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April 21, 2020  |  

Transcriptome analysis reveals multiple signal network contributing to the Verticillium wilt resistance in eggplant

Verticillium wilt is a devastating disease in eggplants. In order to understand the molecular mechanism of disease resistance in eggplants, transcriptomes of Verticillium wilt infected eggplants were detected. A total of 480, 518, 887 and 1 046 Verticillium wilt related differentially expressed genes were identified at 6 (V6), 12 (V12), 24 (V24) and 48?h (V48), respectively. COG function classification revealed that most of DEGs functioned in “Amino acid transport and metabolism”, “Cytoskeleton” and “Cell motility”. In addition, compared the control plants (V0) to infected eggplants (V6-V48), a total of 111 common DEGs were identified. Except for “General function prediction only”, most of the DEGs enriched in “Signal transduction”. DEGs associated to different hormone signals, including GID1B, ROPGAP1, OPT3 and CDPK, were identified throughout the whole infection process. Cross-talk among defense signal pathways plays major roles in the Verticillium wilt disease resistance in eggplants.


April 21, 2020  |  

Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers.

The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174?bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.


April 21, 2020  |  

Closing the Yield Gap for Cannabis: A Meta-Analysis of Factors Determining Cannabis Yield.

Until recently, the commercial production of Cannabis sativa was restricted to varieties that yielded high-quality fiber while producing low levels of the psychoactive cannabinoid tetrahydrocannabinol (THC). In the last few years, a number of jurisdictions have legalized the production of medical and/or recreational cannabis with higher levels of THC, and other jurisdictions seem poised to follow suit. Consequently, demand for industrial-scale production of high yield cannabis with consistent cannabinoid profiles is expected to increase. In this paper we highlight that currently, projected annual production of cannabis is based largely on facility size, not yield per square meter. This meta-analysis of cannabis yields reported in scientific literature aimed to identify the main factors contributing to cannabis yield per plant, per square meter, and per W of lighting electricity. In line with previous research we found that variety, plant density, light intensity and fertilization influence cannabis yield and cannabinoid content; we also identified pot size, light type and duration of the flowering period as predictors of yield and THC accumulation. We provide insight into the critical role of light intensity, quality, and photoperiod in determining cannabis yields, with particular focus on the potential for light-emitting diodes (LEDs) to improve growth and reduce energy requirements. We propose that the vast amount of genomics data currently available for cannabis can be used to better understand the effect of genotype on yield. Finally, we describe diversification that is likely to emerge in cannabis growing systems and examine the potential role of plant-growth promoting rhizobacteria (PGPR) for growth promotion, regulation of cannabinoid biosynthesis, and biocontrol.


April 21, 2020  |  

Cichorium intybus L.?×?Cicerbita alpina Walbr.: doubled haploid chicory induction and CENH3 characterization

Intergeneric hybridization between industrial chicory (Cichorium intybus L.) and Cicerbita alpina Walbr. induces interspecific hybrids and haploid chicory plants after in vitro embryo rescue. The protocol yielded haploids in 5 out of 12 cultivars pollinated; altogether 18 haploids were regenerated from 2836 embryos, with a maximum efficiency of 1.96% haploids per cross. Obtained haploids were chromosome doubled with mitosis inhibitors trifluralin and oryzalin; exposure to 0.05 g L-1 oryzalin during one week was the most efficient treatment to regenerate doubled haploids. Inbreeding effects in vitro were limited, but the ploidy level affects morphology. Transcriptome sequencing revealed two unique copies of CENH3 in Cicerbita alpina Walbr. Comparison of CENH3.1 protein sequences of Cicerbita and Cichorium obtained through transcriptome and whole shotgun genome sequencing revealed two amino-acid substitutions at critical residues of the histone fold domain. These particular changes cause chromosome elimination and reduced centromere loading in several other species and might indicate a CENH3-dependent mechanism causing chromosome elimination of parental chromosomes during Cichorium?×?Cicerbita intergeneric hybridization. Our results provide insights in chromosome elimination and might increase the efficiency of haploid induction in Cichorium.


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