Cytoplasmic diversity of Brassica napus L., Brassica oleracea L. and Brassica rapa L. as determined by chloroplast microsatellite markers

Cytoplasmic genomes in most angiosperms are known to be maternally inherited. Oilseed rape (Brassica napus L.) as a natural amphidiploid species hence may carry the B. oleracea L. or the B. rapa L. cytoplasm, depending on the cross direction. The presence of either the B. oleracea or the B. rapa cytoplasm in oilseed rape has been reported to affect agronomically important traits. However, to date little is known about the cytoplasmic composition and genetic diversity of current winter oilseed rape cultivars and breeding material. The aim of this study was to assess the usefulness of 40 previously published chloroplast cpSSR markers from Brassica species and Arabidopsis thaliana (L.) Heynh. for distinguishing the cytoplasms of 49 different genotypes of B. napus and its diploid ancestor species. Results showed that only 14 out of the 40 tested primer combinations were suitable to distinguish the cytoplasms of a test set of 8 Brassica genotypes. With the 14 primer pairs 64 different cpSSR alleles were identified in the set of 49 genotypes. Cluster analysis indicated distinct groups for the cytoplasms of B. napus, B. rapa, and B. oleracea. However, an unambiguous identification and classification of the cytoplasm types was not possible in all cases with the available polymorphic set of cpSSR primer pairs.     

Using diversity of the chloroplast genome to examine evolutionary history of wheat species

Chloroplast microsatellites (SSRs) are conserved within wheat species, yet are sufficiently polymorphic between and within species to be useful for evolutionary studies. This study describes the relationships among a very large set of accessions of Triticum urartu Thum. ex Gandil., T. dicoccoides (Körn. ex Asch. et Graebn.) Schweinf., T. dicoccon Schrank, T. durum Desf., T. spelta L., and T. aestivum L. s. str. based on their cpSSR genotypes. By characterising the chloroplast diversity in each wheat species in the evolutionary series, the impact on diversity of major evolutionary events such as domestication and polyploidyisation was assessed. We detected bottlenecks associated with domestication, polyploidisation and selection, yet these constrictions were partially offset by mutations in the chloroplast SSR loci that generated new alleles. The discrete cpSSR alleles and haplotypes observed in T. urartu and Aegilops tauschii, combined with other species specific polymorphisms, provide very strong evidence that concur with current opinion that neither species was the maternal and thus cytoplasmic donor for polyploid wheats. Synthetic hexaploid wheats possessed the same chloroplast haplotypes as their tetraploid progenitors demonstrating how the novel synthetic wheat lines have captured chloroplast diversity from the maternal parents, the chloroplast is maternally inherited and novel alleles are not created by genomic rearrangements triggered by the polyploidisation event.     

A-genome cotton as a source of genetic variability for Upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>)

Since Upland cotton (Gossypium hirsutum) is known to have relatively low levels of genetic diversity, a better understanding of variation and relationships among possible sources of novel genes would be valuable. Therefore, analysis of genetic variation of the genus Gossypium, especially the diploids, which are the putative donors of the A and D genomes for the commercially important allotetraploid cottons (AADD), G. hirsutum and G. barbadense, could provide important information about the feasibility of using these genetic resources for cotton improvement. The primary objective of this study was to analyze the genetic diversity in A-genome diploid cotton species, G. herbaceum (A1) and G.␣arboreum (A2) by using microsatellite markers. Forty-one A-genome germplasm accessions were evaluated with 32 microsatellite loci. Genetic similarities between A1 and A2 ranged from 0.62 to 0.86 with a mean of 0.70. Within each A-genome species similarities ranged from 0.80 to 0.97 with a mean of 0.89 for A1 and from 0.82 to 0.98 with a mean of 0.89 for A2. A UPGMA tree and principal coordinate analysis based on genetic similarity matrices showed distinct clusters consistent with the genomic groups.     

Genetic analysis of wheat (Triticum aestivum L.) and related species with SSR markers

Genetic diversity among 19 Triticum aestivum accessions and 73 accessions of closely related species was analyzed using simple sequence repeat (SSR) markers. Forty-four out of 497 SSR markers were polymorphic. In total 274 alleles were detected (mean 6.32 alleles per locus). The polymorphic information content (PIC) of the loci ranged from 0.3589 to 0.8854 (mean 0.7538). The D genome contained the highest mean number of alleles (6.32) followed by the A and B genomes (6.13 and 5.94, respectively). The correlation between PIC and allele number was significant in all genome groups (0.7540, 0.7361 and 0.7482 for A, B and D genomes, respectively). Among the seven homologous chromosome groups, genetic diversity was lowest in group 7 and highest in group 5. In cluster and principal component analyses, all accessions grouped according to their genomes were consistent with their taxonomic classification. Accessions with the A and D genomes were clustered into two distinct groups, and AABB accessions showed abundant genetic diversity and a close relationship. Triticum durum and T. turgidum were clustered together, consistent with their morphological similarity. Cluster analysis indicated emmer is closely related to hexaploid wheat. Compared with common wheat, higher genetic variation was detected in spelt, T. aestivum subsp. yunnanense and subsp. tibetanum. In addition, a close genetic relationship between T. polonicum and T. macha was observed. The results of the clustering and principal component analyses were essentially consistent, but the latter method more explicitly displayed the relationships among wheat and closely related species.     

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers and evaluated 114 Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For those seven, the average heterozygosity was moderate at 0.49, and mean allele number, genetic diversity and polymorphism information index were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor-joining (NJ) clustering and structure analysis agreed with classical taxonomic analysis and supported inclusion of C. maxima within the large polymorphic species, C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated 21 distinct chlorotypes with an average of 3 alleles per locus. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.54. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture related to hybridization during the ancestral diversification of the genus, or to homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they continued to evolve after dispersal from Asia through the Mediterranean to Europe, and across the Atlantic and/or the Bering land bridge to North America.     

Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid <Emphasis Type="Italic">Triticum</Emphasis> and <Emphasis Type="Italic">Aegilops</Emphasis> species

Chloroplast simple sequence repeats (cpSSRs) are widely distributed in the chloroplast genomes of all plant species, and are frequently employed for genotypic and phylogenetic analysis. However, information on intra- and interspecies variation in cpSSRs is lacking. In this study, we sequenced four intergenic (non-coding) chloroplast DNA regions in 57 accessions of 12 tetraploid, and 16 accessions of 4 hexaploid species of Triticum and Aegilops. These sequence data added to our previous data for diploid species in the same chloroplast regions. Intra- and interspecific genetic variation was analyzed for a total of 189 accessions of 13 diploid, 12 tetraploid, and 4 hexaploid species of Triticum and Aegilops, such that all species were represented by multiple accessions. The data were used to infer phylogenetic relationships within and among Triticum and Aegilops species. Based on this robust phylogenetic tree, seven of eight cpSSR loci clearly exhibited “size homoplasy,” referring to the fact that cpSSRs of identical size and DNA sequence can arise even if the alleles are not descended from a common ancestor. These data indicate that cpSSRs should be used with caution in phylogenetic analyzes. Interestingly, as observed from several previous studies, our data also suggest that observed mutation rates may increase significantly when mononucleotide (homopolymer) repeat numbers reach or exceed 9 bp. In the present report, using this sequence data set involving cpSSRs, 81 unique haplotypes among 189 accessions were detected, and five tetraploid Triticum and Aegilops species were successfully identified and genotyped. Our results indicate that combinations of nucleotide substitutions, indels and SSRs of chloroplast nucleotide sequences are available for genotyping at the species accession level.     

Chloroplast Microsatellites to Investigate the Origin of Grapevine

The origin of the grapevine, Vitis vinifera ssp . sativa L., has been investigated with archaeobotanical–archaeological, cultural and historical data indicating a unique domestication centre located in the Caucasian and Middel-East regions about 6–7000 years ago, but, events leading to the domestication of this species are still an open issue. In this work, eight universal chloroplast microsatellites are used to assess genetic relationships among varieties selected as representatives of four distinct geographical groups from Middle-East to Western European regions. Results show that two out of the eight analysed chloroplast loci are polymorphic within the 142 individuals. Allele variants of the cpSSR loci combine in a total of six different haplotypes. The analysis of haplotypes distribution and haplotype diversity (HD) suggest that only three out of the six haplotypes are represented in the Caucasian and Middle-East samples, with 90% of individuals sharing the same haplotype. Moreover, the presence of all six haplotypes in the European accessions, with a high level of haplotype diversity, suggests varietal influx in these areas. Concerning the Western European varieties, especially in Spanish accessions, half of the individuals share haplotype VI which is completely absent in the Caucasian and Middle-East cultivars. This result opens the discussion about the existence of a unique and common domestication centre, located in the Caucasian and Middle-East area, for all the European cultivars. This work suggests the usefulness of chloroplast genome markers to provide information on haplotype distributions that could help to identify further geographical areas for grapevine varietal evolution.     

Phylogenetic relationship of 40 species of genus Aloe L. and the origin of an allodiploid species revealed by nucleotide sequence variation in chloroplast intergenic space and cytogenetic insitu hybridization

Aloe species, which have been used as medicinal plants, belong to the Asphodelaceae family consisting of 530 species. In this study, genetic diversity and phylogenetic relationships among 40 Aloe species including a putative interspecies hybrid were analyzed using PCR band profiles from eight chloroplast intergenic space markers and nucleotide sequence diversity in the psbK–psbI intergenic region. A phylogenetic tree based on psbK–psbI sequences supported the revised classification of the genus Aloe as polyphyletic with several species be re-allocated into three genera Kumara, Aloidendron, and Aloiampelos. Further, the origin of the putative interspecies Aloe hybrid was characterized through molecular cytogenetics. Fluorescence and genomic insitu hybridization illustrated that the hybrid has a bimodal karyotype with a chromosome complement of 2n = 14, of which complementary halves were derived from two parental species, A. vera and A. arborescens. These findings revealed that the hybrid species was allodiploid. The phylogenetic analysis showed that A. arborescens was the maternal genome donor of the hybrid, as both have identical chloroplast genome sequences. We thus conclude that the allodiploid hybrid should be called A. arborescens × A.vera.     

Chloroplast SSR genetic diversity indicates a refuge for Corylus avellana in northern Portugal

The genus Corylus, a member of the birch family Betulaceae, includes several species that are widely distributed throughout temperate regions of the Northern Hemisphere. The development of microsatellites or simple sequence repeats (SSRs) for non-coding regions of the chloroplast genome and their higher sequence variation compared with coding regions has provided a higher resolution tool for the study of cultivars and closely related taxa. Chloroplast polymorphisms provide a marker system to evaluate the genetic structure of plant populations. This study investigated genetic diversity in three cultivars and 32 genotypes of Corylus avellana L. from Portugal: 13 wild genotypes and 19 Portuguese landraces. Four of ten cpSSR loci were polymorphic, with diversity indices ranging from 0.111 to 0.244. Eleven chlorotypes were detected, and their relationships were analyzed using a network model. Haplotype A was most frequent in landraces and cultivars. Four chlorotypes (H, I, J and L) were found only in wild hazelnuts. The diversity of chlorotypes in the wild hazels, and the limited number reported in cultivars, suggests that northern Portugal was a refuge for hazel during the last ice age.     

ISSR analysis shows low genetic diversity versus high genetic differentiation for giant bamboo, Dendrocalamus giganteus (Poaceae: Bambusoideae), in China populations

Dendrocalamus giganteus Munro is a high-value woody bamboo widely grown in Southeast Asia and China’s Yunnan Province. We investigated its genetic diversity in Yunnan as a prelude to considering effective breeding programs and the protection of germplasm resources. Inter-simple sequence repeat (ISSR) markers were used to assess the genetic structure and differentiation of seven populations. Seven ISSR primers generated 140 bands, of which 124 were polymorphic (88.57%). Genetic diversity within populations was relatively low, averaging 11.33% polymorphic bands (PPB), while diversity was considerably higher among populations, with PPB = 88.57%. Greater genetic differentiation was detected among populations (G _ST = 0.8474). We grouped these seven populations into two clusters within an UPGMA dendrogram—one comprised the Xinping and Shiping populations from central Yunnan, the other included the remaining five populations. Mantel tests indicated no significant correlation between genetic and geographic distances among populations. Breeding system characteristics, genetic drift, and limited gene flow (N _m = 0.0901) might be important factors for explaining this differentiation. Based on the overall high genetic diversity and differentiation among D. giganteus populations in Yunnan, we suggest the implementation of in situ conservation measures for all populations and sufficient sampling for ex situ conservation collections.     

Genetic diversity of African wild rice (Oryza longistaminata Chev. et Roehr) at the edge of its distribution

Ethiopia is at the edge of the distribution for African wild rice, Oryza longistaminata. Here, chloroplast (cp) and simple sequence repeat (SSR) markers were applied to wild rice accessions in Ethiopia to evaluate how they differ from control O. longistaminata, O. barthii and O. glaberrima accessions which originated from African countries. Based on the cp genomes of African wild rice species, maternally inherited cpINDEL markers were developed. The cp indels helped to elucidate 20 plastid types. African cultivated rice shared a particular plastid type with one of annual O. barthii. Parts of northern wild rice in Ethiopia shared Type 6 with control O. longistaminata. The north group shared another type with parts of the south group. The 16 SSR markers amplified a total of 155 alleles in 215 rice accessions, with mean allelic richness of 9.688 per locus, observed heterozygosity of 0.241, expected heterozygosity of 0.724, polymorphic information content of 0.700, and a significant genetic differentiation of 0.215. Both cpINDEL and nuclear markers analyses suggested that wild rice in Ethiopia belongs to O. longistaminata. However, they carry both a unique plastid type and different population structure from control O. longistaminata collected from other areas in Africa. We concluded that the edge of its distribution maintains unique variation. These populations are regarded as valuable genetic resources for future rice breeding.

     

Chromosomal distributions of oligo-Am1 and (TTG)<Subscript>6</Subscript> trinucleotide and their utilization in genome association analysis of sixteen <Emphasis Type="Italic">Avena</Emphasis> species

Fluorescence in situ hybridization was used to investigate the physical location of oligo-Am1 and (TTG)₆ trinucleotide repeats in the metaphase chromosomes of seven diploid species (AA or CC genomes), seven tetraploid species (AABB or AACC genomes), and two hexaploid species (AACCDD genomes) belonging to the genus Avena. The oligo-Am1 probe produced signals that were particularly enriched on almost whole C-genome chromosomes, whereas the (TTG)₆ probe was located in the pericentromeric (M), and, occasionally, their telomeric (T) chromosome regions, but showed low matching to C genome. All the species possessed (TTG)₆ loci in M regions, and the CC, AABB, and AACCDD species also possessed (TTG)₆ loci in T regions. The (TTG)₆ signal number is constant in both the AA and CC species but slightly differs in signal intensity, whereas the (TTG)₆ signal pattern shows wide diversity in the AABB, AACC and AACCDD species. The probe hybridization results provide key information that can be used in the physical assignment of genome sequences to chromosomes.     

Cloning of genome-specific repetitive DNA sequences in wild rice (O. rufipogon Griff.), and the development of Ty3-gypsy retrotransposon-based SSAP marker for distinguishing rice (O. sativa L.) indica and japonica subspecies

In the rice genome, insertions and eliminations of transposable elements have generated numerous transposon insertion polymorphisms (TIPs). Common wild rice (O. rufipogon Griff.), the ancestor of Asian cultivated rice (O. sativa L.), carries abundant genetic variations. To find subspecies-specific (SS) markers that can distinguish O. sativa ssp. indica and ssp. japonica, some long terminal repeat (LTR) sequences (sc1-14) of AA genome-specific RIRE retrotransposon were isolated from O. rufipogon genome. Sequences sc1 and sc12 were successfully utilized to develop the SS marker system based on retrotransposon inserted position polymorphisms. Twenty-two SS markers (ssi1-9, ssj1-13) were developed, where ssi1-9 are the indica-specific types, and ssj1-13 the japonica-specific types. The average accuracy of these markers in distinguishing the two subspecies is over 85%. SS marker ssj-10 can distinguish the two subspecies at 100% accuracy. Principal component analysis (PCA) showed that these markers could successfully distinguish indica from japonica varieties, regardless of their geographical origin.     

Genetic variability of wild apricot (Prunus armeniaca L.) populations in the Ili Valley as revealed by ISSR markers

The genetic variability of 14 wild Prunus armeniaca populations was investigated using morphological analysis and inter-simple sequence repeat markers. 10 morphological characters revealed a high level variation, especially Fruit number, Fruit weight, Seed weight and Tree height. Totally, 15 selected primers generated 155 loci, with an average of 10.3 bands per primer. Nei’s gene diversity (H _e ) and Shannon’s index of diversity (I) were fairly high at the species level (H _e  = 0.2741, I = 0.4220). High molecular and morphological variability indicated that wild apricots in the Ili Valley still maintained a relatively high level of diversity. The G _ST of 0.2275 revealed a low level of genetic differentiation among populations, and genetic variation mainly resided within populations (81.51 %), which was identified with the moderate gene flow value (N _m  = 1.6974). The relatively high intraspecific genetic diversity and low inter-population genetic differentiation was largely attributed to long-distance dispersal of pollen, continuous distribution of populations and the self-incompatible breeding system.     

Genetic diversity of <Emphasis Type="Italic">rbc</Emphasis>L gene in <Emphasis Type="Italic">Elymus trachycaulus</Emphasis> complex and their phylogenetic relationships to several Triticeae species

Elymus trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The phylogenetic relationships among the E. trachycaulus complex, and their systematic relation to other species in Triticeae remain unknown. Nucleotide diversity of ribulose-1,5 bisphosphate-carboxylase (rbcL) gene in E. trachycaulus complex species and several other Triticeae was first characterized and compared. A primary conclusion of the present study is that nucleotide diversity for rbcL gene in E. trachycaulus species was detected with the estimates of nucleotide diversity θ = 0.00039 and π = 0.00043. The estimate of nucleotide diversity in rbcL gene for species with different genome constitution here ranged from 0.00099 (π) and 0.00099 (θ) for the species with Ns genome to 0.00226 (π) and 0.00291 (θ) for the species with St genome. The phylogenetic relationships of these species were assessed using these rbcL sequences. A total of 47 variable positions including 19 parsimony-informative sites were detected among 24 accessions of 18 species/subspecies. The species with St, H/I and Ns genomes well separated from each other, and formed a three distinct clades with higher bootstrap values support for both Parsimony and NJ analyses. The St genome containing species is sister group of H/I genome containing species. Our result confirms that Pseudoroegneria is the maternal genome donor to these Elymus species studied here, regardless of their distribution. Elymus trachycaulus complex are more related to each other than to E. glaucescens, E. patagonicus, and E. solandri. This study suggested that Elymus species with StH genomes may form from multiple closely related sets of donors.     

Nuclear intron-targeting markers in genetic diversity analysis of black nightshade (Solanum sect. Solanum,Solanaceae) accessions

Different molecular markers are routinely used in studies of potato (Solanum tuberosum) and the genus Solanum in general. Genome sequence databases provide potential to design new markers for various applications. Here we present the application of a recently developed core set of nuclear intron-targeting (indel) markers. These markers are based on the fact that in the plant genome introns are more variable than exons; therefore primers flanking exons can reveal polymorphisms related to introns. We detected such variation among accessions of the eight different species of black nightshades (Solanum sect. Solanum). Members of this group are important sources of food, mostly in Africa, while others are poisonous weeds with near global distribution. The tested 29 primers were designed previously for potato based on Solanaceae EST and other genomic databases and targeted 16 different genes. Our results showed that Solanum intron-targeting markers are not very polymorphic but identified considerable structure among accessions indicating fairly high interspecies differentiation. Further analyses showed that inbreeding is unlikely to be the major driving force in determining the genetic structure of the analyzed species. All phylogenetic analyses resolved the species included in our study as distinct clades with high support values, but provided weak information about their internal relationships. In summary, indel markers would be useful for the assignment of new Solanum germplasm to taxonomic groups or to identify certain taxa. They could also be used to address important question about genetic diversity and should yield results comparable to other markers covering the whole genome.     

Polymorphisms Among Chloroplast and Mitochondrial Genomes of <Emphasis Type="Italic">Citrullus</Emphasis> Species and Subspecies

Twelve and six DNA clones representing various parts of chloroplast and mitochondrial genomes, respectively, were used to detect polymorphism among five watermelon cultivars and 21 U.S. Plant Introductions (PIs) collected from diverse geographical locations and representing major groups of Citrullus species. Cluster analysis based on 20 chloroplast DNA (cpDNA) and 10 mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) markers differentiated the accessions into three major phenetic groups: PIs and watermelon cultivars of Citrullus lanatus subsp. vulgaris (Schrad. ex Eckl. et Zeyh.) Fursa (also designated as C. lanatus var. lanatus) (group I), PIs of C. lanatus var. citroides (of C. lanatus subsp. lanatus Schrad. ex Eckl. et Zeyh.)(group II), and C. colocynthis (L.) Schrad. PIs (group III). The chloroplast and mitochondrial genomes of watermelon cultivars are distinct, but closely related to those of the C. lanatus var. lanatus PIs. On the other hand, the chloroplast and mitochondrial genomes of the wild species C. colocynthis are more similar to those of C. lanatus var. citroides. Polymorphic cpDNA and mtDNA markers identified in this study can complement isozyme and nuclear DNA data used in earlier phylogenetic and phenetic classifications of Citrullus PIs. These cpDNA and mtDNA markers are being used in experiments designed to enhance watermelon cultivars by replacing the chloroplast and mitochondrial genome of cultivated watermelon with those of the wild species C. colocynthis.     

A retrotransposon-based probe for fingerprinting and evolutionary studies in rice (Oryza sativa)

A genomic DNA fragment (pAA7-2) amplified by a random amplified polymorphic DNA primer from the rice cultivar IR68 was used to assess the genetic variation and genetic relationships among the species of genus Oryza. A Southern hybridization experiment of diverse upland rice accessions using a single restriction enzyme HindIII generated unique DNA fingerprint for each accession. The differential hybridization pattern reflecting the copy number variation of pAA7-2 in a collection of wild species and cultivated species of rice provided insight about the genetic relationships among them. All AA genome species exhibited clear banding pattern suggesting presence of fewer copies of this sequence. Strongest hybridization signal was obtained in species belonging to BB, CC, GG, BBCC, CCDD genomes, whereas weakest hybridization signal was visible in EE, FF, and HHJJ genome species. Oryza brachyantha was the most divergent species. Clear difference in banding pattern was evident between Oryza schlechteri and Oryza coarctata belonging to HHKK genome. Although pAA7-2 had no repetitive sequences often associated with hypervariable loci, homology to a putative unclassified expressed retrotransposon distributed over several rice chromosomes was responsible for the complex banding patterns. There were more sites homologous to pAA7-2 sequence in corn and sorghum genome compared with the rice genome. The study demonstrates the potential of pAA7-2 as a powerful molecular tool for DNA fingerprinting, genetic diversity, phylogenetic, and evolutionary studies in Oryza sativa and its wild relatives and other grasses.     

Synchronous evidence from both phenotypic and molecular signatures for the natural occurrence of sympatric hybridization between cultivated soybean (Glycine max) and its wild progenitor (G. soja)

The genus Glycine subgenus Soja includes two species, the important crop, soybean (G. max), and its wild progenitor (G. soja), and an intermediate semi-wild type (G. gracilis). However, the origin of the semi-wild type is in dispute, from independent evolutionary processes or from sympatric hybridization, although many studies support the hypothesis of a hybridization origin. Here, we reveal conclusive evidence for the natural occurrence of sympatric hybridization between wild and cultivated soybeans leading to G. gracilis by capturing natural F₁ seeds based on phenotypic and molecular signatures. The F₁ hybrids occurred through pollen flow between wild and cultivated soybeans, with many heterozygous loci and similar genetic parameters compared to the maternal wild populations; while paternal soybeans showed the lowest genetic diversity. The F-statistics showed genetic differentiation of the hybrids from the paternal soybeans and maternal wild populations; the differentiation of hybrids from wild soybeans was less than that of hybrids from cultivated soybeans. Natural F₁ hybrids generated various seed sizes in the offspring, suggesting that cultivar-genes introgressed into wild soybeans, and the degree of outcrossing in wild soybeans seems to be very important for gene spread, exchange and recombination in the evolution of populations.     

Genetic diversity and origin of cultivated potatoes based on plastid microsatellite polymorphism

The origin of cultivated potatoes has remaining questions. In this study, 237 accessions of all cultivated species and 155 accessions of wild species closely related to cultivated potatoes, including their putative ancestors, were analyzed using 15 plastid microsatellites (SSRs) to investigate genetic diversity and their relationships with the wild species. We here used polymorphic plastid SSRs we developed from potato plastid genome sequences as well as already known plastid SSR markers. All 15 loci were polymorphic and identified a total of 127 haplotypes. Dramatic decreases in levels of genetic diversity were revealed in landraces in comparison with wild ancestor species. The plastid SSR results showed a decrease in haplotype number and diversity from Peru to both north and south. Phylogenetic analysis revealed two distinct groups. One of them, group A, contained the majority of accessions of cultivated species of the Solanum tuberosum Andigenum group including all accessions of cultivated diploid and triploid cytotypes of this group (S. chaucha, S. phureja, and S. stenotomum by a former taxonomic system) and most of tetraploid accessions of the S. tuberosum Andigenum group (S. tuberosum subsp. andigenum), and the majority of accessions of wild ancestors from the northern members of the S. brevicaule complex. Another group B comprised most of the wild species accessions and almost exclusively hybrid cultivated species which have introgressed plastid genomes from the other wild gene pools. Lack of clustering of traditional cultivated species (as used above) support a revised group classification of S. tuberosum.