Genome analysis of species in the genus Hystrix (Triticeae; Poaceae)

Genomic in situ hybridisation (GISH) and Southern genomic hybridisation were applied in order to gain further knowledge regarding generic delimitation of the genus Hystrix as well as to clarify the genomes of the Hystrix species H. patula, H. longearistata, H. coreana, H. duthiei and H. komarovii. The hybridisation intensity of different genomic probes was compared among the Hystrix species and with other Triticeae species. The Southern- and GISH results confirm that H. patula contains the StH genome and show that H. komarovii most likely has a variant of this StH genome. The other Hystrix species under study, i.e. H. longearistata, H. coreana and H. duthiei, contain an Ns basic genome, and most probably two variants of this basic genome, Ns ¹ Ns ² . The genus Hystrix is thus not a monophyletic group of species.     

Phylogenetic relationships among Hystrix species and related species based on expressed sequence tag‐polymerase chain reaction

Abstract Twelve species, including three Hystrix species, five Leymus species, Hordeum bogdanii, Pseudoroegneria spicata, Psathyrostachys huashanica, and Roegneria ciliaris, were used for expressed sequence tag‐polymerase chain reaction (EST‐PCR) assay. A total of 125 products were amplified by 72 sets of EST‐PCR markers developed in barley, among which 106 (84.8%) products were found to be polymorphic. Each EST‐PCR marker produced 0–6 polymorphic bands, with an average of 1.47. The relationship between H. duthiei ssp. duthiei and H. duthiei ssp. longearistata is close, but they are remote to H. patula. Hystrix duthiei ssp. duthiei and H. duthiei ssp. longearistata were clustered with Leymus species and Psathyrostachys huashanica, which suggested that they have close genetic relationships. The results of EST‐PCR analysis are basically comparable with those obtained from studies on cytology, which indicated that EST‐PCR can be used to assess the genetic relationships among the perennial species in Triticeae.     

Genetic relationships among <Emphasis Type="Italic">Hystrix patula,H. duthiei</Emphasis> and <Emphasis Type="Italic">H. longearistata</Emphasis> according to meiotic studies and genome-specific RAPD assay

Hybrids including Hystrix patula, H. duthiei and H. longearistata were obtained and genetic relationships among them were studied. Meiotic pairing in hybrids of H. duthiei × Psathyrostachys juncea (Ns), H. longearistata × Psa. juncea (Ns), Leymus multicaulis (NsXm) × H. duthiei, L. multicaulis (NsXm) × H. longearistata, Elymus sibiricus (StH) × H. patula, Roegneria ciliaris (StY) × H. patula, R. ciliaris (StY) × H. duthiei and R. ciliaris (StY) × H. longearistata averaged 5.76, 5.44, 11.94, 10.88, 10.08, 3.57, 0.46 and 0.90 bivalents per cell, respectively. The results indicated that H. duthiei and H. longearistata had the NsXm genomes of Leymus, while H. patula contained the StH genomes and had a low genome affinity with the StY genomes of Roegneria. Results of genome-specific RAPD assay were comparable with the chromosome pairing data. According to the genomic system of classification in Triticeae, H. patula should be considered as Elymus hystrix L., while H. duthiei and H. longearistata as Leymus duthiei and Leymus duthiei ssp. longearistata, respectively.     

Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences

To estimate the phylogenetic relationship of polyploid Hystrix in Triticeae, two single-copy nuclear genes (Acc1 and DMC1) and chloroplast trnL-F sequences of six Hystrix taxa were analyzed with those of nine Leymus species (NsXm), four Elymus species (StH) and 13 diploid taxa from seven monogenomic genera. Phylogenetic analyses reveal that Hystrix taxa contain two distinct types of genome constitution, despite the overall morphological and ecological similarity among Hystrix taxa. One type of genome constitution is StH (Hy. patula) as Elymus, the other is NsXm (Hy. californica, Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata and Hy. komarovii) as Leymus. The St, H and Ns genomes in Hystrix are donated by Pseudoroegneria, Hordeum and Psathyrostachys, respectively. The donor of the Xm genome is closely related to Agropyron (P). The trnL-F data especially indicate that there has been a maternal haplotype polymorphism in Hystrix species. Based on these results, we suggest that Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata, Hy. komarovii and Hy. californica should be included in the genus Leymus, and Hy. patula in the genus Elymus.     

Phylogenetic relationships among the species of <Emphasis Type="Italic">Elymus</Emphasis> sensu lato in Triticeae (Poaceae) based on nuclear rDNA ITS sequences

The genus Elymus L. sensu lato includes Roegneria, Elymus, Hystrix, Sitanion and Kengyilia, and they are very important group in the tribe Triticeae. However, the phylogenetic relationships and taxonomic status of them are still in dispute. The ITS sequences were obtained and analyzed for their phylogenetic relationships by using Maximum Parsimony (MP) and Bayesian Inference (BI) methods. The main results were as follows: (1) Most species in Roegneria, Elymus and Sitanion were clustered in the St clade with diploid St genome species, and it was difficult to distinguish the species in Roegneria and Elymus; (2) The polyploid species with St genomes in the St clade were divided into three groups, which suggests that there exists differentiation of St genome in polyploids; (3) Most species of Kengyilia have only P-type of clone and clustered with diploid Agropyron species, which may suggest that Kengyilia is a valid genus; (4) Hy. patula, the type species of Hystrix was clustered with species of Elymus, while Hy. duthiei ssp. duthiei, Hy. duthiei ssp. longearistata, Hy. coreana and Hy. komarovii were grouped with diploid Psathyrostachys species. It indicated that Hy. patula is distinct related to other Hystrix species, and it is reasonable to treat Hystrix patula as Elymus hystrix and other species in Hystrix should be transferred to Leymus; (5) The “clones bias” in ITS sequences are widespread in the allopolyploid species. The article is published in the original.     

Biosystematic studies on Hystrix longearistata from Japan and Hystrix duthiei from China (Poaceae: Triticeae)

Morphological comparison, cytogenetic study and fertility analysis of Hystrix duthiei (2n = 28) from China, Hystrix longearistata (2n= 28) from Japan and their artificial hybrids were carried out. Morphologically H. duthiei was similar to H. longearistata. H. longearistata had longer lemma awn, wider leaf and 2～3 florets per spikelet, while H. duthiei had 1～2 florets per spikelet. These two taxa can be easily crossed. F_l hybrids showed very high degree of bivalent pairing (13～14 bivalents) at the metaphase- I of meiosis. No multivalents were found. The fertility of pollen and seed set of the parents were normal, while the F_l hybrids were of only partial fertility. H. longearistata was closely related to H. duthiei. They should be included in the same species. Because of the differences of their distributions and habitats, some morphological divergency and a little sterility barrier have had appeared between them. It is reasonable to treat Hystrix longearistata as a sub-species of Hystrix duthiei .     

Development of primers to amplify mitochondrial DNA control region of Old World porcupines (subgenus Hystrix)

Eight primers were developed for the amplification of mitochondrial DNA control region of Old world porcupines (subgenus Hystrix). Successful amplifications of low‐quality DNA extracted from old (12 years old) and recent quills were performed, thus facilitating field sampling. Successful cross‐species amplifications were obtained for Hystrix africaeaustralis, H. cristata and H. indica. Length and structure of mitochondrial DNA control region were analysed and its usefulness as genetic marker for interspecific and population investigation was discussed.     

Phylogeny of Hystrix and related genera (Poaceae: Triticeae) based on nuclear rDNA ITS sequences

The taxonomic status of Hystrix and phylogenetic relationships among Hystrix and its related genera of Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), Elymus (StH), Leymus (NsXm), Thinopyrum bessarabicum (E(b)) and Lophopyrum elongatum (E(e)) were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The type species of Hystrix, H. patula, clustered with species of Pseudoroegneria, Hordeum, Elymus, Th. bessarabicum and Lo. elongatum, while H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii were grouped with Psathyrostachys and Leymus species. The results indicate that: (i) H. patula is distantly related to other species of Hystrix, but is closely related to Elymus species; (ii) H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii have a close affinity with Psathyrostachys and Leymus species, and H. komarovii might contain the NsXm genome of Leymus; and (iii) the St, H and Ns genomes in Hystrix originate from Pseudoroegneria, Hordeum and Psathyrostachys, respectively, while the Xm in Hystrix and Leymus has a complex relationship with the E or St genomes. According to the genomic system of classification in Tiritceae, it is reasonable to treat Hystrix patula as Elymus hystrix L, and the other species of Hystrix as species of a section of Leymus, Leymus Sect. Hystrix.     

Morphology and cytology of intergeneric hybrids involvingLeymus multicaulis (Poaceae)

The morphology and meiotic behaviour of pollen mother cells were studied in hybrids involvingLeymus multicaulis (2n = 28) ×Psathyrostachys huashanica (2n = 14),L. multicaulis ×P. juncea (2n = 14), andL. secalinus (2n = 28) ×L. multicaulis. Chromosome pairing was almost identical in theL. multicaulis ×P. huashanica, andL. multicaulis ×P. juncea hybrids, in which it averaged 7.30 univalents + 6.69 bivalents + 0.096 trivalents and 7.48 univalents + 6.75 bivalents, respectively. The meiotic pairing in the two hybrids indicated that oneL. multicaulis genome was closely homologous with theP. huashanica andP. juncea genomes. BothP. huashanica andP. juncea are possibly donors of oneL. multicaulis genome. Chromosome pairing in theL. secalinus ×L. multicaulis hybrid averaged 4.49 univalents + 11.71 bivalents + 0.02 trivalents, indicating that the genomes ofL. multicaulis andL. secalinus are to some degree homologous. However, they are sufficiently differentiated to insure species distinctness.     

Phylogenetic relationships among Hystrix species and related species based on expressed sequence tag-polymerase chain reaction

Twelve species, including three Hystrix species, five Leymus species, Hordeum bogdanii, Pseudoroegneria spicata, Psathyrostachys huashanica, and Roegneria ciliaris, were used for expressed sequence tag-polymerase chain reaction (EST-PCR) assay. A total of 125 products were amplified by 72 sets of EST-PCR markers developed in barley, among which 106 (84.8%) products were found to be polymorphic. Each EST-PCR marker produced 0–6 polymorphic bands, with an average of 1.47. The relationship between H. duthiei s...     

Production and cytogenetic analysis of intergeneric hybrids betweenElymus anthosachnoides andPsathyrostachys huashanica (Poaceae: Triticeae)

Intergeneric hybridization betweenElymus anthosachnoides (2n = 28,SSYY) andPsathyrostachys huashanica (2n = 14,NN) was performed. Three hybrid plants, obtained via embryo rescue, were intermediate between the parents in morphology and developed vigorously, but were completely sterile. The mean chromosome configuration was 19.48 I + 0.76 II per cell in the hybrids at meiotic metaphase I. This result indicates thatE. anthosachnoides andP. huashanica are distantly related and that there is little or no homoeology betweenN (P. huashanica) andS orY (E. anthosachnoides) genomes.     

Cytogenetical studies on artificial hybrids amongElymus sibiricus,E. dahuricus andAgropyron tsukushiense in the tribe Triticeae,Gramineae

To explore the cytogenetical relationships ofElymus andAgropyron of the tribe Triticeae, Gramineae, two species of AsiaticElymus, E. sibiricus (2n=28) andE. dahuricus (2n=42), and a JapaneseAgropyron, A. tsukushiense (2n=42) were crossed. Pentaploid and hexaploid F₁ hybrids were vigorous. All pollen grains were aborted and none of the hybrids produced seed. For the crossE. sibiricus × A. tsukushiense, the average chromosome pairing per cell at the MI of the PMCs in the F₁ was 16.38 univalents, 8.93 bivalents, 0.25 trivalents and 0.01 quadrivalents; for the crossE. dahuricus × A. tsukushiense, it was 4.41 univalents, 17.67 bivalents, 0.32 trivalents, 0.28 quadrivalents and 0.04 quinquevalents; and for the crossE. dahuricus × E. sibiricus, it was 17.11 univalents, 8.74 bivalents, 0.04 trivalents and 0.07 quadrivalents. From the present results, it is concluded thatE. sibiricus contains one genome andE. dahuricus contains two genomes, which are homologous to those ofA. tsukushiense, and that the third genome ofE. dahuricus might be partially homologous to the remaining genome ofA. tsukushiense. This conclusion is also supported by the cytogenetical analysis ofE. dahuricus × E. sibiricus. Contribution No. 27 from the Plant Germ-plasm Institute, Faculty of Agriculture, Kyoto University, Kyoto, Japan.     

Cytogenetics of a Hordeum vulgare x Elymus patagonicus hybrid (n=4x=28)

Summary Hordeum vulgare L. (2n=2x=14) was hybridized with Elymus patagonicus Speg. (2n=6x=42). The hybrid had 28 chromosomes, genomically represented as HSH₁H₂, and was perennial with a codominant phenotype. The chromosomes were meiotically associated as 19.6 univalents + 0.004 ring bivalents + 2.6 rod bivalents + 0.8 trivalents + 0.14 quadrivalents in 1,129 meiocytes, with a chiasma frequency of 4.77 per cell. The bivalent pairing presumably is an autosyndetic but modified expression of the H₁H₂ genomes of E. patagonicus, since ring bivalents were rare. This does not preclude the association of the H. vulgare H genome chromosomes with either H₁ and/or H₂ genomes of E. patagonicus to form bivalent or multivalent associations. A further evaluation of the genome homologies of H. vulgare, H. bogdanii, E. canadensis and E. patagonicus is proposed.     

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC₂DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). QTLs were detected as a marker main effect and/or a marker × environment interaction effect (M × E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs the M × E interaction effect, and at 21 QTLs both the effects were significant. The majority of the M × E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m² and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.     

Cytogenetic studies in the genus Zea

Summary New cytological evidence supporting x = 5 as the basic chromosome number of the genus Zea has been obtained as a consequence of our analysis of the meiotic configurations of Zea mays ssp. mays, Z. diploperennis, Z. perennis and of four F₁ artificial interspecific hybrids. Z. mays ssp. mays (2n = 20) presents regular meiosis with 10 bivalents (II) and is considered here as a typical allotetraploid (A₂A₂B₂B₂). In Z. diploperennis (2n = 20) 10II are formed in the majority of the cells, but the formation of 1III + 8II + 1I or 1III + 711 + 3I in 4% of the cells would indicate its segmental allotetraploid nature (A₁A₁B₁B₁). Z. perennis (2n = 40) had 5IV + 10II in 55% of the cells and would be considered as an auto-allooctoploid (A₁A₁A'₁A'₁C₁C₁C₂C₂). Z. diploperennis x Z. mays ssp. mays (2n = 20) presents 10II in ca. 70% of the cells and no multivalents are formed. In the two 2n = 30 hybrids (Z. mays ssp. mays x Z. perennis and Z. diploperennis x Z. perennis) the most frequent meiotic configuration was 5III + 5II + 5I and in 2n = 40 hybrid (Z. diploperennis x Z. perennis) was 5IV + 10II. Moreover, secondary association was observed in the three abovementioned tetraploid taxa (2n = 20) where one to five groups of two bivalents each at diakinesis-metaphase I was formed showing the affinities between homoeologous genomes. The results, as a whole, can be interpreed by assuming a basic x = 5 in this polyploid complex. The main previous contributions that support this working hypothesis are reviewed and its phylogenetic implications studied are discussed.     

Genetic diversity and phylogeny in Hystrix (Poaceae, Triticeae) and related genera inferred from Giemsa C-banded karyotypes

The phylogenetic relationships of 15 taxa from Hystrix and the related genera Leymus (NsXm), Elymus (StH), Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), and Thinopyrum (E) were examined by using the Giemsa C-banded karyotype. The Hy. patula C-banding pattern was similar to those of Elymus species, whereas C-banding patterns of the other Hystrix species were similar to those of Leymus species. The results suggest high genetic diversity within Hystrix, and support treating Hy. patula as E. hystrix L., and transferring Hy. coreana, Hy. duthiei ssp. duthiei and Hy. duthiei ssp. longearistata to the genus Leymus. On comparing C-banding patterns of Elymus species with their diploid ancestors (Pseudoroegneria and Hordeum), there are indications that certain chromosomal re-arrangements had previously occurred in the St and H genomes. Furthermore, a comparison of the C-banding patterns of the Hystrix and Leymus species with the potential diploid progenitors (Psathyrostachys and Thinopyrum) suggests that Hy. coreana and some Leymus species are closely related to the Ns genome of Psathyrostachys, whereas Hy. duthiei ssp. duthiei, Hy. duthiei ssp. longearistata and some of the Leymus species have a close relationship with the E genome. The results suggest a multiple origin of the polyploid genera Hystrix and Leymus.     

Meiosis,SC-formation,and karyotype structure in diploidPaeonia tenuifolia and tetraploidP. officinalis

The meiosis of the diploidPaeonia tenuifola and the allotetraploidP. officinalis was studied after conventional methanol/acetic acid-fixation and synaptonemal complex (SC) spreading. Meiosis inP. tenuifolia (2n = 10) is normal with five bivalents in metaphase I, and the SCs in pachytene show regular features. InP. officinalis (2n = 4x = 20) univalents, bivalents and multivalents are found in metaphase I. The SCs reveal several abnormalities: a high number of unpaired lateral elements, partner exchanges between three and four lateral elements, loops and lateral element thickenings. These characteristics are compared with the situations found in other polyploid and hybrid species. It is noteworthy that the abnormalities in meiosis ofP. officinalis are not reflected in its somatic karyotype. Its features were analysed after silver staining and fluorescent staining with chromomycin and compared with those ofP. tenuifolia. Synaptonemal Complex Spreading in Plants2; for part1 see Pl. Syst. Evol.154, 129–136 (1986).     

Phylogenetic relationships of species in <Emphasis Type="Italic">Pseudoroegneria</Emphasis> (Poaceae: Triticeae) and related genera inferred from nuclear rDNA ITS (internal transcribed spacer) sequences

To evaluate the phylogenetic relationships of species in Pseudoroegneria and related genera, the nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for eighteen Pseudoroegneria (St), two Elytrigia (E ^e St), two Douglasdeweya (StP), three Lophopyrum (E ^e and E ^b ), three Agropyron (P), two Hordeum (H), two Australopyrum (W) and two Psathyrostachys (Ns) accessions. The main results were: (i) Pseudoroegneria gracillima, P. stipifolia, P. cognata and P. strigosa (2x) were in one clade, while P. libanotica, P. tauri and P. spicata (2x) were in the other clade, indicating there are the differentiations of St genome among diploid Pseudoroegneria species; (ii) P. geniculata ssp. scythica, P. geniculata ssp. pruinifera, Elytriga caespitosa and Et. caespitosa ssp. nodosa formed the E ^e St clade with 6-bp indel in ITS1 regions; and (iii) Douglasdeweya wangii, D. deweyi, Agropyron cristatum and A. puberulum comprised the P clade. It is unreasonable to treat P. geniculata ssp. scythica and P. geniculata ssp. pruinifera as the subspecies of P. geniculata, and they should be transferred to a new genus Trichopyrum, which consists of species with E ^e St genomes. It is also suggested that one of the diploid donor of D. wangii and D. deweyi is derived from Agropyron species, and it is reasonable to treat tetraploid species with StP genomes into Douglasdeweya.     

Comparison of the karyotypes ofPsathyrostachys juncea andP. huashanica (Poaceae) studied by banding techniques

The karyotypes ofP. juncea (Elymus junceus) andP. huashanica (both outbreeders) were investigated by Feulgen-staining and by C-, N-, and Agbanding, based on a single plant in cach case. Both species have 2n=2x=14 and large chromosomes, possibly a generic character. The karyotype ofP. juncea has 8 metacentrics and 6 SAT-chromosomes with minute, heterochromatic satellites while that ofP. huashanica has 9 metacentrics and 5 SAT-chromosomes only, 2 of which with small, heterochromatic satellites. The C-banding patterns ofP. juncea chromosomes comprise from one to five, mostly small, bands at distal, and terminal positions, while those ofP. huashanica chromosomes are characterized by large telomeric bands in most arms. Banding patterns and chromosome morphology allow identification of the homologues of the seven chromosome pairs inP. juncea, but of two pairs inP. huashanica only. The patterns of both taxa are polymorphic, supporting that both taxa are outbreeders. The karyotypic characters suggest thatP. juncea is more closely related toP. fragilis than either is toP. huashanica. N-banding stains weakly. Silver nitrate staining demonstrates that nucleolus organizers of both species have different nucleolus forming capacities. The presence of micronucleoli suggests that both species have an extra unidentified chromosome with nucleolus forming capacity.     

Polyploidy and aneuploidy inOphrys,Orchis, andAnacamptis (Orchidaceae)

Studies on chromosome numbers and karyotypes in Orchid taxa from Apulia (Italy) revealed triploid complements inOphrys tenthredinifera andOrchis italica. InO. tenthredinifera there is no significant difference between the diploid and the triploid karyotypes. The tetraploid cytotype ofAnacamptis pyramidalis forms 36 bivalents during metaphase I in embryo sac mother cells. Aneuploidy was noticed inOphrys bertolonii ×O. tarentina with chromosome numbers n = 19 and 2n = 38. There were diploid (2n = 2x = 36), tetraploid (2n = 4x = 72), hexaploid (2n = 6x = 108) and octoploid (2n = 8x = 144) cells in the ovary wall of the diploid hybridOphrys apulica ×O. bombyliflora. Evolutionary trends inOphrys andOrchis chromosomes are discussed.