New protocol for the indirect regeneration of the Lilium ledebourii Bioss by using bulb explants

Sina Ghanbari,Barat Ali Fakheri,Mohammad Reza Naghavi,Nafiseh Mahdinezhad 한국식물생명공학회 2018 JOURNAL OF PLANT BIOTECHNOLOGY Vol.45 No.2

Lilium ledebourii Bioss is a wild species of Lilium, which grows naturally in some provinces of Iran. Previous studies on Lilium tissue culture have been linked to direct regeneration and a few studies have been conducted on indirect regeneration, which has been studied under bright conditions. In this study, for the first time in the world, all the stages of indirect regeneration (callus induction, shoot and root induction) have been studied under dark conditions. Callus formation and the regeneration levels of L. Ledebourii Bioss were examined for three replicates in an MS (Murashige and Skoog) medium with different hormonal compositions and by using a factorial experiment in the framework of a completely random plan. For callus initiation, 2,4-D and kinetin hormones were used in five and four levels, respectively, as auxin and cytokinin. Results showed that the highest percentage of the callus was found in 3 μM of 2,4-D and 0.5 μM of kinetin. In terms of callus wet weight, the highest amount was found in 3 μM of 2,4-D and 0.5 μM of kinetin. In addition, in terms of diameter, the highest amount was found in 3 μM of 2,4-D, and 0.5 μM of kinetin. In summary, the 2,4-D hormone had a major impact on the percentage of regeneration increase so that the best response was related to the composition of 3 μM of 2,4-D, and 0.1 μM of kinetin. This study contended that auxin and cytokinin can induce long shoots and roots through cell elongation in dark condition.

New protocol for the indirect regeneration of the Lilium ledebourii Bioss by using bulb explants

Ghanbari, Sina,Fakheri, Barat Ali,Naghavi, Mohammad Reza,Mahdinezhad, Nafiseh The Korean Society of Plant Biotechnology 2018 식물생명공학회지 Vol.45 No.2

Lilium ledebourii Bioss is a wild species of Lilium, which grows naturally in some provinces of Iran. Previous studies on Lilium tissue culture have been linked to direct regeneration and a few studies have been conducted on indirect regeneration, which has been studied under bright conditions. In this study, for the first time in the world, all the stages of indirect regeneration (callus induction, shoot and root induction) have been studied under dark conditions. Callus formation and the regeneration levels of L. Ledebourii Bioss were examined for three replicates in an MS (Murashige and Skoog) medium with different hormonal compositions and by using a factorial experiment in the framework of a completely random plan. For callus initiation, 2,4-D and kinetin hormones were used in five and four levels, respectively, as auxin and cytokinin. Results showed that the highest percentage of the callus was found in $3{\mu}M$ of 2,4-D and $0.5{\mu}M$ of kinetin. In terms of callus wet weight, the highest amount was found in $3{\mu}M$ of 2,4-D and $0.5{\mu}M$ of kinetin. In addition, in terms of diameter, the highest amount was found in $3{\mu}M$ of 2,4-D, and $0.5{\mu}M$ of kinetin. In summary, the 2,4-D hormone had a major impact on the percentage of regeneration increase so that the best response was related to the composition of $3{\mu}M$ of 2,4-D, and $0.1{\mu}M$ of kinetin. This study contended that auxin and cytokinin can induce long shoots and roots through cell elongation in dark condition.

Genetic control of some plant growth characteristics of bread wheat (Triticum aestivum L.) under aluminum stress

Sara Farokhzadeh,Barat Ali Fakheri,Nafiseh Mahdinezhad,Sirous Tahmasebi,Abbas Mirsoleimani,C. Lynne McIntyre 한국유전학회 2020 Genes & Genomics Vol.42 No.3

Background Biomass yield is an important trait for wheat breeding programs. Enhancing the yield of the aerial components of wheat cultivars will be an integral part of future wheat improvement. Aluminum (Al) toxicity is one of the main factors limiting wheat growth and production in acid soils, which occur on up to 50% of the arable lands of the world especially in tropical and subtropical regions. Objective Our objective was to identify quantitative trait loci (QTL) of plant growth characteristics and yield in wheat. Methods A recombinant inbred line (RIL) population consisting of 167 lines, derived from a cross between SeriM82 and Babax were evaluated under two Al treatments (+ Al, 800 µM of Al; −Al, 0 µM of Al) in the field based on an alpha lattice design with two replications for two consecutive crop seasons. Results A total of 40 QTLs including nine putative and 31 suggestive QTLs were found for all traits using the composite interval mapping (CIM) method. By mixed model-based composite interval mapping (MCIM) method, 42 additive QTLs and nine pairs of epistatic effects were detected for studied traits, of which 20 additive and six pairs of epistatic QTLs showed significant QTL × environment interactions. Most of the detected QTLs across environments were stable, and the highest number of stable QTLs was related to A genome. Co-localization of QTL was found on linkage groups (LGs) 2B, 4B, 6A-a, and 7A (CIM method) and 2A-d, and 6A-a (MCIM method). Conclusion These results have implications for selection strategies in biomass yield and for increasing the yield of the aerial part of wheat following further evaluations in various genetic backgrounds and environments.

Evaluating phylogenetic relationships in the Lilium family using the ITS marker

Ghanbari, Sina,Fakheri, Barat Ali,Naghavi, Mohammad Reza,Mahdinezhad, Nafiseh The Korean Society of Plant Biotechnology 2018 식물생명공학회지 Vol.45 No.3

Lilium is a perennial bulbous plant belonging to the liriotypes genus. Our aim was to study the phylogenetic relationships of the Lilium family. Two varieties of Lilium ledebourii, 44 varieties of the gene bank, and one variety from the Tulipa family served as the out group. In order to study the diversity between lilium masses, ITS regions were used to design the marker. The results showed that the guanine base is the most abundant nucleotide. Relatively high conservation was observed in the ITS regions of the populations (0.653). Phylogenetic analysis showed that sargentiae and hybrid varieties are older than other varieties of the Lilium family. Also, the location of L. ledebourii varieties (Damash and Namin) was identified in a phylogenetic tree by using the ITS marker. Overall, our research showed that ITS molecular markers are very suitable for phylogenetic studies in the Lilium family.

Phylogenetic relationships of Iranian Allium species using the matK (cpDNA gene) region

Zarei, Hemadollah,Fakheri, Barat Ali,Naghavi, Mohammad Reza,Mahdinezhad, Nafiseh The Korean Society of Plant Biotechnology 2020 식물생명공학회지 Vol.47 No.1

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

Evaluating phylogenetic relationships in the Lilium family using the ITS marker

Sina Ghanbari,Barat Ali Fakheri,Mohammad Reza Naghavi,Nafiseh Mahdinezhad 한국식물생명공학회 2018 JOURNAL OF PLANT BIOTECHNOLOGY Vol.45 No.3

Lilium is a perennial bulbous plant belonging to the liriotypes genus. Our aim was to study the phylogenetic relationships of the Lilium family. Two varieties of Lilium ledebourii, 44 varieties of the gene bank, and one variety from the Tulipa family served as the out group. In order to study the diversity between lilium masses, ITS regions were used to design the marker. The results showed that the guanine base is the most abundant nucleotide. Relatively high conservation was observed in the ITS regions of the populations (0.653). Phylogenetic analysis showed that sargentiae and hybrid varieties are older than other varieties of the Lilium family. Also, the location of L. ledebourii varieties (Damash and Namin) was identified in a phylogenetic tree by using the ITS marker. Overall, our research showed that ITS molecular markers are very suitable for phylogenetic studies in the Lilium family.

Phylogenetic relationships of Iranian Allium species using the matK (cpDNA gene) region

Hemadollah Zarei,Barat Ali Fakheri,Mohammad Reza Naghavi,Nafiseh Mahdinezhad (사)한국식물생명공학회 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.1

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima’s D and -1.19 for Fu’s Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

Assessment of Yield and Yield Component of Soybean Genotypes (Glycine Max L.) in North of Khuzestan

Sina Ghanbari,Ahmad Nooshkam,Barat Ali Fakheri,Nafiseh Mahdinezhad 한국작물학회 2018 Journal of crop science and biotechnology Vol.21 No.5

18 soybean genotypes were examined to investigate the relationships between some principal attributions of morphology with seed yield per soybean, by Random Complete Block Design (RCBD) study. This study was also carried out three replicates to gain reliable results. The results of variance analysis indicated that, there were significance differences among all soybean genotypes. Moreover, the results of correlated analysis revealed that biological yield (0.96), harvest index (0.92), and number of branches (0.92) had the uttermost correlation with seed yield. To data factor analysis, four independent variables justified 99 percent of all data. The first variable, seed yield, justified 96 percent of entire variance. Multiple-Regression Model with method Analytical Regression Model (step-by-step) was utilized to examine soybean seed yield. This model proved that biological yield, thousand seed weight, and harvest index entered into model respectively and justified 98.85 percent of variation of seed yield. Correlated coefficients of considered attributions were equal to 0.96, 0.78, and 0.92, respectively. All of these indexes had significant at 1% in statistical process. Therefore, these traits can be notability used in soybean breeding programs. Also, accordance to cluster analysis, the sample was divided into three groups.

Thymol production in hairy root culture of Sahendian savory (Satureja sahendica Bornm)

Bahmani Helia,Maroufi Asad,Majdi Mohammad,Fakheri Barat Ali 한국식물생명공학회 2021 Plant biotechnology reports Vol.15 No.2

Sahendian savory (Satureja sahendica Bornm) is a medicinal plant species which produces valuable secondary metabolites including thymol, p-cymene and γ-terpinene. In this study, optimization of hairy roots culture in S. sahendica using Agrobac�terium rhizogenes was efciently established. High frequency of genetic transformation was obtained using node and inter�node explants and three bacterial strains (ATCC 15834, A4, and LBA 9402). However, leaf explants showed no susceptibility to induce hairy roots with the A. rhizogenes strains. The node explants and LBA 9402 strain were the best combination for root induction. Infection time of 20 min caused greater transformation occurrence compared to 10 and 30 min, respectively. Node explants infected with LBA 9402 were found to produce more transformants upon co-cultivation for 2 days. The maxi�mum induction of hairy roots was obtained from bacterial infection at a density of OD600=0.8. Polymerase chain reaction by gene-specifc primers from rol B gene confrmed the positive transformation events. S. sahendica efciently provided and produced a large number of hairy roots which could be used for the production of secondary metabolites or other molecular and biotechnological applications. Production of thymol an important secondary metabolite of S. sahendica from hairy root cultures was confrmed by TLC and GC analysis. Elicitor-treated hairy root cultures with methyl jasmonate and ammonium nitrate produced more amount of thymol compared to untreated roots. These results demonstrate that secondary metabolite production such as thymol in hairy root culture of Sahendian savory could be used to increase low secondary metabolite production in this valuable medicinal plant.