Phylogenetic relationships between Leymus and related diploid Triticeae species revealed by ISSR markers

To investigate the genetic diversity and phylogenetic relationships between polyploid Leymus and related diploid species of the Triticeae tribe, inter-simple sequence repeats (ISSR) markers was used to analyze 41 Leymus accessions representing 22 species and 2 subspecies, together with Pseudoroegneria stipifolia (St), Psathyrostachys fragilis (Ns), Australopyrum retrofractum (W), Hordeum bogdanii, H. chilense (H) and Lophopyrum elongatum (E^e). A total of 376 clear and reproducible DNA fragments were amplified by 29 ISSR primers, among which 368 (97.87%) fragments were found to be polymorphic. 8–18 polymorphic bands were amplified by each polymorphic primer, with an average of 12.69 bands. The data of 376 ISSR bands were used to generate Nei’s similarity coefficients and to construct a dendrogram by means of UPGMA. The similarity coefficients data suggested great genetic diversity in genus Leymus and related diploid Triticeae species, the genetic diversity among the different species more abundant than that of the different accessions. The dendrogram and principal coordinate analysis showed explicit interspecific relationships and demonstrated close phylogenetic relationships between Leymus species and Psathyrostachys.     

Phylogenetic relationships among Leymus and related diploid genera (Triticeae: Poaceae) based on chloroplast trnQ–rps16 sequences

To investigate the phylogenetic relationships among Leymus and related diploid genera, the genome donor of Leymus, and the evolutionary history of polyploid Leymus species, chloroplast trnQ–rps16 sequences were analyzed for 36 accessions of Leymus representing 25 species, together with 11 diploid taxa from six monogenomic genera. The phylogenetic analyses (Neighbor‐Joining and MJ network) supported three major clades (Ns, St and Xm). Sequence diversity and genealogical analysis suggested that 1) Leymus species from the same areas or neighboring geographic regions are closely related; 2) most of the Eurasian Leymus species are closely related to Psathyrostachys: P. juncea might serve as the Ns genome donor of polyploid Eurasian Leymus species; 3) the Xm genome may originate from ancestral lineages of Pseudoroegneria (St), Lophopyrum (E^e), Australopyrum (W) and Agropyron (P); 4) the trnQ–rps16 sequences of Leymus are evolutionarily distinct, and may clarify parental lineages and phylogenetic relationships in Leymus.     

Phylogeny and maternal donors of the tetraploid species with St genome (Poaceae: Triticeae) inferred from CoxII and ITS sequences

Mitochondrial CoxII and ITS sequences of 29 tetraploid species with St genome were compared with their related genera and species of Pseudoroegneria (Nevski) Á. Löve (St), Hordeum L. (H), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (E^b), Lophopyrum elongatum (Host) Á. Löve (E^e), Agropyron Gaertner (P), Australopyrum (Tzvelev) Löve (W) and Psathyrostachys Nevski (Ns). The results indicate that: (1) the maternal donors of North American and Eurasian StStHH tetraploid species may have acquired their St genome from distinct Pseudoroegneria gene pools, with Pse. spicata (Pursh) Á. Löve potentially the maternal donor of North American species; (2) Lophopyrum is the maternal donor of StStE^eE^e tetraploid species, hence, Pse. geniculata ssp. scythica (Nevski) Á. Löve, Elytrigia caespitosa (K. Koch) Nevski and El. caespitosa ssp. nodosa (Nevski) Tzvelev should be identified as species of Trichopyrum Á. Löve; (3) tetraploid species with the same maternal donors were more closely related to each other than those with different maternal donors.     

利用RAPD特异标记分析东北猬草染色体组成

选用5个染色体组特异的RAPD引物(St、H、Ns、Ee、Eb),对东北猬草[Hystrix komarovii (Roshev.) Ohwi]等5个猬草属及其8个近缘属物种进行PCR扩增,以探讨东北猬草的染色体组组成.结果显示:Hy.komarovii具有Ns染色体组特异的RAPD标记,而没有St、H、Ee和Eb特异的RAPD标记.表明Hy.komarovii含有Ns染色体组,而不含St和H染色体组,认为其染色体组组成可能与Hy.duthiei、Hy.coreana和Leymus arenarius一样,具有NsXm染色体组.根据染色体组分类原理,支持将东北猬草归于赖草属中.     

Genome- and species-specific markers and genome relationships of diploid perennial species in Triticeae based on RAPD analyses.

Eight different genomes (E, H, I, P, R, St, W, and Ns) represented by 22 diploid species of the tribe Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique. The genome relationships were obtained based on 371 RAPD fragments produced with 30 primers. The four species of the genus Psathyrostachys (having various Ns genomes) were closely related. The genomes Ee and Eb had a similarly close relationship and were distinct from all other genomes analyzed. Genomes P, R, and St were grouped in one cluster and genomes H and I in another. Genome W had a distant relationship with all other genomes. These results agree with the conclusions from studies of chromosome pairing and isozyme and DNA sequence analyses. Twenty-nine and 11 RAPD fragments are considered to be genome- and species-specific markers, respectively. One to six genome-specific markers were identified for each genome. These RAPD markers are useful in studies of genome evolution, analysis of genome composition, and genome identification.     

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase

Background  

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Leymus is a polyploid genus with a diverse array of morphology, ecology and distribution in Triticeae. The genomic constitution of Leymus was assigned as NsXm, where Ns was presumed to be originated from Psathyrostachys, while Xm represented a genome of unknown origin. In addition, little is known about the evolutionary history of Leymus. Here, we investigate the phylogenetic relationship, genome donor, and evolutionary history of Leymus based on a single-copy nuclear Acc1 gene.     

Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae)

Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A^u, B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π = 0.03343 and θ = 0.03536 for polyploid Ns genome sequences and π = 0.03886 and θ = 0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π = 0.0011 and θ = 0.0011. Nucleotide variation of diploid Aegilops speltoides (π = 0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π = 0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A^u, and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A^u, B, and D genomes were linked to T. urartu, A. speltoides, and A. tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum.     

Phylogenetic Analysis of Leymus (Poaceae: Triticeae) Inferred from Nuclear rDNA ITS Sequences

To investigate the phylogenetic relationships of polyploid Leymus (Poaceae: Triticeae), sequences of the nuclear rDNA internal transcribed spacer region (ITS) were analyzed for 34 Leymus accessions representing 25 species, together with three Psathyrostachys species (Ns genome), two Pseudoroegneria (St genome) species, Lophopyrum elongatum (E(e) genome), and Thinopyrum bessarabicum (E(b) genome). The phylogenetic analyses (maximum likelihood and Bayesian inference) supported two major clades, one including 21 Leymus species and three Psathyrostachys species, the other with nine Leymus species and four diploid species. The ITS RNA secondary structure of the Leymus species was compared with that of their putative diploid donor. It is suggested that (1) the species from the same areas or neighboring geographic regions are closely related to each other; (2) L. coreanus, L. duthiei, L. duthiei var. longearistatus, and L. komarovii are closely related to other Leymus species, and it is reasonable to transfer these species from the genus Hystrix to Leymus; (3) the ITS sequences of Leymus are evolutionarily distinct; (4) the different Leymus species and different distribution of a species derived their Ns genome from different Psathyrostachys species; and (5) there is a close relationship among Leymus, Pseudoroegneria, Lophopyrum, and Thinopyrum, but it is difficult to presume that the St, E(e), and E(b) genome may be the Xm genome donor of the Leymus species.     

Phylogenetic analysis of the genus Pseudoroegneria and the Triticeae tribe using the rbcL gene

The Pseudoroegneria species are perennial grasses in the Triticeae tribe, whose St genome has been linked to several important polyploid species. Due to frequent hybridization and complex genetic mechanism, the relationships within Pseudoroegneria, and within the Triticeae have been heavily disputed. Using the chloroplast rbcL gene we estimated the nucleotide diversity of 8 Pseudoroegneria species. We also examined the phylogenetic relationships within Pseudoroegneria and of Pseudoroegneria within the Triticeae. The estimates of nucleotide diversity indicated that Pseudoroegneria tauri and Pseudoroegneria spicata species had the highest diversity, while Pseudoroegneria gracillima had the lowest diversity. The phylogenetic analysis of Pseudoroegneria placed all P. spicata species into a clade separate from the other Pseudoroegneria species, while the relationship of the other Pseudoroegneria species could not be determined. Due to the groupings of Pseudoroegneria with the polyploid Elymus, our results strongly supported Pseudoroegneria as the maternal genome donor to Elymus. There was also weak support that P. spicata may be the maternal donor to the StH Elymus species.     

Genome constitutions of Roegneriaalashanica,R. elytrigioides,R. magnicaespes and R. grandis (Poaceae: Triticeae) via genomic in‐situ hybridization

The genomic constitutions of Roegneria alashanica, R. elytrigioides, R. magnicaespes and R. grandis were studied using GISH. DNA of Pseudoroegneria spicata (St), P. libanotica (St), P. stipifolia (St), R. ciliaris (StY), Lopophyllum elongatum (E^e), Agropyron cristatum (P) and Hordeum bogdanii (H) were used for probing, respectively. The results indicated that: 1) R. alashanica and R. magnicaespes contained one St genome, the other genome was unidentified, however, it was not an E, P, H or Y genome; 2) R. elytrigioides contained two St genomes and should on this basis be included in Pseudoroegneria; 3) R. grandis contained an St and an St^g genome. The St^g genome is suggested to be a modified form of the St genome of Pseudoroegneria and to be homoeologous with the Y genome. It might be an intermediate type between the St and Y genomes. Therefore, R. elytrigioides should be treated as Pseudoroegneriaelytrigioides.Roegneria alashanica, R. magnicaespes and R. grandis does apparently not belong in the genus Roegneria but further studies are needed to establish their correct taxonomic position.     

Phylogeny of the StH genome species in Triticeae (Poaceae): Evidence from chloroplast trnL-F and mitochondria COXII intron sequences

The StH genome species in Triticeae exhibit different morphological variations and extensive geographic distribution. To estimate the phylogenetic relationship of the StH genome species in Triticeae, mitochondria COXII intron and chloroplast trnL-F sequences of 16 StH genome species were analyzed with those of four Pseudoroegneria species (St) and four Hordeum species (H). Sequence diversity and genealogical analysis suggested that (1) the trnL-F and COXII sequence may evolve faster in the polyploid species than in the diploids; (2) the COXII intron has a high evolutionary rate compared to trnL-F sequence and would provide potentially useful phylogenetic analysis in the StH genome species; (3) different Pseudoroegneria species might serve as the maternal donor during the polyploid speciation of the StH genome species; (4) phylogenetic relationships of the StH genome species may be not linked with the inter-continental disjunction between Eurasian and North American.     

Cytogenetic and genomic relationships ofThinopyrum elongatum with twoPsathyrostachys species and withLeymus secalinus (Poaceae)

Intergeneric hybridizations were made betweenT. elongatum, and twoPsathyrostachys and fiveLeymus species. The seed set obtained onT. elongatum ×Leymus hybrids ranged from 5.65% to 20.00%, depending onLeymus species. The seed set obtained onT. elongatum ×Psathyrostachys hybrids ranged from 16.07% to 19.70%. Meiotic pairing at metaphase-I in JN diploid hybrids ofT. elongatum ×Psathyrostachys species revealed a very low level homology between the basic J and N genomes, and further demonstrated that the two genomes are quite diverged. Chromosome pairing in theT. elongatum ×Leymus secalinus hybrid averaged 15.19 univalents + 2.62 rod bivalents + 0.26 ring bivalents + 0.02 trivalents, suggesting that the partial J^e chromosomes ofT. elongatum has homology withLeymus secalinus genomes.L. secalinus might have 3–4 chromosomes originating from J^e genome.     

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.     

Hybridisation,genomic constitution and generic delimitation inElymus s. l. (Poaceae: Triticeae)

Intergeneric crosses were made between representatives of the genomically-defined generaElymus, Agropyron, Elytrigia, Pseudoroegneria, andThinopyrum. The genomic constitution ofElytrigia repens, the type species ofElytrigia, is shown to be SSH, a genomic combination otherwise found only inElymus. The S genome ofPseudoroegneria has almost always a dominant influence on the morphology of the taxa of which it is a component.Wang (1989) showed that the J genome inThinopyrum and the S genome have considerable homoeology, with a mean c-value of 0.35 in diploid SJ hybrids. A genetic coherence from S to SJ^e, J^e, J^eJ^b, and J^b can be expected, agreeing with the continuous morphologic variation pattern observed. Because of the absence of morphological discontinuities between the taxa,Pseudoroegneria (S),Elymus (SH, SY, sometimes with additional genomes),Elytrigia (SSH, SSHX), andThinopyrum (SJ, SJJ, J) are best treated as a single genus,Elymus, following the generic concept ofMelderis in Flora Europaea and Flora of Turkey. The basic genomic constituents ofElymus will then be the S and/or J genomes.Agropyron, with diploids, tetraploids, and hexaploids based on the P genome is morphologically distinct from other genera inTriticeae. In a few species ofElymus andPseudoroegneria, a P genome is an additional constituent. In these cases the P genome has a negligible morphological influence. Therefore, it seems reasonable to maintainAgropyron as a separate genus.     

Identifying the genome of wood barley Hordelymus europaeus (Poaceae: Triticeae)

Wood barley, Hordelymus europaeus, was compared with other Triticeae species by Southern and fluorescence in situ hybridisation using total genomic DNA and repetitive sequences as probes. On Southern blots, the total genomic probe from H. europaeus hybridised strongly to DNA of its own species and to Leymus and Psathyrostachys, indicating the presence of Ns genome in H. europaeus. Furthermore, the total genomic probe from P. fragilis hybridised to DNA of H. europaeus as much as to all of the Psathyrostachys and Leymus species examined. Ns genome-specific DNA sequences isolated from L. mollis (pLmIs1, pLmIs44 and pLmIs53) hybridised essentially to H. europaeus and all of the species of Leymus and Psathyrostachys. Chromosomal localization of these clones on H. europaeus confirmed the presence of Ns genome-specific DNA on all chromosomes, indiscriminately. Under moderate hybridisation stringency the Ns genome-specific probes, together with repetitive sequences pTa71 and pAesKB7, produced species-specific RFLP banding profiles on Southern blots. A phenetic tree based on these profiles revealed a distinct Ns species cluster within the Triticeae, represented by Leymus and Psathyrostachys species. Hordelymus europaeus belonged to this Ns cluster. Chromosomal mapping of the 18S-25S and the 5S ribosomal genes, together with the repetitive sequence pLrTaiI, corroborated that H. europaeus was most probably related to Leymus, especially the European/Eurasian members of sect. Leymus. In an attempt to identify the genome of H. europaeus, different approaches were employed; the results clearly showed that wood barley had the Ns basic genome and nothing else.     

Phylogeny and maternal donor of Kengyilia (Triticeae: Poaceae) based on chloroplast trnT–trnL sequences

The chloroplast DNA regions trnT–trnL was used to analyze to phylogenetic relationships and maternal donor of Kengyilia species and their closely related species. The Neighbor-Joining phylogenetic reconstructions partitioned the species into two reciprocally monophyletic groups. Kengyilia melanthera was related to species of Agropyron, whereas the other species were related to species of Pseudoroegneria and Roegneria. These results indicate that there have been at least two phylogenetically divergent maternal donors within Kengyilia, i.e. Agropyron (P genome) and Pseudoroegneria (St genome). In addition, the St genome of Kengyilia had several origins and diverse species of Pseudoroegneria might have taken part in the formation of polyploid species of Kengyilia.     

Genome origins in Leymus (Poaceae: Triticeae): evidence of maternal and paternal progenitors and implications for reticulate evolution

The polyploid Leymus species have the Ns nuclear genomes evolved from Psathyrostachys and the Xm nuclear genomes from unknown origins. Currently, little is known about the cytoplasmic genomes of Leymus, and the species of Psathyrostachys that transferred the Ns genome to Leymus remain elusive. To determine the origins of the plastid and nuclear genome for Leymus species, sequences of two chloroplast genes, rpoA and rbcL, and partial sequences of the nuclear gene DMC1 of 15 Leymus species were phylogenetically analyzed with those of 71 accessions belonging to 19 monogenomic genera in Triticeae. Both rpoA and rbcL sequences revealed that Psathyrostachys juncea, P. lanuginosa, and P. stoloniformis had close phylogenetic relationships with the Eurasian and one North American Leymus accessions, L. cinereus. Three American Leymus species, L. erianthus, L. triticoides, and L. innovatus had different maternal origins from Eurasian Leymus species. DMC1 sequences of Leymus were grouped into several phylogenetically distant clades indicating that either Ns or Xm originated from different lineages. These results suggest multiple contributions to the chloroplast as well as nuclear genomes in Leymus species. The comprehensive data indicate reticulate evolution in polyploid Leymus.     

Genome origin and phylogenetic relationships of Elymus villosus (Triticeae: Poaceae) based on single-copy nuclear Acc1, Pgk1, DMC1 and chloroplast trnL-F sequences

To investigate the genome origin and phylogenetic relationships of Elymus villosus, three single-copy nuclear gene (Acc1, Pgk1 and DMC1) and chloroplast trnL-F gene sequences of two accessions of E. villosus were analyzed with those of eighteen allotetraploids (StH, StY, StP and StE^e genomes) and thirty-five diploid taxa representing eighteen basic genomes in Triticeae. The results revealed that: (1) the genomic constitution of E. villosus is StH as Elymus; (2) North America Pseudoroegneria species served as the maternal donor during the allotetraploid speciation of E. villosus; (3) E. villosus is closely related to North America Elymus species; (4) it is reasonable to recognize the E. villosus as Elymus L. sensu stricto.     

Multidisciplinary approach to genome analysis in the diploid species,Thinopyrum bessarabicum and Th. elongatum (Lophopyrum elongatum), of the Triticeae

Summary The J and E genome species of the Triticeae are invaluable sources of salt tolerance. The evidence concerning the phyletic relatedness of the J genome of diploid Thinopyrum bessarabicum and the E genome of diploid Th. elongatum (=Lophopyrum elongatum) is discussed. Low level of chromosome pairing between J and E at different ploidy levels, suppression of J-E pairing by the Ph1 pairing regulator that inhibits homoeologous pairing, complete sterility of the diploid hybrids (JE), karyotypic divergence of the two genomes, differences in total content and distribution of heterochromatin along their chromosomes, and marked differences in gliadin proteins, isozymes, 5S DNA, and rDNA indicate that J and E are distinct genomes. Well-defined biochemical markers have been identified in the two genomes and may be useful in plant breeding. The level of distinction between J and E is comparable to that among the universally accepted homoeologous genomes A, B, and D of wheat. Therefore, the J and E genomes are homoeologous and not homologous, although some workers continue to call them homologous. The previous workers' data on chromosome pairing in diploid hybrids and/ or karyotypic differences in the conventionally stained chromosomes do not provide sufficient evidence for the proposed merger of J and E genomes (and, hence, of the genera Thinopyrum and Lophopyrum) specifically and for establishing genome relationships generally. Extra precautions should be exercised before changing the designation of an established genome and before merging two genera. A uniform, standardized system of genomic nomenclature for the entire Triticeae is proposed, which should benefit cytogeneticists, plant breeders, taxonomists, and evolutionists.Cooperative investigations of the USDA-Agricultural Research Service and the Utah Agricultural Experiment Station, Logan, UT 84322, USA. Approved as Journal Paper no. 3832     

Comparison of Acetyl-CoA carboxylase 1 (Acc-1) gene diversity among different Triticeae genomes

It has widely been documented that life form and mating system have significant influences on genetic diversity. In the tribe Triticeae, several genera contain both annual and perennial species, whereas other genera comprise strictly annual or perennial species. It was suggested that Triticeae annuals have originated from Triticeae perennials. The present study aims to analyze nucleotide diversity of Acc-1 gene among different Triticeae genomes, and attempts to link effects of life history (annuals and perennials) and mating systems. The nucleotide diversity of 364 Acc-1 sequences in Triticeae species was characterized. The highest estimates of nucleotide diversity values (π = 0.01919, θ = 0.03515) were found for the Ns genome among the genomes analyzed. Nucleotide diversities in the D genome and Ns genome of polyploids are higher than those in respective genomes of diploids, while in the St genome of polyploids, it is lower than that in the St genome of diploids. The averaged π value (0.013705) in the genomes of perennials is more than twice of the value (0.00508) in the genomes of annuals. The averaged π value (0.01323) in the genomes of outcrossing species is two-fold of the value (0.005664) in the genomes of selfer. Our results suggested that the evolutionary history and mating system may play an important role in determining nucleotide diversity of Acc-1 gene in each genome.