In vitro mutagenesis and identification of mutants via ISSR in lily (Lilium longiflorum)

Application of machine learning in in vitro propagation of endemic Lilium akkusianum R. Gämperle

A successful regeneration protocol was developed for micropropagation of Lilium akkusianum R. Gämperle, an endemic species of Türkiye, from scale explants. The study also aimed to evaluate the effects of Meta-Topolin (mT) and N6-Benzyladenine (BA) on in vitro regeneration. The Murashige and Skoog medium (MS) supplemented with different levels of α-naphthaleneacetic acid (NAA)/BA and NAA/mT were used for culture initiation in the darkness. The highest callus rates were observed on explants cultured on MS medium with 2.0 mg/L NAA + 0.5 mg/L mT (83.31%), and the highest adventitious bud number per explant was 4.98 in MS medium with 0.5 mg/L NAA + 1.5 mg/L mT. Adventitious buds were excised and cultured in 16/8 h photoperiod conditions. The highest average shoot number per explant was 4.0 in MS medium with 2.0 mg/L mT + 1.0 mg/L NAA. Shoots were rooted with the highest rate (90%) in the medium with the 1.0 mg/L IBA, and the highest survival rate (87.5%) was recorded in rooted shoots in the same medium. The ISSR marker system showed that regenerated plantlets were genetically stable. Besides traditional tissue culture techniques used in the current study, the potential for improving the effectiveness of L. akkusianum propagation protocols by incorporating machine learning methodologies was evaluated. ML techniques enhance lily micropropagation by analyzing complex biological processes, merging with traditional methods. This collaborative approach validates current protocols, allowing ongoing improvements. Embracing machine learning in endemic L. akkusianum studies contributes to sustainable plant propagation, promoting conservation and responsible genetic resource utilization in agriculture.

Evaluation of the optimum threshold of gamma-ray for inducing mutation on Polianthes tuberosa cv. double and analysis of genetic variation with RAPD marker

PURPOSE

This experiment aimed to investigate the effect of gamma irradiation on morpho-physiological characteristics and molecular-induced variations in Polianthes tuberosa L.

METHODS

Experiments were designed according to a completely randomized design with eight different gamma-ray doses (0, 20, 30, 40, 50, 60, 70, and 80 Gy) via a source of cobalt-60 with three replications. Some morpho-physiological characteristics of tuberoses were screened and evaluated at the end of the flower growth and development phases. The RAPD-PCR molecular marker technique was further used to identify the mutants of phenotypic variation flowers.

RESULTS

Results indicated that the effect of different levels of γ-rays on some morphological and physiological traits was significant as the gamma-ray level was increased up to 50 Gy. The doses higher than 50 Gy were found to cause stand or no growth. The 50 Gy gamma irradiation reduced germination by 70.59%, germination rate by 66.36%, dry weight by 88.15%, fresh weight by 87.41%, flowering stem height (cm) by 69.22%, leaf area (cm²) by 57.35%, leaf number by 34.41%, chlorophyll content (mg g^-1 FW) by 44.79%, number of florets by 92.57%, spike height (cm) by 27.80%, bulblet number by 32.57%, and bulblet diameter (mm) by 30.21%. On the contrary, gamma radiation at 50 Gy increased relative water content (%) and electrolyte leakage (ds m^-1) by 41.27 and 237.65%, respectively. The results also showed that bulbs treated with 20 Gy gamma ray had the highest germination percentage and dry weight. The RAPD analysis indicated that among 10 primers tested, nine primers showed clear bands as the highest number of amplified fragments (90) was related to the OPM13 primer and the lowest number (40) to the OPM10 primer. However, the DNA polymorphism was dose-dependent.

CONCLUSION

Overall results showed that although the plant morphology was changed with gamma-ray level, no changes occurred in tuberose color.

Determination of the effective radiation dose for mutation breeding in purple carrot (Daucus carota L.) and possible variations formed

BACKGROUND

Plant breeding allows altering the genetic structure of plants to meet human needs. The use of radiation technology for inducing mutations and -thereby- new phenotypic variants has become increasingly common as a tool for developing new crops. The aim of this study was to determine the effective gamma irradiation dose for inducing mutations in purple carrot.

METHODS AND RESULTS

Increasing gamma radiation doses [0, 50, 100, 200, 300, 400, 500, and 600 Gy] were applied to purple carrot seeds. The irradiated seeds were sown in pots and the emergence and survival rates of the seedlings were analyzed. Considering plant emergence (%) as a response variable, the LD₅₀ dose was 387.5 Gy. Analysis of root length, root width (shoulder diameter) and plant height in control (0 Gy) and irradiated plants (50-600 Gy) revealed an inverse association between these morphological traits and radiation dose. SRAP and ISSR markers were used to identify DNA polymorphisms in irradiated and control plants. The range of amplicons per primer set revealed by ISSR and SRAP markers was 4-10 and 2-13, respectively. In the ISSR analysis of the irradiated carrots (for the 8 doses used), we obtained range values for the average Nei's gene diversity, Shannon's information index, and polymorphism information content (PIC) of 0.13-0.25, 0.20-0.35, and 1.39-1.67, respectively, whereas in the SRAP analysis, the range values for these parameters were 0.15-0.25, 0.23-0.37, and 0.43-0.58, respectively. Cluster analysis revealed three main groups; (a) non-irradiated (control) plants, (b) plants from the 600 Gy dose, and (c) a third group with two subgroups: one with individuals from the lowest irradiation doses (50-200 Gy) and a second group with individuals from the highest irradiation doses (300-500 Gy).

CONCLUSIONS

This is the first report on determining effective mutagen doses and genetic characterization of induced mutagenesis via gamma irradiation in purple carrot. ISSR and SRAP markers were successful in detecting variations among different levels of mutagen doses.

Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5'-UTR and 3'-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

Exploration and Exploitation of Novel SSR Markers for Candidate Transcription Factor Genes in Lilium Species

Lilies (Lilium sp.) are commercially important horticultural crops widely cultivated for their flowers and bulbs. Here, we conducted large-scale data mining of the lily transcriptome to develop transcription factor (TF)-associated microsatellite markers (TFSSRs). Among 216,768 unigenes extracted from our sequence data, 6966 unigenes harbored simple sequence repeats (SSRs). Seventy-one SSRs were associated with TF genes, and these were used to design primers and validate their potential as markers. These 71 SSRs were accomplished with 31 transcription factor families; including bHLH, MYB, C2H2, ERF, C3H, NAC, bZIP, and so on. Fourteen highly polymorphic SSRs were selected based on Polymorphic Information Content (PIC) values and used to study genetic diversity and population structure in lily accessions. Higher genetic diversity was observed in Longiflorum compared to Oriental and Asiatic populations. Lily accessions were divided into three sub-populations based in our structure analysis, and an un-rooted neighbor-joining tree effectively separated the accessions according to Asiatic, Oriental, and Longiflorum subgroups. Finally, we showed that 46 of the SSR-associated genes were differentially expressed in response to Botrytis elliptica infection. Thus, our newly developed TFSSR markers represent a powerful tool for large-scale genotyping, high-density and comparative mapping, marker-aided backcrossing, and molecular diversity analysis of Lilium sp.

Effect of Gamma Rays on Sophora davidii and Detection of DNA Polymorphism through ISSR Marker

Sophora davidii (Franch.) Kom. ex Pavol is an important medicinal plant and a feeding scrub with ecological value. The effects of different gamma irradiation doses (20-140 Kr) on seed germination and seedling morphology were investigated in S. davidii, and intersimple sequence repeat (ISSR) markers were used to identify the DNA polymorphism among mutants. Significant variations were observed for seed germination, stem diameter, and number of branches per plant. The improved agronomic traits, such as stem diameter and number of branches per plant, were recorded at 80 Kr dose and 20 Kr dose for seed germination. ISSR analysis generated in total 183 scorable fragments, of which 94 (51.37%) were polymorphic. The percentage of polymorphism ranged from 14.29 to 93.33 with an average of 45.69%. Jaccard's coefficients of dissimilarity varied from 0.6885 to 1.000, indicative of the level of genetic variation among the mutants. The constructed dendrogram grouped the entities into five clusters. Consequently, it was concluded that gamma rays irradiation of seeds generates a sufficient number of induced mutations and that ISSR analysis offered a useful molecular marker for the identification of mutants.

Biotechnological advances in Lilium

Modern powerful techniques in plant biotechnology have been developed in lilies (Lilium spp., Liliaceae) to propagate, improve and make new phenotypes. Reliable in vitro culture methods are available to multiply lilies rapidly and shorten breeding programs. Lilium is also an ideal model plant to study in vitro pollination and embryo rescue methods. Although lilies are recalcitrant to genetic manipulation, superior genotypes are developed with improved flower colour and form, disease resistance and year round forcing ability. Different DNA molecular markers have been developed for rapid indirect selection, genetic diversity evaluation, mutation detection and construction of Lilium linkage map. Some disease resistance-QTLs are already mapped on the Lilium linkage map. This review presents latest information on in vitro propagation, genetic engineering and molecular advances made in lily.

Validation of Reference Genes for Accurate Normalization of Gene Expression in Lilium davidii var. unicolor for Real Time Quantitative PCR

Lilium is an important commercial market flower bulb. qRT-PCR is an extremely important technique to track gene expression levels. The requirement of suitable reference genes for normalization has become increasingly significant and exigent. The expression of internal control genes in living organisms varies considerably under different experimental conditions. For economically important Lilium, only a limited number of reference genes applied in qRT-PCR have been reported to date. In this study, the expression stability of 12 candidate genes including α-TUB, β-TUB, ACT, eIF, GAPDH, UBQ, UBC, 18S, 60S, AP4, FP, and RH2, in a diverse set of 29 samples representing different developmental processes, three stress treatments (cold, heat, and salt) and different organs, has been evaluated. For different organs, the combination of ACT, GAPDH, and UBQ is appropriate whereas ACT together with AP4, or ACT along with GAPDH is suitable for normalization of leaves and scales at different developmental stages, respectively. In leaves, scales and roots under stress treatments, FP, ACT and AP4, respectively showed the most stable expression. This study provides a guide for the selection of a reference gene under different experimental conditions, and will benefit future research on more accurate gene expression studies in a wide variety of Lilium genotypes.