Recent emergence of the wheat Lr34 multi-pathogen resistance: insights from haplotype analysis in wheat, rice, sorghum and Aegilops tauschii

Spontaneous sequence changes and the selection of beneficial mutations are driving forces of gene diversification and key factors of evolution. In highly dynamic co-evolutionary processes such as plant-pathogen interactions, the plant's ability to rapidly adapt to newly emerging pathogens is paramount. The hexaploid wheat gene Lr34, which encodes an ATP-binding cassette (ABC) transporter, confers durable field resistance against four fungal diseases. Despite its extensive use in breeding and agriculture, no increase in virulence towards Lr34 has been described over the last century. The wheat genepool contains two predominant Lr34 alleles of which only one confers disease resistance. The two alleles, located on chromosome 7DS, differ by only two exon-polymorphisms. Putatively functional homoeologs and orthologs of Lr34 are found on the B-genome of wheat and in rice and sorghum, but not in maize, barley and Brachypodium. In this study we present a detailed haplotype analysis of homoeologous and orthologous Lr34 genes in genetically and geographically diverse selections of wheat, rice and sorghum accessions. We found that the resistant Lr34 haplotype is unique to the wheat D-genome and is not found in the B-genome of wheat or in rice and sorghum. Furthermore, we only found the susceptible Lr34 allele in a set of 252 Ae. tauschii genotypes, the progenitor of the wheat D-genome. These data provide compelling evidence that the Lr34 multi-pathogen resistance is the result of recent gene diversification occurring after the formation of hexaploid wheat about 8,000 years ago.

High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H

Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC7F3 nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

Identificación de QTL para dormición y análisis molecular de la interacción ABA-GAs en cariopses de sorgo granífero

El objetivo de esta tesis fue contribuir a la dilucidación de los mecanismos moleculares y genéticos que participan en la expresión de la dormición de semillas de cereales, utilizando Sorghum bicolor (L.) Moench como sistema modelo. Para ello se utilizaron dos aproximaciones complementarias: la identificación de QTL para el carácter dormición y la evaluación de la ocurrencia de interacciones in vitro entre componentes de la señalización del ácido abscísico (ABA) y el catabolismo de las giberelinas (GAs), candidatos a tener un rol importante durante la expresión de la dormición en granos de sorgo inmaduros (i.e. antes de madurez fisiológica). Los resultados obtenidos permitieron identificar tres QTL (qDOR-5; qDOR-9 y qDOR-10) que explican una proporción de la variabilidad que se observa en el patrón de expresión de dormición de granos de sorgo maduros (i.e. después de madurez fisiológica). Un análisis in silico de las secuencias abarcadas por estos QTL mostró que ninguno ellos incluye genes considerados como candidatos para dormición de sorgo. En ese sentido, esta tesis aportó nuevas regiones genómicas que contienen genes hasta ahora desconocidos, que serían importantes en la expresión del carácter dormición en granos maduros. Por otra parte, los análisis de unión in vitro realizados mostraron que las proteínas SbABI4 y SbABI5 (componentes de la señalización del ABA) pueden interactuar de manera específica con el ABRC (complejo de respuesta al ABA) del promotor del gen SbGA2ox3, responsable de la degradación de giberelinas activas. Este mecanismo de cross-talk ABA-GAs podría ser uno de los responsables del mantenimiento de la dormición en cariopses inmaduros resistentes al brotado pre-cosecha. Más aún, el ABRC del promotor de SbGA2ox3, involucrado en las interacciones, se encontró además en los promotores de genes GA2ox de otras especies monocotiledóneas como Brachypodium y arroz (Oryza sativa), pero no así en las dicotiledóneas analizadas, sugiriendo que el cross-talk ABA-GAs podría tener lugar en otras especies además de sorgo. Los resultados de esta tesis en forma conjunta aportaron nuevas evidencias acerca del rol preponderante que tienen ciertas regiones del genoma o genes puntuales en la expresión de la dormición tanto en granos maduros como inmaduros de sorgo granífero.

Identificación de QTL para dormición y análisis molecular de la interacción ABA-GAs en cariopses de sorgo granífero

El objetivo de esta tesis fue contribuir a la dilucidación de los mecanismos moleculares y genéticos que participan en la expresión de la dormición de semillas de cereales, utilizando Sorghum bicolor (L.)Moench como sistema modelo. Para ello se utilizaron dos aproximaciones complementarias: la identificación de QTL para el carácter dormición y la evaluación de la ocurrencia de interacciones in vitro entre componentes de la señalización del ácido abscísico (ABA)y el catabolismo de las giberelinas (GAs), candidatos a tener un rol importante durante la expresión de la dormición en granos de sorgo inmaduros (i.e. antes de madurez fisiológica). Los resultados obtenidos permitieron identificar tres QTL (qDOR-5; qDOR-9 y qDOR-10)que explican una proporción de la variabilidad que se observa en el patrón de expresión de dormición de granos de sorgo maduros (i.e. después de madurez fisiológica). Un análisis in silico de las secuencias abarcadas por estos QTL mostró que ninguno ellos incluye genes considerados como candidatos para dormición de sorgo. En ese sentido, esta tesis aportó nuevas regiones genómicas que contienen genes hasta ahora desconocidos, que serían importantes en la expresión del carácter dormición en granos maduros. Por otra parte, los análisis de unión in vitro realizados mostraron que las proteínas SbABI4 y SbABI5 (componentes de la señalización del ABA)pueden interactuar de manera específica con el ABRC (complejo de respuesta al ABA)del promotor del gen SbGA2ox3, responsable de la degradación de giberelinas activas. Este mecanismo de cross-talk ABA-GAs podría ser uno de los responsables del mantenimiento de la dormición en cariopses inmaduros resistentes al brotado pre-cosecha. Más aún, el ABRC del promotor de SbGA2ox3, involucrado en las interacciones, se encontró además en los promotores de genes GA2ox de otras especies monocotiledóneas como Brachypodium y arroz (Oryza sativa), pero no así en las dicotiledóneas analizadas, sugiriendo que el cross-talk ABA-GAs podría tener lugar en otras especies además de sorgo. Los resultados de esta tesis en forma conjunta aportaron nuevas evidencias acerca del rol preponderante que tienen ciertas regiones del genoma o genes puntuales en la expresión de la dormición tanto en granos maduros como inmaduros de sorgo granífero.

Nomenclature and syntaxonomic notes on some high-rank syntaxa of the European grassland vegetation

We present descriptions of a new order (Ranunculo cortusifolii-Geranietalia reuteri and of a new alliance (Stachyo lusitanicae-Cheirolophion sempervirentis) for the herbaceous fringe communities of Macaronesia and of the southwestern Iberian Peninsula, respectively. A new alliance, the Polygalo mediterraneae-Bromion erecti (mesophilous post-cultural grasslands), was introduced for the Peninsular Italy. We further validate and typify the Armerietalia rumelicae (perennial grasslands supported by nutrient-poor on siliceous bedrocks at altitudes characterized by the submediterranean climate of central-southern Balkan Peninsula), the Securigero-Dasypyrion villosae (lawn and fallow-land tall-grass annual vegetation of Italy), and the Cirsio vallis-demoni-Nardion (acidophilous grasslands on siliceous substrates of the Southern Italy). Nomenclatural issues (validity, legitimacy, synonymy, formal corrections) have been discussed and clarified for the following names: Brachypodio-Brometalia, Bromo pannonici-Festucion csikhegyensis, Corynephoro-Plantaginion radicatae, Heleochloion, Hieracio-Plantaginion radicatae, Nardetea strictae, Nardetalia strictae, Nardo-Callunetea, Nardo-Galion saxatilis, Oligo-Bromion, Paspalo-Heleochloetalia, Plantagini-Corynephorion and Scorzoneret alia villosae. 

Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals

Comparative mapping is an important component of map-based cloning in large-genome cereal species. We describe evidence of a segmental chromosomal duplication harbouring CONSTANS-like genes in barley that predates the divergence of the Oryzoideae (rice) and Pooideae (brachypodium, barley, wheat) clades, and discuss the implications of such events for comparative mapping and QTL cloning in temperate cereal crops.

Biogeographische Beziehungen zwischen den Alpen, dem Kaukasus und den asiatischen Hochgebirgen

Hintergrund: Biogeographische Verbindungen der Alpen nach Asien wurden schon im 19. Jahrhundert durch floristische Vergleiche entdeckt. Ziele: In den vorliegenden drei Artikeln wird untersucht, ob diese Verbindung entlang einer nördlichen, arktisch-borealen Route oder entlang einer südlichen Route über dazwischen liegende Gebirge wie den Kaukasus bestand. Methoden: Molekulare Phylogenien von Epimedium (Berberidaceae) und der Tribus der Hyoscyameae (Solanaceae), deren Vertreter disjunkt in den Alpen, dem Kaukasus und in asiatischen Gebirgen vorkommen, wurden mit nukleären und plastidären Markern erstellt und bio¬geographisch ausgewertet. Zur Datierung der Diversifizierungsereignisse und Arealbil¬dung diente eine molekulare Uhr. Ein aktueller floristischer Vergleich von Gattungen, die in den Alpen, den asiatischen Gebirgen und in Gebieten entlang der potentiellen Routen vor¬kom¬men, wurde unternommen und ausgewertet. Daran anschließend wurde nach molekular-phylogenetischer Literatur für interessante Gruppen aus diesem Ver¬gleich recherchiert, um diese biogeogra¬phisch bezüglich der Fragestellung zu interpretieren. Ergebnisse: Von 429 Gattungen, die in den Alpen und im Himalaya vorkommen, wachsen 218 entlang der nördlichen und der südlichen Route. 203 kommen nur entlang der süd¬lichen und drei nur entlang der nördlichen Route vor. Fünf kommen nur in den Alpen und im Himalaya vor. Epimedium, Scopolia/Physochlaina aus den Hyoscyameae und Primula sect. Auricula sind Beispiele für eine nördliche biogeographische Verbindung zwischen den Alpen und Asien. Diese bestand zumindest in den ersten beiden Fällen wahrscheinlich aus einem durchgängigen Laubwaldgürtel, der durch das abkühlende und trockener werdende Klima im Pliozän und Pleistozän fragmentiert wurde und heute nicht mehr besteht. Es handelt sich also um ein Vikarianzmuster und weniger um eine Migrationsroute. Die größere Diver¬sität dieser Guppen, die in Asien beobachtet werden kann ist sekundär entstanden. Atropa aus den Hyoscyameae, Brachypodium, die Subtribus Loliinae aus den Poaceae, Bupleurum und Doronicum sind Beispiele für eine südliche Verbindung. Hier liegen die Diversitätszentren im Mediterraneum und die Vorkommen im Osten sind abgeleitet. Schlussfolgerungen: Die Datengrundlage aus der Literaturrecherche ist nicht sehr breit und die meisten Phylogenien waren für die Fragestellung nicht aussagekräftig. Die histori¬schen Erkenntnisse und die Ideen über den Zusammenhang der Alpenflora mit der asiatischer Gebirge werden grundsätzlich bestärkt. Die Flora der Alpen enthält ein Element das über eine nördliche Verbindung noch lange mit asiatischen Gebirgen in Kontakt stand und ein südliches Element, das aus dem Mittelmeer¬raum bzw. aus SW Asien stammt. Die Beispiele für eine nördliche Verbindung sprechen allerdings nicht für eine Migration von Asien nach Europa sondern zeigen ein Vikarianzmuster auf.

Plant species decline due to abandonment of meadows cannot easily be reversed by mowing. A case study from the southern Alps

Abstract. We resumed mowing in two plots of ca. 100 m2 in an abandoned meadow dominated by Brachypodium pinnatum on the slope of Monte Generoso (Switzerland). We monitored species composition and hay yield using point quadrats and biomass samples. Species frequencies changed little during 10 yr (1988–1997) while hay yields showed large fluctuations according to mean relative humidity in April-June. We performed a seed-addition experiment to test whether the establishment of meadow species is limited by lack of diaspores or favourable microsites for germination and recruitment from the seed bank. We sowed ca. 12 000 seeds of 12 species originating from a nearby meadow individually in plots of a 4 × 6 unbalanced Latin square with four treatments, burning, mowing, mowing and removal of a layer of decayed organic matter, and a control. We monitored the fate of seedling individuals for 24 months. Seedlings of all species were established and survived for 12 months, 10 species survived during at least 24 months, some reached a reproductive stage. Species responded to different qualities of microsites provided by the different treatments thus required different regeneration niches. Spontaneous long-distance immigration was insignificant. We conclude that the former species composition of abandoned meadows cannot easily be restored by mowing alone because many plant species of meadows do not have persistent seed banks and immigration over distances of more than 25 m and successful establishment is very unlikely.

Community attributes determine facilitation potential in a semi-arid steppe

Studies on positive plant–plant relations have traditionally focused on pair-wise interactions. Conversely, the interaction with other co-occurring species has scarcely been addressed, despite the fact that the entire community may affect plant performance. We used woody vegetation patches as models to evaluate community facilitation in semi-arid steppes. We characterized biotic and physical attributes of 53 woody patches (patch size, litter accumulation, canopy density, vegetation cover, species number and identity, and phylogenetic distance), and soil fertility (organic C and total N), and evaluated their relative importance for the performance of seedlings of Pistacia lentiscus, a keystone woody species in western Mediterranean steppes. Seedlings were planted underneath the patches, and on their northern and southern edges. Woody patches positively affected seedling survival but not seedling growth. Soil fertility was higher underneath the patches than elsewhere. Physical and biotic attributes of woody patches affected seedling survival, but these effects depended on microsite conditions. The composition of the community of small shrubs and perennial grasses growing underneath the patches controlled seedling performance. An increase in Stipa tenacissima and a decrease in Brachypodium retusum increased the probability of survival. The cover of these species and other small shrubs, litter depth and community phylogenetic distance, were also related to seedling survival. Seedlings planted on the northern edge of the patches were mostly affected by attributes of the biotic community. These traits were of lesser importance in seedlings planted underneath and in the southern edge of patches, suggesting that constraints to seedling establishment differed within the patches. Our study highlights the importance of taking into consideration community attributes over pair-wise interactions when evaluating the outcome of ecological interactions in multi-specific communities, as they have profound implications in the composition, function and management of semi-arid steppes.

Successional stage after land abandonment modulates fire severity and post-fire recovery in a Mediterranean mountain landscape

This study analyses the effect of successional stage after farmland terrace abandonment on post-fire plant recovery in a Mediterranean landscape. Specific objectives of the study were to (1) compare fuel characteristics and fire severity in three successional stages after farmland abandonment – dry grassland, dense shrubland and pine stands; (2) analyse the effect of pre-fire successional stage and fire severity on vegetation recovery and (3) analyse the relative vulnerability (i.e. potential for ecosystem shift and soil degradation) to wildfires of the successional stages. We assessed 30 abandoned terraces (15 unburned and 15 burned), with diverse successional stages, on the Xortà Range (south-east Spain). Post-fire recovery was measured 1, 4 and 7 years after fire. The successional stages varied in aboveground biomass, litter amount, vertical structure and continuity of plant cover, and flammability. Dry grassland showed the lowest fire severity, whereas no differences in severity were found between shrubland and pine stands. One year after fire, plant cover was inversely related to fire severity; this relationship attenuated with time after fire. Post-fire recovery of pine stands and shrubland led in both cases to shrublands, contributing to landscape homogenisation. The pine stands showed the largest changes in composition due to fire and the lowest post-fire plant recovery – a sign of high vulnerability to fire.

Arrangement of gene pairs, retrotransposon insertions, and regulation of gene expression in plants

Plant genomes are extremely complex. Myriad factors contribute to their evolution and organization, as well as to the expression and regulation of individual genes. Here we present investigations into several such factors and their influence on genome structure and gene expression: the arrangement of pairs of physically adjacent genes, retrotransposons closely associated with genes, and the effect of retrotransposons on gene pair evolution. All sequenced plant genomes contain a significant fraction of retrotransposons, including that of rice. We investigated the effects of retrotransposons within rice genes and within a 1 kb putative promoter region upstream of each gene. We found that approximately one-sixth of all rice genes are closely associated with retrotransposons. Insertions within a gene’s promoter region tend to block gene expression, while retrotransposons within genes promote the existence of alternative splicing forms. We also identified several other trends in retrotransposon insertion and its effects on gene expression. Several studies have previously noted a connection among genes between physical proximity and correlated expression profiles. To determine the degree to which this correlation depends on an exact physical arrangement, we studied the expression and interspecies conservation of convergent and divergent gene pairs in rice, Arabidopsis, and Populus trichocarpa. Correlated expression among gene pairs was quite common in all three species, yet conserved arrangement was rare. However, conservation of gene pair arrangement was significantly more common among pairs with strongly correlated expression levels. In order to uncover additional properties of gene pair conservation and rearrangement, we performed a comparative analysis of convergent, divergent, and tandem gene pairs in rice, sorghum, maize, and Brachypodium. We noted considerable differences between gene pair types and species. We also constructed a putative evolutionary history for each pair, which led to several interesting discoveries. To further elucidate the causes of gene pair conservation and rearrangement, we identified retrotransposon insertions in and near rice gene pairs. Retrotransposon-associated pairs are less likely to be conserved, although there are significant differences in the possible effect of different types and locations of retrotransposon insertions. The three types of gene pair also varied in their susceptibility to retrotransposon-associated evolutionary changes.