11”和“Bellemont”的零等位,而RG131揭示了“金南凤M”和“Bellemont”的零等位。利用“南京11”/“金南凤M”的杂交F_2群体,对其中58个单株进行了7个零等位RFLP标记及程氏指数法中的6个形态性状的测验,据此计算出各植株的零等位基因型及籼、粳分类指数,结果表明:零等位标记在F_2群体中呈显性遗传。在F_2群体中进一步对G93、G122、G261、G402、G1318、C397、RG573零等位标记与程氏指数之间进行了成组数据t测验,发现G93、G122、G402、G1318、G397差异达显著或极显著水平,G261、RG573的t值也较大,显示出零等位标记在籼、粳交后代,可特异鉴定籼、粳差异。     

水稻籼粳亚种杂交1代的光合光抑制特性

用４个粳稻品种,５个籼稻品种进行正反交,得到１６个籼粳杂交Ｆ１,测定其光合光抑制特性。结果表明：通常籼稻对光抑制的敏感性大于粳稻,但籼稻中也有耐性强的品种。籼粳杂交稻Ｆ１的光抑制介于双亲之间,并偏向其母本。光抑制程度与ＰＳⅡ活性一致,其机理与双亲核编码的ＳＯＤ诱导活性和母本质体编码的Ｄ１蛋白量有关。比较釉粳杂交稻“３０３７／０２４２８”和税型杂交稻“汕优６３”的光抑制特性发现,在光抑制条件下,籼粳杂交稻ＳＯＤ诱导活性和Ｄ１蛋白量保持能力较高,因而ＰＳⅡ和光合能力表现比较稳定。因此,为培育耐光抑制的籼粳杂交稻,筛选耐性强的品种作母本是籼粳亚种配组的重要原则。     

地中海地区稻种资源的籼粳分类及遗传多样性

利用SSR标记及程氏综合指数法分析了109份从地中海引进的水稻种质资源的遗传多样性和籼粳类型,同时利用籼粳测交法分析了其中37份资源的籼粳亲和性.结果表明,大部分引进的水稻种质属粳稻类型,基于SSR聚类、程氏综合指数法分析所确定的粳型品种数分别占引进种质的80.73%和77.98%,基于籼粳亲和性分类所确定的粳型品种数占供试37份资源的75.68%.地中海稻种资源具有较高的遗传多样性,平均有效等位基因数为3.84个,Nei多样性指数平均值为0.482,其中籼稻群与粳稻群的Nei多样性指数分别为0.459和0.340,籼稻遗传多样性高于粳稻.研究结果对于科学引进、合理保存和有效利用国外水稻种质改良国内水稻品种具有指导意义.     

基于表型性状和SSR分子标记的云南省水稻主要育成品种（系）的遗传相似性分析

为了揭示云南省水稻主要育成品种（系）的遗传相似性。本文利用株高等17个表型性状和48个微卫星（SSR）分子标记,对云南省18个育种部门（或课题组）60年代以来选育的40个品种（系）进行遗传相似性评价。结果显示表型遗传相似性低于DNA水平。40个品种（系）基于17个表型性状的平均遗传相似系数为0.244,籼型为0.289,粳型为0.309,籼粳亚种间为0.162;基于48个SSR分子标记的平均遗传相似系数为0.383,籼型为0.318,粳型为0.478,籼粳亚种间为0.267。48个SSR分子标记共检测到等位基因214个,每个标记2～8,平均4.458个;平均有效等位基因数为2.8336,变幅为1.1515～5.2981;多态性信息含量（PIC）平均值为0.6058,变幅为0.2118～0.8816;基因型多样性指数（H′）平均值为1.1328,变幅为0.3768～1.8087。RM84、RM249、RM152、RM222和RM528是评价云南省水稻选育品种（系）遗传相似性比较理想的SSR分子标记。聚类分析显示,云南省水稻主要选育品种（系）表现为亚种间遗传差异明显,亚种内遗传差异较小,粳型遗传相似性高于籼型。表明云南省选育的粳型品种（系）遗传多样性低,且同一育种部门（或育种人）选育的品种遗传相似度高。     

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.     

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。     

Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions showed three major groups and nine subgroups. Group I corresponded to the classical indica subspecies, whereas groups II and III belong to the japonica subspecies. Indica and japonica differentiation accounted for only 6.5% of the total variation in the entire sample and 93.5% was due to within-subspecies diversity. Differentiation among eco-geographic regions accounted for 24% of the diversity within the subspecies. Larger amounts of the eco-geographical differentiation were resolved within japonica than within indica. The largest indica-japonica differentiation based on the single locus level was detected by markers on chromosomes 9 and 12, while the smallest differentiation was detected by markers on chromosomes 4 and 8. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between indica and japonica and among the main geographic regions. The multilocus analysis in genetic diversity showed a higher proportion of variation caused by predominant non-random associations of different loci within and among the classified subspecies and geographic subdivisions. The results suggest that selection for eco-geographical adaptation on multilocus associations was largely responsible for the maintenance of the extensive variation in the primary gene pool of rice.Communicated by Q. ZhangS.B. Yu and W.J. Xu contributed equally to the work     

Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication.

The three quantitative trait loci (qSH1, qSH3, and qSH4) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication. The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering, compared with the qSH3 locus. Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes. A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci, showing that qSH1 is genetically epistatic to the other loci. The level of the reduction in sequence diversity was compared between the qSH1 and qSH4 regions. The sequence diversity was severely reduced in the qSH1 region of Oryza sativa subsp. japonica compared with that of O. sativa subsp. indica, despite that the level of diversity was similarly reduced at the qSH4 region in the 2 subspecies. Phylogenetic reconstruction based on the combined sequences of the flanking sites showed different patterns in the 2 subspecies. The 2 subspecies formed a single clade with respect to qSH4, whereas they were separated into different lineages with respect to qSH1, suggesting that these loci had different histories during rice domestication.     

Molecularmarker diversity and hybrid sterility in indica-japonica rice crosses

 The partial sterility of hybrids between the indica and japonica rice subspecies of Asian cultivated rice is a serious constraint for utilizing inter-subspecific heterosis in hybrid rice breeding. In this study, we have investigated the relationship between molecular-marker polymorphism and indica-japonica hybrid fertility using a diallel set involving 20 rice accessions including 9 indica and 11 japonica varieties. Spikelet fertility of the resulting 190 F₁s and their parents was examined in a replicated field trial. Intra-subspecific hybrids showed much higher spikelet fertility than inter-subspecific hybrids except in crosses involving wide-compatibility varieties. The parents were surveyed for DNA polymorphism using 96 RFLP and ten SSR markers, which revealed extensive genetic differentiation between indica and japonica varieties. A large number of markers detected highly significant effects on hybrid fertility. The chromosomal locations for many of the positive markers coincided well with previously identified loci for hybrid sterility. The correlation between hybrid fertility and parental distance was low in both intra- and inter-subspecific crosses. The results suggest that the genetic basis of indica-japonica hybrid sterility is complex. It is the qualitative, rather than the quantitative, difference between the parents that determines the fertility of hybrids. Received: 3 January 1997/Accepted: 17 January 1997     

Classification of rice germplasm. II. Discrimination of indica from japonica via analysis of amplicon length polymorphisms

The polymerase chain reaction (PCR) was used to survey DNA sequence variation among 12 indica and 10 japonica rice cultivars. Of the 143 primer pairs used, 37 detected amplicon length polymorphism (ALP) and 11 revealed PCR banding patterns paralleled with the indica/japonica differentiation. Thus the 11 primer pairs were used to discriminate the two rice subspecies. A collection of 116 accessions representing the breadth of rice germplasm was analyzed for ALP at the 11 loci. Rice accessions with scores of 0.3 or more were classified as indica while those with –0.3 or less were classified as japonica. Those with scores from –0.3 to 0.3 were considered intermediate. With this criterion, 70 accessions were classified as indica, 35 accessions as japonica, and 11 accessions as intermediate. The concept and the approach used here for rice should be equally applicable for classifying other plant species. Received: 1 July 1997 / Revision received: 4 December 1997 / Accepted: 29 December 1997     

Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice)

A dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast Asia up to now. Before the first sd1-d-carrying variety IR8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. Inter-subspecific difference of the tall (wild-type) allele SD1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting sd1-d of the recurrent parent IR36 by SD1s of two indica varieties, two temperate-japonica varieties and one tropical-japonica variety. The two indica -donor isogenic lines had longer culms than the three japonica-donor isogenic lines consistently in two different environmental conditions. Moreover, nonsynonymous single-nucleotide polymorphism between the two subspecies was detected at two sites in Exon 1 and Exon 3 of the sd1 locus. It is demonstrated that the inter-subspecific differentiation of SD1 contributes height difference between indica and japonica. The indica-originating and japonica-originating alleles at the sd1 locus were designated as SD1-in(t) and SD1-ja(t), respectively.     

Distribution and Organization of AA Genome- specific and Tandemly Repetitive Sequences in Chinese Common Wild Rice and Cultivated Rice

Repetitive DNA sequences are useful molecular markers for studying plant genome evolution and species diversity. The authors report the isolation and characterization of repetitive DNA sequences (pOs139) from Oryza sativa cuhivars "Zhaiyeqing". By Southern blot analysis, the authors discovered that pOs139 sequences were organized not only tandemly, but also highly specifc for the AA genome of Oryza genus. Sequence analysis revealed that the clone pOs139 contains a 355 bp repetitive unit. The genomic DNA of 29 Chinese common wild accessions, and 43 cultivated rice accessions, were analyzed by Southern blot with pOs139 as a probe. The results illustrated that there was significant difference in hybridization patterns between japonica and indica subspecies. Hybridization bands of indica subspecies were much more than those of japonica, and the Chinese common wild rice was similar to indica in hybridization patterns. The copy number estimated by dot blot hybridization analysis indicated that a considerable degree of variation existed among different accessions of O. sativa and the Chinese common wild rice. It is interesting to note that japonica subspecies contains relatively low copy numbers of pOs139-related repetitive DNA sequences, while the indica and Chinese common wild rice contain relatively high copy numbers.     

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(Oryz a 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。