Plant Genomics

Biography

Annamaria Bevivino has her expertise in soil microbial diversity. She is Se­nior Scientist at ENEA, Italian National Agency for New Technologies, Energy and Sustainable Development, and Professor in Agro-Food Microbiology at University Campus Bio-Medico, Rome, Italy. Actually, she is a Management Committee Substitute for Italy of FPS COST Action FP1305: Linking below­ground biodiversity and ecosystem function in European forests (BioLink), actively participating in the activities of WG3: Belowground biodiversity in plantations and tree crops. She is Academic Editor for PlosOne and Fron­tiers in Microbiology and Member of Italian Society of General Microbiology and Microbial Biotechnology, Federation of European Microbiological soci­eties, Italian Society of Agro-Food and Environmental Microbiology, Interna­tional Union of Microbiological Societies. She is author of 43 peer-reviewed published papers in international journals, and more than 150 communica­tions to national and international congresses.

Abstract

Soil is a complex and dynamic ecosystem whose functionality is related to the equilibrium existing among chemical, physical and biological parameters and the resident microbial communities. Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling, and have direct and indirect effects on both crop growth and quality, as well as on the sustainability of soil productivity. In addition, soil microorganisms substantially contribute to the resistance and resilience of agro-ecosystems to biotic and abiotic disturbance and stress. Therefore, changes in microbial communities may directly affect soil ecosystem function since microbes can respond rapidly to environmental changes because of the vastness of microbial biomass and diversity. Given the role of soil microbes in soil safeness and function, there is the need to improve our knowledge about the ecology of microbial populations for proper agriculture management, at both levels of whole population structure and defined taxonomic/ functional groups, such as those involved in inorganic nitrogen turnover and biogeochemical cycles. Different approaches can be followed for studying diversity and community structure and evaluating dynamics processes at a global level or at the level of distinct taxonomic groups, for identification and typing, and for functional characterization. Here, author summarise the methodological approaches to unravel the composition and function of belowground microbiota, ranging from classical and culture-based methods to molecular and high-throughput sequencing-based metagenomic analyses.

A holistic approach taking into consideration all of potential factors and drivers is necessary when examining the structure–function relationships of soil microbial communities for providing insight into the long-standing questions of which species of microorganisms are present?, what are they doing? who is active out there? and how do the activities of these microorganisms relate to ecosystem functions? An in-depth analysis of these interactions could be of crucial importance in designing new and effective microbial consortia for optimizing plant production and developing new strategies for disease control.

Biography

Maciej Majka is working in the Cereal Genomics Team in the Institute of Plant Genetics in Poznan, Poland. He has completed his MSc in Molecular Cytogenetics at the University of Silesia in Katowice, Poland. He is a Princi­pal Investigator of his three years long scientific project financed by the Na­tional Science Centre (Poland): Genetic improvement of triticale by distant crosses with Aegilops tauschii × Secale cereale amphiploid forms in order to transfer the leaf rust resistance genes. He is an Executor in four other sci­entific projects. He is an author/co-author of 14 papers in reputed journals from the JCR list.

Abstract

Leaf rust caused by the Puccinia triticina Eriks is one of the most dangerous diseases of cereals. Genetic manipulation of host resistance is both cost-effective and safe for environment method of controlling leaf rust. Wild Aegilops species, characterized by a high genetic variability, constitute the rich source of genetic resources especially resistance to fungal diseases. The main goal of this work was to examine the resistance of (Ae. tauschii × S. cereale) × Triticosecale hybrids to leaf rust in inoculation tests with isolates of P. triticina with different virulence patterns. Hybrid plants were selected for the presence of 2D chromosomes in triticale background using fluorescent and genomic in situ hybridization. Presence of Leaf rust (Lr) resistance genes was confirmed with associated molecular markers. Resistance was determined at macroscopic and microscopic level at two stages of development: seedlings and adult plants (flag leaf). Our results revealed the decreased reaction of hybrid plants at the seedling stage followed by the increasement of resistance in further stages of development, what indicates that obtained hybrid plants may especially exhibit Adult Plant Resistance

(APR) resistance conferred by Lr22a introgressed from Ae. tauschii. On the basis of the macroscopic and microscopic analysis, this resistance can be determined as additive and race-specific. We selected Monosomic 2D Addition (M2DA) triticale genotypes highly resistant to P. triticina infection from which, we obtained double haploid lines that can be used for further breeding work to increase the agronomic value of cultivated triticale.

Biography

Akiko Kozaki has studied the function of indeterminate domain family pro­teins, which are plant specific group of transcription factors. She is also interested in the TOR signaling pathway in plants and the regulation of oil synthesis in plants.

Abstract

Seed germination is a crucial process in the life cycle of plants and the control of the timing of germination is important not only for plants but also for agriculture. Plant growth depends on several environmental conditions, such as light, moisture, nutrients, temperature, and so on. Therefore, seeds have to monitor the environmental condition to germinate at proper timing. Previous studies have shown that germination is regulated by these environmental conditions and many components, including plant hormones, such as Gibberellins (GA) and Abscisic Acid (ABA) and have identified several genes involved in the regulation of seed germination. We found that several INDETERMINATE DOMAIN (IDD) family transcription factors in Arabidopsis expressed in seeds are involved in the regulation of seed germination. The IDD family transcription factor was first identified as a regulator of maize flowering and recent studies show that some IDD transcription factors play important roles in GA signaling pathway, root patterning and gravitropism. Here, we present the results about IDD4 gene. The T-DNA tag line of IDD4 gene (idd4) showed delayed germination compared to Wild Type (WT) and the addition of 1 M ABA further delayed the germination of idd4. These results indicated that IDD4 gene promotes germination and suppress the sensitivity to ABA. In contrast, 50% of idd4 seeds germinated in the dark while WT seeds did not germinate. The result indicated that IDD4 gene inhibits germination in the dark. We analyzed the expression of gene involved in the synthesis, catabolism and signaling of GA and ABA, and germination regulation. In this presentation.

Biography

Chongling Yan has his expertise on the biogeochemical Process of heavy metals and Organic Pollutants (POPs) in wetland ecosystem (water/sedi­ment/plant). He has made some progress in distribution of heavy metals and the relationship between them and plants, environmental conditions and chemical-physical properties in estuary sediments, speciation distribu­tion of heavy metal in the mangrove sediment and the influence of man­grove roots on bio-availability of heavy metals.

Abstract

Mangrove ecosystem, a bushy woody plant community in the intertidal shores, mainly distributes in tropic and subtropic estuaries and plays an important role in estuarine ecosystems. Meanwhile, mangrove is severely polluted by heavy metals in consequence of human activities, notably cadmium. In this study, transcriptome sequencing was performed and the complex regulatory networks of cadmium tolerance in K. obovata were revealed. K. obovata was selected as research materials and treated with 5 mg/L cadmium for five days, then the total RNA of six samples (namely Ctrl-root, Ctrl-stem, Ctrl-leaf, Cd-root, Cd- stem, Cd-leaf) was extracted and prepared for RNA-seq and sRNA-seq base on Illumina HiSeq 2500 sequencing platform. Clean data obtained from sequencing was used for de novo assembly, differential expression analysis, function annotation, pathway enrichment analysis and other personalized analysis. Comprehensive dissection of molecular regulatory network of Cd tolerance involving Cd transport, chelation, plant hormone signaling, transcriptional regulation, phenylpropanoid metabolism, lignification and miRNA regulation was achieved in K. obovata. Notably this research is great important and may help in elucidating the gene networks involved in plant responses to various kinds of stress.

Biography

Danielle Keidar Friedman is a PhD Candidate at Ben Gurion University, Isra­el. Her study focuses on transposable elements dynamics in allopolyploid wheat species. She is studying SINE (Short Interspersed Nuclear Elements) and MITE (Miniature Inverted-repeat Transposable Elements) proliferation following polyploidization events, their possible impact on gene expression and regulation and their mode of transposition.

Abstract

The impact of Transposable Elements (TEs) on genome structure and function is intensively studied in eukaryotes, especially in plants where TEs can reach up to 90% of the genome in some cases, such as in wheat. We have performed a genome-wide in silico analysis using the updated publicly available genome draft of bread wheat (T. aestivum), in addition to the updated genome drafts of the diploid donor species, T. urartu and Ae. tauschii, to retrieve and analyze a non-LTR retrotransposon family, termed Au SINE (Short Interspersed Nuclear Elements), which was found to be widespread in plant species. Then, we have performed site-specific PCR and realtime RT-PCR analyses to assess the possible impact of Au SINE on gene structure and function. To this end, we retrieved 133, 180 and 1886 intact Au SINE insertions from T. urartu, Ae. tauschii and T. aestivum genome drafts, respectively. The 1886 Au SINE insertions were distributed in the seven homoeologous chromosomes of T. aestivum, while ~67% of the insertions were associated with genes. Detailed analysis of 40 genes harboring Au SINE revealed allelic variation of those genes in the Triticum-Aegilops genus. In addition, expression analysis revealed that both regular transcripts and alternative Au SINE-containing transcripts were simultaneously amplified in the same tissue, indicating retention of Au SINE-containing introns. Analysis of the wheat transcriptome revealed that hundreds of protein-coding genes that harbor Au SINE in at least one of their mature splice variants. Au SINE might play a prominent role in speciation by creating transcriptome variation.