Relationships among <Emphasis Type="Italic">Avena</Emphasis> species as revealed by consensus chloroplast simple sequence repeat (ccSSR) markers

Consensus chloroplast simple sequence repeat (ccSSR) makers were used to assess the genetic variation and genetic relationships of 80 accessions from 25 taxa of the genus Avena. Fifteen out of 16 ccSSR markers (93.75%) were polymorphic. A total of 51 alleles were detected at the 16 ccSSR loci. The number of alleles per locus ranged from 1 to 6, with an average of 3.2 alleles. Among these ccSSR loci, the highest polymorphism information content (PIC) value was 0.754, while the lowest PIC value was 0. The mean genetic similarity index among the 80 Avena accessions was 0.545, ranging from 0.188 to 1.000. To assess the usefulness of ccSSRs in separating and distinguishing between haplome (genome) groups, we used ordination by canonical discriminant analysis and classificatory discriminant analysis. Although discriminant analysis separated the haplome groups unequivocally, it was up to 69% predictive of correctly classifying an individual plant whose haplome(s) is unknown in the case where it belonged to the A haplome group, 75% where it belonged in the AC group, and almost 80% where it belonged in the ACD group. The analysis of genetic similarity showed that diploid species with the A haplome were more diverse than other species, and that the species with the As haplome were more divergent than other diploid species with the A haplome. Among the species with the C haplome, A. clauda was more diverse than A. eriantha and A. ventricosa. In the cluster analysis, we found that the Avena accessions with the same genomes and/or belonging to the same species had the tendency to cluster together. As for the maternal donors of polyploid species based on this maternally inherited marker, A. strigosa served as the maternal donor of some Avena polyploidy species such as A. sativa, A. sterilis and A. occidentalis from Morocco. A. fatua is genetically distinct from other hexaploid Avena species, and A. damascena might be the A genome donor of A. fatua. Avena lusitanica served as the maternal parents during the polyploid formation of the AACC tetraploids and some AACCDD hexaploids. These results suggested that different diploid species were the putative A haplome donors of the tetraploid and hexaploid species. The C genome species A. eriantha and A. ventricosa are largely differentiated from the Avena species containing the A, or B, or D haplomes, whereas A. clauda from different accessions were found to be scattered within different groups. Wei-Tao Li and Yuan-Ying Peng have contributed equally to this paper.     

Eco-geographical assessment of <Emphasis Type="Italic">Avena</Emphasis> L. wild species at the VIR herbarium and genebank collection

On the bases of analysis of the collecting sites of 1160 herbarium specimens and 1640 genebank accessions of wild Avena L. species from the world collection of the Vavilov Institute of Plant Genetic Resources maps of areas of the species were produced data base. A comparison of the climate conditions of the Mediterranean, Southwestern Asiatic and Abyssinian centers of diversity with those of the oat species distribution areas shows that all oat species mostly prefer the moderately hot, semi-arid and dry climate. An analysis of the range of soils in the areas of wild oat species distribution has shown that the collected accessions, preferred different types of soil. When considering the soil diversity within the areas of natural distribution of wild oat species, it could be established that the majority of diploid and tetraploid taxa prefer to grow on mountain or plain cinnamon soils; the hexaploid taxa favorites were the mountain forest brown or red-brown soils, as well as subtropical desert soils. An analysis of the database of geographic distribution on wild oat species showed a full picture of oat species diversity, and a basis to make plans concerning further collecting activities or a basis for selecting potential sources of novel genes that can improve some valuable traits and characters to use them for practical purposes.     

Assessment of distribution and diversity of <Emphasis Type="Italic">Avena</Emphasis><Emphasis Type="Italic"> sterilis</Emphasis> L. and <Emphasis Type="Italic">Avena fatua</Emphasis> L. in cereal crops of Greece based on a 3-year survey and selected morphological traits

Under the view of species genetic erosion and the need of better crops, wild species could become important germplasm sources for breeding. At present, several wild Avena species are used as donors of valuable characters in oat breeding. In this study, wild oat distribution and diversity in wheat, barley and oat fields of Greece was examined by means of a 3-year survey in some typical cereal producing regions in the central part of the country. Greenhouse experiments were also conducted in order to compare seedlings grown from wild oat accessions of these regions under the same conditions. A total of 151 fields were surveyed and 158 accessions of wild oats were studied in terms of some morphological traits. The occurrence and distribution of A. sterilis was very high, while a noticeable and first-time analytically reported presence of A. fatua was evident in some of the surveyed wheat fields. The high diversity of wild oat was furthermore indicated by means of the pot experiments. The high degree of phenotypic variation in A. sterilis could be attributed to the earlier introduction of this species in the sampling area, compared to A. fatua. Wild oat distribution and diversity in a region seems crucial for the cereal production and is an important parameter which must be considered in evaluating efficacy of weed control strategies, while genes controlling these characters could be potentially used to improve cultivated forms of oats or other cereals.     

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.     

Identification of genomic constitutions of <Emphasis Type="Italic">Oryza</Emphasis> species with the B and C genomes by the PCR-RFLP method

Oryza officinalis complex is the largest and the most complicated group in the genus Oryza L., consisting of about ten species with the B, C, BC, CD, and E genomes. Taxonomy and identification of the species, particularly those with the B, C and BC genomes, are difficult due to the similar morphology and overlapping distribution of some species. The difference in ploidy levels of some species adds more complexity. In the present study, we surveyed 64 accessions of rice germplasm in the O. officinalis complex using RFLP analysis of PCR-amplified Adh genes in addition to chromosome counting. The results confirmed that all O. rhizomatis accessions are diploids with the C genome, whereas all O. minuta accessions are tetraploids having the BC genome. However, both diploid and tetraploid forms were found for the accessions identified in the genebank as O. officinalis, O. punctata and O. eichingeri. The tetraploid form of O. officinalis with the BC genome is exclusively distributed in India and has been described as O. malampuzhaensis. The tetraploid form of O. punctata which has been called O. schweinfurthiana by some workers was found to be as widely distributed as its diploid form in Africa. It is noteworthy that two accessions that had been determined as tetraploid O. officinalis were actually belonging to a species with the CD genome (O. latifolia). Our results promote a better understanding of the genomic constitutions of many accessions in the O. officinalis complex and correct determination of the genebank material, which serves as an important basis of germplasm cataloguing for further research and utilization.     

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.     

Genetic relationships among Arachis hypogaea L. (AABB) and diploid Arachis species with AA and BB genomes

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid, with two types of genomes, classified as AA and BB, according to cytogenetic characters. Similar genomes to those of A. hypogaea are found in the wild diploid species of section Arachis, which is one of the nine Arachis sections. The wild species have resistances to pests and diseases that affect the cultivated peanut and are a potential source of genes to increase the resistance levels in peanut. The aim of this study was to analyze the genetic variability within AA and BB genome species and to evaluate how they are related to each other and to A. hypogaea, using RAPD markers. Eighty-seven polymorphic bands amplified by ten 10-mer primers were analyzed. The species were divided into two major groups, and the AA and the BB genome species were, in general, separated from each other. The results showed that high variation is available within species that have genomes similar to the AA and the BB genomes of A. hypogaea.     

Assessments of genetic diversity within a world collection of cultivated hexaploid oat (<Emphasis Type="Italic">Avena sativa</Emphasis> L.) based on qualitative morphological characters

A characterization of 10,105 accessions of hexaploid cultivated oat (Avena sativa L. sensu lato) from 85 countries of the Plant Gene Resources of Canada (PGRC) collection was conducted at Saskatoon, Saskatchewan, Canada. Eight environmentally stable morphological characters (panicle type, panicle erectness, panicle density, lemma colour, dorsal awn of lemma, ligula, major infraspecific group), differentiated into 18 character states, were used to define genetically distinct morphological groups. Comparisons of oat diversity from different countries, among the major infraspecific groups and among Canadian oat cultivars registered between 1886 and 2002 were possible. The 10,105 accessions represented 118 different morphological groups. The number of accessions in each morphological group was unevenly distributed with the 13 most frequent morphological groups including 90% of the accessions. The most frequent morphological groups in the PGRC collection were identical with the most frequent types of Canadian oat cultivars. The greatest richness of diversity was found in oat from countries with temperate climates and intensive oat breeding programmes. The oat accessions comprised 8,754 accessions of common hulled oat, 183 accessions of hull-less oat and 1,168 accessions of red oat. For red oat (A. byzantina C. Koch), West Asia was richest in diversity. The USA could be considered a secondary centre of diversity for red oat and Canada a secondary centre of diversity for hull-less oat. Morphological diversity of oat cultivars released in Canada increased during the twentieth century. The morphological groups were related to formal taxonomical infraspecific classifications of A. sativa. Applications of the concept of defining morphological groups for phenotyping a large germplasm collection are demonstrated discussed.     

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.     

Genetic Diversity of the Greater Yam (<Emphasis Type="Italic">Dioscorea alata</Emphasis> L.) and Relatedness to <Emphasis Type="Italic">D. nummularia</Emphasis> Lam. and <Emphasis Type="Italic">D. transversa</Emphasis> Br. as Revealed with AFLP Markers

Amplified fragment length polymorphism markers were used to assess the genetic relatedness between Dioscorea alata and nine other edible Dioscorea. These species include D. abyssinica Hoch., D. bulbifera L., D. cayenensis-rotundata Lamk. et Poir., D. esculenta Burk., D. nummularia Lam., D. pentaphylla L., D. persimilis Prain. et Burk., D. transversa Br. and D. trifida L. Four successive studies were conducted with emphasis on the genetic relationship within D. alata and among species of the Enantiophyllum section from Vanuatu. Study 1 was carried out to select a set of polymorphic primer pairs using 11 combinations and eight species belonging to five distinct sections. The four most polymorphic primer pairs were used in study 2 among six species of the Enantiophyllum section. Study 3 focussed mainly on the genetic relationship among 83 accessions of D. alata, mostly from Vanuatu (78 acc.) but also from Benin, Guadeloupe, New Caledonia and Vietnam. The ploidy level of 53 accessions was determined and results indicated the presence of tetraploid, hexaploid and octoploid cultivars. Study 4, included 35 accessions of D. alata, D. nummularia and D. transversa and was conducted using two primer pairs to verify the taxonomical identity of the cultivars `langlang', `maro' and `netsar' from Vanuatu. The overall results indicated that each accession can be fingerprinted uniquely with AFLP. D. alata is an heterogeneous species which shares a common genetic background with D. nummularia and `langlang', `maro' and `netsar'. UPGMA cluster analysis revealed the existence of three major groups of genotypes within D. alata, each assembling accessions from distant geographical origins and different ploidy levels. The analysis also revealed that `langlang', `maro' and `netsar' clustered together with the cultivar `wael' (D. transversa) from New Caledonia. Results are discussed in the paper.     

Cytogenetic and systematic analyses of Kengyilia gobicola, K. zhaosuensis and K. batalinii var. nana (Poaceae)

Kengyilia batalinii var. nana J.L. Yang, Yen et Baum, K. gobicola Yen et J.L. Yang, K. zhaosuensis J.L. Yang, Yen et Baum are short-lived perennial grasses of the family Triticeae distributed throughout the upper and middle mountain ranges of west China. They were cytogenetically studied with testers R. kamoji Ohwi (StStHHYY) and K. hirsuta (Keng) J. L. Yang, Yen et Baum (PPStStYY). Analysis of metaphase I pairing configurations in the F₁ indicate that K. batalinii var. nana, K. gobicola, K. zhaosuensis possess the P, St, and Y genomes, with o nly minor structural rearrangements. These results showed that the three target taxa are good species in the genus Kengyilia.     

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 diversity of the D-genome in <Emphasis Type="Italic">T. aestivum</Emphasis> and <Emphasis Type="Italic">Aegilops</Emphasis> species using SSR markers

Simple sequence repeats (SSRs), highly dispersed nucleotide sequences in genomes, were used for germplasm analysis and estimation of the genetic relationship of the D-genome among 52 accessions of T. aestivum (AABBDD), Ae. tauschii (D^tD^t), Ae. cylindrica (CCD^cD^c) and Ae. crassa (MMD^cr1D^cr1), collected from 13 different sites in Iran. A set of 21 microsatellite primers, from various locations on the seven D-genome chromosomes, revealed a high level of polymorphism. A total of 273 alleles were detected across all four species and the number of alleles per each microsatellite marker varied from 3 to 27. The highest genetic diversity occurred in Ae. tauschii followed by Ae. crassa, and the genetic distance was the smallest between Ae. tauschii and Ae. cylindrica. Data obtained in this study supports the view that genetic variability in the D-genome of hexaploid wheat is less than in Ae. tauschii. The highest number of unique alleles was observed within Ae. crassa accessions, indicating this species as a great potential source of novel genes for bread wheat improvement. Knowledge of genetic diversity in Aegilops species provides different levels of information which is important in the management of germplasm resources.     

Phylogenetic analysis of complete 5′ external transcribed spacers of the 18S ribosomal RNA genes of diploid Aegilops and related species (Triticeae, Poaceae)

PCR systems were designed to amplify the entire 5 external transcribed spacer (ETS) region of the 18S rRNA gene of all the diploid species of Aegilops and several other taxa closely related to domesticated wheat. Phylogenetic analysis was performed on the complete ETS sequences using the neighbor-joining, maximum parsimony, and maximum likelihood methods. Among the individual taxa studied, speciation in Secale is very recent. In the case of the A genome diploids, the results support the theory that the A genomes of wheat have experienced reticulate evolution owing to introgression. The B and G genomes of tetraploid domesticated wheats form a clade with Ae. speltoides in which the B genome diverged first and the G genome more recently. It was demonstrated that the complete ETS sequences of the Triticeae yield coherent phylogenetic information. The ETS is a useful tool for studying the phylogeny of closely related species.     

Genetic diversity among <Emphasis Type="Italic">Jatropha</Emphasis> species as revealed by RAPD markers

The genus Jatropha is native of tropical America with more than 200 species that are widely distributed in tropics with a promise for use as an oil crop for biodiesel. This investigation was carried out to assess the genetic diversity of 12 Jatropha species based on random amplified polymorphic DNA markers. From 26 random primers used, 18 primers gave reproducible amplification banding patterns of 112 polymorphic bands out of 134 bands scored accounting for 80.2% polymorphism across the genotypes. Three primers viz., OPA 4, OPF 11, and OPD 14 generated 100% polymorphic patterns. The polymorphic information content was highest for the primer OPD 14 (0.50) followed by the primers OPF 11 and OPAD 11 (0.48). Jaccard’s coefficient of similarity varied from 0.00 to 0.85, indicative of high level of genetic variation among the genotypes studied. UPGMA cluster analysis indicated three distinct clusters, one comprising all accessions of J. curcas L., while second included six species viz., J. ramanadensis Ramam., J. gossypiifolia L., J. podagrica Hook., J. tanjorensis J. L. Ellis et Saroja J. villosa Wight and J. integerrima Jacq. J. glandulifera Roxb. remained distinct and formed third cluster indicating its higher genetic distinctness from other species. The overall grouping pattern of clustering corresponds well with principal component analysis confirming patterns of genetic diversity observed among the species. The result provides valid guidelines for collection, conservation and characterization of Jatropha genetic resources.     

Molecular Confirmation of the Position of <Emphasis Type="Italic">Gossypium trifurcatum</Emphasis> Vollesen

Taxonomic understanding is a necessary prerequisite for intelligent germplasm maintenance and evaluation. Here, we use molecular evidence to address the generic position of the poorly known and morphologically unusual taxon Gossypium trifurcatum Vollesen. This species possesses dentate leaves, a feature not otherwise found in Gossypium L. but one that is common in Cienfuegosia Cav., a related genus in the small Malvaceous tribe Gossypieae. G. trifurcatum is a rare plant, restricted to deserts of Eastern Somalia and known from only two collections, the last in 1980. Using DNA extracted from an herbarium specimen, we amplified and sequenced the chloroplast gene ndhF. Phylogenetic analysis reveals G. trifurcatum to be cladistically nested within Gossypium. These data diagnose dentate leaves as an autapomorphy within a genetically diverse assemblage of African–Arabian species, which remain the least well-represented cottons in germplasm collections.     

Diversity of seed globulins in Lathyrus sativus L. and some related species

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of reduced seed globulins covered 141 accessions of Lathyrus sativus and the following related species: L. amphicarpos, L. blepharicarpus, L. cicera, L. gorgoni, L. marmoratus, L. pseudocicera and L. stenophyllus. In the total examined material 71 globulin polypeptide bands were distinguished. The number of polypeptide bands detected in particular species varied from 14 in L. amphicarpos to 29 in L. sativus; all the species under study showed intraspecific variation due to individual variation and/or differences among accessions. Electrophoretic data were subjected to statistical analysis using hierarchical UPGMA grouping. Frequency distribution of polypeptide bands in L. sativus showed some correlations with geographical origin and certain seed characteristics (seed coat colour, seed weight) of the studied accessions. As regards interspecific relationships, the studied species showed to be distantly related taxa except for the rather closely allied L. cicera and L. marmoratus. The obtained results are compared with the electrophoretic seed albumin data reported earlier for the same taxa.     

Isozyme polymorphism and genetic differentiation in natural populations of an endemic tetraploid species <Emphasis Type="Italic">Avena maroccana</Emphasis> in Morocco

A wild tetraploid oat Avena maroccana Gdgr. was collected from the 11 populations in the periphery of Rommani and Casablanca geographic groups of Morocco. Genetic diversity of the species was investigated using six allozyme systems. Allelic frequencies were scored representing eight polymorphic and five monomorphic loci. Coefficient of gene differentiation (Gst) was 0.3019, which indicated great genetic differentiation. The number of alleles per locus was 2.6154, the percentage of polymorphic loci was 61.54, and the expected heterozygosity was 0.2462 in all populations. Genetic diversity in A. maroccana was high in comparison to self-pollinated species. In total, nine heterozygotes resulting from outcrossing were found in the progeny from M1, M3, M4, M22 and M26. The population of M7 had peculiar alleles Pgd–2SS and Pgd-1SS in high frequency. M9 had the lowest level of diversity out of the 11 populations. Geographic and genetic distances between all the populations were not significantly correlated with each other (r = 0.0996). Cluster analysis showed that two groups, (M1, M22, M2 and M4) and (M3, M23, M8, M5 and M26) were apparently differentiated. Two populations of the Casablanca group, M7 and M9 were independent from each other, and were separated distinctly from the other populations. Genetic diversity of the Rommani and Casablanca groups was almost the same in all the parameters. This was due to the similar man-made habitat such as roadside or rich fertile soil and brown clay soils. The population size of A. maroccana was small and restricted to the narrow central Morocco with great genetic differentiation so that genetic diversity may be reflected from the results of genetic drift and outcrossing heterozygote segregation.     

A novel genome of C and the first autotetraploid species in the <Emphasis Type="Italic">Setaria</Emphasis> genus identified by genomic <Emphasis Type="Italic">in situ</Emphasis> hybridization

Genomic in situ hybridization (GISH) was used to investigate the genomic relationships among some newly collected species of genus Setaria. Previous work identified that S. viridis and S. adhaerens carry genomes A and B, respectively. GISH patterns obtained in this report clearly distinguished the genome of S. grisebachii from the known genomes A and B, and indicated its new genomic constitution which we suggest to name genome C of the Setaria genus. The two sets of chromosomes of tetraploid S. queenslandica hybridized well with the A genome of S. viridis indicating its autotetraploid nature. This is the first autotetraploid identified in the Setaria genus, which should be classified into the primary A genome gene pool rather than the tertiary gene pool as previously classified. GISH patterns did not distinguish the genome of S. leucopila from the A genome of S. viridis and S. italica, suggesting its close relation with foxtail millet. Strong hybridization signals were observed when S. adhaerens genomic DNA was used as probe to hybridize the chromosomes of diploid S. verticillata, inferring its B genome nature. Combined with morphological observation and previous work, we deduce that diploid S. verticillata and S. adhaerens are probably taxonomically the same species with different names. Y. Wang and H. Zhi contributed equally to this article.