Development of an efficient in vitro mutagenesis protocol for genetic improvement of saffron (Crocus sativus L.)

In vitro mutagenesis using habituation and PBR autotrophy based indirect somatic embryogenesis (ISE) system in Kinnow mandarin

Solid mutant induction using specialized habituation and PBR (Plant bio-regulator) autotrophy-mediated suspension-based ISE system was the prime aim of present investigation. Based on survival of cell clumps after mutagen treatment, the probit analysis was calculated. The result revealed LD50 at 54.31 Gy in gamma, while for EMS (ethyl methanesulfonate), it was 0.1% for 3 h and 0.5% for 1 h. Based on embryogenesis efficiency, a dose rate of 100 Gy and 0.1% EMS for a 3-h exposure were selected for regeneration. As compared to control, significant decrease in the embryogenesis efficiency was recorded at 100 Gy (85.92%) with similar reduction trends in embryo production (79.49%), germination (13.43%), conversion (2.48%), establishment (15.78%) and acclimatization (60.92%). The growth-related parameters such as root and shoot length and number of leaves/regenerant were also significantly reduced to 67.29%, 30.19% and 5.03%, respectively, in the regenerated plants after gamma irradiation as compared to control. In the EMS treatment, at the dose rate of 0.1% for 3-h, the embryogenesis efficiency was reduced to 43.67% with similar diminution trends in embryo production (59.49%), germination (8.95%), conversion (1.94%), establishment (4.37%) and acclimatization (29.9%). The growth-related parameters in the EMS treatment, decreased to 91.00% (root length), 71.34% (shoot length) and 35.03% (no. of leaves). The molecular marker based varied amplifications confirmed the occurrence of mutations in both gamma and EMS induced M1 regenerants. The study highlights the alternative high frequency in vitro mutagenesis protocol for induction of solid mutants in Kinnow mandarin and related citrus species.

Graphical Abstract

Recombination of endophytic bacteria in asexual plant Ligusticum chuanxiong Hort. caused by transplanting

Background

Long-term asexual reproduction can easily lead to the degradation of plant germplasm, serious diseases and insect pests, reduction of production and even catastrophic crop failure. "Mountain Breeding and Dam Cultivation" is the main cultivation mode of Ligusticum chuanxiong Hort., which successfully avoided the germplasm degradation caused by long-term asexual reproduction. The recombination of endophytic fungi of L. chuanxiong caused by off-site transplantation was considered to be an important reason for its germplasm rejuvenation. However, whether bacteria have the same regularity is not yet known.

Methods

In this study, we carried out the experiment of cultivating propagation materials of L. chuanxiong in different regions and transplanting them to the same region. High-throughput sequencing was performed to analyze the bacterial communities in L. chuanxiong and its soil.

Results

The results showed that after transplanting, the plant height, tiller number, fresh weight, etc. of L. chuanxiong in mountainous areas were significantly higher than those in dam areas. At the same time, significant changes had taken place in the endophytic bacteria in reproductive material stem nodes (Lingzi, abbreviated as LZ). The diversity and abundance of bacteria in dam area LZ (YL) are significantly higher than those in mountainous area LZ (ML). The relative abundance of bacteria such as Xanthobacteraceae, Micromonosporaceae, Beijerinkiaceae, Rhodanobacteria, in ML is significantly higher than YL, mainly classified in Proteobateria and Actinobacteriota. In addition, the abundance advantage of Actinobacteriota still exists in MY (underground mature rhizomes obtained by ML). Meanwhile, the bacterial community was different in different area of transplanting. The diversity of bacterial communities in dam soil (YLS) is significantly higher than that in mountain soil (MLS). MLS had more Acidobacteriota than YLS. Comparative analysis showed that 74.38% of bacteria in ML are found in MLS, and 87.91% of bacteria in YL are found in YLS.

Conclusions

We can conclude that the community structure of endophytic bacteria recombined after the transplantation of L. chuanxiong, which was related to the bacterial community in soils. Moreover, after transplanting in mountainous areas, LZ accumulated more potentially beneficial Actinobacteriota, which may be an important reason for promoting the rejuvenation of germplasm in L. chuanxiong. However, this hypothesis requires more specific experiments to verify. This study provided a new idea that off-site transplanting may be a new strategy to restore vegetative plant germplasm resources.

Development of EST-based methylation specific PCR (MSP) markers in Crocus sativus

BACKGROUND

Saffron (Crocus sativus) is high valued spice crop, but due to its sterile nature, the crop is propagated exclusively through corms. Thus, the genetic base of this crop is very narrow, however, frequency of phenotypic variability is observed; and suggested the potential role of epigenetics in saffron crop growth and development.

METHODS AND RESULTS

To facilitate epigenetic studies in saffron, we developed 1525 methylation-specific PCR (MSP) markers using MethPrimer. For this purpose, we used 6767 EST sequences of saffron available on the NCBI database. We also mine CpG islands (2555) and found that 32.7% of EST sequences had CpG islands. Out of 1525 MSP markers developed during the present study, 725 covered the CpG islands and 800 were without CpG islands. PCR amplification was found successful for 82% of MSP markers. A preliminary analysis suggested that 53.7% of genomic sites were methylated and more prominent (60% methylations) in non-CpG island regions, although, more comprehensive studies are required to validate it further.

CONCLUSIONS

The epigenetic resource developed during the present study will strengthen the epigenetic studies like epiQTL mapping, epiGWAS to explore the molecular mechanisms and genomic/epigenomic regions associated with phenotype; and further may be utilized for saffron improvement programs through epibreeding.

Morphological, molecular and phytochemical variations induced by colchicine and EMS chemical mutagens in Crocus sativus L

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The highest expression level of the ALDH, BGL, and CCD2 genes was found in 0.025% colchicine for 12 h treatment.

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The content of crocetin esters, picrocrocin, and safranal in colchicine treatments was changed.

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The stigmas of the C. sativus flowers with two, four, five, and six threads were observed.

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Various differences in morphological traits were observed in both colchicine and ethyl methanesulfonate (EMS) treatments.

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The lowest survival rate of corms was related to ethyl methanesulfonate (EMS) treatments.

Crocus sativus L., also known as saffron, is one of the most important medicinal and spice plants throughout the world. The plant is a rich source of apocarotenoids such as crocetin esters, picrocrocin, and safranal. The purpose of this study was to investigate the effect of colchicine and ethyl methanesulfonate (EMS) mutagens on possible inducing new variation in C. sativus. Accordingly, corms were exposed to EMS (0.1% and 0.2%) and colchicine (0.05% and 0.025%) for three incubation times. The lowest survival rate of corms was related to EMS treatments. The relative expression of ALDH, BGL, and CCD2 genes under 0.025% colchicine treatment for 12 h revealed a 2 fold increase compared with the control. The flow cytometric measurements (FCM) of the nuclear DNA content of the colchicine-treated plants did not reveal any significant changes in 2C DNA content. The results, manifest the potential of mutagens to create new variations in the plant.

Random mutagenesis in vegetatively propagated crops: opportunities, challenges and genome editing prospects

In order to meet the growing human food and nutrition demand a perpetual process of crop improvement is idealized. It has seen changing trends and varying concepts throughout human history; from simple selection to complex gene-editing. Among these techniques, random mutagenesis has been shown to be a promising technology to achieve desirable genetic gain with less time and minimal efforts. Over the decade, several hundred varieties have been released through random mutagenesis, but the production is falling behind the demand. Several food crops like banana, potato, cassava, sweet potato, apple, citrus, and others are vegetatively propagated. Since such crops are not propagated through seed, genetic improvement through classical breeding is impractical for them. Besides, in the case of polyploids, accomplishment of allelic homozygosity requires a considerable land area, extensive fieldwork with huge manpower, and hefty funding for an extended period of time. Apart from induction, mapping of induced genes to facilitate the knowledge of biological processes has been performed only in a few selected facultative vegetative crops like banana and cassava which can form a segregating population. During the last few decades, there has been a shift in the techniques used for crop improvement. With the introduction of the robust technologies like meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) more and more crops are being subjected to gene editing. However, more work needs to be done in case of vegetatively propagated crops.

Development of a system for efficient callus production, somatic embryogenesis and gene editing using CRISPR/Cas9 in Saffron (Crocus sativus L.)

BACKGROUND

Crocus sativus is a recalcitrant plant for genetic transformation and genetic improvement, largely due to difficulties in Agrobacterium mediated transformation and vegetative reproduction. Effective genome editing requires proficient callus production and an efficient method to deliver Cas9 and sgRNAs into the plant. Here, we demonstrate Agrobacterium-mediated transformation of saffron. Further, we developed a CRISPR-Cas9 based system in this plant, for efficient gene knockout or edits in future.

RESULTS

Efficient callus production and regeneration confers important benefits in developing competent transformation system in plants. More than 70% multiplication rate of callus initiation was achieved from corm slices of saffron subjected to a two-step sterilization procedure and grown on complete MS medium supplemented with 2,4-D (0.5 mg/L), BAP (1 mg/L), IAA (1 mg/L), photoperiod of 16/8 h and 45% relative humidity at 20 ± 2 °C. In vitro cormlet generation was accomplished in 8 weeks by using mature somatic embryos on MS medium supplemented with TDZ (0.5 mg/L) + IAA (1 mg/L) + Activated charcoal (0.1 g/L) at 15 ± 2 °C. The attempt of using Agrobacterium-mediated transformation resulted in successful integration of the binary vector into the somatic embryos of saffron with a transformation efficiency of 4%. PCR and Southern blot analysis confirmed the integration of Cas9 into saffron.

CONCLUSION

The protocol for callus production, somatic embryogenesis and regeneration was standardised. Successful demonstration of integrated Cas9 in this study constitutes first step in developing strategies for genetic manipulation of saffron, which has so far been considered recalcitrant. Furthering the development of this technology holds significant potential for advancing genetic research in saffron by integrating multigene targeting and/or use of recyclable cassettes.