Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ~28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.

Belowground ABA boosts aboveground production of DIMBOA and primes induction of chlorogenic acid in maize

Plants are important mediators between above- and belowground herbivores. Consequently, interactions between root and shoot defences can have far-reaching impacts on entire food webs. We recently reported that infestation of maize roots by the root feeding larvae of the beetle Diabrotica virgifera virgifera boosts shoot resistance against herbivores and pathogens. Root herbivory also induced DIMBOA levels and primed for enhanced induction of chlorogenic acid, two secondary metabolites that have been associated with biotic stress resistance. Interestingly, ABA emerged as a putative long-distance signal, possibly responsible for this effect. In this addendum, we investigate the role of root-derived ABA in the systemic regulation of aboveground DIMBOA, and the phenolic compounds chlorogenic acid, caffeic and ferulic acid. We discuss the relevance of the plant hormone in relation to defence against the leaf herbivore Spodoptera littoralis. Soil-drench treatment with ABA mimicked root herbivore-induced accumulation of DIMBOA in the leaves. Similarly, ABA mimicked aboveground priming of chlorogenic acid production, resulting in augmented accumulation of this compound upon subsequent shoot attack by S. littoralis. These findings confirm our notion that ABA acts as an important signal in the regulation of aboveground defence upon belowground herbivory. However, based on our previous finding that ABA alone is not sufficient to trigger aboveground resistance against S. littoralis caterpillars, the results suggest that the ABA-inducible effects on DIMBOA and chlorogenic acid are not solely responsible for root herbivore-induced resistance against S. littoralis. Full text HTML PDF

Drought Adaptation in Millets

Millets are major food and feed sources in the developing world especially in the semi-arid tropical regions of Africa and Asia. The most widely cultivated millets are pearl millet [Pennisetum glaucum (L.) R. Br.], finger millet [Eleusine coracana (L.) Gaertn], foxtail millet [Setaria italica (L.) P. Beauvois], Japanese barnyard millet [Echinochloa esculneta (A. Braun) H. Scholz], Indian Barnyard millet [Echinochloa frumetacea Link], kodo millet [Paspalum scrobiculatum L.], little millet [Panicum sumatrense Roth.ex.Roem. & Schult.], proso millet [Panicum miliaceum L.], tef [Eragrostis tef (Zucc.) Trotter] and fonio or acha [Digitaria exilis (Kippist) Stapf and D. iburua Stapf]. Millets are resilient to extreme environmental conditions especially to inadequate moisture and are rich in nutrients. Millets are also considered to be a healthy food, mainly due to the lack of gluten (a substance that causes coeliac disease) in their grain. Despite these agronomic, nutritional and health-related benefits, millets produce very low yield compared to major cereals such as wheat and rice. This extremely low productivity is related to the challenging environment in which they are extensively cultivated and to the little research investment in these crops. Recently, several national and international initiatives have begun to support the improvement of diverse millet types.

A fungal endophyte helps plants to tolerate root herbivory through changes in gibberellin and jasmonate signaling

Plant–microbe mutualisms can improve plant defense, but the impact of root endophytes on below-ground herbivore interactions remains unknown. We investigated the effects of the root endophyte Piriformospora indica on interactions between rice (Oryza sativa) plants and its root herbivore rice water weevil (RWW; Lissorhoptrus oryzophilus), and how plant jasmonic acid (JA) and GA regulate this tripartite interaction. Glasshouse experiments with wild-type rice and coi1-18 and Eui1-OX mutants combined with nutrient, jasmonate and gene expression analyses were used to test: whether RWW adult herbivory above ground influences subsequent damage caused by larval herbivory below ground; whether P. indica protects plants against RWW; and whether GA and JA signaling mediate these interactions. The endophyte induced plant tolerance to root herbivory. RWW adults and larvae acted synergistically via JA signaling to reduce root growth, while endophyte-elicited GA biosynthesis suppressed the herbivore-induced JA in roots and recovered plant growth. Our study shows for the first time the impact of a root endophyte on plant defense against below-ground herbivores, adds to growing evidence that induced tolerance may be an important root defense, and implicates GA as a signal component of inducible plant tolerance against biotic stress.

The importance of biotic interactions and local adaptation for plant response to environmental changes: field evidence along an elevational gradient

Predicting the response of species to environmental changes is a great and on-going challenge for ecologists, and this requires a more in-depth understanding of the importance of biotic interactions and the population structuration in the landscape. Using a reciprocal transplantation experiment, we tested the response of five species to an elevational gradient. This was combined to a neighbour removal treatment to test the importance of local adaptation and biotic interactions. The trait studied was performance measured as survival and biomass. Species response varied along the elevational gradient, but with no consistent pattern. Performance of species was influenced by environmental conditions occurring locally at each site, as well as by positive or negative effects of the surrounding vegetation. Indeed, we observed a shift from competition for biomass to facilitation for survival as a response to the increase in environmental stress occurring in the different sites. Unlike previous studies pointing out an increase of stress along the elevation gradient, our results supported a stress gradient related to water availability, which was not strictly parallel to the elevational gradient. For three of our species, we observed a greater biomass production for the population coming from the site where the species was dominant (central population) compared to population sampled at the limit of the distribution (marginal population). Nevertheless, we did not observe any pattern of local adaptation that could indicate adaptation of populations to a particular habitat. Altogether, our results highlighted the great ability of plant species to cope with environmental changes, with no local adaptation and great variability in response to local conditions. Our study confirms the importance of taking into account biotic interactions and population structure occurring at local scale in the prediction of communities’ responses to global environmental changes.