Table of Contents

13 November 2014, Volume 52 Issue 6
Cover illustration: Tetraploid wild emmer wheat (TD). A, Premature plants. B, A natural TD population in eastern Upper Galilee, Israel. C, Spike color polymorphism of mature TD spikes. D, A TD population in Yehudiyya, Israel. Photographed by Eviatar NEVO. See NEVO, pp. 673–696 in this issue.
  • Commentary
  • Mary E. BARKWORTH, Roland von BOTHMER
    J Syst Evol. 2014, 52(6): 667-672.
    The International Triticeae Symposia were initiated to encourage scientists working on different aspects of the Triticeae1 to share information and examine the distant relatives of its cereal species. There have now been seven symposia, each in a different country. The scope of these symposia is briefly reviewed. The merits of the symposium series are identified as their interdisciplinary nature and small size.
  • Reviews & Research Articles
  • Eviatar NEVO
    J Syst Evol. 2014, 52(6): 673-696.
    Allotetraploid wild emmer wheat, Triticum dicoccoides (TD) 2n = 28, the progenitor of most cultivated bread wheat, is an ecological specialist and excellent model organism for advancing evolutionary theory, wheat evolution, and wheat improvement. The center of origin and diversity of TD is northeastern Upper Galilee and the Golan. Elsewhere in the Fertile Crescent, it occurs in semi-isolated and isolated populations. The genetic structure is generally an “archipelago.” Regional and localgenetic patterns are partly or largely adaptive at the protein and DNA levels, both at coding and noncoding genomes, correlated with and predictable by environmental abiotic and biotic stresses. TD is a rich, mostly untapped, genetic resource for improving cultivated wheat, harboring drought, salt, mineral, and disease resistances, grain proteins, and with high variation in photosynthetic yield. TD was chromosomally mapped with 549 molecular markers and 70 QTLs for 11 traits of agricultural importance and domestication. Prospects include sequencing its genome; including 80% repeat elements for structural, functional, and regulatory polymorphisms, epigenetics, and genetic resources for wheat improvement. TD is affected by global warming both phenotypically (advancing flowering time) and genotypically (genetic erosion, SSR allelic turn-over, and novel drought resistant alleles). Hence, it should be conserved in situ and ex situ, to safeguard the arguably best source for wheat improvement and future food production in an exploding world population.
  • Richard R. C. WANG, Baorong LU
    J Syst Evol. 2014, 52(6): 697-705.
    Understanding the classification and biosystematics of species in Triticeae Dumort., an economically important tribe in the grass family (Poaceae), is not an easy task, particularly for some perennial species. Does genomic analysis facilitate the understanding of evolutionary relationships of these Triticeae species? We reviewed literature published after 1984 to address questions concerning: (1) genome relationships among the monogenomic diploid species; (2) progenitors of the unknown Y genome in Elymus polyploids, X genome in Thinopyrum intermedium, and Xm genome in Leymus; and (3) genome constitutions of some perennial Triticeae species that were unknown or misidentified. A majority of publications have substantiated the close affinity of the Eb and Ee genomes in Th. bessarabicumand Th. elongatum, supporting the use of a common basic genome symbol. The E genome is close to the St genome of Pseudoroegneria and ABD genomes ofTriticum/Aegilops complex, providing an explanation for transferring genes from the E to ABD genomes with relative ease. Although the solid proof is still lacking, theW, P, and especially Xp genomes are possible origins for the Y genome of polyploid Elymus. The absence of the E genome and the allopolyploidy nature of tetraploidLeymus species have been unequivocally confirmed by both cytogenetic and molecular studies. However, the donor of the Xm genomes of Leymus was only speculated to be related to the P genome of Agropyron and F genome of Eremopyrum. Intermediate wheatgrass (Th. intermedium) has been extensively studied. The presence of the St (as the previously designated X) genome in Th. intermedium is now unequivocal. Its two more closely related E1 and E2 genomes are shown to be older versions of the E genome rather than the current Eb and Ee genomes. Speciation of Th. intermedium was similar to that of Triticum aestivum, in which the Js/Es(like B) genomes had the greatest differentiation from the current J (Eb) genome owning to repetitive sequences of the V genome, whereas its St (like D) had the least differentiation from the current St genome. Species with unknown or misidentified genomes have been correctly designated, including those with the ESt, StP, StPY,StWY, EStP, HW, StYHW, and NsXm genomes. Some of those species have been transferred to and renamed in appropriate genera.
  • Genlou SUN
    J Syst Evol. 2014, 52(6): 706-711.
    Recent molecular phylogenetic studies on Elymus have added to our understanding of the origination of Elymus species. However, evolutionary dynamics and speciation of most species in Elymus are unclear. Molecular phylogeny has demonstrated that reticulate evolution has occurred extensively in the genus, as an example, the largest subunit of RNA polymerase II (rpb2) and phosphoenolpyruvate carboxylase (pepC) data revealed two versions of the St genome, St1 and St2contributing to speciation of E. caninus. Phylogenetic analyses of E. pendulinus uncovered additional genome-level complexity. Our data indicated that both chloroplast and nuclear gene introgression have occurred in the evolutionary process of E. pendulinus. Non-donor species genomes have been detected in severalElymus species, such as in allohexaploid E. repens (StStStStHH), a Taeniatherum-like (Ta genome in Triticeae) GBSSI sequence, Bromus- (Bromeae) and Panicum-like (Paniceae) ITS sequences have been detected. The chloroplast DNA data indicated that Pseudoroegneria is the maternal genome donor to Elymus species, but whether different Elymus species originated from different St donors remains an open question. The origin of the Y genome in Elymus is puzzling. It is clear that the Ygenome is distinct from the St genome, but unclear on the relationships of Y to other genomes in Triticeae. Introgressive hybridization may be an important factor complicating the evolutionary history of the species in Elymus. The extent of introgression and its role in creating diversity in Elymus species should be the objective of further investigations.
  • Hai-Qin ZHANG, Rui-Wu YANG, Cai-Rong YANG,Yan HUANG,Xing FAN,Li-Na SHA,Hou-Yang KANG,Yi WANG, Yong-Hong ZHOU
    J Syst Evol. 2014, 52(6): 712-715.
    Hystrix Moench was a perennial genus of the Triticeae. Its members differed from those of other genera in the tribe in lacking glumes. The type species is H. patulaMoench, a North American taxon. When it became accepted that H. patula should be included in Elymus, Hystrix could not be used as a generic name. The problem became how to treat the other species that had been included in Hystrix. Hystrix patula, like many other species of Elymus, has the StH genomic composition but H. coreana (Honda) Ohwi, H. californica (Bol.) Kuntze, H. duthiei (Stapf) Bor ssp. duthiei, and H. duthiei ssp. longearistata have the NsXm genomic composition that is associated with Leymus. Using genomic in situ hybridization analysis, we showed that H. komarovii (Roshev.) Ohwi has an NsEe genomic composition, a combination not known from any other species. Hystrix sibirica (Trautv.) Kuntze and H. duthiei ssp. japonica are included in Leymus on morphological grounds. The status of H. kunlunensis K. S. Hao is not clear. In this paper, we summarize our results and those of others concerning what is now known and the problems that remain concerning the species that used to be included in Hystrix.
    J Syst Evol. 2014, 52(6): 716-721.
    The objective of this paper is to summarize the work in my group on FISH (fluorescent in situ hybridization) mapping of Ns-specific repetitive DNA sequences fromLeymus and discuss the results in the context of classification based on the genome system currently used among Triticeae researchers. The key question here is whether the genome composition of a tetraploid Leymus species should be NsXm or NsNs (Ns1Ns2). Different types of Leymus-specific dispersed retroelement-like repeats have been isolated and characterized. Because the sequences occur in significantly high copy number in Leymus, based on strong hybridization signal in Southern blots, they are considered essentially specific to Leymus. They are also abundant in Psathyrostachys, the progenitor of Ns genome in Leymus. These dispersed repeats are found to distribute over the whole of all Leymus chromosomes, without any differentiation between chromosomes that have been suggested to be of different genomic origins, meaning that all genomes in Leymus are the same. GISH (genomic in situ hybridization) experiments on Leymus chromosomes using Psathyrostachys genomic DNA as probes further support the NsNs (Ns1Ns2) genome constitution for Leymus. The Xm genome of an unknown origin might have been there in the beginning of the allopolyploidization process, but the Ns genome-specific elements must have spread predominantly and rapidly across genomes, thus homogenizing the nuclear genomes of Leymus. I present here for the first time evidence that Ns-specific dispersed repeats can spread in a very short time, from Leymus over to wheat in Triticum × Leymus hybrids growing in artificial conditions.
  • Li-Na SHA, Xing FAN, Hai-Qin ZHANG, Hou-Yang KANG, Yi WANG, Xiao-Li WANG, Li ZHANG, Chun-Bang DING, Rui-Wu YANG, Yong-Hong ZHOU
    J Syst Evol. 2014, 52(6): 722-734.
    Leymus Hochst. is a polyploid genus with a diverse array of morphology, cytology, ecology, and distribution in Triticeae. To investigate the phylogenetic relationships and maternal genome donor of polyploid Leymus, the chloroplast trnH-psbA region and mitochondrial coxII intron sequences of 33 Leymus taxa were analyzed with those of 36 diploid perennial species representing 19 basic genomes in Triticeae. The results showed that reticulate evolution occurred in Leymus species, with the cytoplasmic lineage of Leymus contributed by different progenitors. Interspecific relationships of Leymus were also elucidated on the basis of orthologous comparison. Our data suggested that: (i) due to incomplete lineage sorting and/or difference in the pattern of chloroplast and mitochondrial inheritance, the genealogical conflict between the two genealogical patterns suggest the contribution of Psathyrostachys Nevski, Agropyron J. Gaertn, Eremopyrum (Ledeb.) Jaub. & Spach, Pseudoroegneria (Nevski) Á. Löve, Thinopyrum Á. Löve, and Lophopyrum (Host) Á. Löve to the cytoplasmic lineage of Leymus; (ii) there is a close relationship among Leymus species from the same area or neighboring geographic regions; (iii) L. coreanus (Honda) K. B. Jensen & R. R.-C. Wang, L. duthiei (Stapf) Y. H. Zhou & H. Q. Zhang ex C. Yen, J. L. Yang & B. R. Baum, L. duthiei var. longearistatus (Hack.) Y. H. Zhou & H. Q. Zhang ex C. Yen, J. L. Yang & B. R. Baum, and L. komarovii(Roshev.) C. Yen, J. L. Yang & B. R. Baum are closely related to other Leymus species, and it is reasonable to transfer these species from the genus Hystrix Moench to Leymus; (iv) Leymus species from North America are closely related to L. coreanus from the Russian Far East and L. komarovii from northeast China but are evolutionarily distinct from Leymus species from Central Asia and the Qinghai–Tibet Plateau. The occurrence of multiple origin and introgression could account for the rich diversity and ecological adaptation of Leymus species.
  • Jun LI, Hong-Shen WAN, Wu-Yun YANG
    J Syst Evol. 2014, 52(6): 735-742.
    Synthetic hexaploid wheat (SHW) that combines novel and elite genes from the tetraploid wheat Triticum turgidum L. and wild ancestor Aegilops tauschii Coss., has been used to genetically improve hexaploid common wheat. The abundant genetic diversity in SHW can effectively make breakthroughs in wheat genetic improvement through the inclusion of increased variation. In this paper, we reviewed the current advances in research and utilization of the primary SHW lines and SHW-derived wheat varieties that have enhanced evolution of modern wheat under conditions of natural and artificial selection in southwestern China. Using primary SHW lines, four high-yielding wheat varieties have been developed. In addition, using the SHW-derived varieties as breeding parents, 12 new wheat varieties were also developed. Results of genotype–phenotype and fingerprint analysis showed that the introgressed alleles from SHW lines have contributed a great number of elite characters to the new wheat varieties, and these elite characters include disease resistance, more spikes per plant, more grains per spike, larger grains, and higher grain-yield potential. We found that the primary SHW lines and SHW-derived varieties have identifiable effects to enhance genetic variation and adaptive evolution of modern hexaploid wheat, which significantly increased the grain yields of hexaploid wheat in recent years. These findings have significant implications in the breeding of high-yielding wheat varieties resistant to biotic and abiotic stresses using SHW as genetic resources.
  • Reviews & Research Articles
  • Yun-Ze LU, Le WANG, Hong YUE, Meng-Xing WANG, Ping-Chuan DENG, David EDWARDS, Song WEINING
    J Syst Evol. 2014, 52(6): 743-749.
    Miniature inverted repeat transposable elements (MITEs) are the most ubiquitous transposable elements in eukaryotic genomes; they play a prominent role in sequence divergence and genome evolution. There are many well-characterized Stowaway-like MITE families in wheat, but their distribution, abundance, and composition at the chromosome level are still not well understood. In this study, we systematically investigated the Stowaway-like MITEs in wheat group 7 chromosomes based on the survey sequences of isolated wheat chromosomes, to compare them at the chromosome level and to reveal their evolutionary role on wheat polyploidization. In summary, 2026 MITEs were identified, of which 587, 714, and 725 were distributed on 7A, 7B, and 7D chromosomes, respectively. There are more MITEs present on 7D, compared to 7A and 7B, suggesting A and B subgenomes eliminated some repetitive elements during two hybridization processes. Furthermore, some chromosome/arm-specific MITEs were also identified, providing information on the function and evolution of MITEs in wheat genomes. The sequence diversity of the MITE insertions was also investigated. This study for the first time investigated the abundance and composition of MITEs at the chromosome level, which will be beneficial to improve our understanding of the distribution of wheat MITEs and their evolutionary role in polyploidization.
  • Jutta C. BURGER, Norman C. ELLSTRAND
    J Syst Evol. 2014, 52(6): 750-764.
    Feral rye is an invasive North American weed that evolved from domesticated rye in the last century. In order to determine how this weed diverged from its cultivated ancestor and whether it has evolved regional differences across its new range in the western United States, we planted both feral rye from different regions and its progenitor in three common garden sites spanning the North-South axis of that range (eastern Washington, northern California, and southern California, respectively). We measured seedling emergence, survival, vegetative growth, flowering phenology, and reproductive output concurrently across sites over a single growing season. All traits were found to be genetically based. All feral populations were typically shattering contrasting with domesticated rye's typically non-shattering seed head. They also flowered later, tillered more, grew shorter, and produced smaller seeds in at least one population. Near the center and proposed origin of its introduced range, all feral rye populations produced significantly more seed than cultivars. Northern feral populations flowered later than southern populations and cultivars. Shifts were not symmetrical: southern populations performed well at all sites. But northern populations showed more evidence of local adaptation, faring poorly in southern California. Clearly, feral rye has evolved from its cultivated progenitor by more than just acquiring shattering. Furthermore, it has diverged regionally, although not all populations are fully locally adapted. Notably, feral rye populations exhibited a greater range of phenotypes than rye cultivars, suggesting that its evolution is not simply due to selection acting on existing variation within individual cultivars.
  • Ya-Xi LIU, Ji-Rui WANG, Ze-Hou LIU, Yan WANG, Xing CHEN, Robert J HENRY, Yu-Ming WEI, Eviatar NEVO, You-Liang ZHENG
    J Syst Evol. 2014, 52(6): 765-778.
    Alpha-amylases play essential roles in germination, and the malting and brewing processes, by hydrolyzing starch granules present in the endosperm of barley.Hordeum spontaneum C. Koch, the progenitor of cultivated barley that harbors rich genetic diversity, was collected from seven different environments. To investigate the influence of microclimatic ecological divergence on α-amylase, single nucleotide polymorphisms (SNPs) in amy genes from these populations were determined. A total of 16 and 17 SNPs were detected in the coding sequences of amy1 and amy2, respectively, from the seven wild barley populations. Among these SNPs, three in amy1-2 and nine in amy2-2 were significantly associated with ecological factors. The genetic divergence of amy sequences was significantly different among the populations. Natural microclimatic selection was apparently the major evolutionary driving force causing interslope divergence and adaptive evolution of these genes. The genetic variation in amy1-2 and amy2-2 was at least partly ecologically determined in these populations, representing adaptive patterns generated by natural selection. The SNPs were apparently generated by natural selection in climatic environmental patterns at both the micro (“Evolution Canyon”) and macro (across Israel, Galilee, and Negev) scales.
    J Syst Evol. 2014, 52(6): 779-782.
    The barley (Hordeum vulgare) spike exists in two alternative forms: six-rowed or two rowed. The genetic basis of this difference lies in the single gene Vrs1, the recessive allele of which is responsible for the six-rowed phenotype. The gene encodes a homeodomain-leucine zipper I class transcription factor. Its paralogHvHox2 is well conserved among the cereals, whereas Vrs1 acquired its function after the speciation of barley. To determine whether it is the mode of expression or neofunctionalization which accounts for the action of Vrs1, a comparative analysis was carried out between HvHox2 and Vrs1. This revealed that HvHOX2 and VRS1 share the same transcriptional activation activity. In situ hybridization analysis showed that HvHox2 mRNA is concentrated in the vascular bundles of the immature spike, whereas Vrs1 message is deposited exclusively in the pistil, lemma, palea, and lodicule of the lateral spikelets. The transcript abundance of Vrs1 was over 10-fold higher than that of HvHox2 during the pistil developmental stage, suggesting that the key function of Vrs1 is to inhibit gynoecial development. An analysis of six-rowed spike mutants which are non-allelic to vrs1 showed that Vrs1 was up-regulated by Vrs4, whereas HvHox2 expression was not. These data demonstrate that it is most likely a divergence in gene expression which has determined the function of Vrs1.
    J Syst Evol. 2014, 52(6): 783-789.
    Aegilops distribution was revised on localities in the territory of the Czech Republic and the former Czechoslovakia, based on herbarium data, literature and floristic databases. The only surviving species Ae. cylindrica forms the northern limit of distribution in the Danube basin, other sites are secondary. In situ conservation was proposed for two Czech sites where Aegilops have been naturalized. An ex situ gene bank collection has been maintained in the Gene Bank Prague since 1985. The collection includes 21 species and 1099 accessions. The whole collection was evaluated for breeding-valuable characters: resistance to leaf diseases, cereal aphids, viral diseases, and qualitative parameters. Recently, the collection was retested for the present races of leaf and stem rust including new introductions from Kazakhstan. Six different leaf rust races and five different stem rust races collected from the Czech Republic were applied in the older tests, and three races from each rust species in the recent tests. The highest number of accessions resistant both to wheat leaf rust and wheat stem rust and powdery mildew was found in Ae. speltoides (90%). Different reactions of individual accessions of the tested species to the three different pathotypes of each rust species indicates that several diverse genes for specific resistance are present in the accessions of the tested species.
  • Qiu-Xia WANG, Ai-Nong GAO, Xin-Ming YANG, Li-Hui LI
    J Syst Evol. 2014, 52(6): 790-793.
    Chromosome changes are common in Triticeae, and they occur widely in natural and resynthesized polyploidy. Two important factors, nucleocytoplasmic interaction (internal) and the environment (external), can significantly influence chromosome changes after polyploidization. And chromosomal DNA changes play key roles during the initial formation, gradual stabilization, and establishment of polyploids. Hybrid breeding between common wheat and related wild species of Triticeae is an example of polyploidization, and many of the chromosome changes occurring after hybridization could be useful for improving wheat varieties. The famous chromosomal translocation 1BL/1RS that occurred after ancestral hybridization between wheat and rye is distributed widely among modern wheat varieties and makes a big contribution to wheat breeding; xiaoyan 6 is a similarly distant hybridization between wheat and Agropyron elongatum (Host) P. Beauv. in China. This chromosome translocation line was cultivated as the main variety in Shaanxi Province for 16 years and has also been used as a core parent for wheat breeding in China during the past 20 years because of its outstanding merits.
  • Wayne R. SIMPSON, Marty J. FAVILLE, Roger A. MORAGA, Warren M. WILLIAMS, Michael T. MCMANUS, Richard D. JOHNSON
    J Syst Evol. 2014, 52(6): 794-806.
    This review examines two classes of organism that live in symbiosis; grasses, and fungi. Specifically it deals with grasses of the tribe Hordeeae (formerly Triticeae) of the subfamily Poöideae and the Epichloë fungi of family Clavicipitaceae. Epichloë endophytes, particularly asexual forms, have important roles in pastoral agricultural systems in the Americas, Australia, and New Zealand. Selected strains add value to some grass-based forage systems by providing both biotic and abiotic stress resistance. The importance of cereal grasses such as wheat, barley, rye, and oats to human and animal nutrition and indeed to the foundation and maintenance of human civilization is well documented. Both organism classes, Epichloë endophytes and cereal grasses, are of great importance in their own contexts. Here, we seek to review these two classes of organism and examine the possibility of bringing them together in symbiosis with the ultimate goal of improving cereal production systems.