Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

BACKGROUND: The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide.
RESULTS: GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus.
CONCLUSIONS: Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

Background

The grass genus Setaria Beauv., a member of the tribe Paniceae, in the subfamily Panicoideae of the Poaceae, has approximately 125 species worldwide in tropical, sub-tropical and temperate regions, including crop and weed species with different life cycles and ploidy levels [1,2]. However, the actual number of species in this genus is confused by the presence of multiple names for some species and multiple species under the same name, as well as overlapping morphological characters both within and between species [3,4]. There are approximately 74 species native to Africa, 25 species in America and the remainder in Eurasia [2]. Setaria italica (foxtail millet), a crop that was domesticated more than 10 thousand years ago [5], is still cultivated in China, India, Japan and other countries in more arid and semi-arid regions as a stable food grain, and is used as a forage crop in North America, Africa and Australia [6]. Setaria glauca (Weigel) Hubb. (yellow foxtail) is also domesticated and cultivated in India as to complement other food sources [3,4]. Most other species of the genus are problematic weeds for agricultural crop production [2], including S. verticillata (L.) Beauv. (bristly foxtail) and S. faberi Herrm. (giant foxtail). S. viridis (L.) Beauv. (green foxtail) is a wide spread species in Eurasia and is known for its repeated evolution of herbicide resistance in North America farms [7]. In the latest phylogenetic analysis, Setaria was found to be polyphyletic, with separate groups correlated by geography rather than the existing sub-generic classification [8].

Evolutionary relationships within Setaria remain unclear, even after several molecular phylogenetic studies [8,9]. However, several groups within Setaria were shown to be monophyletic, including the close relationship between S. viridis and S. italica. Numerous studies have shown that the domesticated S. italica has been shown to be most likely derived from the wild S. viridis, including cytological genetical studies [10], RAPDs [11], RFLPs [12], ISSRs [13] and molecular phylogenetic studies [8,9,14]. Detailed studies of the phylogenetic relationships of Setaria, using more than 50 species from all over the world and the knotted1 and ndhF gene markers, found that Setaria is polyphyletic, with some species of the New World classified into other genera [8,9].

The basic chromosome number of the genus and its close relatives is x = 9 [15,16], but the genome constitution of the group is so far poorly studied. The diploid genome of S. italica (2n = 2x = 18) was designated as genome A by Li et al [10]. Diploid S. viridis shares the same A genome as S. italica, verified by hybrid fertility and cytogenomic, enzymatic and molecular marker studies [12,14,17-19]. S. adhaerans (Forssk.) Link ex Chiov. (2n = 2x = 18) was identified as carrying a distinct genome from genome A (labeled B) by genomic in situ hybridization (GISH) [19]. The genome constitution of the tetraploid S. faberi (giant foxtail) and S. verticillata (bristle foxtail) was identified as being AABB, with 2n = 4x = 36 [19]. GISH studies also indicated that S. glauca bears an unknown genome type that is not related to either the A or B genome [19]. The diploid genome of S. grisebachii Fourn. ex Hemsl (2n = 2x = 18) was identified as genome C due to their poor hybridization signals with both A of S. viridis and B of S. adhaerans by GISH [20]. S. queenslandica (Domin) was detected as being the first autotetraploid in the genus, with a genome constitution of AAAA, with 2n = 4x = 36 [20]. The genome constitutions of most other species of the Setaria genus remain unknown.

The most recent phylogenetic analysis of the genus using the chloroplast marker ndhF shows accessions of S. faberi and S. verticillata grouping with S. viridis and S. italica[8]. However, other accessions of S. verticillata are placed elsewhere, and the authors suggest that this is caused either by the multiple origins of the polyploid and/or homoplasy in the distinguishing characteristic of the retrorse barbs on the sterile bristles in the inflorescence. An earlier study that used the knotted1 nuclear marker found both multiple placements of separate accessions of S. verticillata as well as multiple placements of copies from single accessions [9]. Benalbdelmouna [19] showed that the genome constitution of both S. faberi and S. verticillata was AABB, which supports the placement of one gene copy of S. verticillata with the A genome species S. italica and S. viridis, and the other copy elsewhere. In the ndhF phylogeny two accessions of S. verticillata are placed with S. adhaerens, shown by Benalbdelmouna to possess genome B. The relationships of S. faberi are less clear, primarily because of insufficient sampling, as the ndhF phylogeny only contains a single accession of S. faberi, and the knotted1 phylogeny does not contain that species.

Due to its small genome size, diploid nature and self-fertilization, S. italica is becoming a new model for functional and evolutionary studies in the grasses, while S. viridis is a model for C4 photosynthesis [21-23]. The release of the genomic sequences of foxtail millet has accelerated the establishment of these model systems [23,24]. Understanding the genetic relationships of Setaria genome types will be helpful in managing Setaria germplasm, and contribute to our understanding of the evolution history of this group of species. Genomic in situ hybridization (GISH) provides a visual and direct method for investigating genomic composition among species, and is especially useful in elucidating the complex origins of polyploid plants. This technique has been already applied in many groups such as Triticeae[25], Brassica[26], Nicotiana[27], Andropogon[28], and Setaria species [19,20]. In this report, GISH was applied to chromosome preparations of Setaria species of Eurasian origin with unknown genome constitution. The known genome types of A, B and C were used as probes to detect the genome composition of these species and to identify new genomes in the Setaria group. To further confirm the results obtained by GISH, 5S rDNA and knotted1 gene sequences were analyzed using Bayesian methods to elucidate their phylogenetic relationships. Sequences of 5S rDNA and knotted1 genes have already useful in the phylogenetic study of many plant species and of Setaria relationship in particular [9,14,27].

Methods

Plant material

The three diploid known genomes of S. viridis (genome A), S. adhaerans (genome B) and S. grisebachii (genome C) were used as testers to determine the genome constitution of other diploid and polyloid Eurasian species. The polyploid species examined in this paper include S. glauca, S. parviflora (Poir.) Kerguelen, S. palmifolia (Koen.) stapf, S. lachnea (Nees) Kunth, S. plicata (Lam.) T. Cooke and S. arenaria (Kitag.). The chromosome number of the accessions studied was identified by squashing root tips, as previously reported [20,29]. The chromosome preparations of at least one sample of each species were hybridized with probes made from the known diploid A, B and C species genomes (Table 1). For phylogenetic analysis with genomic sequences of the 5S rDNA and knotted1 genes, more accessions were added (Table 1). One sample of S. viridis (Qing 9) appeared morphologically distinct from other accessions and was analyzed along with representative accessions. Plant material used in this study, as well as their polyploid characteristics and geographical origin are listed in Table 1.

Table 1

Origin of the samples used, chromosome numbers, genome constitution if known, and the copy numbers of DNA fragments from each accession used for phylogenetic analysis

Species	Origin	Accession number	Code	Ploidy level	Genome	Copy 5SrDNA	Copy knotted1
S. viridis*	China (Hebei)	N033	S. vir-Q24	2n = 2x = 18	AA	1	1
S. viridis	Russia	09005	S. vir-W56	2n = 2x = 18	AA	1	1
S. italica+	China (Henan)	00024169	S. ita-Y1	2n = 2x = 18	AA	1	1
S. italica	South Africa, (Transvaal)	PI 209909	S. ita-C238	2n = 2x = 18	AA	1	1
Qing 9*+ (unidentified species)	China (Hebei)	N011	Qin9	2n = 2x = 18	BB	1	1
S. adhaerans*+	Spain	02448	S. adh-W94	2n = 2x = 18	BB	1	1
S. adhaerans	Hawaii	25001	S. adh-W41	2n = 2x = 18	BB	1	1
S. grisebachii*	Mexico	03001	S. gri-W8	2n = 2x = 18	CC	1	1
S. plicata*	China (Kunming)	25001	S. pli-N195	2n = 4x = 36	X(EE)	1	2
S. glauca*+	Iowa	04004	S. gla-W12	2n = 4x = 36	X(DD)	1	1
S. glauca	Canada	04005	S. gla-W13	2n = 4x = 36	X(DD)	1	1
S. glauca	Japan	04002	S. gla-W10	2n = 8x = 72	X(DD)	2	2
S. glauca	France	14003	S. gla-W82	2n = 4x = 36	X(DD)	1	1
S. lachnea+	Australia	11001	S. lac-W74	2n = 4x = 36	CCC’C’	1	2
S. palmifolia+	China (Kunming)	26001	S. pal-N193	2n = 6x = 54	X(EE)	3	2
S. parviflora+	Brazil	13002	S. par-W79	2n = 4x = 36	X(DD)	2	2
S. arenaria+	China (Kunming)	27001	S. are-N196	2n = 6x = 54	X(FF)	4	2
S. verticillata	France	08006	S. ver-W42	2n = 4x = 36	AABB	2	2
S. faberi	Russia	02005	S. fab-W5	2n = 4x = 36	AABB	2	1
S. faberi	Japan	02006	S. fab-W7	2n = 4x = 36	AABB	2	2
S. queenslandica	Australia	PI 316342	S. que-W89	2n = 4x = 36	AAAA	2	1

Note: The materials marked with * was used to be labeled as probe. The materials marked with + was used to make chromosome preparations. All materials were used for phylogenetic analysis. The putative genome constitution X represents an unknown genome constitution and the capital letter in the bracket of the Genome column indicated the novel genomes identified in the paper.

Chromosome and probe preparation

All seeds were germinated on moistened filter paper at 27°C in Petri dishes until the roots were 2 cm long, and then treated with 2 mM 8-hydroxyquinoline for 2 h at room temperature to accumulate metaphases. After rinsing with distilled water, the whole seedlings were fixed in a mixture of freshly prepared 1:3 glacial acetic and ethanol (100%), and stored at −20°C until use. For DNA probes, plants were grown in autoclaved soil, transferred into an open air field at the seedling stage, and DNA extracted from young leaves for PCR amplification of 5S rDNA gene and knotted1 gene fragments and for probe preparation for GISH.

Chromosome preparations were done according to Benabdelmouna et al [30], with some modifications. A single root tip was transferred in a drop of 45% acetic acid onto a clean slide before squashing. After squashing, the slides were then scanned for good chromosome spreads at prophase or metaphase stages with phase contrast microscopy, then slips were removed by immersing slides into liquid nitrogen for 10–15 min, and the air-dried slides were stored at room temperature until use.

In situ hybridization

For genomic in situ hybridization, total nuclear DNA from S. viridis (AA), S. adherans (BB), S. grisebachii (CC), Qing 9, S. glauca-W12, and S. plicata, were extracted from young plants and genomic DNA was labeled by the nick translation method with digaoxigenin-11-dUTP, (Roche). The method of GISH followed that of Bisht et al [31] with some modifications. The hybridization mixture (20 μl/per slide) included 100–150 ng DNA probe, 1 ng/μl salmon sperm DNA, 50%(v/v) deionized formamide, 2 × SSC, 0.1% SDS, and 10% dextran sulfate. DNA probes were denatured for 10 min at 95°C, immediately quenched on ice for least 10 min, denatured by immersion in 70% formamide-2 × SSC for 3 min at 80°C, then the chromosome preparations were dehydrated for 3 min each in a graded series of 70%, 90%, and 100% ethanol at −20°C. Probe mix was applied to each air-dried slide and hybridized overnight in a moist chamber at 37°C. After hybridization the slides were washed twice in 2 × SSC at 37°C for 3 min and 4 × SSC at room temperature for 5 min, and then the slides were treated with BSA blocking solution (5% BSA-2 × SSC) for 15 min at 37°C. Immunodetection of digoxigenated probes was carried out with Rhodamine conjugated anti-digoxigenin antibodies (Roche). Slides were then washed two times in 4 × SSC for 5 min at room temperature, chromosomes were counter-stained with DAPI in the antifade buffer (10 mg/ml, blue fluorescence). For visualization, chromosome preparations were analyzed using an Olympus epifluorescence microscope with appropriate filters. GISH hybridization results between Setaria species are list in Table 2.

Table 2

GISH hybridization results between species

Probe/Chromosome	S.ita-Y1(c)	Qing 9(c)	S.adh-W94(c)	S.lac-W74(c)	S.par-W79(c)	S.pal-N193(c)	S.gla-W12(c)	S. are-N196(c)	S. pli-N195(c)
S. vir-Q24(p)	√	×	×*	×	×	×	×*	×	×
S. adh-W94(p)	×*	√		×	×	×	×*	×	×
S. gri-W8(p)	×*		×*	√	×	×	×	×	×
Qing 9(p)			√
S. gla-W12(p)					√	×		×	×
S. pli-N195(p)						√		×

Note: (1) The p in the brackets following each accession indicates corresponding genomic DNA as probes used in GISH performance.

(2) The c in the brackets following each accession indicates corresponding chromosome preparation used in the GISH experiment.

(3) The √ indicates that positive signal was detected between the two samples in this paper, × indicates that no significant signal was detected between the two samples in this paper. × with superscripts * indicates the result with no significant signal was reported previously [19,20].

Phylogenetic analysis

Total genomic DNA was extracted from fresh leaves using the CTAB procedure [32]. The 5S rDNA gene fragments from each sample were amplified using primers designed on conserved regions of the 5S rDNA sequences from barley and wheat [33] with FP: 5′-GGACCTCCTGCGAAGTCCT-3′ and RP: 5′-CCCATCCGTGTACTACTCTC-3′. The PCR conditions were 95°C for 5 min, 32 cycles of 94°C for 55 s, 62°C for 25 s and 72°C for 35 s, followed by a final extension of 72°C for 10 min. The PCR mixture (20 μl) contained 100 ng template DNA, 250 μM of each dNTP (Takara), 0.5 μM of each primer, 2.0 μl of reaction buffer, and 1 unit of Ex Taq DNA polymerase (Takara). The knotted1 (kn1) gene fragments including part of the first intron, the whole sequences of the second intron and the second exon as described by Doust et al [9] were amplified using the primers pair of kn211-402F: 5′-TCAGAACTTTTGGCCGTGGGT-3′ and kn612-402R: 5′-GAGATGGACAGCGAGTTGAGC-3′. PCR reactions were denatured for 5 min at 95°C and then followed a step-down procedure where annealing temperature was stepped down from 65°C to 59°C, and then 35 amplification cycles were performed, each cycle including denaturation at 95°C for 30 s, annealing at 57°C for 1 min, primer extension at 72°C for 1 min, and a final extension of 72°C for 10 min. Products were separated by electrophoresis on 1.5% agrose gels, and the major band of each sample was isolated from the gel, cleaned using Qiagen columns, cloned into the PUCm-T or PMD18-T vector system, and then transformed into the DH5a strain of E. coli. After identification of recombinant clones, for diploid species, a minimum of two clones were sequenced, for tetraploid species, at least six clones were picked and sequenced. Kn1 and 5S rDNA fragments obtained were confirmed by comparison with Genbank. Sequences from the same accession were aligned using DNAMAN, and redundant sequences were deleted. Accession number for each clone has been deposited in Gene Bank and listed in Additional file 1: Table S1. Outgroup sequences [AB023618, DQ351339, JQ947589, X61308] were obtained from Genbank.

Multiple alignments of unique sequences from each sample were carried out using T-Coffee [34-36]. The phylogenetic trees based on 5S rDNA and kn1 sequences were analyzed under neighbor joining (Mega version 5.1) [37] and Bayesian approaches (Mr Bayes 3.1.2) [38,39]. Evolutionary models were chosen using jModeltest version 0.1.1 [40,41], and in both cases were a general time reversible model with a 4 category gamma rate model. Neighbor-joining analyses were run under the Maximum-composite likelihood model, with gamma values estimated in jModeltest, and tree support estimated with 1,000 bootstrapped sample sets. Mr Bayes was run using a GTR plus gamma model, with branch length unconstrained, branch length priors set to an exponential distribution with a parameter of 10, and shape parameter priors set to an exponential distribution with a parameter of 10. Bayesian analyses were run for 5,000,000 generations, with 4 chains on each of two nodes. Chains were compared every generation and nodes compared every 1,000 generations. Tracer version 1.5 [42] was used to estimate burnin, and a conservative 1,000,000 generations from the beginning of each run were removed. The remaining trees from each run were combined and a majority rule consensus tree used computed to summarize the data.

Results

GISH analysis

Genome identification of a novel diploid Setaria species

GISH hybridization patterns were investigated using genomic DNA probes to mitotic chromosomes. When the probe prepared from total genomic DNA of S. virdis-Q24 was hybridized on the chromosome of S. italica, a strong and total painting on all the chromosomes of S. italica was observed (Figure 1a). However, when the S. viridis-Q24 genomic DNA was used as a probe on chromosome preparations of Qing 9, little hybridization was observed except for two major signal points in the nucleolar organizer region (Figure 1b). When total DNA probe from Qing 9 was applied to chromosome preparations of S. adhaerans-W94, all 18 chromosomes strongly hybridized (Figure 1c-d). The same hybridization pattern was obtained in the reciprocal experiment when genomic DNA from S. adhaerans-W94 was hybridized to chromosome preparations of Qing 9 (Figure 1e-f).

Figure 1

GISH patterns obtained on different species. (a) GISH was carried out using S. viridis-Q24 genomic DNA as probe hybridizing on the chromosome preparation of S. italica-Y1. (b) Metaphase of Qing 9 probed with S. viridis-Q24 total genomic DNA probe, two major spots were detected in the nucleolar organizing regions (arrows). (c) DAPI counterstained metaphase plate from S. adhaerans-W94. (d) The same metaphase plate was hybridized with Qing 9 genomic DNA (red). (e) The metaphase of Qing 9 was counterstained with DAPI. (f) The same metaphase hybridized with genomic DNA of S. adhaerans-W94 (red). (g-h) Genomic DNA of S. viridis-Q24 (g) and S. adhaerans-W94 (h) was applied to S. lachnea chromosomes respectively. (i) DAPI counterstained metaphase plate from S. lachnea. (j) The same metaphase hybridized with the total genomic DNA of S. grisebachii. (k) The metaphase of S. palmifolia was counterstained with DAPI. (l) The same metaphase plate was hybridized with the genomic DNA of S. plicata (red). (m) DAPI counterstained metaphase plate from S. parviflora-W79. (n) The same metaphase hybridized with S. glauca-W12 genomic DNA. (o-r) The metaphases of S. arenaria respectively hybridized with the genomic DNA of S. viridis-Q24 (o), S. adhaerans-W94 (p), S. grisebachii (q), and S. glauca-W12 (r). (s) Metaphase of S. palmifolia probed with S. viridis-Q24 total genomic DNA probe. (t) Metaphase plate from S. glauca-W12 hybridized with probe from S. grisebachii. Bar = 5 μm.

Genome constitution of S. lachnea

We performed separate GISH experiments hybridizing chromosome preparations of S. lachnea with the three diploid species genomic DNA as probes. When total genomic DNA from S. viridis-Q24 (A genome) was used as a probe, no hybridization signals could be detected except for two major signals clustered at pericentromeric regions (Figure 1g), these being regions that are rich in repeat sequences to accumulate hybridization signals. The same patterns were obtained when using B genome of S. adhaerans-W94 genomic DNA as probe (Figure 1h). However, a completely different hybridization pattern was obtained when GISH was carried out using genomic DNA of S. grisebachii as probe, as all the 36 chromosomes were strongly hybridized with signal painting over most of the length of each chromosome (Figure 1i-j). Although multiple independent hybridizations with different washing protocol with higher stringency were carried out, the same result was obtained and no difference between the two sets of chromosomes was detected (Additional file 2: Figure S1).

Genome constitution of S. glauca and S. parviflora

The genome constitution of S. glauca, which is a tetraploid with 2n = 4x = 36 and which was previously identified as being neither A nor B genome by GISH [19], was tested by hybridizing its chromosomes with probes from the genomic DNA of S. viridis-Q24, S. adhaerans-W94 and S. grisebachii (Figure 1t) respectively. All those hybridizations were found to give little or no hybridization signal, except in the pericentromeric regions, which confirms the result obtained by Benabdelmouna et al [19], implying that the two sets of genomes of S. glauca are all different from the known genomes of A, B and C.

Chromosome preparations of S. parviflora, which is also a tetraploid, were hybridized with probes from the genomic DNA of S. viridis-Q24, S. adhaerans-W94 and S. grisebachii respectively, with the same results obtained as for S. glauca. Moreover, the chromosomes of S. parviflora-W79 were strongly hybridized with probes from genomic DNA of S. glauca-W12 (Figure 1m-n), implying that these two species have a close genetic relationship and they share very similar or the same genome.

Genome constitution of S. plicata and S. palmifolia

Chromosome preparations of the tetraploid species S. plicata were hybridized with probes made from the genomic DNA of S. viridis-Q24, S. adhaerans, S. grisebachii and S. glauca respectively. All the hybridization gave little or no signals, indicating that the two sets of genomes in S. plicata are different from the genome A, B, C and the genome of S. glauca. Chromosome preparations of hexaploid species with 2n = 6x = 54 of S. palmifolia were also hybridized with genomic DNA probes from S. viridis-Q24 (Figure 1s), S. adhaerans-W94, S. grisebachii and S. glauca-W12 respectively and no hybridization signal results were obtained, indicating that the 3 sets of genomes in S. palmifolia were quite different from the genomes of A, B, C and that of S. glauca. However, when total DNA probes from S. plicata were hybridized to chromosomes of S. palmifolia, a very strong hybridization pattern distributing all over the chromosomes were obtained (Figure 1k-l), indicating that these two species share the same or similar genome.

Genomic constitution of S. arenaria

Probes from total genomic DNA of S. viridis-Q24 (Figure 1o), S. adhaerans-W94 (Figure 1p), S. grisebachii (Figure 1q), tetroploid S. glauca-W12 (Figure 1r) and S. plicata were all hybridized with chromosome preparations of hexaploid species of S. arenaria (2n = 6x = 54), but little or no hybridization signal was obtained on the chromosomes. Those GISH hybridizations indicated that the 3 sets of genomes in S. arenaria are neither related with the known genomes of A, B and C, nor related with the unknown genomes in species of tetroploid S. glauca and S. plicata.

Phylogeny based on 5SrDNA sequences

All PCR amplifications for 5S rDNA sequences from primers designed by D’Hont et al [33] were successful using our Setaria genomic DNA as template, and target bands were isolated and subcloned for sequencing. For diploid species, such as S. viridis, S. italica, S. adhaerans and S. grisebachii, single sequences were obtained from a sample accession, but for polyploid species, such as S. verticillata, S. faberi, S. glauca, S. parviflora, S. palmifolia, S. plicata and S. arenaria, multiple isolates were sequenced and sequences obtained were first aligned to delete redundant sequences, before the unique ones were used for phylogenetic tree construction. The number of unique sequences obtained varied between the different polyploid species (Table 1).

A consensus tree generated from the Bayesian analysis of the 5S rDNA sequences is displayed in Figure 2, and six groups can be clearly identified (similar results were found for the neighbor joining tree, although with less resolution). The first group, which corresponds with the A genome, is composed of sequences from S. viridis, S. italica, S. verticillata, S. faberi and S. queenslandica. The sequence of S. faberi-W7-37 was somewhat divergent from the others of the A group sequences and also carried a large deletion of 41 bp compared to the others in this group. Group B is composed of sequences from S. adhaerans, S. verticillata, and Qing 9, which corresponds with the B genome. Two sequences of S. verticillata deposited in Genbank [AF227011, AF227012] were separately included in A and B group. Group C is composed of two sequences, one from S. grisebachii and the other from S. lachnea, which corresponds with the known C genome. Although S. lachnea is a tetraploid, only one 5S rDNA was amplified. Sequences in group D were all from two tetraploid species of S. glauca and S. parviflora with high support, indicating a new genome that is different from the known A, B and C genomes. High support values were also seen in Group E, which is composed of sequences from tetraploid S. plicata (one sequence) and hexaploid S. palmifolia (3 sequences), indicating another novel genome in the Setaria species group. Four unique sequences were obtained from hexaploid S. arenaria and they were classified into Group F, which implies yet another new genome in the Setaria genus.

Figure 2

Bayesian analyses for 5S rDNA sequences amplified in . Support value are Bayesian posterior probability. Two sequences deposited in Genbank [GenBank: AB023618, DQ351339] were used as outgroups. In some polyploid accessions, more than one copy that different in sequence were obtained, and they are distinguished in the tree by corresponding clone number following each sequence code.

Phylogeny based on kn1 sequences

Twenty-nine kn1 unique sequences were included in the phylogenetic analysis, obtained from the samples we used as well as one from S. palmifolia in GenBank [EF189834]. The consensus Bayesian tree in Figure 3 was similar in the groups that were delimited in the 5S tree (and similar results were found for the neighbor joining tree, although with less resolution). Group A was composed of the A genome sequences from 5 species, which include S. viridis, S. italica, S. verticillata, S. faberi and S. queenslandica. Group B was made up of 4 sequences corresponding with the known B genome from S. adhaerans, S. verticillata, and Qing 9, however, we did not detect any sequences from S. faberi in this group, albeit its tetraploid AABB genome constitution [19]. For the known C genome only two sequences were amplified from S. grisebachii and S. lachnea respectively, which form Group C in the tree constructed. However, one sequence from S. lachnea (W74-31) was aligned closely to the E group clade with high support. All sequences of kn1 from S. glauca and S. parviflora were classified into Group D, which agrees with the GISH result that S. glauca and S. parviflora share the same or similar genomes. Two sequences of kn1 from S. plicata, two sequences from S. palmifolia and the accession of S. palmifolia from GenBank [EF189834] were aligned into Group E, which also agrees with the GISH result and 5S rDNA tree. Only two unique sequences of kn1 were amplified from the hexaploid S. arenaria, which forms Group F in the phylogenetic tree, and their clear differences from other kn1 sequences is further evidence that the corresponding genomes in S. arenaria are distinct from the known A, B, C genomes and from the S. glauca and S. palmifolia genomes.

Figure 3

Bayesian analyses for sequences amplified in . Support values are Bayesian posterior probability. Two sequences deposited in Genbank [GenBank: JQ947589, X61308] are used as outgroup. In some polyploid accessions, more than one copy that different in sequence were obtained, and they are distinguished in the tree by the corresponding clone number following each sequence code.

Differences in the relationships between the genome types are evident by comparison of the 5S rDNA and kn1 trees. In particular, the relationships of genome E (S. plicata, S. palmifolia) is strongly supported as being with genome B in the kn1 tree but with genome A and C (albeit with less support) in the 5S rDNA tree. Likewise, in the kn1 tree genomes A and D are strongly supported as a phylogenetic group whereas in the 5S rDNA tree genome D is sister to a clade of A, C, and E genome species. In both trees, genome F (S. arenaria) is basal.

Discussion

Novel genomes identified by GISH and phylogenetic trees in the genus Setaria

There are over 125 species in the genus of Setaria[2], yet differences in genome constitution have been poorly studied. The genome of diploid species of green foxtail and foxtail millet was first designated as A genome by Li et al [10], and the genomes of diploid S. adhaerans and S. grisebachii were designated as B and C genomes respectively [19,20]. The genome constitutions of two tetraploid species, S. verticillata and S. faberi, were identified being AABB by GISH [19], and that of S. queenslandica as AAAA using GISH in our lab [20]; S. queenslandica being the only autotetraploid found in the Setaria genus. So far no other reports on genomes or genome constitution of Setaria species have been published.

Previous reports by GISH identified that the genomes in S. glauca were neither A nor B [19], and our result in this report from both GISH and phylogenetic trees indicates that genomes in S. glauca were also quite distinct from the newly identified C genome, suggesting a new genome in S. glauca which we designated as genome D. A close relationship between S. glauca and S. parviflora was identified by GISH and phylogenetic trees, imply that they share the D genome. Little or no signals were detected when chromosomes of S. plicata and S. palmifolia were hybridized with probes from genomic DNA of genomes A, B, C and that of S. glauca, and this is supported by the phylogenetic analyses that also show that the sequences from S. plicata and S. palmifolia are clearly distinguished from those of the known genomes and that of S. glauca and S. parviflora. This indicates another new genome in Setaria, designated as genome E, shared by S. plicata and S. palmifolia. The GISH pattern and phylogenetic result also indicate that the three sets of genomes in S. arenaria are distantly related with the known genome of A, B, C and that of S. glauca and S. plicata, suggesting another new genome in S. arenaria, designated genome F. Thus three new genomes are suggested by combined data from GISH and phylogenetic analyses, although the corresponding species of these new genomes are all polyploid. So far six distinct genome-types coexist in the genus of Setaria, reflecting the diversified and diverged genetic composition of this group of grasses, and in good concordance with ISSR result [13] and phylogenetic analyses [8,9]. Setaria is suspected to be polyphyletic, based on phylogenetic analysis using both chloroplast and nuclear markers [8,9], so it will be interesting to know whether related taxa outside the various groups of Setaria studied here share these genome types.

The B genome in S. faberi is distinct from the B genome in S. verticillata

S. verticillata and S. faberi were all identified as being allotetraploids with a genome constitution of AABB [19]. However, the two primer pairs amplifying the 5S rDNA and kn1 gene fragments only amplified from both the B genome diploid of S. adhaerans and the B genome of allotetraploid of S. verticillata, but gave no amplification from the putative B genome in S. faberi (Figures 2 &3), even though multiple PCR amplifications were tried and multiple clones sequenced. The same results were also obtained by Benabdelmouna et al [14] for the 5S rDNA marker. This suggests that the B genome in S. faberi has either diverged from the B genome of S. adhaerans and S. verticillata, or further recombination or backcrossing has occurred that led to the loss of those gene copies. Analysis of more molecular markers and a greater number of accessions will be necessary to distinguish between these possibilities. S. adhaerans and S. verticillata are both characterized by bristles with retrorse barbs, but the bristles of S. faberi are the common straight ones. S. verticillata appears to have originated from genome duplication of a hybrid between an A genome diploid and a B genome diploid, and the B genome diploid is genetically closely related with the current S. adhaerans. The origin of S. faberi was from genome duplication of a hybrid between an A genome diploid and an unknown diploid that are relatively distantly related to S. adhaerans B genome. Previous hypotheses have suggested that S. faberi originated from S. italica x S. adhaerens, based on the presence of large seeds [43]. Our results do not specifically address this hypothesis, but we suspect that large seeds in S. italica are the result of human selection during the last 10,000 years, and that S. faberi is of older origin than this. However, genetic diversity analysis of S. faberi accessions show little genetic variation [44], indicating that this taxon requires more study.

Genome constitution of S. lachnea was probably CCC’C’

Our GISH experiments clearly show that the two sets of chromosomes of S. lachnea had strong hybridization signals covering the entire chromosomes with probe from genomic DNA of diploid S. grisebachii, suggesting that S. lachnea is probably an autotetroploid species with genome constitution of CCCC (Figure 1i-j). To confirm this conjecture, multiple independent hybridizations with different washing protocol with higher stringency were carried out, giving the same results, and no differences between the two sets of chromosomes were detected (Additional file 2: Figure S1). However, only one of the two unique sequences of kn1 from S. lachnea was closely related to S. grisebachii representing the C genome, while the other (W74-31) was more closely related to the E genome sequences (Figure 3). We did not test hybridization of E genome probes to S. lachnea, so it remains a possibility that the second genome is related to the E genome. The evidence suggests that one genome set of S. lachnea is C, and the other set is a genome closely related with C with some sequence divergence, thus we describe the genome constitution of S. lachnea as CCC’C’.

Qing 9 is probably a newly identified species in B genome of Setaria

Qing 9 is a Setaria accession collected from Qiema of Luancheng, Shijiazhuang, Hebei province in China in 2003, and treated as a S. viridis sample. However, its morphology is clearly distinct from that of S. viridis, and ISSR data also indicated that it was distantly related with S. viridis samples with A genome, but closely related with B genome species S. adhaerans[13]. Our GISH results show that the chromosomes of Qing 9 hybridized well with probe from the B genome S. adhaerans, whereas no signal was detected when using the A genome S. viridis as probe. This clearly indicated that it is a B genome species and that it was misclassified as a S. viridis sample. The 5S rDNA and kn1 gene phylogenetic trees also clearly show that Qing 9 is closely related with S. adhaerans and distantly related with S. viridis, which well support our conjecture. So, Qing 9 is clearly a B genome diploid sample.

Morphological observations also clearly distinguishes Qing 9 from S. adhaerans. As a typical B genome species, S. adhaerans is characterized with bristles of deep retrorse barbs, tall and slim stem, and narrow leaf blade. But Qing 9 is characterized with shorter and sturdy stem, wide leaf blade, and especially its bristles are weakly retrorse hooked, which is not only clearly different from the deep retrorse hooked S. adhaerans but also clearly different from the straight ones of S. viridis. Qing 9 does not correspond to any of the twenty three indigenous species described in the Flora of China [45], suggesting that it is a newly identified species. Combine all those data, we make the hypothesis that Qing 9 is probably a not yet detected resident species in China. S. adhaerans is a sub-tropical B genome diploid species found around the Mediterranean area (including South Europe and North Africa), thus the identification of novel B genome diploid species indigenous to China will be important for the evolutionary study of the Setaria group and the grass family. Detailed studies of this taxon are currently under way.

Conclusions

The combined data provided by the GISH and phylogenetic analysis indicates that the diploid genome constitutions containing in the polyploid species S. glauca, S. plicata, and S. arenaria are clearly different from the known genomes of S. viridis (A), S. adherans (B) and S. grisebachii (C). These new genomes were designated as genome D, E and F respectively. The genome constitution of S. lachnea is probably CCC’C’, and Qing 9 is a B genome species indigenous to China. The results obtained provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

XD designed the study and supervised the experiment. HZ, WL, YW and HL participated in the growing of all the materials used. MZ, YW and NZ performed the GISH and sequence cloning. MZ, AND, JG and XD analyzed the Data and drafted the manuscript. All authors discussed the results and conclusion and read and approved the final manuscript.

Additional file 1: Table S1

Each clone was added to accession number deposited in Gene Bank.

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Additional file 2: Figure S1

Hybridization between S. grisebachii and S. lachnea with high stringency. The stringency was strengthened by additional wash of 0.1 × SSC at 37°C for 5 min each, 2 × SSC at 37°C for 5 min two times, the genome of S. grisebachii hybridized well with the two sets of chromosome of S. lachnea. Bar = 5 μm.

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