Non-essential heavy metals and toxic concentrations of essential metals negatively affect various metabolic and cellular processes. Although only few studies have performed the regulation of heavy metals transport in plants, heavy metal ions are known to enter cells in a non-selective manner. Plant cyclic nucleotide-gated channels (CNGCs), a type of Ca²⁺-permeable-channel, have been suggested to be involved in transporting both essential and toxic heavy metal ions. To determine the candidates responsible for heavy metal ion transport, a series of Arabidopsis CNGC mutants were examined for their response to Pb²⁺ and Cd²⁺ ions. Results, based on the analysis of primary root length and ion content analysis verified that at least four AtCNGCs play roles in Pb²⁺ and/or Cd²⁺ accumulation in plants. These findings provide functional evidence which support the roles of these AtCNGCs in the uptake and transport of Pb²⁺ or Cd²⁺ ion in plants.

The genome-encoded small RNAs have emerged as critical regulators of gene expression in higher eukaryotes.  In plants, on the basis of their biogenesis, size and their roles as transcriptional or posttranscriptional gene regulators, these are divided into two major sub classes, microRNAs and small interfering RNAs. MicroRNAs fine-tune target gene expression at the posttranscriptional level either by degrading or inhibiting the protein production of the mRNA target(s) and this regulation is essential for plant growth and development as well as adaptation to stress conditions. Our research mainly focused on identifying plant microRNAs that could be important for adapting to diverse abiotic stresses such as the drought, salt and heat including nutrient deprivation. Additionally, some of our work also has been focused on identifying and engineering microRNAs that could improve biomass accumulation in biofuel and medicinally important plant species. I will discuss these results including identification of upstream signaling events that are required for regulating stress-responsive microRNAs in plants.

Setaria viridis is rapidly emerging as the premier model system for studies of C₄ photosynthesis in the grasses (1).  With a rapid life cycle of just 6 to 8 weeks, a short stature that is similar to A. thaliana and relatively simple growth requirements, S. viridis is an attractive system for conducting forward and reverse genetic screens to probe the genetic networks underlying the function and regulation of C₄ photosynthesis.  To exploit Setaria as a model system, we have been developing a number of genetic and genomics tools, methods and resources for the community (2).  Here I will present on methods we have developed to rapidly identify candidate genes underlying phenotypes of interest and to identify putative rate limiting steps in C₄ photosynthesis through cross-species selection scans (3).  I will also discuss new methods and approaches to engineering synthetic circuits in plants and discuss how these methods could be applied to altering metabolic flux in a C₄ system as well as engineering C₄ traits into C₃ systems.

Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, whose excessive use is responsible of environmental damages. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake (NUpE), utilize (NUtE) and remobilize N available in soils, could be challenging to maintain high yields. The aim of this study was to explore the natural variation among 19 eggplant accessions in response to low and high NO₃^- supply to identify NUE-contrasting genotypes, in hydroponic and greenhouse experiments. AM222 and AM22 accessions were identified in both growing systems as N-use efficient and inefficient, respectively. Overall, the results indicated the key role of N-utilization component (NUtE) to confer high NUE. The higher N-content in AM222 fruits suggesting the efficient N-remobilization as a strategy to enhance NUtE, suggesting GS as a key enzyme.

To deeply understanding the mechanisms underlying NUE complex trait, AM222 and AM22 were employed for both transcriptomics and metabolomics approaches. Short- and long-term N-stress were adopted in the same experimental design for both -omics approaches. Metabolomics results highlighted that alanine, aspartate and glutamate metabolism was highly affected in AM222, while RNA-seq analysis underlined differential gene transcripts involved in processes of reactive oxygen species (ROS) rate‐limiting production that could be attributed to a higher antioxidant activity ability of N-use efficient genotype.

Overall, here we demonstrated the predominant role of NUtE to confer high NUE in eggplant. More interestingly, an integrated network of differential expressed genes and metabolites belong NUtE between AM222 and AM22 were discovered.

Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, whose excessive use is responsible of environmental damages. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake (NUpE), utilize (NUtE) and remobilize N available in soils, could be challenging to maintain high yields. The aim of this study was to explore the natural variation among 19 eggplant accessions in response to low and high NO₃^- supply to identify NUE-contrasting genotypes, in hydroponic and greenhouse experiments. AM222 and AM22 accessions were identified in both growing systems as N-use efficient and inefficient, respectively. Overall, the results indicated the key role of N-utilization component (NUtE) to confer high NUE. The higher N-content in AM222 fruits suggesting the efficient N-remobilization as a strategy to enhance NUtE, suggesting GS as a key enzyme.

To deeply understanding the mechanisms underlying NUE complex trait, AM222 and AM22 were employed for both transcriptomics and metabolomics approaches. Short- and long-term N-stress were adopted in the same experimental design for both -omics approaches. Metabolomics results highlighted that alanine, aspartate and glutamate metabolism was highly affected in AM222, while RNA-seq analysis underlined differential gene transcripts involved in processes of reactive oxygen species (ROS) rate‐limiting production that could be attributed to a higher antioxidant activity ability of N-use efficient genotype.

Overall, here we demonstrated the predominant role of NUtE to confer high NUE in eggplant. More interestingly, an integrated network of differential expressed genes and metabolites belong NUtE between AM222 and AM22 were discovered.

Fusarium oxysporum f. sp. cubense (Foc) is a disease that attacks bananas causing great economic losses to banana production worldwide. Conventional banana breeding to introgress resistance from wild relatives to susceptible cultivars is complicated and takes a long time. Markers assisted selection is a modern tool thought to over some barriers of banana breeding by increasing the breeding efficiency and shortening the breeding period. The aim of this study was to genotype two unrelated mapping populations developed Foc race 1 resistance and identify markers for analysis of Foc race 1 resistance QTL. Two F₁ mapping populations were developed for Foc race 1 resistance: First population of 140 hybrids, by crossing a resistant Monyet with a susceptible Kokopo and the second of 138 hybrids by crossing a susceptible Mshale with a resistant Calcutta 4. The parents contrasting for Foc race 1 resistance were screened using IRAP, ISSR, and SSR markers. IRAP primer GyLTRev had the highest polymorphism of 76.9% between Mshale and Calcutta 4 parents and 69.2% among their F₁ hybrids and  64.3 % between Monyet and Kokopo parents of and 42.9% their F₁ hybrids among all the primers. One major QTL associated with Foc race 1 in an F₁ population of Monyet x Kokopo was mapped at linkage groups 1 (LG1) with a  LOD score of 4.0 using 32 polymorphic markers. Results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers.

Fusarium oxysporum f. sp. cubense (Foc) is a disease that attacks bananas causing great economic losses to banana production worldwide. Conventional banana breeding to introgress resistance from wild relatives to susceptible cultivars is complicated and takes a long time. Markers assisted selection is a modern tool thought to over some barriers of banana breeding by increasing the breeding efficiency and shortening the breeding period. The aim of this study was to genotype two unrelated mapping populations developed Foc race 1 resistance and identify markers for analysis of Foc race 1 resistance QTL. Two F₁ mapping populations were developed for Foc race 1 resistance: First population of 140 hybrids, by crossing a resistant Monyet with a susceptible Kokopo and the second of 138 hybrids by crossing a susceptible Mshale with a resistant Calcutta 4. The parents contrasting for Foc race 1 resistance were screened using IRAP, ISSR, and SSR markers. IRAP primer GyLTRev had the highest polymorphism of 76.9% between Mshale and Calcutta 4 parents and 69.2% among their F₁ hybrids and  64.3 % between Monyet and Kokopo parents of and 42.9% their F₁ hybrids among all the primers. One major QTL associated with Foc race 1 in an F₁ population of Monyet x Kokopo was mapped at linkage groups 1 (LG1) with a  LOD score of 4.0 using 32 polymorphic markers. Results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers.

Sunflower (Helianthus annuus L.) is one of the main oil crops and grows commonly non irrigated lands in the world, therefore it influences from environmental conditions especially during grain filling period. Some diseases, weeds and broomrape parasite are main limiting factors of sunflower yield in addition to abiotic stresses. Hybrids have been using largely in sunflower production since 1980s almost in all of the world. However, plant breeders have to combine many different traits to new cultivars biotic and abiotic resistance in addition to higher seed and oil yielding and higher adaptation capability. Therefore, we need seriously new molecular tools both developing new hybrids and inbred lines and accelerating breeding program in sunflower, and also gene pyramiding in such as drought tolerance, higher oleic, etc. Helianthus family has 51 species so it has huge genetic resources keeping very useful genes for plant breeders both developing new plant designs to increase leaf area then new hybrids could catch higher heterosis on seed yield etc. New developments on molecular breeding will help to breeders both screening enormous genetic materials and then determining and transferring to cultivated ones shortly utilizing from molecular markers. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies enabled these identification of new markers from huge wild species and interspecific hybrids in sunflower. On the other hand, new image analysis methods and drone technology will facilitate to work for phenotyping on huge genetic materials giving the opportunities to look different angles to breeders while analyzing to plants.  As results, the future targets will be more complex both combining classical and molecular tools together in sunflower breeding programs and also help to develop new hybrids associated multi useful genes together.

Rhizobia are known to induce nodulation signal in legumes. In this research Canadian Wonder common bean, Phaseolus valgaris was grown in different growth media up to flowering to test how soil nutrition control nodulation signal. The different growth medium were saw dust, pure sand, saw dust + sand, loam soil, saw dust + loam soil and pure tap water as the control. Plants were sacrificed to count the level of nodulation. Pure sand significantly induced higher number of nodulation than others and no nodulation was noticed in the sawdust and loam soil.  The objective was to test effectiveness of different medium-growth environment in inducing nodulation in common bean. Conclusion is that soils like pure sand that was presumed to contain minimum nutrients induced nodulation signals better than the richer soils and pure tap water control samples. Therefore, maximum advantage of using beans as a fertility restoring crop is best realized in soils with little nutrient than well-nourished soils. 

Key Words: Bean, Growth Media, Legumes, Nodulation, Signal.

Abaca (Musa textilis Nee) is susceptible to abaca bunchy top virus (ABTV).  An abaca BC2 hybrid derived from a cross between abaca variety Abuab and the ABTV resistant donor parent Pacol (M. balbisiana), was observed to be resistant to ABTV.  The molecular mechanism underlying ABTV disease resistance in the hybrid has not been elucidated.  Currently, transcriptomic data are available to understand the molecular mechanism of resistance of the abaca BC2 hybrid to ABTV.  RNA Seq transcriptome data were obtained from the inner whorl of the pseudostems of Abuab, pacol, BC2-A2 non-inoculated, BC2-A2 two weeks post inoculated and BC2-A2 four weeks post inoculated with ABTV.  Transcriptome were assembled using CLC Bio Genomics Workbench based on reference-guided assembly with CDS of M. acuminate and M. balbisiana.  There are 349 differentially expressed (DEGs), eighty-seven of which were putatively classified as defense response genes.  These include: four pattern triggered immunity (PTI); signal receptor genes/pattern recognition receptors (PRRs); 35 effector triggered immunity (ETI)-based effector genes or R genes; four photosynthetic genes; two ER resident chaperones involved in unfolded protein response (UPR) and ER-mediated program cell death; two genes involved in molecular Ubiquitin Proteasome System (UPS); four regulatory receptors and thirty-one ABTV responsive transcription factors.  It was also observed that some genes have similar patterns of expression in the BC2 hybrid and the donor parent, Pacol.  Quantitative real-time PCR analysis validated the RNA-Seq expression results for six genes which include germin-like protein (GLP3), glutathione S-transferase F11 (GST), heat shock coat protein 70-1 (HSCP 70-1), lipid transfer protein (LTP3), senescence associated gene (SAG20) and thioredoxin superfamily protein (TXN).  This is the first report on the possible complex molecular mechanisms involved in antiviral defense response in Musa textilis Nee.

Keywords: abaca buncy top virus, abaca antiviral resistance genes, abaca transcriptome, innate immunity in abaca

Jatropha curcas is an important perennial, drought tolerant plant identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of Jatropha curcas generated using Illumina and PacBio sequencing technologies and identification of quantitative loci responsible for geminivirus resistance. In this study, we generated scaffolds of 265.7 Mbp in length which is corresponding to 84.8% of the gene space using BUSCO analysis. Additionally, 96.4% of predicted protein-coding genes were captured in corresponding tissues transcriptome data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide repeat SSR markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 250, polymorphic SSR markers were employed to construct a genetic linkage map for Jatropha Mosaic Virus (JMV) resistance using interspecific F₂ mapping population involving Jatropha curcas and Jatropha integerrima as parents. QTL analysis showed the identification of three minor quantitative trait locus (QTL) for JMV resistance and validated in an alternate recipient genetic background F₂ mapping population. These validated QTLs were utilized in Marker Assisted Breeding (MAS) for developing Jatropha Mosaic Virus resistance hybrids in Jatropha. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2,986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha and serves as source for the development of agronomically improved virus resistant and oil producing species.