Phylogeny of wild and cultivatedSolanum species based on nuclear restriction fragment length polymorphisms (RFLPs)

Analysis of Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata (L.) Walp) Genotypes Using Single Nucleotide Polymorphism Markers

Cowpea (Vigna unguiculata (L.) Walp) is an important legume crop with immense potential for nutritional and food security, income generation, and livestock feed in Sub-Saharan Africa. The crop is highly tolerant to heat and drought stresses which makes it an extremely important crop for improving resilience in crop production in the face of climate change. This study was carried out to assess the genetic diversity and population structure of 90 cowpea accessions using single nucleotide polymorphism (SNP) markers. Out of 11,940 SNPs used, 5864 SNPs were polymorphic and maintained for genome diversity analysis. Polymorphic information content (PIC) values ranged from 0.22 to 0.32 with a mean value of 0.27. The model-based Bayesian STRUCTURE analysis classified 90 cowpea accessions into four subpopulations at K = 4, while the distance-based cluster analysis grouped the accessions into three distinct clusters. The analysis of molecular variance (AMOVA) revealed that 59% and 69% of the total molecular variation was attributed to among individual variation for model-based and distance-based populations, respectively, and 18% was attributed to within individual variations. Furthermore, the low heterozygosity among cowpea accessions and the high inbreeding coefficient observed in this study suggests that the accessions reached an acceptable level of homozygosity. This study would serve as a reference for future selection and breeding programs of cowpea with desirable traits and systematic conservation of these plant genetic resources.

Identifying SSR Markers Related to Seed Fatty Acid Content in Perilla Crop (Perilla frutescens L.)

Perilla seed oil has been attracting attention in South Korea as a health food. Five fatty acids of 100 Perilla accessions were identified as follows: palmitic acid (PA) (5.10-9.13%), stearic acid (SA) (1.70-3.99%), oleic acid (OA) (11.1-21.9%), linoleic acid (LA) (10.2-23.4%), and linolenic acid (LNA) (54.3-75.4%). Additionally, the 100 Perilla accessions were divided into two groups (high or low) based on the total fatty acid content (TFAC). By using an association analysis of 40 simple sequence repeat (SSR) markers and the six Perilla seed oil traits in the 100 Perilla accessions, we detected four SSR markers associated with TFAC, five SSR markers associated with LNA, one SSR marker associated with LA, two SSR markers each associated with OA and PA, and four SSR markers associated with SA. Among these SSR markers, four SSR markers (KNUPF14, KNUPF62, KNUPF72, KNUPF85) were all associated with TFAC and LNA. Moreover, two SSR markers (KNUPF62, KNUPF85) were both associated with TFAC, LNA, and OA. Therefore, these SSR markers are considered to be useful molecular markers for selecting useful accessions related to fatty acid contents in Perilla germplasm and for improving the seed oil quality of Perilla crop through marker-assisted selection (MAS) breeding programs.

Taxonomy and Genetic Differentiation among Wild and Cultivated Germplasm of Solanum sect. Petota

Because of their adaptation to a diverse set of habitats and stresses, wild species of cultivated crops offer new sources of genetic diversity for germplasm improvement. Using an Infinium array representing a genome-wide set of 8303 single nucleotide polymorphisms (SNPs), phylogenetic relationships and allelic diversity were evaluated within a diversity panel of germplasm from Solanum sect. Petota. This panel consists of 74 plant introductions (PIs) representing 25 species and provides a diverse representation of tuber-bearing Solanum germplasm. Unlike other molecular markers, genome-wide SNPs have not been widely implemented in potato. To determine relatedness between current species classifications and SNP-based genetic distances, a phylogeny was generated based on random individuals from each core collection PI. With few exceptions, SNP-based estimates of species relationships revealed general agreement with the existing taxonomic grouping of species in Solanum sect. Petota. Genotype comparisons between the Solanum sect. Petota diversity panel and a panel of 213 tetraploid cultivars and breeding lines indicated a greater extent of diversity between populations of native Andean landraces than among modern cultivated varieties. Comparison of SNP allele frequencies between the Solanum sect. Petota panel and tetraploid cultivars identified loci with extreme divergence between cultivated potato and its tuber-bearing relatives. Several of these loci are associated with genes related to carbohydrate metabolism and tuber development, suggesting potential roles in potato domestication. The Infinium SNP data offer a new taxonomic view of potato germplasm, while further identifying candidate alleles likely to differentiate wild germplasm and cultivated potato, possibly underlying key agronomic traits.

Molecular marker technologies for plant improvement

The exploitation of DNA polymorphisms by an ever-increasing number of molecular marker technologies has begun to have an impact on plant genome research and breeding. Restriction fragment length polymorphisms, micro- and mini-satellites and PCR-based approaches are used to determine inter- and intra-specific genetic diversity and construct molecular maps of crops using specially designed mapping populations. Resistance genes and other agronomically important loci are tagged with tightly linked DNA markers and the genes isolated by magabase DNA technology and cloning into yeast artificial chromosomes (YAC). This review discusses some recent developments and results in this field.

Overcoming crossing barriers between nontuber-bearing and tuber-bearing Solanum species: towards potato germplasm enhancement with a broad spectrum of solanaceous genetic resources

The first direct sexual hybrids between diploid nontuber-bearing species and diploid potato breeding lines are reported here. Three nontuberous species of Solanum, S. brevidens, S. etuberosum, and S. fernandezianum, were used for sexual crosses, achieved by a combination of rescue pollinations and embryo rescue. Initial hybrid selection was made using an embryo spot marker, followed by the evaluation of morphological and reproductive traits. Putative hybrids were first tested for resistance to potato leaf roll virus derived from the wild species, and then were tested with molecular markers using species-specific DNA probes. Finally, the tuberization of several 2x hybrids was tested for actual potato germplasm enhancement. These hybrids are unique in terms of their potential to enhance recombination between chromosomes of wild species and those of cultivated potatoes in germplasm utilization, and to exploit the genetic nature of tuber formation. The finding that nontuber-bearing Solanum spp. can be directly crossed with tuber-bearing species also has important implications for the regulatory aspects of the use of genetically modified organisms.

Genomic in situ hybridization reveals both auto- and allopolyploid origins of different North and Central American hexaploid potato (Solanum sect. Petota) species

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2n = 2x = 24) to hexaploids (2n = 6x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes's series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAA(a)A(a) genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa.

A model of the C14-EPIC complex indicates hotspots for a protease-inhibitor arms race in the oomycete-potato interaction

The oomycete pathogen Phytophthora infestans secretes cystatin-like effector proteins (EPICs) that inhibit secreted host proteases during infection. We recently found that the C14 protease is a relevant target of EPICs and that this protease is under diversifying selection in wild potato species with which P. infestans has coevolved. Here we generated a model of the EPIC-C14 complex based on cystatin-papain crystal structures and discovered three regions where variant residues in C14 might be the result of an arms race between enzyme and inhibitor at the plant-pathogen interface.

An effector-targeted protease contributes to defense against Phytophthora infestans and is under diversifying selection in natural hosts

Since the leaf apoplast is a primary habitat for many plant pathogens, apoplastic proteins are potent, ancient targets for apoplastic effectors secreted by plant pathogens. So far, however, only a few apoplastic effector targets have been identified and characterized. Here, we discovered that the papain-like cysteine protease C14 is a new common target of EPIC1 and EPIC2B, two apoplastic, cystatin-like proteins secreted by the potato (Solanum tuberosum) late blight pathogen Phytophthora infestans. C14 is a secreted protease of tomato (Solanum lycopersicum) and potato typified by a carboxyl-terminal granulin domain. The EPIC-C14 interaction occurs at a wide pH range and is stronger than the previously described interactions of EPICs with tomato defense proteases PIP1 and RCR3. The selectivity of the EPICs is also different when compared with the AVR2 effector of the fungal tomato pathogen Cladosporium fulvum, which targets PIP1 and RCR3, and only at apoplastic pH. Importantly, silencing of C14 increased susceptibility to P. infestans, demonstrating that this protease plays a role in pathogen defense. Although C14 is under conservative selection in tomato, it is under diversifying selection in wild potato species (Solanum demissum, Solanum verrucosum, and Solanum stoliniferum) that are the natural hosts of P. infestans. These data reveal a novel effector target in the apoplast that contributes to immunity and is under diversifying selection, but only in the natural host of the pathogen.

Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping

Comparative genetic linkage mapping using a common set of DNA markers in related species is an important methodology in plant genome research. Here, we demonstrate a comparative fluorescence in situ hybridization (FISH) mapping strategy in plants. A set of 13 bacterial artificial chromosome clones spanning the entire length of potato chromosome 6 was used for pachytene chromosome-based FISH mapping in seven distantly related Solanum species including potato, tomato, and eggplant. We discovered one paracentric inversion and one pericentric inversion within specific lineages of these species. The comparative FISH mapping data revealed the ancestral structure of this chromosome. We demonstrate that comparative FISH mapping is an efficient and powerful methodology to study chromosomal evolution among plant species diverged for up to 12 million years.

Mitochondrial DNA variation in cultivated and wild potato species (Solanum spp.)

The European cultivated potato, Solanum tuberosum subsp. tuberosum, has 6 related cultivated species and more than 200 wild relatives. In Solanum spp., studies of cytoplasmic organelles have been mainly confined to the plastid DNA composition of cultivated and wild species. In this study, 53 genotypes of 30 potato species belonging to the subsections Estolonifera and Potatoe, 2 tomato species, and a black nightshade genotype were examined using PCR markers to evaluate mitochondrial DNA diversity and assess whether mtDNA variability was correlated with series classification, geographical origin, ploidy, and endosperm balance number (EBN). The markers used revealed interspecific mtDNA variability in Solanum spp. and identified 13 different haplotypes. Intraspecific variability was also observed in a few species and genomic regions. Cluster analysis allowed arrangement of the 13 haplotypes into 7 subgroups, and statistical association tests showed significant relationships between mitochondrial patterns detected by molecular analysis and ploidy, EBN, and geographical origin. On the whole, the evolutionary patterns for the genomic regions analyzed reflected the species relationships established on the basis of morphological and molecular (nuclear and plastidial DNA) data. The mtDNA variability shown is also important for better characterization of genetic resources for potato breeding.

Origin and evolution of Andigena potatoes revealed by chloroplast and nuclear DNA markers

Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are important, native-farmer-selected cultivars in the Andes, which form a primary gene pool for improving a worldwide grown potato (S. tuberosum subsp. tuberosum). To elucidate the origin of Andigena, 196 Andigena accessions were compared with 301 accessions of 33 closely related cultivated and wild species using several types of chloroplast DNA (ctDNA) markers and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Fourteen ctDNA types (haplotypes) and 115 RFLP bands were detected in Andigena, of which the main haplotypes and frequent RFLP bands were mostly shared with a cultivated diploid species, S. stenotomum Juz. et Buk. Principal component analysis of nDNA polymorphisms revealed a progressive and continuous variation from Peruvian wild species with C-type ctDNA to a group of wild species having S-type ctDNA in its variation range (S. bukasovii, S. canasense, S. candolleanum, and S. multidissectum), to cultivated diploid potatoes (S. phureja and S. stenotomum), and to cultivated tetraploid potatoes (Andigena and Chilean S. tuberosum subsp. tuberosum). These results suggest that the initial Andigena population arose with multiple origins exclusively from S. stenotomum. The overall evolutionary process toward the present-day Andigena was discussed.

Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.)

Microsatellites, or simple sequence repeats (SSRs) are very useful molecular markers for a number of plant species. They are commonly used in cultivar identification, plant variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Early development of SSRs was hampered by the high cost of library screening and clone sequencing. Currently, large public SSR datasets exist for many crop species, but the number of publicly available, mapped SSRs for potato is relatively low (approximately 100). We have utilized a database mining approach to identify SSR-containing sequences in The Institute For Genomic Research Potato Gene Index database (http://www.tigr.org), focusing on sequences with size polymorphisms present in this dataset. Ninety-four primer pairs flanking SSR sequences were synthesized and used to amplify potato DNA. This study rendered 61 useful SSRs that were located in pre-existing genetic maps, fingerprinted in a set of 30 cultivars from South America, North America, and Europe or a combination thereof. The high proportion of success (65%) of expressed sequence tag-derived SSRs obtained in this work validates the use of transcribed sequences as a source of markers. These markers will be useful for genetic mapping, taxonomic studies, marker-assisted selection, and cultivar identification.

Nuclear and chloroplast DNA differentiation in Andean potatoes

Over 3500 accessions of Andean landraces have been known in potato, classified into 7 cultivated species ranging from 2x to 5x (Hawkes 1990). Chloroplast DNA (ctDNA), distinguished into T, W, C, S, and A types, showed extensive overlaps in their frequencies among cultivated species and between cultivated and putative ancestral wild species. In this study, 76 accessions of cultivated and 19 accessions of wild species were evaluated for ctDNA types and examined by ctDNA high-resolution markers (ctDNA microsatellites and H3 marker) and nuclear DNA restriction fragment length polymorphisms (RFLPs). ctDNA high-resolution markers identified 25 different ctDNA haplotypes. The S- and A-type ctDNAs were discriminated as unique haplotypes from 12 haplotypes having C-type ctDNA and T-type ctDNA from 10 haplotypes having W-type ctDNA. Differences among ctDNA types were strongly correlated with those of ctDNA high-resolution markers (r = 0.822). Differentiation between W-type ctDNA and C-, S-, and A-type ctDNAs was supported by nDNA RFLPs in most species except for those of recent or immediate hybrid origin. However, differentiation among C-, S-, and A-type ctDNAs was not clearly supported by nDNA RFLPs, suggesting that frequent genetic exchange occurred among them and (or) they shared the same gene pool owing to common ancestry.

Molecular evolution of rDNA external transcribed spacer and phylogeny of sect. Petota (genus Solanum)

The 5(') external transcribed spacer (ETS) region of ribosomal DNA of 30 species of Solanum sect. Petota and the European Solanum dulcamara were compared. Two structural elements can be distinguished in the ETS: (i). a variable region (VR), demonstrating significant structural rearrangements and (ii). a conservative region (CR), evolving mainly by base substitutions. In VR, a conservative element (CE) with similarity to the ETS of distantly related Nicotiana is present. The ancestral organization of ETS (variant A) was found for non-tuber-bearing species of ser. Etuberosa, tuber-bearing wild potatoes of Central American ser. Bulbocastana, Pinnatisecta, and Polyadenia and S. dulcamara. Duplication of CE took place in the ETS of species from ser. Commersoniana and Circaeifolia (variant B). South American diploids and Mexican polyploids from superser. Rotata also possess two CE, and additionally two duplications around CE1 are present in VR (variant C). Three major lineages could be distinguished: non-tuber-bearing species of ser. Etuberosa, tuber-bearing Central American diploids and all South American species radiated from a common ancestor at early stages of evolution, indicating a South American origin of the tuber-bearing species. Later, Central and South American diploids evolved further as independent lineages. South American species form a monophyletic group composed of series with both stellata and rotata flower morphology. Solanum commersonii represents a sister taxon for all rotata species, whereas ser. Circaeifolia diverged earlier. Two main groups, C1 and C2, may be distinguished for species possessing ETS variant C. C1 contains ser. Megistacroloba, Conicibaccata, Maglia, and Acaulia, whereas all diploids of ser. Tuberosa are combined into C2. A closer relationship of Solanum chacoense (ser. Yungasensa) to the C2 group was found. The origin of polyploid species Solanum maglia, Solanum acaule, Solanum tuberosum, Solanum iopetalum, and Solanum demissum is discussed.

Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses

Three genomic libraries were constructed using a mixture of DNA from Solanum phureja Juz. & Buk., and S. chacoense Bitt. Two of the libraries were enriched for ATT and GT repeats (a 27-fold enrichment was achieved). In total, 3500 clones of the conventional library, 1000 of the library enriched for ATT, and 12 000 of the one enriched for GT were screened with five different repeat motifs, and a total of 18 primer pairs was obtained. Another group of 12 primer pairs was obtained from the SSR-containing sequences in the public databases (18 SSR-containing sequences were utilized). From among 30 newly developed primer pairs, 12 previously published ones, and 12 pairs developed for tomato, 7 were used to identify 12 different potato cultivars and introductions, and 12 were used to study phylogenetic distance among seven wild and cultivated potato species. Two SSR markers were sufficient to discriminate the 12 cultivars. The mean number of alleles per polymorphic locus was 5 for the 12 cultivars and 4.5 for the seven species. The results obtained in this study confirm those achieved in similar studies in other plant species regarding the abundance and use of SSR markers in identifying species and cultivars.Key words: Solanum, simple sequence repeats, SSRs, genomic library.

Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers

Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Three DNA marker techniques, restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and inter simple sequence repeat amplification (ISSR), were employed to analyze 22 accessions belonging to 5 species of Eleusine. An 8 probe--3 enzyme RFLP combination, 18 RAPD primers, and 6 ISSR primers, respectively, revealed 14, 10, and 26% polymorphism in 17 accessions of E. coracana from Africa and Asia. These results indicated a very low level of DNA sequence variability in the finger millets but did allow each line to be distinguished. The different Eleusine species could be easily identified by DNA marker technology and the 16% intraspecific polymorphism exhibited by the two analyzed accessions of E. floccifolia suggested a much higher level of diversity in this species than in E. coracana. Between species, E. coracana and E. indica shared the most markers, while E. indica and E. tristachya shared a considerable number of markers, indicating that these three species form a close genetic assemblage within the Eleusine. Eleusine floccifolia and E. compressa were found to be the most divergent among the species examined. Comparison of RFLP, RAPD, and ISSR technologies, in terms of the quantity and quality of data output, indicated that ISSRs are particularly promising for the analysis of plant genome diversity.

Successive domestication and evolution of the Andean potatoes as revealed by chloroplast DNA restriction endonuclease analysis

Five chloroplast DNA (ctDNA) types (W, T, C, S, and A) have previously been identified in the Andean tetraploid cultivated potatoes (Solanum tuberosum ssp. andigena) and three types (C, S, and A) in diploid cultivated potatoes (S. stenotomum). In this study, ctDNA types were determined for an additional 35 accessions of S. stenotomum and 97 accessions of putative ancestral wild species (15 of S. brevicaule, 26 of S. bukasovii, 4 of S. candolleanum, 25 of S. canasense, 17 of S. leptophyes, and 10 of S. multidissectum). The first five ctDNA types were also identified in S. stenotomum. The wild species were also polymorphic for ctDNA types except for S. brevicaule, which had only W-type ctDNA. T-type ctDNA was not found in any of the wild species and could have originated from W-type ctDNA after S. stenotomum arose. The other types of ctDNA evolved in wild species. The geographical distribution of each ctDNA type indicated that A-type ctDNA arose in central Peru and T-type ctDNA in the Bolivia-Argentine boundary. It is implied that potatoes were successively domesticated and that, in parallel, several wild species were differentiated from time to time and place to place from the 'ancestral species' complex. Subsequent sexual polyploidization formed a wide ctDNA diversity among the Andean tetraploid potatoes, and selection from them formed the limited ctDNA diversity found in Chilean tetraploid potatoes (ssp. tuberosum).

Similarities and relationships among populations of the bulb onion as estimated by nuclear RFLPs

Random nuclear restriction fragment length polymorphisms (RFLPs) were used to assess similarities and relationships among open-pollinated (OP) populations of the cultivated bulb onion (Allium cepa). Seventeen OP populations and 2 inbreds of contrasting daylength response [termed by convention as long (LD) and short (SD) day], 1 shallot (A. cepa var. ascalonicum), and one cultivar of bunching onion (Allium fistulosum) were examined with 104 cDNA clones and two to four restriction enzymes. Sixty (58%) clones detected at least 1 polymorphic fragment scorable among the OP populations and were used for analyses. The average number of polymorphic fragments per polymorphic probe-enzyme combination was 1.9, reflecting that numerous monomorphic fragments were usually present. Similarities were estimated as the proportion of polymorphic fragments shared by 2 populations. Average similarity values among LD, among SD, and between LD and SD OP populations were 0.79, 0.67, and 0.68, respectively. Relationships among the OP populations were estimated by parsimony, cluster analysis of similarities using the unweighted-pair-group method (UPGMA), and multivariate analysis using principle components. Parsimony analysis generated a strict consensus tree that grouped all but 1 LD onion with unresolved relationships to the SD OP populations. The UPGMA analysis placed together the LD storage OP populations. Principal component analysis grouped all but 2 LD onions; the other OP populations were dispersed. The results suggest that LD and SD onions do not represent distinct germ plasm, but that LD storage onions represent a derived group selected for production at higher latitudes. If it is assumed that the sampled populations are representative of all onion OP populations, the lower similarities among SD OP populations indicate that their collection and maintenance in germ plasm collections is important for the preservation of genetic diversity.

Isolation, characterization and RFLP linkage mapping of a DNA repeat family of Solanum spegazzinii by which chromosome ends can be localized on the genetic map of potato

In a random sample of 2263 cloned genomic DNA fragments of the wild potato species Solanum spegazzinii six related, highly repetitive fragments (SPG repeat family) were identified that were present in much higher copy numbers in S. spegazzinii when compared with the closely related cultivated potato S. tuberosum. The SPG repeat family was organized in long arrays of multiple copies. Cross hybridization experiments with 29 wild and cultivated Solanum species and with the related tomato showed specificity of the SPG repeat family for tuber-bearing Solanum species. Among tuber bearing Solanum species a high degree of variation was observed for restriction fragment length and copy number. The variation in copy number was not correlated with established taxonomic relationships between tuber-bearing Solanum species. DNA sequence analysis revealed a subrepeat structure of 120-140 base pairs embedded in longer repeat units of variable length. Length polymorphisms between highly repeated restriction fragments detected by the SPG probes were used for segregation- and linkage analysis in four mapping populations of potato, for which RFLP maps had been constructed. Twelve loci were identified, eleven of which mapped to the distal ends of nine linkage groups. All the evidence suggested that the SPG repeat family represents a satellite repeat members of which are localized in the subtelomeric region of potato chromosomes. The SPG repeat family could be used, therefore, for completing the genetic map of potato.

Estimation of sampling variance of molecular marker data using the bootstrap procedure

Knowledge of genetic relationships among genotypes is useful in a plant breeding program because it permits the organization of germplasm and provides for more efficient sampling. The genetic distance (GD) among genotypes can be estimated using random restriction fragment length polymorphisms (RFLPs) as molecular markers. Knowledge of the sampling variance associated with RFLP markers is needed to determine how many markers are required for a given level of precision in the estimate of GD. The sampling variance for GD among all pairs of 37 maize (Z. mays L.) inbred lines was estimated from 1202 RFLPs. The 1202 polymorphisms were generated from 251 enzyme-probe combinations (EPC). The sampling variance was used to determine how large a sample of RFLPs was required to provide a given level of precision. The coefficient of variation (CV) associated with GD has a nearly linear relationship between its expected standard deviation and mean. The magnitude of the decrease in the mean CV for GD with increasing numbers of bands was dependent upon the sampling unit; e.g., individual polymorphic bands vs EPC, and the degree of relatedness among the inbreds compared. The rate of reduction in mean CV with increasing sample size was the same regardless of the restriction enzyme used, BamHI, EcoRI or HindIII, when the bootstrap sampling units were individual polymorphic bands. In constrast, although the rate of reduction (slopes) was the same, the intercepts of the mean CVs were different when EPCs were used as the bootstrap sampling unit. This difference was due to the higher number of bands per EPC in BamHI (4.94) compared with EcoRI (4.83) and HindIII (4.63).

PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation to potato diseases

Using a sequenced pectate lyase-encoding gene (pel gene), we developed a PCR test for Erwinia carotovora. A set of primers allowed the amplification of a 434-bp fragment in E. carotovora strains. Among the 89 E. carotovora strains tested, only the Erwinia carotovora subsp. betavasculorum strains were not detected. A restriction fragment length polymorphism (RFLP) study was undertaken on the amplified fragment with seven endonucleases. The Sau3AI digestion pattern specifically identified the Erwinia carotovora subsp. atroseptica strains, and the whole set of data identified the Erwinia carotovora subsp. wasabiae strains. However, Erwinia carotovora subsp. carotovora and Erwinia carotovora subsp. odorifera could not be separated. Phenetic and phylogenic analyses of RFLP results showed E. carotovora subsp. atroseptica as a homogeneous group while E. carotovora subsp. carotovora and E. carotovora subsp. odorifera strains exhibited a genetic diversity that may result from a nonmonophyletic origin. The use of RFLP on amplified fragments in epidemiology and for diagnosis is discussed.

Phylogenetic relationships between cultivated and wild species of the genusBeta revealed by DNA "fingerprinting"

Forty-one accessions of the genusBeta representing wild and cultivated species of all sections were analyzed by DNA "fingerprinting". Four sugar beet minisatellite DNA probes revealed characteristic banding patterns with Southern-hybridizedBeta DNA restricted withHindIII. A total of 111 polymorphic RFLP bands were scored across all accessions. Cluster analysis based on genetic similarity estimates for all 820 combinations of accessions revealed the following results. (1) All accessions could unambiguously be identified by a characteristic RFLP banding pattern. (2) The sugar beet cultivars examined displayed a low level of genetic diversity; they showed high similarity toB. Vulgaris ssp.maritima but low genetic similarity to the other wild species of section I. (3) In most cases, the present taxonomic classification of the genusBeta was confirmed. Species of sections II, III, and IV were clearly distinguishable from those of section I except forB. Macrocarpa, which showed high similarity to wild species of section II. In a second experiment, 108 single-copy RFLP probes from sugar beet were Southern hybridized withB. procumbens DNA. A surprisingly low degree of homology (34%) was found. The results are discussed with regard to the taxonomic classification of the genusBeta.

Molecular taxonomic relationships in the genus Vigna based on RFLP analysis

The taxonomy of the genus Vigna has been primarily based on morphological attributes. We have used 27 genomic clones from soybean, common bean, mungbean and cowpea to examine restriction fragment length polymorphism (RFLP) among 44 accessions of different species belonging to four subgenera of the genus Vigna. One accession each of common bean (Phaseolus vulgaris) and soybean (Glycine max) was included in the study. Total DNA from the various genotypes was digested with one restriction enzyme (Eco RV). Results of a numerical taxonomic analysis showed a high level of genetic variation within the genus with a remarkably higher amount of variation associated with Vigna sp. from Africa relative to those from Asia. The distinctness of the Asiatic grams in subgenus Ceratotropis, cowpea in section Catiang, bambara groundnut (V. subterranean) and members of the subgenus Plectotropis was elucidated by this study. Members of the subgenus Plectotropis were closer in genome homology to those of subgenus Vigna section Catiang than to those of subgenus Ceratotropis. The relative positions of some genotypes to one another on the dendrogram and minimum spanning tree were discussed in regard to hybridisations aimed generating well-saturated genomic maps and interspecies transfer of desirable genes.

Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars

Highly repeated DNA of potato (Solanum sp.) was characterized by cloning various major repeated elements of the nuclear genome. The percentage of the nuclear genome of the specific fractions and the restriction enzyme patterns were determined in order to show the distribution and organization of the respective repeats in the genome of Solanum tuberosum cultivars, dihaploid breeding lines and in wild species of Solanum. Several of the clones obtained were represented in a high copy number but showed no informative RFLP patterns. More information was gained from 'restriction satellite' repeats. The clone pR1T320 was found to contain satellite repeats (360 bp in length) that are proportionally present in the genome of all Solanum species at frequencies, between 0.5% and 2.6% and which are differently organized. This repeat was also found in the genera Lycopersicon, Datura and Nicotiana. With various restriction enzymes characteristic RFLP patterns were detected. A more or less genus-specific element for Solanum was the 183-bp repeat (clone pSA287; between 0.2-0.4% of the nuclear genome) that was present in the majority of the Solanum species analyzed except S. kurtzianum, S. bulbocastanum and S. pinnatisectum. In a few wild species (prominently in S. kurtzianum, S. demissum and S. acaule) a specific repeat type was detected (clone pSDT382; repeat length approximately 370 bp) that could be used to trace the wild species introduced into S. tuberosum cultivars. The repeats analyzed together with the 18S, 5.8S and 25S ribosomal DNA (1.9-5.2%, corresponding to 1800-5500 rDNA copies) comprised approximately 4-7% of the Solanum genome.

Genetic variation in agronomically important species of Stylosanthes determined using random amplified polymorphic DNA markers

Random amplified polymorphic DNA (RAPD) markers were generated from 20 cultivars and accessions representing four agronomically important species of Stylosanthes, S. scabra, S. hamata, S. guianensis, and S. humilis. Approximately 200 fragments generated by 22 primers of arbitrary sequence were used to assess the level of DNA variation. Relatively low levels of polymorphism (0-16% of total bands in pairwise comparisons) were found within each species, while polymorphisms between the species were much higher (up to 46%). Very few polymorphisms (0-2%) were detected between the individuals of the same cultivar or accession. A phenogram of relationships among the species was constructed based on band sharing. Four main clusters corresponding to each species were readily distinguished on this phenogram. The allotetraploid species S. hamata and its putative diploid progenitor, S. humilis, were more similar to each other than to S. scabra and S. guianensis. No variation in RAPD markers was found between the two commercial S. hamata cvs 'Verano' and 'Amiga'. Cultivar 'Oxley' in S. guianensis was considerably different from the other cultivars and accessions of this species. The phylogenetic distinctions obtained with RAPDs were in agreement with other studies from morphology, cytology, and enzyme electrophoresis. The low level of polymorphisms observed within each species suggested that interspecific crosses may be a better vehicle for the construction of RAPD linkage maps in Stylosanthes.

RFLP analysis of the wild potato species, Solanum acaule Bitter (Solanum sect. Petota)

Intraspecific variation of a wild potato species, Solanum acaule Bitt., was analyzed by RFLPs of genomic DNA. One hundred and five accessions were selected throughout the distribution area, including all subspecies, i.e., ssp. albicans (hexaploid), ssp. punae (tetraploid), ssp. acaule (tetraploid) and ssp. aemulans (tetraploid). Twenty-seven low-copy DNA clones (probes) were Southern hybridized with EcoRI, EcoRV, HindIII, and XbaI digests of total DNA of all accessions. In total, 238 RFLPs were detected from 94 enzyme x probe combinations. Among them, 49 RFLPs were specific to ssp. albicans, suggesting that the additional third genome is distinct from its two other genomes. RFLPs between and within subspecies were analyzed by principal component analysis. DNA similarities between subspecies coincided with a former taxonomic treatment in the sense that ssp. albicans is the most distantly related to ssp. acaule and ssp. aemulans is distantly related. Subspecies acaule and ssp. punae were indistinguishable. In addition, RFLPs could be used to distinguish groups within subspecies. Subspecies aemulans, confined to Argentina, was divided into two populations, one from the province of La Rioja and the other from the province of Jujuy. In ssp. acaule, some accessions from the southernmost distribution area were clearly distinguishable, while the others varied continuously, showing a geographical cline from Peru to Argentina.

RFLP-based phylogeny of Musa species in Papua New Guinea

Random genomic probes were used to detect restriction fragment length polymorphisms (RFLPs) in 26 accessions of Musa representing eight species from Papua New Guinea (PNG), M. textilis, M. jackeyi and one accession of Ensete. Ninety-eight phylogenetically informative characters were scored and analyzed cladistically and phenetically. Results generally agreed with previous morphology-based phylogenetic analyses. However, the closest wild relative of the edible M. fehi (fe'i banana) appears to be M. lolodensis. Musa angustigemma is sister species with M. boman and M. jackeyi and is distinct from M. peekelii, with which it is often united. Musa boman is unambiguously placed in section Australimusa. The diploid parthenocarpic landraces of section Musa unique to PNG are closely related to, but apparently distinct from, M. acuminata ssp. banksii. The evolution of the fe'i bananas and the M. acuminata-derived diploid landraces of PNG are discussed.

Restriction fragment length polymorphism (RFLP)-based phylogenetic analysis of Musa

Random genomic probes were used to detect RFLPs in 19 Musa species and subspecies. A total of 89 phylogenetically informative alleles were scored and analyzed cladistically and phenetically. Results were in general agreement with morphology-based phylogenetic analyses, with the following exceptions: our data unambiguously places M. boman in section Australimusa, and indicates M. beccarii is very closely related to M. acuminata. Additionally, no support was found for the separation of section Rhodochlamys from section Musa. A comparison of morphology-based and RFLP-based phylogenetic analyses is presented.

Taxonomic and evolutionary implications of the Endosperm Balance Number hypothesis in potatoes

The Endosperm Balance Number (EBN) hypothesis can explain to a considerable degree the crossability between tuber-bearing Solanum species. It has been shown to be genetically controlled and is dosage dependent. There is a good correlation between EBN and the postulated evolution and present taxonomy of potatoes. The primitive white stellate-flowered species from Mexico are 1EBN, and this condition is also found in species from South America with flowers of the same colour and shape. The evolution of a rotate corolla seems to be correlated with 2EBN. It is postulated that the 2EBN state arose as a reproductive isolating mechanism in South America. The taxonomic and evolutionary implications of the EBN hypothesis are discussed.

Similarity of maize and sorghum genomes as revealed by maize RFLP probes

Densely saturated genetic maps of neutral genetic markers are a prerequisite either for plant breeding programs to improve quantitative traits in crops or for evolutionary studies. cDNA and genomic clones from maize were utilized to initiate the construction of a RFLP linkage map in Sorghum bicolor. To this purpose, an F2 population was produced from starting parental lines IS 18729 (USA) and IS 24756 (Nigeria) that were differentiated with regard to many morphological and agronomical traits. A total of 159 maize clones were hybridized to the genomic DNA of the two parents in order to detect polymorphism: 154 probes hybridized to sorghum and 58 out of these were polymorphic. In almost all of the cases hybridization patterns were similar between maize and sorghum. The analysis of the segregation of 35 polymorphic clones in an F2 population of 149 individuals yielded five linkage groups. The three principal ones recall regions of maize chromosomes 1, 3 and 5: in general, colinearity was maintained. A possible inversion, involving a long region of maize chromosome 3, was detected. Simulations were also performed to empirically obtain a value for the lowest number of individuals of the F2 population needed to obtain the same linkage data.

Construction of an RFLP map of barley

In order to construct an RFLP map of barley, two populations were analyzed using 251 genomic and cDNA markers: one population comprised 71 F1 antherderived double haploid (DH) individuals of an intraspecific cross (IGRI x FRANKA), and the other 135 individuals of an interspecific F2/F3 progeny (VADA x H. spontaneum). The distribution of nonrepetitive clones over the seven barley chromosomes revealed a maximum for chromosome 2H and a minimum for 6H. The polymorphism of the interspecific progeny (76%) clearly exceeded that of the intraspecific progeny (26%) although, based on their pedigrees, IGRI and FRANKA are only distantly related. The contribution of individual chromosomes of the DH parents to the overall polymorphism varied between 8% and 50%. A significant portion (44% versus 10% of the interspecific progeny) of the markers mapped on the DH offspring showed distorted segregation, caused mainly by the prevalence of variants originating from the parent that better responded to in vitro culture (IGRI). In contrast to the interspecific map, probes displaying skewed segregation were clustered on the DH map on discrete segments. The colinear arrangement of both maps covers a distance of 1,453 cM and identifies regions of varying map distances.

Plant genome studies: restriction fragment length polymorphism and chromosome mapping information

The detection of sequence variation with restriction fragment length polymorphisms is advancing our knowledge of plant genetics on several fronts. In the past year, there has been progress in genetic map construction, phylogeny studies, and the dissection of multigenic traits. In addition, new methods that are independent of restriction sites are being developed for polymorphism detection.