Genetic diversity of the Andean tetraploid cultivated potato (Solanum tuberosum L. subsp. andigena Hawkes) evaluated by chloroplast and nuclear DNA markers.

Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are native farmer-selected important cultivars that form a primary gene pool of the common potato (Solanum tuberosum L. subsp. tuberosum). The genetic diversity of 185 Andigena accessions and 6 Chilean native potatoes (S. tuberosum subsp. tuberosum) was studied using chloroplast DNA (ctDNA) microsatellites and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Andigena potatoes had 14 ctDNA haplotypes and showed higher variability in the central Andes, particularly in Bolivia, whereas those in the northern regions of the distribution area were remarkably uniform with A1 ctDNA and Chilean subsp. tuberosum with T ctDNA. Most of 123 clearly scored RFLP bands using 30 single-copy probes were randomly distributed throughout the distribution area and proved the same gene pool shared among these widely collected accessions. Nevertheless, the geographic trend of the nDNA differentiation from north to south along the Andes and the correlated differentiation between nDNA and ctDNA (r = 0.120) could also be revealed by canonical variates analysis. These results suggest that the genetic diversity in Andigena was brought about primarily from cultivated diploid species but considerably modified through sexual polyploidization and intervarietal and (or) introgressive hybridization and long-distance dispersal of seed tubers by humans.     

Origin of chloroplast DNA diversity in the Andean potatoes

Summary Wide chloroplast DNA (ctDNA) diversity has been reported in the Andean cultivated tetraploid potato, Solanum tuberosum ssp. andigena. Andean diploid potatoes were analyzed in this study to elucidate the origin of the diverse ctDNA variation of the cultivated tetraploids. The ctDNA types of 58 cultivated diploid potatoes (S. stenotomum, S. goniocalyx and S. phureja), 35 accessions of S. sparsipilum, a diploid weed species, and 40 accessions of the wild or weed species, S. chacoense, were determined based on ctDNA restriction fragment patterns of BamHI, HindIII and PvuII. Several different ctDNA types were found in the cultivated potatoes as well as in weed and wild potato species; thus, intraspecific ctDNA variation may be common in both wild and cultivated potato species and perhaps in the higher plant kingdom as a whole. The ctDNA variation range of cultivated diploid potatoes was similar to that of the tetraploid potatoes, suggesting that the ctDNA diversity of the tetraploid potato could have been introduced from cultivated diploid potatoes. This provided further evidence that the Andean cultivated tetraploid potato, ssp. andigena, could have arisen many times from the cultivated diploid populations. The diverse but conserved ctDNA variation noted in the Andean potatoes may have occurred in the early stage of species differentiation of South American tuber-bearing Solanums.     

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.     

Reclassification of landrace populations of cultivated potatoes (Solanum sect. Petota)

Cultivated potatoes have been classified as species under the International Code of Botanical Nomenclature (ICBN) and as cultivar-groups under the International Code of Nomenclature of Cultivated Plants (ICNCP); both classifications are still widely used. This study examines morphological support for the classification of landrace populations of cultivated potatoes, using representatives of all seven species and most subspecies as outlined in the latest taxonomic treatment. These taxa are S. ajanhuiri, S. chaucha, S. curtilobum, S. juzepczukii, S. phureja subsp. phureja, S. stenotomum subsp. stenotomum, S. stenotomum subsp. goniocalyx, S. tuberosum subsp. andigenum, and S. tuberosum subsp. tuberosum. The results show some phenetic support for S. ajanhuiri, S. chaucha, S. curtilobum, S. juzepczukii, and S. tuberosum subsp. tuberosum, but little support for the other taxa. Most morphological support is by using a suite of characters, all of which are shared with other taxa (polythetic support). These results, combined with their likely hybrid origins, multiple origins, evolutionary dynamics of continuing hybridization, and our classification philosophy, leads us to recognize all landrace populations of cultivated potatoes as a single species, S. tuberosum, with the eight cultivar-groups: Ajanhuiri Group, Andigenum Group, Chaucha Group, Chilotanum Group, Curtilobum Group, Juzepczukii Group, Phureja Group, and Stenotomum Group. We defer classification of modern cultivars, traditionally classified in Tuberosum Group, to a later study.     

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).Hawkes' (1990) classification system is tentatively adopted throughout this text. Synonyms indicated by Hawkes (1990) for the species names described by various authors are presented in parentheses.     

Evolutionary trends of microsatellites during the speciation process and phylogenetic relationships within the genus Secale

Eleven weedy or wild species or subspecies of the genus Secale L. were compared with a set of cultivated rye accessions, based on inter-simple sequence repeat (ISSR) markers to analyze their phylogenetic relationships. A total of 846 bands were amplified from reactions using 12 screening primers, including 79 loci with a mean of 10.1 alleles per locus. The number of amplified bands for each primer ranged from 12 to 134, with a mean of 70.5 amplified bands per primer. The presence and distribution of amplified bands in different accessions demonstrate that a rapid evolutionary trend of microsatellite repeats occurred during the speciation process from the perennial wild form to annual cultivated rye. In addition, variation, amplification, and deletion of microsatellites in genomes revealed phylogenetic relationships in the genus Secale. Analysis of the presence, number, and distribution of amplified bands in genomes, as well as the comparison with genetic similarity (GS) indices based on ISSR, indicate that Secale strictum subsp. africanum (Stapf) Hammer, Secale strictum anatolicum (Boiss.) Hammer, Secale sylvestre Host, and Secale strictum subsp. strictum (C. Presl) Hammer emerged in succession from a common ancestor of Secale following geographic separation and genetic differentiation. The annual weedy rye evolved from S. strictum subsp. strictum, which was domesticated as present-day cultivated rye. Data from ISSR analyses separated all investigated accessions of the genus Secale into three distinct groups. These results support the division of the genus Secale into three species: the annual wild species S. sylvestre; the perennial wild species S. strictum, including several differential subspecies forms such as strictum, africanum, and anatolicum; and S. cereale, including cultivated and weedy rye as subspecies forms.     

Elucidation of the evolution and taxonomy of cultivated potatoes with electrophoresis

Summary A recently developed polyacrylamide gel electrophoresis technique for tuber proteins is used to help elucidate the evolution and taxonomy of some cultivated potatoes. The results substantiate the theory that Group Tuberosum evolved from Group Andigena, that Group Andigena evolved from a cultivated diploid × wild diploid hybrid, and that Group Phureja evolved from Group Stenotomum. Furthermore, the results suggest these groups are closely enough related to merit classification within a single species.Scientific Journal Series Article 10,172 of the Minnesota Agricultural Experiment Station     

Production of inbred progenies of diploid potatoes using an S-locus inhibitor (Sli) gene, and their characterization.

To develop inbred lines from self-incompatible, cultivated diploid potatoes, an S-locus inhibitor (Sli) gene derived from a self-compatible variant of a wild potato species, Solanum chacoense, was incorporated into various cultivated diploid potatoes. The progeny was selfed twice by the action of the Sli gene to obtain 74 S2 inbred clones belonging to 8 families. More than 40% of them were either non-flowering or pollen sterile. Among the pollen fertile clones, self-compatible clones occurred with a much lower frequency (20.9%) than expected (83.3%). The result demonstrated that self-compatibility was introduced and expressed in the gene pool of cultivated diploid potatoes by an action of the Sli gene, although serious inbreeding depression associated with selfing occurred. The genotypes of S2 inbreds were surveyed using 46 S. chacoense-specific RFLP (restriction fragment length polymorphism) markers covering the whole potato genome. More than half of the markers (67.4%) showed distorted segregation. Particularly, all markers on chromosome 12 were overrepresented in the S2 inbreds. This confirms our earlier finding that the Sli gene locates on chromosome 12 and the alleles linked with this gene are preferentially transmitted because of its essential requirement for selfing.     

Allozyme variability and phylogenetic relationships in the cultivated potato (Solanum tuberosum) and related species

Gene frequencies at 13 isozyme loci were determined in three South American taxa of cultivated potatoes [the diploid group (gp.) Stenotomum, the diploid subgroups (subgp.) Goniocalyx, and the tetraploid gp. Andigena ofS. tuberosum], in the diploid weed speciesS. sparsipilum, and in most of the main cultivars now raised in the Northern Hemisphere (the tetraploid gp. Tuberosum ofS. tuberosum). High levels of genetic variability (mean number of alleles per locus, percentage of polymorphic loci, and mean heterozygosity) were detected, being higher in tetraploid potatoes. An equilibrium among the evolutionary factors which increase genetic variability and artificial selection for maximum yield would explain the high uniformity of heterozygosity values we observed in both Andigena (0.36 ± 0.02) and Tuberosum (0.38 ± 0.01) cultivars.—The low value of genetic distance (D = 0.044) between Stenotomum and Goniocalyx does not support the status of species forS. goniocalyx.—In most isozyme loci, the electromorphs of gp. Andigena were a combination of those found in both gp. Stenotomum andS. sparsipilum, suggesting an amphidiploid origin of gp. Andigena from that two diploid taxa. The presence in Andigena of unique electromorphs, which were lacking in both gp. Stenotomum andS. sparsipilum, suggests that other diploid species could be also implied in the origin of tetraploid Andean potatoes. Furthermore, since Andigena were more related to Stenotomum (D = 0.052) than toS. sparsipilum (D = 0.241), the autopolyploidization of Stenotomum individuals and the subsequent hybridization with gp. Andigena may also have occurred. Thus, our study suggests a multiple origin (amphidiploidy, autoploidy, and hybridization at tetraploid level) of gp. Andigena.—Most of the electromorphs of gp. Tuberosum were also found in gp. Andigena; both the direct derivation of that group from the Andean tetraploid potatoes and the repeated introgression provided by breeding programmes could explain this result. However, the allele c of Pgm-B, present in 30 out of 76 Tuberosum cultivars from Northern Hemisphere as well as in 3 Chilean Tuberosum cultivars, lacks in the 258 Andigena genotypes sampled, suggesting that Chilean germplasm could have taken part in the origin of at least the 39% of the potato cultivars from Europe and North America analyzed here.—The distanceWagner procedure provides an estimate of a 30% of heterogeneity in the evolutionary divergence shown by different groups of cultivated potatoes. Diploid groups show a higher (22.5%) evolutionary rate than tetraploids, which can be attributed to both tetrasomic inheritance and facultative autofecundation that exists in Andigena and Tuberosum groups. Thus, artificial selection acting since 10000 years has not resulted in a higher rate of molecular evolution at the isozyme level in the tetraploids.     

Genetic diversity in european and Argentinian cultivated potatoes (Solanum tuberosum subsp. tuberosum) detected by inter-simple sequence repeats (ISSRs).

In this study, the use of inter-simple sequence repeats (ISSR) to assess genetic diversity between cultivated potatoes (Solanum tuberosum subsp. tuberosum) is reported. ISSR technology rapidly reveals high polymorphic fingerprints and thus determines the genetic diversity among potato cultivars. Nine primers were selected according to the number of amplified markers and the level of polymorphism detected. Three primers (GAG(CAA)5, CTG(AG)8, and (AG)8) were used to cluster the 28 potato accessions and 77 polymorphic markers were sufficient to identify all of the accessions. Among the 15 simple sequence repeat (SSR) motifs tested, the most abundant were CAA and AG. Argentinian- and European-grown potatoes were easily distinguished, with a higher level of genetic diversity among potatoes from Argentina. An ISSR study using a limited number of cultivars and very few primers clearly differentiated between all cultivars, thus ISSR was revealed to be a good tool for the genetic identification of potato and for future germplasm-management programs.     

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.     

Simple sequence repeat diversity in diploid and tetraploid Coffea species.

Thirty-four fluorescently labeled microsatellite markers were used to assess genetic diversity in a set of 30 Coffea accessions from the CENICAFE germplasm bank in Colombia. The plant material included one sample per accession of seven East African accessions representing five diploid species and 23 wild and cultivated tetraploid accessions of Coffea arabica from Africa, Indonesia, and South America. More allelic diversity was detected among the five diploid species than among the 23 tetraploid genotypes. The diploid species averaged 3.6 alleles/locus and had an average polymorphism information content (PIC) value of 0.6, whereas the wild tetraploids averaged 2.5 alleles/locus and had an average PIC value of 0.3 and the cultivated tetraploids (C. arabica cultivars) averaged 1.9 alleles/locus and had an average PIC value of 0.22. Fifty-five percent of the alleles found in the wild tetraploids were not shared with cultivated C. arabica genotypes, supporting the idea that the wild tetraploid ancestors from Ethiopia could be used productively as a source of novel genetic variation to expand the gene pool of elite C. arabica germplasm.     

Ecogeography of ploidy variation in cultivated potato (Solanum sect. Petota)

? Premise of the study: The taxonomy of cultivated potatoes has been highly controversial, with estimates of species numbers ranging from 3 to 17. Ploidy level has been one of the most important taxonomic characters to recognize cultivated potato species, containing diploid (2n = 2x = 24), triploid (2n = 3x = 36), tetraploid (2n = 4x = 48), and pentaploid (2n = 5x = 60) cultivars. We tested the environmental associations of different ploidy levels in cultivated potato species that traditionally have been recognized as Linnaean taxa to see whether, in combination with prior morphological, molecular, and crossing data, some of the ploidy variants can be recognized as distinct taxa. ? Methods: We summarize 2780 chromosome counts of landrace cultivated potatoes, provide georeferences to 2048 of them, and analyze these data for 20 environmental variables at 10-min resolution using the randomForest algorithm to explore associations with taxa and ploidy variants. ? Key results: Except for the S. tuberosum Chilotanum Group and extreme northern and southern range extensions of the Andigenum Group, it is impossible to find distinct habitats for the ploidy variants of the S. tuberosum Andigenum Group. ? Conclusions: Our distributional and ecological data, in combination with prior results from morphology, microsatellites, and crossing data, provide yet additional data to support a major reclassification of cultivated potato species. A rational, stable, and universally accepted taxonomy of this major crop plant will greatly aid all users of wild and cultivated potatoes from breeders to gene bank managers to ecologists and evolutionary biologists.     

Molecular marker analysis of 24- and 25-chromosome plants obtained from Solanum tuberosum L. subsp. andigena (2n = 4x = 48) pollinated with a Solanum phureja haploid inducer.

Clones with 24 or 25 chromosomes were obtained by pollinating an Andean cultivated tetraploid potato (Solanum tuberosum subsp. andigena clone 94H94, 2n = 4x = 48) with the Solanum phureja haploid-inducer clone 1.22. Their genetic composition was analyzed in an RAPD assay using 135 decamer primers and in an RFLP assay using 45 single-copy DNA probes. In total, 22 RAPD and 20 RFLP markers were found to be specific to S. phureja. None of these markers were found in the 24- and 25-chromosome clones. RFLP genotypes for the 45 RFLP loci were further determined for each clone. Genotypes of the 24-chromosome clones were characterized using two alleles randomly selected from four alleles of the parental tetraploid clone for almost all RFLP loci. Five 25-chromosome clones had extra alleles for all of the RFLP loci of chromosomes 4, 8, 10, 11, and 12, respectively, suggesting primary trisomy for one of these chromosomes. Clones with genotypes showing double reduction were also identified. Therefore, the obtained clones likely originated from random samples of female gametes, and hence are euhaploids or aneuhaploids of S. tuberosum subsp. andigena, strongly supporting parthenogenesis to be a primary mechanism for haploid induction in potato.     

Restriction Fragment Length Polymorphism and Random Amplified Polymorphic DNA Analysis of Chickpea Accessions

Genetic diversity analysis was carried out in chickpea accessions using restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) techniques. RFLP analysis using 26 Pst I sub-genomic clones on ten chickpea accessions in 130 probe-enzyme combinations detected polymorphism with only two clones. Pst I clones, CG 141 detected polymorphism in ICC 4918 and Pusa 209 while CG 500 detected polymorphism in Pusa 261, ILC 26 and in ILC 13326. These clones detected very few polymorphic markers. Analysis using 10 Eco RI clones on twelve chickpea accessions have shown better hybridisation signal and one clone detected polymorphism in Pusa 256. RFLP analysis of both cultivated and wild Cicer species using heterologous DNA probe Cab3C revealed polymorphism only in wild Cicer species (Cicer reticulatum L., JM 2100). RAPD analysis of 13 chickpea accessions which includes mutants of C 235 and E100Y showed greater degree of polymorphism with 1 - 5 unique DNA bands for all the accessions. Phylogenetic analysis of the RAPD data helped to group the accessions. C 235 and its mutants were found to be closely grouped while E100Y and its mutant E100Ym grouped apart. Desi and kabuli chickpea accessions however, could not be separately grouped. This revised version was published online in July 2006 with corrections to the Cover Date.     

RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species

Summary RFLP variability was studied in eight U.S. peanut cultivars, representing the four market types, and in 14 wild Arachis species accessions, using random genomic clones from a PstI library. Very low levels of RFLP variability were found among the allotetraploids, which included the U.S. cultivars and Arachis monticola, a wild species. The diploid wild species were very diverse, however. RFLP patterns of the allotetraploids were more complex than the diploids, and the two constituent genomes could usually be distinguished. On the basis of RFLP band sharing, A. ipaensis, A. duranensis, and A. spegazzinii appeared most closely related to the diploid progenitor species of the allotetraploids. A dendrogram of relationships among the diploid wild species was constructed based on band sharing.     

RFLP Analysis of Chromosomal Segregation in Progeny from an Interspecific Hexaploid Somatic Hybrid between Solanum Brevidens and Solanum Tuberosum

Segregation of restriction fragment length polymorphism (RFLP) loci was monitored to determine the degree of homeologous pairing and recombination in a hexaploid somatic hybrid, A206, the result of protoplast fusion between Solanum tuberosum (PI 203900, a tetraploid cultivated potato) and Solanum brevidens (PI 218228), a diploid, sexually incompatible, distant relative harboring several traits for disease resistance. Somatic hybrid A206 was crossed to Katahdin, a tetraploid potato cultivar, to generate a segregating population of pentaploid progeny. Although the clones of the tetraploid S. tuberosum lines PI 203900 and Katahdin were highly polymorphic, the diploid S. brevidens clone was homozygous at all but two of the tested RFLP loci. Thus, homeologous recombination could be detected only when S. tuberosum and S. brevidens chromosomes paired and the S. brevidens homologs then segregated into separate gametes. A bias toward homologous pairing was observed for all 12 chromosomes. At least four and perhaps six chromosomes participated in homologous pairing only; each of 24 progeny contained all S. brevidens-derived RFLP markers for chromosomes 4, 8, 9 and 10. The remaining six chromosomes paired with their homolog(s) about twice as often as expected if hexaploid pairings were completely random. Where detectable with RFLPs, homeologous recombinations (both single and double) occurred at a frequency of 1.31 per chromosome. Cytological observations of meiosis I in the somatic hybrid indicated that homeologous pairing had occurred. Enhanced recombinational activity was observed for chromosome 2. A specific small deletion from chromosome 4 was detected in A206 and 11 other somatic hybrids out of 14 screened. These hybrids represent 13 independent fusion events between the same clones of S. brevidens and S. tuberosum. In one instance, this deletion occurred in one of two plants resulting from the same callus, indicating that the loss occurred in culture after fusion had taken place. It is possible that this deletion contributes to somaclonal variation.     

Genetic diversity within the species Arachis duranensis Krapov. &W.C. Gregory, a possible progenitor of cultivated peanut.

Eighteen accessions of a diploid wild peanut species (Arachis duranensis) were analyzed using morphological, intercrossing, cytological, and RFLP data. Abundant variation was found for morphological characters and for RFLP patterns both between and within accessions, and each accession could be uniquely identified by RFLP pattern. Several plants were found to be F1 hybrids between different accessions, indicating that intercrossing had occurred when these were planted for seed increase. Patterns of RFLP diversity were found to correspond with geographic distribution. Analysis of the number of RFLP fragments observed per accession indicates that additional field collections of this complex of taxa will yield additional genetic variability.     

Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs

Summary Ninety-three accessions representing 21 species from the genus Oryza were examined for restriction fragment length polymorphism. The majority (78%) of the accessions, for which five individuals were tested, were found to be monomorphic. Most of the polymorphic accessions segregated for only one or two probes and appeared to be mixed pure lines. For most of the Oryza species tested, the majority of the genetic variation (83%) was found between accessions from different species with only 17% between accessions within species. Tetraploid species were found to have, on average, nearly 50% more alleles (unique fragments) per individual than diploid species reflecting the allopolyploid nature of their genomes.Classification of Oryza species based on RFLPs matches remarkably well previous classifications based on morphology, hybridization and isozymes. In the current study, four species complexes could be identified corresponding to those proposed by Vaughan (1989): the O. ridleyi complex, the O. meyeriana complex, the O. officinalis complex and the O. sativa complex. Within the O. sativa complex, accessions of O. rufipogon from Asia (including O. nivara) and perennial forms of O. rufipogon from Australia clustered together with accessions of cultivated rice O. sativa. Surprisingly, indica and japonica (the two major subspecies of cultivated rice) showed closer affinity with different accessions of wild O. Rufipogon than to each other, supporting a hypothesis of independent domestication events for these two types of rice. Australian annual wild rice O. meridionalis (previously classified as O. rufipogon) was clearly distinct from all other O. rufipogon accessions supporting its recent reclassification as O. meridionalis (Ng et al. 1981). Using genetic relatedness as a criterion, it was possible to identify the closest living diploid relatives of the currently known tetraploid rice species. Results from these analyses suggest that BBCC tetraploids (O. malampuzhaensis, O. punctata and O. minuta) are either of independent origins or have experienced introgression from sympatric C-genome diploid rice species. CCDD tetraploid species from America (O. latifolia, O. alta and O. grandiglumis) may be of ancient origin since they show a closer affinity to each other than to any known diploid species. Their closest living diploid relatives belong to C genome (O. eichingeri) and E genome (O. Australiensis) species. Comparisons among African, Australian and Asian rice species suggest that Oryza species in Africa and Australia are of polyphyletic origin and probably migrated to these regions at different times in the past.Finally, on a practical note, the majority of probes used in this study detected polymorphism between cultivated rice and its wild relatives. Hence, RFLP markers and maps based on such markers are likely to be very useful in monitoring and aiding introgression of genes from wild rice into modern cultivars.     

iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Lack of requisite genetic variation in cultivated species has necessitated systematic collection, documentation and evaluation of wild Cicer species for use in chickpea variety improvement programs. Cicer arietinum has very narrow genetic variation, and the use of a wild relative in chickpea breeding could provide a good opportunity for increasing the available genetic variation of cultivated chickpea. Genetic diversity and the relationship of 71 accessions, from the core area of chickpea origin and domestication (Southeastern Turkey), belonging to five wild annual species and one cultivated species (Cicer arietinum) were analysed using iPBS-retrotransposon and ISSR markers. A total of 136 scorable bands were detected using 10 ISSR primers among 71 accessions belonging to 6 species, out of which 135 were polymorphic (99.3 %), with an average of 13.5 polymorphic fragments per primer, whereas iPBS detected 130 bands with 100 % polymorphism with an average of 13.0 bands per primer. C. echinospermum and C. pinnatifidum were the most diverse among species, whereas C. arietinum exhibited lower polymorphism. The average polymorphism information contents (PIC) value for both marker systems was 0.91. The clustering of the accessions and species within groups was almost similar, when iPBS and ISSR NeighborNet (NNet) planar graphs were compared. Further detailed studies are indispensable in order to collect Cicer germplasm, especially C. reticulatum, from southeastern Turkey particularly, from Karacada? Mountain for preservation, management of this species, and to study their genetic diversity at molecular level. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in wild chickpea and in cultivated chickpea.