Somatic hybrids between Solanum bulbocastanum and potato: a new source of resistance to late blight

 Solanum bulbocastanum, a wild, diploid (2n=2x=24) Mexican species, is highly resistant to Phytophthora infestans, the fungus that causes late blight of potato. However this 1 EBN species is virtually impossible to cross directly with potato. PEG-mediated fusion of leaf cells of S. bulbocastanum PI 245310 and the tetraploid potato line S. tuberosum PI 203900 (2n=4x=48) yielded hexaploid (2n= 6x=72) somatic hybrids that retained the high resistance of the S. bulbocastanum parent. RFLP and RAPD analyses confirmed the hybridity of the materials. Four of the somatic hybrids were crossed with potato cultivars Katahdin or Atlantic. The BC₁ progeny segregated for resistance to the US8 genotype (A-2 mating type) of P. Infestans. Resistant BC₁ lines crossed with susceptible cultivars again yielded populations that segregated for resistance to the fungus. In a 1996 field-plot in Wisconsin, to which no fungicide was applied, two of the BC₁ lines, from two different somatic hybrids, yielded 1.36 and 1.32 kg/plant under a severe late-blight epidemic. In contrast, under these same conditions the cultivar Russet Burbank yielded only 0.86 kg/plant. These results indicate that effective resistance to the late-blight fungus in a sexually incompatible Solanum species can be transferred into potato breeding lines by somatic hybridization and that this resistance can then be further transmitted into potato breeding lines by sexual crossing. Received: 27 October 1997 / Accepted: 11 November 1997     

PCR primed with minisatellite core sequences yields DNA fingerprinting probes in wheat

 Four minisatellite core sequences were used as primers in a polymerase chain reaction (PCR) technique, known as the directed amplification of minisatellite-region DNA (DAMD), to detect polymorphisms in three pairs of hexaploid/tetraploid wheat cultivars. In each pair, the tetraploid cultivar (genomic formula AABB) was extracted from its corresponding hexaploid (genomic formula AABBDD) parent. Reproducible profiles of the amplified products revealed characteristic bands that were present only in the hexaploid wheats but not in their extracted tetraploids. Some polymorphisms were observed among the hexaploid cultivars. Twenty-three DAMD-PCR amplified fragments were isolated and screened as molecular probes on the genomic DNA of wild wheat species, hexaploid wheat and triticale cultivars. Subsequently, 8 of the fragments were cloned and sequenced. The DAMD-PCR clones revealed various degrees of polymorphism among different wild and cultivated wheats. Two clones yielded individual-specific DNA fingerprinting patterns which could be used for species differentiation and cultivar identification. The results demonstrated the use of DAMD-PCR as a tool for the isolation of informative molecular probes for DNA fingerprinting in wheat cultivars and species. Received: 13 May 1996/Accepted: 11 October 1996     

A potato hypersensitive resistance gene against potato virus X maps to a resistance gene cluster on chromosome 5

 The dominant Nb gene of potato confers strain-specific hypersensitive resistance against potato virus X (PVX). A population segregating for Nb was screened for resistance by inoculating with PVX strain CP2, which is sensitive to Nb. Through a combination of bulked segregant analysis and selective restriction fragment amplification, several amplified fragment length polymorphism (AFLP) markers linked to Nb were identified. These were cloned and converted into dominant cleaved amplified polymorphic sequence (CAPS) markers. The segregation of these markers in a Lycopersicon esculentum×L. pennellii mapping population suggested that Nb is located on chromosome 5. This was confirmed by examining resistant and susceptible potato individuals with several tomato and potato chromosome-5-specific markers. Nb maps to a region of chromosome 5 where several other resistance genes– including R1, a resistance gene against Phytophthora infestans, Gpa, a locus that confers resistance against Globodera pallida, and Rx2, a gene that confers extreme resistance against PVX–have previously been identified. Received: 2 January 1997/Accepted: 7 February 1997     

Organelle DNA analysis of Solanum and Brassica somatic hybrids by PCR with ’universal primers’

In order to set up a quick and easy procedure for determining the cytoplasmic composition of somatic hybrids, we tested a set of ’universal primers’ for plastidial and mitochondrial DNA on 13 genotypes belonging to the following species: Nicotiana tabacum, Solanum commersonii, Solanum tuberosum, Solanum etuberosum, Solanum phureja, Brassica oleracea, Brassica rapa, ’Anand’ CMS B. rapa, ’Chiang’ CMS B. oleracea, and ’Ogura’ CMS B. oleracea. Such primers are homologous to conserved coding sequences and amplify polymorphic intergenic or intronic regions. cpDNA polymorphism within Solanum and Brassica spp. was found with two and four primer pairs, respectively. The primers for the intergenic region between the trnF and trnV genes gave polymorphism among several tested species and were used in S. commersonii (+) S. tuberosum somatic hybrids,and B. oleracea (+) ’Anand’ CMS B. rapacybrids. Two primer pairs for mtDNA revealed polymorphism between S. commersonii and S. tuberosum, and one showed intraspecific polymorphism in S. tuberosum. The primer pair for the intergenic region between the rps14 and cob genes (pumD) showed a fragment of about 1.5 kb in S. tuberosum and S. phureja. A shorter fragment and no amplification were found in S. etuberosum and S. commersonii, respectively, suggesting frequent intrageneric rearrangements in this genome region. All Brassicaceae evidenced a fragment about 150-bp longer than in S. tuberosum. The same primers were also used with interspecific Solanum spp. somatic hybrids. Both PCR with pumD primers and hybridization with rpl5/rps14 genes indicated lack of linkage between rpl5/rps14 and cob genes in S. commersonii. Compared to direct visualization of restricted organellar DNA or Southern analysis with labelled probes, amplification of cpDNA and mtDNA with universal primers, followed by electrophoresis of either entire or restricted amplified fragments, is a simpler, more rapid and less expensive method to determine the organelle genome composition of interspecific Solanum and Brassica somatic hybrids. Received: 2 August 2000 / Accepted: 22 September 2000     

Expanding informativeness of microsatellite motifs through the analysis of heteroduplexes: a case applied to Solanum tuberosum

The incorporation of heteroduplex analysis into conventional strategies for the study of polymorphisms at microsatellite loci has allowed us to obtain information useful in determining genetic diversity and relationships among organisms. We have chosen, as a model for the testing of this strategy, several Solanum tuberosum varieties cultivated on Tenerife Island (Canary Archipelago) and a (TCT)_n microsatellite located in intron I from the gene for granule-bound starch synthase. The data obtained confirm the high degree of agreement between molecular and farmer taxonomy. Received: 21 September 1998 / Accepted: 28 December 1998     

Identification of DNA amplification fingerprinting (DAF) markers close to the symbiosis-ineffective sym31 mutation of pea (Pisum sativum L.)

 We demonstrate efficient genome mapping through a combination of bulked segregant analysis (BSA) with DNA amplification fingerprinting (DAF). Two sets of 64 octamer DAF primers, along with two PCR programs of low- and high-annealing temperatures (30°C and 55°C, respectively), appeared to be enough to locate molecular markers within 2–5 cM of a gene of interest. This approach allowed the rapid identification of four BSA markers linked to the pea (Pisum sativum L.) Sym31 gene, which is responsible for bacteroid and symbiosome differentiation. Three of these markers are shown to be tightly linked to the sym31 mutation. Two markers flanking the Sym31 gene, A21-310 and B1-277, cover a 4–5 cM interval of pea linkage group 3. Both markers were converted to sequence-characterized amplified regions (SCARs). The flanking markers may be potential tools for marker-assisted selection or for positional cloning of the Sym31 gene. Received: 2 July 1998 / Accepted: 8 October 1998     

Anchored simple-sequence repeats as primers to generate species-specific DNA markers in Lolium and Festuca grasses

Simple-sequence repeats (SSRs) comprising three tetranucleotide repeat sequences with two-base ’anchors’, namely 5′-(AGAC)₄GC, 5′-AC(GACA)₄ and 5′-(GACA)₄GT, were used in PCR reactions as primers to develop inter-SSR DNA fingerprints of the outbreeding grass species Lolium multiflorum, L. perenne, Festuca pratensis and F. arundinacea. Each species was represented by DNA samples from 3 to 6 varieties. In all four species distinctive species-specific DNA profiles were produced that were common across a number of varieties despite their diverse origin. While the fingerprints of the two ryegrasses, L. multiflorum and L. perenne, were the most similar, a number of inter-SSR DNA markers were generated that enabled them to be distinguished from each other. Some slight variations were found between varieties, which provided putative variety-specific markers for cultivar identification. In addition, variations in the DNA profiles of the genotypes of L. multiflorum and F. pratensis were examined, and the results showed that variety-specific fingerprints are integrated patterns made up from the profiles of individual genotypes. Amongst the primers used, AC(GACA)₄ generated the best distinction between Lolium and Festuca individuals and provides an effective new tool for genome identification. A number of species-discriminating sequences, ranging in size between 550 bp and 1,600 bp, were cloned: three clones for F. pratensis, one clone for L. multiflorum and one clone for F. arundinacea. A F. pratensis fragment pFp 78H582 was sequenced. Southern hybridization confirmed the presence of this fragment in F. arundinacea (which contains one genome of F. pratensis), but no homology was found with L. multiflorum. However, a F. arundinacea clone amplified with (GACA)₄GT, pFa 104H1350, was found to be unique to the F. arundinacea genome. Received: 23 June 1999 / Accepted: 27 August 1999     

Allozyme polymorphisms in tetraploid potato gene pools and the effect on human selection

The need for broadening a crop’s genetic base may be determined by comparing allele frequencies within the gene pools of farmer selections in their centers of diversity with that of modern breeding populations. The genetic structure of Andean and Chilean potato farmer selections was investigated with the aid of nine isozymes, which have been studied in detail and used to characterize North American cultivars and advanced breeding lines. These isozymes are associated with the most-important agronomic or quality characters in the North American gene pool. By comparing these data with previous analyses of the North American gene pool, allozyme frequency changes for nine loci were monitored. Allozyme frequency changes were not always due to genetic drift, but resulted also from directional selection of isozyme marker linked quantitative trait loci (QTLs) affecting agronomic or quality characters. Changes in allozyme frequency can also occur as a consequence of pleiotropy, i.e. the isozyme itself may be involved in the expression of a phenotype. These allozyme frequency changes may reflect the manipulation of the potato genome by breeders. There were allozymes in some North American cultivars that were not observed in the farmer selections from the Andes and Chile. This confirms that breeders have already introgressed exotic genes from wild and other primitive cultivated tuber-bearing Solanum species. On this basis, the need for broadening the genetic base for specific chromosomes (or chromosome regions) should be based on analysis with these and other genetic markers available in potato. Received: 20 November 2000 / Accepted: 27 December 2000     

Sucrose utilization during potato microtuber growth in bioreactors

 Potato microtubers are used as pathogen-tested in vitro stocks for certified seed potato production. Microtubers grown in a rotating bioreactor grew at a faster rate when the medium was replaced frequently. Although the total microtuber number was not affected, the number of microtubers over 1 g quadrupled when 75% of the medium was replaced every 2 weeks when compared with no medium refreshment. Significantly slower microtuber growth rates resulted when a lower sugar concentration (40 g 1⁻¹ instead of 80 g 1⁻¹) was used or when a mixture of glucose and fructose replaced sucrose. Although high sucrose levels are necessary for optimal microtuber production, the sucrose supplied was rapidly hydrolyzed into glucose and fructose, making the long-term maintenance of desirable sucrose levels difficult. These results indicate that successful strategies to reduce sucrose hydrolysis without inhibiting microtuber growth will improve the efficiency of sucrose utilization in potato microtuber bioreactors. Received: 1 December 1998 / Revision received: 6 May 1999 · Accepted: 19 May 1999     

Design of grapevine (Vitis vinifera L.) cultivar-specific SCAR primers for PCR fingerprinting

Among 34 grapevine cultivars (Vitis vinifera L.), eight putative genotype-specific RAPD markers, from ’Albariño’, ’Caíño blanco’, ’Chardonnay’, ’Folle blanche’, ’Grenache blanc’, ’Malvasía Sitges’, ’Torrontés’ and ’Treixadura’ respectively, were selected to transform into SCAR markers. Of these, seven markers were cloned and then five which showed a positive specific hybridization signal were sequenced. For these five markers, 30 sequence-specific primers ranging from 14 to 29 bases were designed to amplify genomic DNA from 64 grapevine cultivars under more-stringent PCR conditions. Only, two primer pairs, OpA11₁₁₇₅p17R/ p17F and OpD10₈₀₀p14R/p14F, still produced a specific SCAR marker, the ’Folle blanche’ ScA11₁₁₇₅ and the ’Malvasía Sitges’ ScD10₈₀₀ respectively. Moreover, the ScA11₁₁₇₅ marker was amplified only in ’Folle blanche’ among the 64 cultivars tested with a large annealing temperature range using either two different Taq DNA polymerases or two separate thermocyclers. In addition, we discuss the initial polymorphism originated by the RAPD technique and suggest a new design of SCAR primers to obtain reliable cultivar-specific SCAR markers from single PCR-based bands for identification purposes.     

DNA fingerprinting of Indian isolates of Xanthomonas oryzae pv. oryzae

 A high level of genetic polymorphism was detected among Indian isolates of Xanthomonas oryzae pv. oryzae using hypervariable probes such as a microsatellite oligonucleotide, probe (TG)₁₀, a human minisatellite probe, pV47, an avirulence gene probe, avrXa10 and a repeat clone, pBS101. These DNA probes detected multiple loci in the bacterial genome generating complex DNA fingerprints and differentiated all of the bacterial isolates. Analysis of fingerprints indicated that pV47, (TG)₁₀ and pBS101 have a lower probability of identical match than avrXa10 and therefore are potential probes for DNA fingerprinting and variability analysis of Xanthomonas oryzae pv. oryzae pathogen populations. Cluster analysis based on hybridization patterns using all of the above probes showed five groups at 56% similarity. Studies on the methylation patterns of isolates representing the three important races of X. oryzae pv. oryzae indicated more methylation in the most virulent isolate, suggesting a possible role of methylation in pathogenicity. Received: 8 December 1996 / Accepted: 20 December 1996     

A new gene,Ny (tbr), for hypersensitivity to Potato virus Y from Solanum tuberosumMaps to Chromosome IV

A diploid backcross population derived from a cross between Solanum tuberosum and Solanum berthaultii segregated for monogenic dominant hypersensitivity to Potato virus Y (PVY). We propose the symbol Ny _tbr for this locus because plants carrying this gene develop necrosis after inoculation with PVY and the allele originated in S. tuberosum. The gene mapped to chromosome IV between TG316 and TG208 at LOD=2.72. This location does not correspond to any other mapped resistance genes in potato. Received: 13 April 2001 / Accepted: 20 July 2001     

Two additive QTLs conferring broad-spectrum resistance in potato to Globodera pallida are localized on resistance gene clusters

Broad-spectrum resistance in potato to the potato cyst nematode (PCN) is commonly regarded as a complex inherited trait. Yet, in this paper we show that, by use of a selected set of PCN test populations, broad-spectrum resistance to the species Globodera pallida can be fully ascribed to the action of two loci: Gpa5 and Gpa6. These loci were readily mapped by means of a strategy based on two steps. Firstly, the chromosomal localization of both loci was assessed by use of an online catalogue of AFLP markers covering a substantial part of the potato genome (http://www.spg.wau.nl/pv/aflp/catalog.htm). Subsequently the chromosomal regions of both loci were identified by means of CAPS markers based on RFLP insert sequences. Locus Gpa5 explains at least 61% of the genetic variation. This locus maps to chromosome 5 on a region which has previously been shown to harbor resistance factors to viral (Nb, Rx2), fungal (R1) and nematodal (Gpa, Grp1) pathogens. The Gpa6 locus exhibits a minor effect on the resistance (24%) and acts additively to Gpa5. Interestingly, the Gpa6 locus maps to a region on chromosome 9 where, in the homoeologous tomato genome, the virus resistance gene Sw-5 resides as part of a resistance gene cluster. In potato, resistance to potato virus X has been reported in the vicinity of this region. The map location of Gpa6 indicates the presence of a resistance gene cluster at the end of the long arm of chromosome 9 of potato. Received: 10 January 2000 / Accepted: 31 January 2000     

Specific PCR primers to identify arbuscular mycorrhizal fungi within colonized roots

 A set of PCR primers targeted at five major phylogenetic subgroups of arbuscular mycorrhizal fungi (Glomales) was designed to facilitate specific amplification of internal transcribed spacers and 18 S rRNA gene fragments from colonized roots in the absence of spores. The subgroups include the recently discovered deeply divergent lineages of Glomales, which could not be detected by previously reported PCR primers, and the former genus Sclerocystis. Restriction fragment length polymorphism patterns presented allow identification of presently known members of these groups. The resulting PCR products can be used to identify the fungal symbionts at the genus or species level by restriction digests or DNA sequencing. A novel DNA extraction method allows visual control of the analyzed roots by staining procedures after analysis by PCR. Accepted: 2 April 2000     

Transmission of alien tomato chromosomes from BC1 to BC2 progenies derived from backcrossing potato (+) tomato fusion hybrids to potato: the selection of single additions for seven different tomato chromosomes

 By backcrossing three BC₁ genotypes of potato (+) tomato fusion hybrids to different tetraploid potato pollinators, BC₂ populations were produced. A combined total of 97 BC₂ plants from three BC₂ populations were analysed with chromosome-specific probes through restriction fragment length polymorphism (RFLP) for the presence of alien tomato chromosomes. The number of different alien tomato chromosomes transmitted through the female BC₁ parent ranged from 0 to 6, and the average number of different alien chromosomes transmitted per BC₂ plant varied between 1.7 and 3.4 in the different populations. This variation corresponded to the chromosome constitution of the individual BC₁ parents: parent 6739, which possessed 11 different alien chromosomes in a single condition, gave rise to progeny with a lower average number of alien chromosomes per plant than the BC₁ parent 2003 that possessed 2 of the 12 alien chromosomes in a disomic condition. In the latter case, the higher transmission rate was attributed to the more regular distribution of the two alien chromosomes in the disomic condition because of regular bivalent formation during meiosis as revealed by genomic in situ hybridisation (GISH) and fluorescent in situ hybridisation (FISH). The transmission frequencies of individual alien chromosomes were subjected to statistical analysis to test whether the maternal genotypes had an effect on alien-chromosome transmission. Among the BC₂ plants, a total of 27 single additions were detected for as many as seven different chromosomes (1, 2, 4, 6, 8, 10 and 12) out of the 12 possible types. Received: 4 March 1997 / Accepted: 28 August 1997     

Low-Cot DNA sequences for fingerprinting analysis of germplasm diversity and relationships in Amaranthus

We examined genetic diversity and relationships among 24 cultivated and wild Amaranthus accessions using the total low-Cot DNA and five individual repetitive sequences as probes. These low-Cot DNA probes were obtained by the isolation of various classes of repetitive-DNA sequences, including satellites, minisatellites, microsatellites, rDNA, retrotransposon-like sequences, and other unidentified novel repetitive sequences. DNA fingerprints generated by different types of repetitive-DNA probes revealed different levels of polymorphism in the Amaranthus genomes. A repetitive sequence containing microsatellites was found to be a suitable probe for characterizing intraspecific accessions, whereas more conservative sequences (e.g. rDNA) were informative for resolving phylogenetic relationships among distantly related species.Genetic diversity, measured as restriction fragment length polymorphism (RFLP) and the similarity index at the low-Cot DNA level, was equally high among intraspecific accessions between the two species groups: grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus) and their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis). At the interspecific level, however, the grain amaranth species are less divergent from each other than their wild progenitors. With the rare exceptions of certain A. caudatus accessions, grain amaranths were found to be closely related to A. hybridus. The results based on low-Cot DNA were comparable with previous RAPD and isozyme studies of the same set of species/accessions of Amaranthus, indicating that low-Cot DNA sequences are suitable probes for a fingerprinting analysis of plant germplasm diversity and for determining phylogenetic relationships. Received: 19 October 1998 / Accepted: 8 January 1999     

基于ISSR标记的猕猴桃品种 遗传多样性分析及指纹图谱构建

采用ISSR标记对中华猕猴桃(Actinidia chinensis Planch.)、美味猕猴桃〔A.chinensis var.deliciosa(A.Chev.)A.Chev.〕、软枣猕猴桃〔A.arguta(Sieb.et Zucc.)Planch.ex Miq.〕和毛花猕猴桃(A.eriantha Benth.)的32个样本进行了遗传多样性分析,并以ISSR标记为基础构建了DNA指纹图谱.结果表明:筛选的10个多态性高且条带清晰的引物共扩增出200个条带(位点),其中,多态性位点195个,多态性位点百分率(PPL)达97.50%;各引物的多态性信息含量(PIC)以及供试样本的观测等位基因数(Na)、有效等位基因数(Ne)、Nei's基因多样性指数(H)和Shannon's多样性指数(I)的总均值分别为0.9080、1.9800、1.3569、0.2255和0.3613,4个猕猴桃种间的遗传分化系数(Gst)为0.4146,基因流(Nm)为0.7059,且32个样本间的Na、Ne、H和I值差异极显著(P<0.001).供试32个样本间的遗传相似系数(GS)为0.5650~0.9650,平均值为0.7164;基于GS值进行UPGMA聚类分析,在GS值为0.76处将32个样本分为4组,基本对应供试的4个猕猴桃种类,其中,第Ⅰ组的大多数样本属于美味猕猴桃品种,第Ⅱ组的样本均属于中华猕猴桃品种,第Ⅲ组的样本属于毛花猕猴桃品种,第Ⅳ组的样本均属于软枣猕猴桃品种.分子方差分析结果表明:4个猕猴桃的种间变异占总变异的40.84%,种内变异占总变异的59.16%.研究结果表明:供试的猕猴桃品种间遗传分化程度较高,基因交流频率较低,且总遗传变异的近60%存在于种内,说明供试的猕猴桃品种具有较丰富的遗传多样性.另外,根据10个ISSR引物的扩增结果,筛选出引物UBC818、UBC824、UBC854和UBC895扩增的15个多态性位点构建的DNA指纹图谱可用于供试32个猕猴桃样本的鉴定.     

Asymmetric protoplast fusions between wild species and breeding lines of potato – effect of recipients and genome stability

 The objective of this study was to investigate if in asymmetric protoplast fusion experiments the ploidy of the recipient line (di-haploid and tetraploid) has an influence on the extent of the asymmetry of the regenerating fusion products. Nineteen different experiments with the wild species Solanum bulbocastanum and Solanum circaeifolium as donors (irradiated with 210 Gy) and different breeding lines (di-haploid and tetraploid) were carried out. The degree of genome elimination was determined by measuring the relative DNA content using flow cytometry. The data showed that the loss of DNA in hybrid plants was significantly higher for 4x, compared to 2x, plants as recipients. In addition, the stability of asymmetry in the fusion products was studied. For this purpose differences in asymmetry in individual shoots originating from the same callus were analysed. A large variation in the DNA content of individual shoots was detected. Of the 4x to 6x shoots 44% had the same DNA content as another shoot originating from the same callus, 19% had a DNA content between 4x and 6x but different from any other analysed shoot originating from the same callus, 2% were chimeras and 35% had a completely different DNA content (eutetraploid, euhexaploid, eupolyploid or asymmetric with a ploidy level above 6x). RFLP-analysis with single-copy probes of 12 regenerates from six calli (two regenerates per callus) confirmed the assumption that the different regenerates of one callus originate from the same single cell. The analysis of selected regenerates cultivated for a period of more than 1 year demonstrated that the genome of asymmetric regenerates might change during cultivation. Received: 30 April 1998 / Accepted: 24 July 1998     

Progeny selection for agronomic characters in early generations of a potato breeding programme

 Repeatabilities of progeny means, and the univariate cross prediction method were used to study the effectiveness of progeny selection for agronomically important characters in early generations of potato (Solanum tuberosum L.) breeding. The study was based on 90 progenies (72 crosses+18 selfs) evaluated for three successive generations, i.e. seedling, first clonal and second clonal generations. Repeatabilities of progeny means were measured as correlation coefficients between generations. In the univariate cross prediction method, progeny means and within-progeny standard deviations were used to calculate the proportions of clones exceeding the target values, and correlation coefficients between generations for predicted and observed proportions of clones, were calculated. Population means varied from generation to generation. Correlation coefficients between generations for progeny means for most of the characters were significant, but moderate. These were higher than the correlation coefficients between predicted and observed proportions of clones exceeding the target values. The possibility of using progeny means as a selection parameter to reduce the number of genotypes to be examined in later stages by rejecting the poor crosses in seedling generation is discussed. Received: 8 January 1997/Accepted: 28 February 1997     

Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.)

 Inter-simple sequence repeat (ISSR) amplification was used to analyze microsatellite motif frequency in the rice genome and to evaluate genetic diversity among rice cultivars. A total of 32 primers, containing different simple sequence repeat (SSR) motifs, were tested for amplification on a panel of 59 varieties, representative of the diversity of cultivated rice (Oryza sativa L.). The ISSR analysis provided insights into the organization, frequency and levels of polymorphism of different simple sequence repeats in rice. The more common dinucleotide motifs were more amenable to ISSR analysis than the more infrequent tri-, tetra- and penta-nucleotide motifs. The ISSR results suggested that within the dinucleotide class, the poly(GA) motif was more common than the poly(GT) motif and that the frequency and clustering of specific tri- and tetra-nucleotide simple sequence repeats was variable and motif-specific. Furthermore, trinucleotide ISSR markers were found to be less polymorphic than either dinucleotide or certain tetranucleotide ISSR markers, suggesting which motifs would be better targets for microsatellite marker development. The ISSR amplification pattern was used to group the rice genotypes by cluster analysis. These results were compared to surveys of the same varieties for amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP) and isozyme markers. The ISSR fingerprint could be used to differentiate the genotypes belonging to either Japonica or Indica sub species of cultivated rice and to dissect finer levels of diversity within each subspecies. A higher percentage of polymorphic bands was produced with the ISSR technique than the AFLP method, based on a similar PCR reaction. Therefore, ISSR amplification proved to be a valuable method for determining genetic variability among rice varieties and for rapidly identifying cultivars. This efficient genetic fingerprinting technique would be useful for characterizing the large numbers of rice accessions held in national and international germplasm centers. Received: 25 May 1998 / Accepted: 17 September 1998