Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is p... more Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks < 1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.
Tomato (Solanum lycopersicum) is one of the most cultivated vegetables in the world due to its co... more Tomato (Solanum lycopersicum) is one of the most cultivated vegetables in the world due to its consumption in a large variety of raw, cooked, or processed foods. Tomato breeding and productivity highly depend on the use of hybrid seeds and their higher yield, environmental adaption, and disease tolerance. However, the emasculation procedure during hybridization raises tomato seed production costs and labor expenses. Using male sterility is an effective way to reduce the cost of hybrid seeds and ensure cultivar purity. Recent developments in CRISPR genome editing technology enabled tomato breeders to investigate the male sterility genes and to develop male-sterile tomato lines. In the current study, the tomato Acotinase (SlACO) gene family was investigated via in silico tools and functionally characterized with CRISPR/Cas9-mediated gene disruption. Genome-wide blast and HMM search represented two SlACO genes located on different tomato chromosomes. Both genes were estimated to have a segmental duplication in the tomato genome due to their identical motif and domain structure. One of these genes, SlACO2, showed a high expression profile in all generative cells of tomato. Therefore, the SlACO2 gene was targeted with two different gRNA/Cas9 constructs to identify their functional role in tomatoes. The gene was mutated in a total of six genome-edited tomato lines, two of which were homozygous. Surprisingly, pollen viability was found to be extremely low in mutant plants compared to their wild-type (WT) counterparts. Likewise, the number of seeds per fruit also sharply decreased more than fivefold in mutant lines (10–12 seeds) compared to that in WT (67 seeds). The pollen shape, anther structures, and flower colors/shapes were not significantly varied between the mutant and WT tomatoes. The mutated lines were also subjected to salt and mannitol-mediated drought stress to test the effect of SlACO2 on abiotic stress tolerance. The results of the study indicated that mutant tomatoes have higher tolerance with significantly lower MDA content under stress conditions. This is the first CRISPR-mediated characterization of ACO genes on pollen viability, seed formation, and abiotic stress tolerance in tomatoes.
Current cultivation and breeding strategy based on selections from local and wild vegetation does... more Current cultivation and breeding strategy based on selections from local and wild vegetation does not meet the hazelnut demand. This situation would benefit from the development of high-yielding cultivars with greater tolerance to abiotic and biotic stress conditions. Molecular markers are useful tools to support these breeding efforts. In the current study, EST-SSR markers were developed from RNA-sequencing data obtained from three hazelnut varieties. The transcriptome sequences contained 86,542 unigenes and a total of 25,391 SSRs, most of which (50.9%) were di-nucleotide repeats. A set of 40 primer pairs were randomly selected to validate their usefulness for investigating genetic diversity in 19 C. avellana cultivars and one accession of Corylus colurna. Of the 40, 28 were highly polymorphic with average values of observed heterozygosity, polymorphism information content and number of alleles per locus of 0.45, 0.67 and 6.11, respectively. The principal coordinate and dendrogram analysis separated the C. colurna accession from the C. avellana cultivars, and separated the cultivars for date of leaf bud burst. These new EST-SSRs and others that could be developed from the transcriptome sequences increase the number of markers for cultivar fingerprinting and may be useful for identifying marker-trait associations and further genetic diversity analyses.
Tomato (Solanum lycopersicum) is the second most important horticultural crop worldwide that is w... more Tomato (Solanum lycopersicum) is the second most important horticultural crop worldwide that is widely used as a model plant in genetic manipulation of Solanaceae. CRISPR/Cas9 system has been successfully utilized in several studies for genome edition of model tomato cultivars. However, these genome editing systems should be also optimized for commercial tomato cultivar for direct application of genome editing in field conditions. In this study, we have optimized an Agrobacterium-mediated gene transfer and regeneration system for CRISPR/Cas9 genome editing in two commercial tomato cultivars for the first time. The effect of explant type, genotype, pre-transformation time, Agrobacterium concentration, infection time, and different co-culture periods of bacteria were evaluated to optimize the regeneration and transformation parameters. The highest regeneration capacity of 83% was obtained from cotyledons of Crocker incubated in a medium supplemented with BA (3 mg/L) and IAA (0.1 mg/L). The maximum transformation frequency was obtained by using the following parameters: cotyledon explants of commercial Crocker cultivar that were left for 2 days of pre-transformation incubation, infected with Agrobacterium for 10 min at a concentration of OD600 of 0.6 and co-cultivated with Agrobacterium cells for 48 h. CRISPR/Cas9 system was tested with two gRNAs targeting the phytoene desaturase gene. Fully albino and chimeric plants were successfully produced with optimized transformation and culture conditions in up to 71% of all regenerated plants. In the current study, we optimized the implementation of the CRISPR/Cas9 technique in a commercial tomato cultivar and our method will enable breeders to make necessary changes in traits of interest to improve tomato crops for commercial applications.
Plant-specific BURP domain-containing proteins have an essential role in the plant's development ... more Plant-specific BURP domain-containing proteins have an essential role in the plant's development and stress responses. Although BURP domain-containing proteins have been identified in several plant species, genome-wide analysis of the BURP gene family has not been investigated in the common bean. In the present study, we identified 11 BURP family members in the common bean (Phaseolus vulgaris) genome with a comprehensive in silico analysis. Pairwise alignment and phylogenetic analyses grouped PvBURP members into four subfamilies [RD-22 like (3), PG1β-like (4), BNM2-like (3), and USP-like (1)] according to their amino acid motifs, protein domains and intron–exon structure. The physical and biochemical characteristics of amino acids, motif and intron–exon structure, and cis-regulatory elements of BURPs members were determined. Promoter regions of BURP members included stress, light, and hormone response-related cis-elements. Therefore, expression profiles of PvBURP genes were identified with in silico tools and qRT-PCR analyses under stress (salt and drought) and hormone treatment (ABA, IAA) in the current study. While significant activity changes were not observed in BURP genes in RNA-seq data sets related to salt stress, it was determined that some BURP genes were expressed differently in those with drought stress. We identified 12 different miRNA, including miRNA395, miRNA156, miRNA169, miRNA171, miRNA319, and miRNA390, targeting the nine PvBURP genes using two different in silico tools based on perfect or near‐perfect complementarity to their targets. Here we present the first study to identify and characterize the BURP genes in common bean using whole-genome analysis, and the findings may serve as a reference for future functional research in common bean.
Beet curly top disease (BCTD) is a yield-limiting viral infection of sugar beet (Beta vulgaris) t... more Beet curly top disease (BCTD) is a yield-limiting viral infection of sugar beet (Beta vulgaris) throughout the arid and semi-arid regions of the world. Two virus species, belonging to two different genera of the family Geminiviridae (Curtovirus and Becurtovirus) had been described as the disease’s causative agents on sugar beet. Despite the detection of the BCTD in some sugar beet fields of Turkey sixty years ago, the genome based characterization of BCTD-associated viruses have not been studied previously. In this study, 628 sugar beet plants exhibiting BCTD symptoms were collected from fourteen cities in central Anatolia, the major sugar beet production areas in Turkey. PCR assays of these samples using the respective Curtovirus and Becurtovirus genus-specific primers indicated that the Turkish sugar beet samples' viral sequences belong only to the genus Becurtovirus. The results of sequencing and phylogenetic analysis of the partial genome of the virus obtained from fourteen cities confirmed that BCTD-associated virus in Turkish sugar beet fields is beet curly top Iran virus (BCTIV-Becurtovirus) species. The whole genome of the collected viruses from fourteen cities were amplified by the rolling circle amplification (RCA) and the five most phylogenetically diverse viruses obtained from Afyon, Ankara, Adapazarı, Yozgat and Aksaray were sequenced. The results of whole genome sequence analysis indicated >98 % sequence identities with that of a BCTIV variants reported from Urmia province (bordering Turkey) of Iran. A virus genome from Yozgat city had a genomic sequence identity of >97 % with those of BCTIV isolated from cowpea, tomato, pepper and sugar beet in the northern part of Iran. These results suggested that the spread of BCTIV through the region could create a significant threat to the production of sugar beet as well as other agricultural crops. A tandem dimer of a BCTIV-Turkish variant isolated from Ankara city was cloned into Agrobacterium plasmid to be used for agro-infection studies. Agroinoculation of this construct on sugar beet leaves generated severe BCTD symptoms (84 %) which were also confirmed by RCA and qPCR analysis. These results constituted the first genome based characterization of BCTIV Turkish variants and the first report of BCTIV spreading out of Iran
The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of p... more The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. A comprehensive genome-wide analysis was performed in its genome to understand the role of DDP genes (DUF221) in the common bean (Phaseolus vulgaris L.). A total of 12 DDP genes were identified and distributed in 8 chromosomes in the common bean genome. The physical and biochemical characteristics of amino acids, motif and intron–exon structure, and cis-regulatory elements of DDP members were determined. Phylogenetically all PvDDPs were clustered into nine clades, subsequently supported by their gene structure and conserved motifs distribution. The PvDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. A total of 45 different cis-regulatory elements in the putative promoter regions of the PvDDPs were identified. ERE and ABRE were discovered to be present in all PvDDPs, indicating that they may be regulated by ethylene and ABA, both of which are strongly associated with biotic stress response in plant species. Additionally, PvDDPs were targeted by multiple miRNA gene families as well. In this context, the most targeted DDP family members are PvDD10 and PvDDP11. The miRNA target analysis showed that Pvu-miR2594, Pvu-miR169, Pvu-miR2584, Pvu-miR530, Pvu-miR156, and Pvu-miR2592 target these genes. There is a strong correlation between abiotic stress and PvDDPs expression in both leaf and root tissues. PvDDP11 is the unique and highest upregulated gene with hormone treatment and abiotic stress among all the members. Expression of the PvDDP11 gene indicated a strong correlation with drought and salt stress in the common bean roots and leaves, respectively. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in common bean.
CRISPR/Cas9 knock-out of SlPHD_MS1 (Solyc04g008420) gene results in complete male sterility in to... more CRISPR/Cas9 knock-out of SlPHD_MS1 (Solyc04g008420) gene results in complete male sterility in tomato
Flowering time is a very important phase in transition to reproductive stage of life in higher pl... more Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L. an important crop worldwide. Fifteen different SBP-box transcription factor genes were identified in potato genome. They were found to be distributed in nine chromosomes and eight of them included miR156 and miRNA157 target sites. Characterization of amino acid sequences were performed and protein interactions were predicted. In addition, expression levels of five S. tuberosum SBP-box genes were analysed by both in silico and qRT-PCR. All these results provide a better understanding of functional role of SBP-box gene family members in flowering time in potato.
GENOME-WIDE INVESTIGATION AND EXPRESSION ANALYSIS OF
AP2-ERF GENE FAMILY IN SALT TOLERANT COMMON ... more GENOME-WIDE INVESTIGATION AND EXPRESSION ANALYSIS OF AP2-ERF GENE FAMILY IN SALT TOLERANT COMMON BEAN
In this study, the effects of long-term NaCl treatment were investigated in two cultivars of
pean... more In this study, the effects of long-term NaCl treatment were investigated in two cultivars of peanut designated as drought-resistant and drought-sensitive. Growth parameters, changes in the concentrations of MDA, H2O2 and proline, and the activities of antioxidant enzymes were determined under salinity stress. Growth parameters indicated the superiority of cv. Florispan to cv. Gazipaşa under milder salinity stress treatment. However, comparative analysis of the two cultivars showed that MDA, H2O2, ion leakage levels and photosystem II activities were not significantly different, except for the proline activity, which increased only in Florispan leaf tissues under 100 mM salt treatment. Among the processes that govern the tolerance in peanut tissues, proline level and the activity of glutathione reductase (GR) appeared to be only components that play an important part in salt stress protection.
Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles i... more Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon–intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.
Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is p... more Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks < 1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.
Tomato (Solanum lycopersicum) is one of the most cultivated vegetables in the world due to its co... more Tomato (Solanum lycopersicum) is one of the most cultivated vegetables in the world due to its consumption in a large variety of raw, cooked, or processed foods. Tomato breeding and productivity highly depend on the use of hybrid seeds and their higher yield, environmental adaption, and disease tolerance. However, the emasculation procedure during hybridization raises tomato seed production costs and labor expenses. Using male sterility is an effective way to reduce the cost of hybrid seeds and ensure cultivar purity. Recent developments in CRISPR genome editing technology enabled tomato breeders to investigate the male sterility genes and to develop male-sterile tomato lines. In the current study, the tomato Acotinase (SlACO) gene family was investigated via in silico tools and functionally characterized with CRISPR/Cas9-mediated gene disruption. Genome-wide blast and HMM search represented two SlACO genes located on different tomato chromosomes. Both genes were estimated to have a segmental duplication in the tomato genome due to their identical motif and domain structure. One of these genes, SlACO2, showed a high expression profile in all generative cells of tomato. Therefore, the SlACO2 gene was targeted with two different gRNA/Cas9 constructs to identify their functional role in tomatoes. The gene was mutated in a total of six genome-edited tomato lines, two of which were homozygous. Surprisingly, pollen viability was found to be extremely low in mutant plants compared to their wild-type (WT) counterparts. Likewise, the number of seeds per fruit also sharply decreased more than fivefold in mutant lines (10–12 seeds) compared to that in WT (67 seeds). The pollen shape, anther structures, and flower colors/shapes were not significantly varied between the mutant and WT tomatoes. The mutated lines were also subjected to salt and mannitol-mediated drought stress to test the effect of SlACO2 on abiotic stress tolerance. The results of the study indicated that mutant tomatoes have higher tolerance with significantly lower MDA content under stress conditions. This is the first CRISPR-mediated characterization of ACO genes on pollen viability, seed formation, and abiotic stress tolerance in tomatoes.
Current cultivation and breeding strategy based on selections from local and wild vegetation does... more Current cultivation and breeding strategy based on selections from local and wild vegetation does not meet the hazelnut demand. This situation would benefit from the development of high-yielding cultivars with greater tolerance to abiotic and biotic stress conditions. Molecular markers are useful tools to support these breeding efforts. In the current study, EST-SSR markers were developed from RNA-sequencing data obtained from three hazelnut varieties. The transcriptome sequences contained 86,542 unigenes and a total of 25,391 SSRs, most of which (50.9%) were di-nucleotide repeats. A set of 40 primer pairs were randomly selected to validate their usefulness for investigating genetic diversity in 19 C. avellana cultivars and one accession of Corylus colurna. Of the 40, 28 were highly polymorphic with average values of observed heterozygosity, polymorphism information content and number of alleles per locus of 0.45, 0.67 and 6.11, respectively. The principal coordinate and dendrogram analysis separated the C. colurna accession from the C. avellana cultivars, and separated the cultivars for date of leaf bud burst. These new EST-SSRs and others that could be developed from the transcriptome sequences increase the number of markers for cultivar fingerprinting and may be useful for identifying marker-trait associations and further genetic diversity analyses.
Tomato (Solanum lycopersicum) is the second most important horticultural crop worldwide that is w... more Tomato (Solanum lycopersicum) is the second most important horticultural crop worldwide that is widely used as a model plant in genetic manipulation of Solanaceae. CRISPR/Cas9 system has been successfully utilized in several studies for genome edition of model tomato cultivars. However, these genome editing systems should be also optimized for commercial tomato cultivar for direct application of genome editing in field conditions. In this study, we have optimized an Agrobacterium-mediated gene transfer and regeneration system for CRISPR/Cas9 genome editing in two commercial tomato cultivars for the first time. The effect of explant type, genotype, pre-transformation time, Agrobacterium concentration, infection time, and different co-culture periods of bacteria were evaluated to optimize the regeneration and transformation parameters. The highest regeneration capacity of 83% was obtained from cotyledons of Crocker incubated in a medium supplemented with BA (3 mg/L) and IAA (0.1 mg/L). The maximum transformation frequency was obtained by using the following parameters: cotyledon explants of commercial Crocker cultivar that were left for 2 days of pre-transformation incubation, infected with Agrobacterium for 10 min at a concentration of OD600 of 0.6 and co-cultivated with Agrobacterium cells for 48 h. CRISPR/Cas9 system was tested with two gRNAs targeting the phytoene desaturase gene. Fully albino and chimeric plants were successfully produced with optimized transformation and culture conditions in up to 71% of all regenerated plants. In the current study, we optimized the implementation of the CRISPR/Cas9 technique in a commercial tomato cultivar and our method will enable breeders to make necessary changes in traits of interest to improve tomato crops for commercial applications.
Plant-specific BURP domain-containing proteins have an essential role in the plant's development ... more Plant-specific BURP domain-containing proteins have an essential role in the plant's development and stress responses. Although BURP domain-containing proteins have been identified in several plant species, genome-wide analysis of the BURP gene family has not been investigated in the common bean. In the present study, we identified 11 BURP family members in the common bean (Phaseolus vulgaris) genome with a comprehensive in silico analysis. Pairwise alignment and phylogenetic analyses grouped PvBURP members into four subfamilies [RD-22 like (3), PG1β-like (4), BNM2-like (3), and USP-like (1)] according to their amino acid motifs, protein domains and intron–exon structure. The physical and biochemical characteristics of amino acids, motif and intron–exon structure, and cis-regulatory elements of BURPs members were determined. Promoter regions of BURP members included stress, light, and hormone response-related cis-elements. Therefore, expression profiles of PvBURP genes were identified with in silico tools and qRT-PCR analyses under stress (salt and drought) and hormone treatment (ABA, IAA) in the current study. While significant activity changes were not observed in BURP genes in RNA-seq data sets related to salt stress, it was determined that some BURP genes were expressed differently in those with drought stress. We identified 12 different miRNA, including miRNA395, miRNA156, miRNA169, miRNA171, miRNA319, and miRNA390, targeting the nine PvBURP genes using two different in silico tools based on perfect or near‐perfect complementarity to their targets. Here we present the first study to identify and characterize the BURP genes in common bean using whole-genome analysis, and the findings may serve as a reference for future functional research in common bean.
Beet curly top disease (BCTD) is a yield-limiting viral infection of sugar beet (Beta vulgaris) t... more Beet curly top disease (BCTD) is a yield-limiting viral infection of sugar beet (Beta vulgaris) throughout the arid and semi-arid regions of the world. Two virus species, belonging to two different genera of the family Geminiviridae (Curtovirus and Becurtovirus) had been described as the disease’s causative agents on sugar beet. Despite the detection of the BCTD in some sugar beet fields of Turkey sixty years ago, the genome based characterization of BCTD-associated viruses have not been studied previously. In this study, 628 sugar beet plants exhibiting BCTD symptoms were collected from fourteen cities in central Anatolia, the major sugar beet production areas in Turkey. PCR assays of these samples using the respective Curtovirus and Becurtovirus genus-specific primers indicated that the Turkish sugar beet samples' viral sequences belong only to the genus Becurtovirus. The results of sequencing and phylogenetic analysis of the partial genome of the virus obtained from fourteen cities confirmed that BCTD-associated virus in Turkish sugar beet fields is beet curly top Iran virus (BCTIV-Becurtovirus) species. The whole genome of the collected viruses from fourteen cities were amplified by the rolling circle amplification (RCA) and the five most phylogenetically diverse viruses obtained from Afyon, Ankara, Adapazarı, Yozgat and Aksaray were sequenced. The results of whole genome sequence analysis indicated >98 % sequence identities with that of a BCTIV variants reported from Urmia province (bordering Turkey) of Iran. A virus genome from Yozgat city had a genomic sequence identity of >97 % with those of BCTIV isolated from cowpea, tomato, pepper and sugar beet in the northern part of Iran. These results suggested that the spread of BCTIV through the region could create a significant threat to the production of sugar beet as well as other agricultural crops. A tandem dimer of a BCTIV-Turkish variant isolated from Ankara city was cloned into Agrobacterium plasmid to be used for agro-infection studies. Agroinoculation of this construct on sugar beet leaves generated severe BCTD symptoms (84 %) which were also confirmed by RCA and qPCR analysis. These results constituted the first genome based characterization of BCTIV Turkish variants and the first report of BCTIV spreading out of Iran
The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of p... more The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. A comprehensive genome-wide analysis was performed in its genome to understand the role of DDP genes (DUF221) in the common bean (Phaseolus vulgaris L.). A total of 12 DDP genes were identified and distributed in 8 chromosomes in the common bean genome. The physical and biochemical characteristics of amino acids, motif and intron–exon structure, and cis-regulatory elements of DDP members were determined. Phylogenetically all PvDDPs were clustered into nine clades, subsequently supported by their gene structure and conserved motifs distribution. The PvDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. A total of 45 different cis-regulatory elements in the putative promoter regions of the PvDDPs were identified. ERE and ABRE were discovered to be present in all PvDDPs, indicating that they may be regulated by ethylene and ABA, both of which are strongly associated with biotic stress response in plant species. Additionally, PvDDPs were targeted by multiple miRNA gene families as well. In this context, the most targeted DDP family members are PvDD10 and PvDDP11. The miRNA target analysis showed that Pvu-miR2594, Pvu-miR169, Pvu-miR2584, Pvu-miR530, Pvu-miR156, and Pvu-miR2592 target these genes. There is a strong correlation between abiotic stress and PvDDPs expression in both leaf and root tissues. PvDDP11 is the unique and highest upregulated gene with hormone treatment and abiotic stress among all the members. Expression of the PvDDP11 gene indicated a strong correlation with drought and salt stress in the common bean roots and leaves, respectively. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in common bean.
CRISPR/Cas9 knock-out of SlPHD_MS1 (Solyc04g008420) gene results in complete male sterility in to... more CRISPR/Cas9 knock-out of SlPHD_MS1 (Solyc04g008420) gene results in complete male sterility in tomato
Flowering time is a very important phase in transition to reproductive stage of life in higher pl... more Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L. an important crop worldwide. Fifteen different SBP-box transcription factor genes were identified in potato genome. They were found to be distributed in nine chromosomes and eight of them included miR156 and miRNA157 target sites. Characterization of amino acid sequences were performed and protein interactions were predicted. In addition, expression levels of five S. tuberosum SBP-box genes were analysed by both in silico and qRT-PCR. All these results provide a better understanding of functional role of SBP-box gene family members in flowering time in potato.
GENOME-WIDE INVESTIGATION AND EXPRESSION ANALYSIS OF
AP2-ERF GENE FAMILY IN SALT TOLERANT COMMON ... more GENOME-WIDE INVESTIGATION AND EXPRESSION ANALYSIS OF AP2-ERF GENE FAMILY IN SALT TOLERANT COMMON BEAN
In this study, the effects of long-term NaCl treatment were investigated in two cultivars of
pean... more In this study, the effects of long-term NaCl treatment were investigated in two cultivars of peanut designated as drought-resistant and drought-sensitive. Growth parameters, changes in the concentrations of MDA, H2O2 and proline, and the activities of antioxidant enzymes were determined under salinity stress. Growth parameters indicated the superiority of cv. Florispan to cv. Gazipaşa under milder salinity stress treatment. However, comparative analysis of the two cultivars showed that MDA, H2O2, ion leakage levels and photosystem II activities were not significantly different, except for the proline activity, which increased only in Florispan leaf tissues under 100 mM salt treatment. Among the processes that govern the tolerance in peanut tissues, proline level and the activity of glutathione reductase (GR) appeared to be only components that play an important part in salt stress protection.
Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles i... more Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon–intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.
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AP2-ERF GENE FAMILY IN SALT TOLERANT COMMON BEAN
peanut designated as drought-resistant and drought-sensitive. Growth parameters, changes in the
concentrations of MDA, H2O2 and proline, and the activities of antioxidant enzymes were determined
under salinity stress. Growth parameters indicated the superiority of cv. Florispan to cv. Gazipaşa under
milder salinity stress treatment. However, comparative analysis of the two cultivars showed that MDA,
H2O2, ion leakage levels and photosystem II activities were not significantly different, except for the
proline activity, which increased only in Florispan leaf tissues under 100 mM salt treatment. Among the
processes that govern the tolerance in peanut tissues, proline level and the activity of glutathione reductase
(GR) appeared to be only components that play an important part in salt stress protection.
AP2-ERF GENE FAMILY IN SALT TOLERANT COMMON BEAN
peanut designated as drought-resistant and drought-sensitive. Growth parameters, changes in the
concentrations of MDA, H2O2 and proline, and the activities of antioxidant enzymes were determined
under salinity stress. Growth parameters indicated the superiority of cv. Florispan to cv. Gazipaşa under
milder salinity stress treatment. However, comparative analysis of the two cultivars showed that MDA,
H2O2, ion leakage levels and photosystem II activities were not significantly different, except for the
proline activity, which increased only in Florispan leaf tissues under 100 mM salt treatment. Among the
processes that govern the tolerance in peanut tissues, proline level and the activity of glutathione reductase
(GR) appeared to be only components that play an important part in salt stress protection.