Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate

Despite the availability of whole genome assemblies, the identification and utilization of gene-based marker systems has been limited in pomegranate. In the present study, we performed a genome-wide survey of intron length (IL) markers in the 36,524 annotated genes of the Tunisia genome. We identified and designed a total of 8,812 potential intron polymorphism (PIP) markers specific to 3,445 (13.40%) gene models that span 8 Tunisia chromosomes. The ePCR validation of all these PIP markers on the Tunisia genome revealed single-locus amplification for 1,233 (14%) markers corresponding to 958 (27.80%) genes. The markers yielding single amplicons were then mapped onto Tunisia chromosomes to develop a saturated linkage map. The functional categorization of 958 genes revealed them to be a part of the nucleus and the cytoplasm having protein binding and catalytic activity, and these genes are mainly involved in the metabolic process, including photosynthesis. Further, through ePCR, 1,233 PIP markers were assayed on multiple genomes, which resulted in the identification of 886 polymorphic markers with an average PIC value of 0.62. In silico comparative mapping based on physically mapped PIP markers indicates a higher synteny of Tunisia with the Dabenzi and Taishanhong genomes (>98%) in comparison with the AG2017 genome (95%). We then performed experimental validation of a subset of 100 PIP primers on eight pomegranate genotypes and identified 76 polymorphic markers, with 15 having PIC values ≥0.50. We demonstrated the potential utility of the developed markers by analyzing the genetic diversity of 31 pomegranate genotypes using 24 PIP markers. This study reports for the first time large-scale development of gene-based and chromosome-specific PIP markers, which would serve as a rich marker resource for genetic variation studies, functional gene discovery, and genomics-assisted breeding of pomegranate

Not Available

Not AvailableNot AvailableNot Availabl

Fast pyrolysis of lignins with different molecular weight: Experiments and modelling

Lignins with number average molecular weights between 350 Da and 1900 Da were characterised and subsequently pyrolysed in a screen-heater at pressures of 500 Pa and 105 Pa between 425 °C and 793 °C. Upwards of 530 °C, the temperature turned out to have only a minor influence on the yields and composition of the oils produced. Clear trends were observed as a function of the molecular weight and pressure – (1) at increasing molecular weight of the lignin, the oil yield decreases while yields of char and gas increase, (2) the molecular weight of the oil is lower for oils produced at 105 Pa as compared to the ones obtained at 500 Pa, (3) above a certain molecular weight of the lignins, ∼400 Da for 105 Pa and ∼800 Da for 500 Pa, the molecular weight of the oil becomes independent of the molecular weight of the lignin. A mathematical model has been developed, which includes three concurrently occurring processes, viz. cracking and polymerisation reactions and removal, hence mass transport, of unconverted lignin and reaction products from the reaction zone. This model can describe all the trends observed experimentally and provides, after parametrisation, reasonable qualitative predictions of the yield and molecular weight of the oils. Knowledge of the role of the interplay between mass transport and chemistry in the pyrolysis process is further accumulating, and from this the development of lignin valorisation can avail. For instance, it has become clear that in the pyrolysis process the molecular weight of lignin oil, which is an important characteristic for the upgrading of the oil to chemicals and/or fuels, can be steered with the pressure

Not Available

Not AvailableNot AvailableNot Availabl

Fast pyrolysis of cellulose in vacuum: The effect of potassium salts on the primary reactions

In this work we investigated the effects of K2CO3 (1, 100, 1000 and 10,000 mg kg−1), KOH (1000 mg kg−1) and KCl (1000 mg kg−1) on the primary products of cellulose fast pyrolysis in vacuum (5 mbar) and at atmospheric pressure (1000 mbar) using a dedicated screen-heater set-up. The screen-heater combines fast heating of the cellulose sample with very fast (milliseconds) removal (high escape rate) and quenching of the reaction products. The solid residue, condensed product, non-condensable gas, levoglucosan and glucose yields obtained from the screen-heater experiments are compared with the product yields from the fluidized bed reactor to elucidate potassium catalysed reactions in the hot vapour phase. Potassium was found to be catalytically active even when the escape rate (milliseconds) of the product was extremely high. Consequently, significantly lower condensed product and sugar yields were obtained. The production of non-condensable gas could almost completely be ascribed to thermal reactions in the vapour phase when the potassium content is low but was predominately produced at the hot reacting particle when the potassium content is high. It was found that in the case of levoglucosan the anions were active in potassium the following order Cl− > OH− > CO3 2−. The activity in reducing the hydrolysable anhydro-sugars (levoglucosan and oligomers), expressed as glucose recovery, shows the following order, OH− > Cl− > CO3 2−. Vacuum could help to improve the oil and sugar yield by fast removal of the products from the hot reacting sample. However, this only holds for cellulose with a low potassium (<100 mg kg−1) content

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)

Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate

The interplay between chemistry and heat/mass transfer during the fast pyrolysis of cellulose

Biomass derived sugars are expected to play an important role as platform chemicals. Herein, we have shown that in the temperature range of 370 °C to 765 °C of the heat source a constant high sugar yield of ∼70% (C-basis) can be obtained from the fast pyrolysis of Avicel cellulose while producing hardly any gas (<1%) and solid residue (<1% above 450 °C). This opens the opportunity to combine the advantages of thermochemical processes, such as high conversion rates and products not being heavily diluted with water, with an increased value of the product slate. In this paper, firstly the screen-heater used to study the very early stages of cellulose pyrolysis is introduced and characterized. Secondly, yield data as a function of process and pyrolysis conditions are presented and interpreted, also using mathematical models, with respect to chemistry, heat transfer, mass transfer and their interplay. It has been shown that next to heat transfer and the residence time in the vapor phase also the escape rate of products from the reacting particle (mass transfer) is a key process determining the overall mass loss rate and/or the product distribution

Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate

This study reports genome wide characterization and development of first set of microsatellite markers through in silico analysis of eight sequenced Xanthomonas axonopodis pv. punicae strains available in the public database. SSR survey resulted in identification of ~ 4638 perfect SSRs, with mean marker frequency 901 SSRs/Mb and densitiy of 11,006 bp/Mb aross the eight genomes. Frequency distribution graphs revealed hexa-nucleotide repeats were more prominent fowllowed by tri-, tetra-, di- and penta-nucleotides in the analysed genomes. We desinged 2927 SSR primers that are specific to the strain LMG 859 and ePCR confirmed on seven other Xap genomes. This resulted in identification of 542 informative SSRs that are producing single amplicons, from which 66 primers were successfully validated through wet lab experiments on eight Xap isolates of pomegranate. Furthermore, utility of these SSRs were demostrated by analysing molecular diversity among 22 Xap isolates using 20 Xap_SSR primers. SSRs revealed moderate genetic diversity among Xap isolates (61%) and grouped 11 isolates that are repersenting six different states into one cluster. This proved the earlier evidence of wider spread of ST3 type Xap acoss India using Multi locus Sequence Typing (MLST) technique. In summary, Xap_SSR will serve as powerful genomics tools that would helps in monitoring of population dynamics, taxonomy, epidomology and quarantine aspects in bacterial blight pathogen through development of microsatellite based Multilocus Variable number of Tandem repeat analysis (MLVA) in future