Joining smallholder farmers’ traditional knowledge with metric traits to select better varieties of Ethiopian wheat

Smallholder farming communities face highly variable climatic conditions that threaten locally adapted, low-input agriculture. The benefits of modern crop breeding may fail to reach their fields when broadly adapted genetic materials do not address local requirements. To date, participatory methods only scratched the surface of the exploitability of farmers’ traditional knowledge in breeding. In this study, 30 smallholder farmers in each of two locations in Ethiopia provided quantitative evaluations of earliness, spike morphology, tillering capacity and overall quality on 400 wheat genotypes, mostly traditional varieties, yielding altogether 192,000 data points. Metric measurements of ten agronomic traits were simultaneously collected, allowing to systematically break down farmers’ preferences on quantitative phenotypes. Results showed that the relative importance of wheat traits differed by gender and location. Farmer traits were variously contributed by metric traits, and could only partially be explained by them. Eventually, farmer trait values were used to produce a ranking of the 400 wheat varieties identifying the trait combinations most desired by farmers. The study scale and methods lead to a better understanding of the quantitative basis of Ethiopian smallholder farmer preference in wheat, broadening the discussion for the future of local, sustainable breeding efforts accommodating farmers’ knowledge

TRANSCRIPTIONAL ANALYSIS OF EIGHT MAGIC MAIZE PARENTAL LINES INFECTED WITH FUSARIUM VERTICILLIOIDES

Maize (Zea mays L.) is among the most important crops worldwide for food, feed, biofuels, and industrial applications. Its cultivation faces significant constraints due to Fusarium species that affect the quality and quantity of maize products. Among these, Fusarium verticillioides is responsible for severe diseases including seedling blights, stalk rot, and ear rot. The impact of the fungus is worsened by the fact that chemical and agronomic measures used to control Fusarium infection are often inefficient. Hence, genetic resistance is considered the most reliable resource to reduce damages caused by F. verticillioides. This study aims to elucidate the genetic basis of resistance to this fungus in maize. Young seedlings of eight divergent maize lines, founder of the MAGIC population, were artificially inoculated with a F. verticillioides strain using the rolled towel assay method. Total RNA was extracted from both control and treated samples after 72 hours of artificial inoculation and underwent paired-end sequenced with Illumina technology. Here we report the use this large transcriptomic dataset to identify the early transcriptional changes and the differentially expressed genes (DEGs) involved in fungal infection. The analysis identified several hundred DEGs, whose functions were explored through Gene Ontology enrichment analysis. A co-expression network analysis further refined the set of genes with potential implications in disease response. The results identify a limited set of genes that might play an important roles in maize resistance to F. verticillioides providing new insights into the molecular resistance mechanisms against the pathogen

Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

The version of this article published in BMC Genomics 2009, 10:558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted by these unreliable data. In this full-length correction, new data replace those found to be unreliable, leading to a more straightforward interpretation without altering the principle conclusions of the study. Table 1 and associated methods have been corrected, Figure 1 deleted, supplementary file 1 added, and modifications made to the sections "Deep sequencing of small RNAs from grapevine leaf tissue" and "Microarray analysis of miRNA expression". The editors and authors regret the inconvenience caused to readers by premature publication of the original paper

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (<it>Vitis vinifera </it>L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families.</p> <p>Results</p> <p>Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts.</p> <p>Conclusion</p> <p>Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.</p

CHARACTERIZING HETEROSIS IN A SET OF RECOMBINANT INTERCROSSES (RIXS) DEVELOPED FROM A MULTIPARENTAL MAIZE POPULATION

The exploitation of heterosis is key in modern maize breeding to capture the superior performance of heterozygous genotypes. Here, we developed a recombinant intercross (RIX) population in maize by crossing pairs of multiparental MAGIC recombinant inbred lines (RILs) to evaluate the heterosis across mosaics of eight maize haplotypes. Field phenotyping was performed on 400 RIX genotypes considering 11 agronomic traits as well as the resistance to Fusarium Ear Rot (FER), caused by Fusarium verticillioides (Sacc.) Nirenberg, in 2018 and 2019 in Piacenza, northern Italy. Phenotypic data showed a broad range of diversity in production and phenology traits thanks to the high level of allelic diversity available in parental genomes. The heterotic response of agronomic traits was computed based on RIL values as mid parent heterosis (MPH) and best parent heterosis (BPH). Both heterosis measures showed different magnitudes for different traits, with higher level of heterosis in yield and lower in flowering time, suggesting effects from partial dominance to over-dominance. No correlation was observed between phenotypic performance and heterozygosity level of RIXs for most of the agronomic traits. A preliminary quantitative trait locus (QTL) mapping detected a number of significant associations with agronomic traits across all chromosomes. The RIX collection showed a moderate heritability of FER resistance, and QTL were associated to this trait as well. The allelic effect estimates by our mapping model indicated the presence of minor effect QTL with relatively small additive effects on disease resistance in both years. Our findings confirm the usefulness of the RIX population to decipher heterotic loci in maize and support utilizing this resource in future to accelerate crop improvement

A comprehensive molecular and morphological study of the effects of space flight on human capillary endothelial cells: sample quality assessment and preliminary results.

ESA (ESA ILSRA-2009-1026); ASI (contract no. 5681); Regione Toscana (POR FSE 2007-2013-FORTEC); Kayser Italia; Lions Club International, District 108LA, Toscana, Italy

Microgravity and space radiation inhibit autophagy in human capillary endothelial cells, through either opposite or synergistic effects on specific molecular pathways

Availability of data and materials: All transcriptome analysis raw data were deposited in GEO as GSE157937.Code availability: Not applicable.Microgravity and space radiation (SR) are two highly influential factors affecting humans in space flight (SF). Many health problems reported by astronauts derive from endothelial dysfunction and impaired homeostasis. Here, we describe the adaptive response of human, capillary endothelial cells to SF. Reference samples on the ground and at 1g onboard permitted discrimination between the contribution of microgravity and SR within the combined responses to SF. Cell softening and reduced motility occurred in SF cells, with a loss of actin stress fibers and a broader distribution of microtubules and intermediate filaments within the cytoplasm than in control cells. Furthermore, in space the number of primary cilia per cell increased and DNA repair mechanisms were found to be activated. Transcriptomics revealed the opposing effects of microgravity from SR for specific molecular pathways: SR, unlike microgravity, stimulated pathways for endothelial activation, such as hypoxia and inflammation, DNA repair and apoptosis, inhibiting autophagic flux and promoting an aged-like phenotype. Conversely, microgravity, unlike SR, activated pathways for metabolism and a pro-proliferative phenotype. Therefore, we suggest microgravity and SR should be considered separately to tailor effective countermeasures to protect astronauts’ health.European Space Agency (ESA ILSRA-2009-1026), Agenzia Spaziale Italiana (contract number 5681)