Y. H. Zhou

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.

Phylogenetic relationships among the species of Elymus 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.

Cloning and characterization of four novel SnRK2 genes from Triticum polonicum

SnRK2 are plant-specific serine/threonine kinases that are involved in plant responses to abiotic stresses. In this study, four novel genes SnRK2s:TpSnRK2.11, TpSnRK2.2, TpSnRK2.5, and TpSnRK2.10 from dwarf Polish wheat (Triticum polonicum L.) were characterized and classified into three groups. TpSnRK2.5 and TpSnRK2.11 were members of group 1; TpSnRK2.2 was member of group 2; TpSnRK2.10 belonged to group 3. The expression of TpSNRK2.2 was strongly regulated by polyethylene glycol (PEG), NaCl, and cold in roots and leaves, as well as by ABA in leaves. The transcript of TpSnRK2.5 was intensely induced by all the treatments in roots and leaves. The distinct expression patterns of TpSnRK2.10 indicate that this gene was very sensitive to ABA and NaCl, less sensitive to cold and PEG. The transcript of TpSnRK2.11 was activated significantly by PEG, NaCl, and cold, but weakly by ABA. Our results indicate that these four genes were probably involved in wheat responses to different abiotic stresses in different tissues.

Transcriptome-wide identification and expression analyses of ABC transporters in dwarf polish wheat under metal stresses

ABC transporters, which comprise one of the largest protein families, are involved in maintaining osmotic homeostasis, nutrient uptake, pathogen resistance, and metal tolerance. In this study, 30 ABC genes in dwarf polish wheat were characterized and classified into seven subfamilies (ABCA - ABCG). Among them, 24 ABC transporters were newly found in wheat. The expressions of 13 ABC genes in roots and leaves under six metal stresses were also analyzed. All these genes were differentially regulated by Cd (except ABCE2, ABCF4, and ABCF6 in roots), suggesting that these genes participate in Cd transport, sequestration, or uptake. These genes were also differentially regulated by other metals including Cu, Mg, Zn, Fe, and Ni. Results suggest that the expressions of ABC transporters in dwarf polish wheat played important roles in metal transport and detoxification.

Nucleotide polymorphism pattern and multiple maternal origin in Thinopyrum intermedium inferred by trnH-psbA sequences

Thinopyrum intermedium is an important species with potential utilization value in breeding of wheat. In this study, the non-coding intergenic region of trnH-psbA was investigated to assess the genetic diversity and infer the maternal origin within T. intermedium accessions. Eleven haplotypes were distinguished among the thirty-five accessions of T. intermedium. They showed a relatively low nucleotide diversity (π) of 0.00473 ± 0.00037 and a moderately high haplotype diversity (Hd) of 0.733 ± 0.061. In the phylogenetic analysis, all accessions of T. intermedium were positioned into two clades, which corresponded to the different diploid donors. These results suggested that there were two phylogenetically divergent maternal donors in T. intermedium.

The origin of Triticum petropavlovskyi Udacz. et Migusch.: demonstration of the utility of the genes encoding plastid acetyl-CoA carboxylase sequence

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. Based on the sequences of a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase (Acc-1), a total of 47 accessions Triticum and Aegilops representing diploid, tetraploid and hexaploid were used to estimate the origin of Triticum petropavlovskyi. Phylogenetic analysis was performed based on the intron, intronxa0+xa0sy and exon data sets sequence using maximum likelihood, neighbor-joining and median-joining networks. The A and B genome sequences from Acc-1 loci show that T. petropavlovskyi shares the highest averaged sequence identity with T. polonicum from Xinjiang and exotic landraces of T. aestivum, and reveals specific progenitor-descendant relationships. The D genome sequences of the Acc-1 genes from T. petropavlovskyi are identical to the sequences of the D genome orthologs in T. aestivum, while the relationship of T. petropavlovskyi and Ae. tauschii are most distant. Our findings do not suggest the probability of an independent allopolyploidization event and a single mutation in T. aestivum in the origin of T. petropavlovskyi, but indicate a greater degree of gene flow between T. aestivum and T. polonicum leading to origin of T. petropavlovskyi. It is most likely that T. petropavlovskyi was originated from T. polonicum from Xinjiang to exotic landraces of T. aestivum via a spontaneous introgression or breeding effort.

Production of intergeneric hybrid between dwarfing polish wheat (Triticum polonicum L.) and Aegilops tauschii Cosson. with reference to wheat origin.

Dwarfing polish wheat is a dwarfing accession of Triticum polonicum L. from Xinjiang of China. In the present study, the artificial hybridization between dwarfing polish wheat and two accessions of Aegilops tauschii Cosson. (AS60 and AS65) was carried out, and the F1 hybrids were obtained successfully without using embryo rescue techniques for the first time. The crossabilities of hybrids T. polonicum × Ae. tauschii (AS60) and T. polonicum × Ae. tauschii (AS65) were 1.67% and 0.60% respectively. Only the hybrids of T. polonicum × Ae. tauschii (AS60) germinated well, and 24 F1 hybrid plants were obtained. All the F1 hybrid plants grew vigorously, and the morphological traits were similar to bread wheat. The F1 plants had some obvious traits inherited from T. polonicum and Ae. tauschii and were completely sterile. Chromosome pairing in the hybrid was characterized by a large number of univalents, with an average of 20.56 and 0.22 bivalents per PMC, and no ring bivalents and multivalents were observed. Furthermore, the potential value of the F1 hybrids between T. polonicum and Ae. tauschii for studying wheat origin and breeding are discussed.

Phylogeny and maternal donor of Roegneria and its affinitive genera (Poaceae: Triticeae) based on sequence data for two chloroplast DNA regions (ndhF and trnH–psbA)

Roegneria C. Koch is a relatively large polyploid perennial genus with 130 species in the Triticeae, and consisting of the St and Y genomes. There are different opinions about whether Roegneria is an independent genus, or whether it should be included in the genus Elymus L. For many species of Roegneria, their genome constitution and phylogenetic relationship are still unknown. More research about the maternal genome donor of the Roegneria species is needed. To investigate the phylogenetic relationships and maternal genome donor of Roegneria and its affinitive genera, phylogenetic analyses of two chloroplast regions ndhF and trnH–psbA sequences were carried out in this study. The results showed that: (i) Campeiostachys Drobow (StYH) and all Roegneria (StY, StStY) species were scattered with Pseudoroegneria Á. Löve (St) species; (ii) R. sinica Keng, R. schugnanica (Nevski) Nevski, R. seriotina Keng, and Elymus calcicolus (Keng) Á. Löve containing the St genome; (iii) there was differentiation among species of Pseudoroegneria; and (iv) the St genome in diploid, tetraploid, and hexaploid species are divergent. Thus, it is suggested that: (i) Pseudoroegneria served as the maternal genome donor of Roegneria, including four species with unknown genomic constitutions (R. sinica, R. schugnanica, R. seriotina, and E. calcicolus); (ii) species of Roegneria or Pseudoroegneria might serve as the maternal genome donor of Campeiostachys; and (iii) the St genome has undergone differentiation during polyploidization in diploid, tetraploid, and hexaploid species.

The complete chloroplast genome sequence of Pseudoroegneria libanotica, genomic features, and phylogenetic relationship with Triticeae species

Pseudoroegneria libanotica is an important herbage diploid species possessing the St genome. The St genome participates in the formation of nine perennial genera in Triticeae (Poaceae). The whole chloroplast (cp) genome of P. libanotica is 135 026 bp in length. The typical quadripartite structure consists of one large single copy of 80 634 bp, one small single copy of 12 766 bp and a pair of inverted regions (20 813 bp each). The cp genome contains 76 coding genes, four ribosomal RNA and 30 transfer RNA genes. Comparative sequence analysis suggested that: 1) the 737 bp deletion in the cp of P. libanotica was specific in Triticeae species and might transfer into its nuclear genome; 2) hot-spot regions, indels in intergenic regions and protein coding sequences mainly led to the length variation in Triticeae; 3) highly divergence regions combined with negative selection in rpl2, rps12, ccsA, rps8, ndhH, petD, ndhK, psbM, rps3, rps18, and ndhA were identified as effective molecular markers and could be considered in future phylogenetic studies of Triticeae species; and 4) ycf3 gene with rich cpSSRs was suitable for phylogeny analysis or could be used for DNA barcoding at low taxonomic levels. The cpSSRs distribution in the coding regions of diploid Triticeae species was shown for the first time and provided a valuable source for developing primers to study specific simple sequence repeat loci.

Cloning and characterization of four TpSnRK2s from dwarf Polish wheat

Protein phosphorylation/dephosphorylation is a major signalling event induced by abiotic stresses in plants. Sucrose nonfermenting 1-related protein kinase 2 (SnRK2) plays important roles in response to osmotic stress. In the present study, four SnRK2s, TpSnRK2.1/3/7/8, were cloned and characterized from Triticum polonicum L. (dwarf Polish wheat, DPW, AABB). All of these were individually located on 2AL, 1AL, 2AL, and 5BL. Two spliced isoforms of TpSnRK2.8 (TpSnRK2.8a and TpSnRK2.8b) were observed. TpSnRK2.1 and TpSnRK2.3 were classified into the group II; TpSnRK2.7 was classified into the group I; and TpSnRK2.8a/b were classified into the group III. Expression patterns revealed that TpSnRK2.1 responded to cold, NaCl, polyethylene glycol (PEG), and abscisic acid (ABA) in both roots and leaves; TpSnRK2.3 was strongly regulated by cold, NaCl, and ABA in both roots and leaves, and by PEG in roots; TpSnRK2.7 was induced by NaCl and PEG in roots, but was not activated by ABA; and TpSnRK2.8s were significantly activated by cold, NaCl, PEG, and ABA in both roots and leaves. From the above results, we inferred that TpSnRK2.1/3/8 may participate in the responses to environmental stresses in ABA-dependent signal transduction pathway but TpSnRK2.7 is possibly involved in responses to environmental stresses in a non-ABA-dependent manner. They play important roles in specific tissues under different stresses.