Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwid... more Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that Traes...
The average sowing date of crops in temperate climate zones has been shifted forwards by several ... more The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. Th...
Additional file 1: Table S1. Overview of reads processing and reference genome mapping from all l... more Additional file 1: Table S1. Overview of reads processing and reference genome mapping from all libraries.
Additional file 4: Table S3. Reference genome coordinates from the novel salt-responsive transcri... more Additional file 4: Table S3. Reference genome coordinates from the novel salt-responsive transcripts identified in the four genotypes.
Additional file 3: Fig. S1. Density plots with the log10 normalized expression values of the libr... more Additional file 3: Fig. S1. Density plots with the log10 normalized expression values of the libraries from the four genotypes studied.
Additional file 11: Fig. S3. Melting curves of some PCR products derived from the amplification o... more Additional file 11: Fig. S3. Melting curves of some PCR products derived from the amplification of reference and target genes.
Additional file 8: Table S6. Gene ontology terms over-represented in the gene clusters from Syn86... more Additional file 8: Table S6. Gene ontology terms over-represented in the gene clusters from Syn86 and Zentos.
Two field experiments were conducted in April and August, 2007 cropping season at the Department ... more Two field experiments were conducted in April and August, 2007 cropping season at the Department of Crop Science research farm, University of Nigeria, Nsukka, to evaluate the pollen germination potentials, rate of pollen tube growth, floral, agronomic and yield attributes of thirteen bambara groundnut cultivars. The first experiment (early planting) was in April and the second (late planting) was in August 2007. The results obtained showed that genotypes had significant effect on the pollen germination only at the late planting. In the early and late planting, pollen grains incubated immediately after harvest had the highest germination percentage, while pollen grains exposed for five minutes prior to in vitro germination showed very poor germination. Pollens exposed beyond five minutes after harvest did not germinate. Genotypes significantly (P<0.05) affected the pollen tube growth at both early and late planting dates. The pollen tube growth decreased drastically with increase ...
Ten Nigerian pumpkin accessions were evaluated during the 2007 and 2008 planting seasons to estim... more Ten Nigerian pumpkin accessions were evaluated during the 2007 and 2008 planting seasons to estimate the magnitude of genetic variability and the character association among some yield characters. The results revealed wide genetic variability among the accessions. The genotypic and heritabilty estimates were high in days to 50% emergence, days to 50% flowering, fruit diameter and number of seeds/fruit in both planting seasons. However, genotypic and heritability estimates were low in number of male and female flowers at both planting seasons. At both plantings, the number of seeds/fruit had a significant (P < 0.01) positive correlation with the number of male flowers/plant and fruit diameter. A significant positive correlation was also obtained between the number of female flowers and the number of fruits/plant in both planting seasons, an indication that both traits increased or decreased simultaneously. Thus, increasing the number of female flowers would favour fruiting in pump...
Drought is one of the major abiotic stress factors limiting wheat production worldwide, thus thre... more Drought is one of the major abiotic stress factors limiting wheat production worldwide, thus threatening food security. The dissection of the genetic footprint of drought stress response offers strong opportunities toward understanding and improving drought tolerance (DT) in wheat. In this study, we investigated the genotypic variability for drought response among 200 diverse wheat cultivars (genotypes) using agronomic, developmental, and grain quality traits (GQT), and conducted genome-wide association studies (GWAS) to uncover the genetic architectures of these important traits. Results indicated significant effects of genotype, water regime and their interactions for all agronomic traits. Grain yield (GY) was the most drought-responsive trait and was highly correlated with kernels number per meter square (KN). Genome-wide association studies revealed 17 and 20 QTL regions under rainfed and drought conditions, respectively, and identified one LD block on chromosome 3A and two othe...
Background Bread wheat is one of the most important crops for the human diet, but the increasing ... more Background Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Results Among the over-represented s...
Bread wheat is one of the most important crops for human diet but the increasing soil salinizatio... more Bread wheat is one of the most important crops for human diet but the increasing soil salinization is causing yield reductions worldwide. Physiological, genetic, transcriptomics and bioinformatics analyses were integrated to study the salt stress adaptation response in bread wheat. A comparative analysis to uncover the dynamic transcriptomic response of contrasting genotypes from two wheat populations was performed at both osmotic and ionic phases in time points defined by physiologic measurements. The differential stress effect on the expression of photosynthesis, calcium binding and oxidative stress response genes in the contrasting genotypes supported the greater photosynthesis inhibition observed in the susceptible genotype at the osmotic phase. At the ionic phase genes involved in metal ion binding and transporter activity were up-regulated and down-regulated in the tolerant and susceptible genotypes, respectively. The stress effect on mechanisms related with protein synthesis ...
Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwid... more Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that Traes...
The average sowing date of crops in temperate climate zones has been shifted forwards by several ... more The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. Th...
Additional file 1: Table S1. Overview of reads processing and reference genome mapping from all l... more Additional file 1: Table S1. Overview of reads processing and reference genome mapping from all libraries.
Additional file 4: Table S3. Reference genome coordinates from the novel salt-responsive transcri... more Additional file 4: Table S3. Reference genome coordinates from the novel salt-responsive transcripts identified in the four genotypes.
Additional file 3: Fig. S1. Density plots with the log10 normalized expression values of the libr... more Additional file 3: Fig. S1. Density plots with the log10 normalized expression values of the libraries from the four genotypes studied.
Additional file 11: Fig. S3. Melting curves of some PCR products derived from the amplification o... more Additional file 11: Fig. S3. Melting curves of some PCR products derived from the amplification of reference and target genes.
Additional file 8: Table S6. Gene ontology terms over-represented in the gene clusters from Syn86... more Additional file 8: Table S6. Gene ontology terms over-represented in the gene clusters from Syn86 and Zentos.
Two field experiments were conducted in April and August, 2007 cropping season at the Department ... more Two field experiments were conducted in April and August, 2007 cropping season at the Department of Crop Science research farm, University of Nigeria, Nsukka, to evaluate the pollen germination potentials, rate of pollen tube growth, floral, agronomic and yield attributes of thirteen bambara groundnut cultivars. The first experiment (early planting) was in April and the second (late planting) was in August 2007. The results obtained showed that genotypes had significant effect on the pollen germination only at the late planting. In the early and late planting, pollen grains incubated immediately after harvest had the highest germination percentage, while pollen grains exposed for five minutes prior to in vitro germination showed very poor germination. Pollens exposed beyond five minutes after harvest did not germinate. Genotypes significantly (P<0.05) affected the pollen tube growth at both early and late planting dates. The pollen tube growth decreased drastically with increase ...
Ten Nigerian pumpkin accessions were evaluated during the 2007 and 2008 planting seasons to estim... more Ten Nigerian pumpkin accessions were evaluated during the 2007 and 2008 planting seasons to estimate the magnitude of genetic variability and the character association among some yield characters. The results revealed wide genetic variability among the accessions. The genotypic and heritabilty estimates were high in days to 50% emergence, days to 50% flowering, fruit diameter and number of seeds/fruit in both planting seasons. However, genotypic and heritability estimates were low in number of male and female flowers at both planting seasons. At both plantings, the number of seeds/fruit had a significant (P < 0.01) positive correlation with the number of male flowers/plant and fruit diameter. A significant positive correlation was also obtained between the number of female flowers and the number of fruits/plant in both planting seasons, an indication that both traits increased or decreased simultaneously. Thus, increasing the number of female flowers would favour fruiting in pump...
Drought is one of the major abiotic stress factors limiting wheat production worldwide, thus thre... more Drought is one of the major abiotic stress factors limiting wheat production worldwide, thus threatening food security. The dissection of the genetic footprint of drought stress response offers strong opportunities toward understanding and improving drought tolerance (DT) in wheat. In this study, we investigated the genotypic variability for drought response among 200 diverse wheat cultivars (genotypes) using agronomic, developmental, and grain quality traits (GQT), and conducted genome-wide association studies (GWAS) to uncover the genetic architectures of these important traits. Results indicated significant effects of genotype, water regime and their interactions for all agronomic traits. Grain yield (GY) was the most drought-responsive trait and was highly correlated with kernels number per meter square (KN). Genome-wide association studies revealed 17 and 20 QTL regions under rainfed and drought conditions, respectively, and identified one LD block on chromosome 3A and two othe...
Background Bread wheat is one of the most important crops for the human diet, but the increasing ... more Background Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. Results Among the over-represented s...
Bread wheat is one of the most important crops for human diet but the increasing soil salinizatio... more Bread wheat is one of the most important crops for human diet but the increasing soil salinization is causing yield reductions worldwide. Physiological, genetic, transcriptomics and bioinformatics analyses were integrated to study the salt stress adaptation response in bread wheat. A comparative analysis to uncover the dynamic transcriptomic response of contrasting genotypes from two wheat populations was performed at both osmotic and ionic phases in time points defined by physiologic measurements. The differential stress effect on the expression of photosynthesis, calcium binding and oxidative stress response genes in the contrasting genotypes supported the greater photosynthesis inhibition observed in the susceptible genotype at the osmotic phase. At the ionic phase genes involved in metal ion binding and transporter activity were up-regulated and down-regulated in the tolerant and susceptible genotypes, respectively. The stress effect on mechanisms related with protein synthesis ...
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