Background The transition from vegetative to floral phase is the result of complex crosstalk of e... more Background The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. Results In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL int...
Background The frequency of droughts has dramatically increased over the last 50 years, causing y... more Background The frequency of droughts has dramatically increased over the last 50 years, causing yield declines in cereals, including wheat. Crop varieties with efficient root systems show great potential for plant adaptation to drought stress, however; genetic control of root systems in wheat under field conditions is not yet well understood. Results Natural variation in root architecture plasticity (phenotypic alteration due to changing environments) was dissected under field-based control (well-irrigated) and drought (rain-out shelter) conditions by a genome-wide association study using 200 diverse wheat cultivars. Our results revealed root architecture and plasticity traits were differentially responded to drought stress. A total of 25 marker-trait associations (MTAs) underlying natural variations in root architectural plasticity were identified in response to drought stress. They were abundantly distributed on chromosomes 1 A, 1B, 2 A, 2B, 3 A, 3B, 4B, 5 A, 5D, 7 A and 7B of the...
Organic farming has the potential to tackle the imminent task of sustainable food production, if ... more Organic farming has the potential to tackle the imminent task of sustainable food production, if the yields could be raised. Here, the benefits of additional exotic alleles, the necessity of increased genetic heterogeneity in organically farmed systems and the buffering capacities by the pronounced plasticity of root traits are demonstrated. Two barley populations, naturally adapted for more than two decades to organic and conventional farming systems, were compared by a novel strategy of whole genome resequencing of pooled samples. Substantial allele frequency deviations between the farming systems were uncovered (for various agronomically relevant chromosomal regions) by testing multiple generations. In contrast to the organic adapted population, an early equilibrium in the conventional population was observed, accompanied reduced genetic diversity. Differences between the populations were revealed in root morphology, developmental processes and abiotic stress responses. These fin...
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...
Developing stress tolerant plants continues to be the goal of breeders due to their realized yiel... more Developing stress tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought in particular have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation are not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This particular ability could enable training of plants to face future challenges that increase in frequency and intensity in changing climates. A better understanding of stress memory and the associated mechanisms is required to breed stress tolerant genotypes. Contrary to the use of genetic modification tools that has brought controversial hype, misinformation and fear among consumers, epigenetic technology is a powerful tool capable of offering potential benefits. In this perspective, this review discuss...
Key message The genetic response to changing climatic factors selects consistent across the teste... more Key message The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Abstract Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays...
BackgroundIn addition to heterogeneity and artificial selection, natural selection is one of the ... more BackgroundIn addition to heterogeneity and artificial selection, natural selection is one of the forces used to combat climate change and improve agrobiodiversity in evolutionary plant breeding. Accurate identification of the specific genomic effects of natural selection will likely accelerate transfer between populations. Thus, insights into changes in allele frequency, adequate population size, gene flow and drift are essential. However, observing such effects often involves a trade-off between costs and resolution when a large sample of genotypes for many loci is analysed. Pool genotyping approaches achieve high resolution and precision in estimating allele frequency when sequence coverage is high. Nevertheless, high-coverage pool sequencing of large genomes is expensive.ResultsThree pool samples (n = 300, 300, 288) from a barley backcross population were generated to assess the population's allele frequency. The tested population (BC2F21) has undergone 18 generations of natu...
A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore... more A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore, it is critically important to evaluate the root system variation for breeding crop plants towards stress adaptation. We phenotyped root architectural traits of naturally adapted populations from organic and conventional cropping systems under hydroponic and field trails. Long-term natural selection under these two cropping systems resulted a microevolution in root morphological and anatomical traits. Barley lines developed under organic system possessed longer roots with narrow root angle, larger surface area, increased root mass density, and a thinner root diameter with an increased number of metaxylem vessels. In contrast, lines adapted to the conventional system tend to have a shorter and wider root system which possess a larger root volume with thicker diameter, but has fewer metaxylem vessels. Allometry analysis established a relationship between root traits and plant size among b...
Water deficit, which is increasing with climate change, is a serious threat to agricultural susta... more Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain...
Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under diff... more Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under different soil available N. Knowing how wheat responds to or interacts with N to produce grains is essential in the selection of N use efficient cultivars. We assessed in this study variations among wheat genotypes for productivity-related traits under three cropping systems (CS), high-nitrogen with fungicide (HN-WF), high-nitrogen without fungicide (HN-NF) and low-nitrogen without fungicide (LN-NF) in the 2015, 2016 and 2017 seasons. ANOVA results showed genotypes, CS, and their interactions significantly affected agronomic traits. Grain yield (GY) increased with higher leaf chlorophyll content, importantly under CS without N and fungicide supply. Yellow rust disease reduced the GY by 20% and 28% in 2015 and 2016, respectively. Moreover, averaged over growing seasons, GY was increased by 23.78% under CS with N supply, while it was greatly increased, by 52.84%, under CS with both N and fungi...
Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultiva... more Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, “Cardos” (registered in 1998) which was the first among the panel to contain this transloc...
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...
BackgroundBread wheat is one of the most important crops for the human diet, but the increasing s... more BackgroundBread 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.ResultsAmong the over-represented salt...
Flowering time is a complex trait and has a key role in crop yield and adaptation to environmenta... more Flowering time is a complex trait and has a key role in crop yield and adaptation to environmental stressors such as heat and drought. This study aimed to better understand the interconnected dynamics of epistasis and environment and look for novel regulators. We investigated 534 spring barley MAGIC DH lines for flowering time at various environments. Analysis of quantitative trait loci (QTLs), epistatic interactions, QTL × environment (Q×E) interactions, and epistasis × environment (E×E) interactions were performed with single SNP and haplotype approaches. In total, 18 QTLs and 2420 epistatic interactions were detected, including intervals harboring major genes such as Ppd-H1, Vrn-H1, Vrn-H3, and denso/sdw1. Epistatic interactions found in field and semi-controlled conditions were distinctive. Q×E and E×E interactions revealed that temperature influenced flowering time by triggering different interactions between known and newly detected regulators. A novel flowering-delaying QTL a...
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 ...
Potato,Solanum tuberosum, is one of the highest consumed food in the world, being the basis of th... more Potato,Solanum tuberosum, is one of the highest consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused byPhytophtora infestans. Here, we present a multi-environmental analysis of the response toP. infestansusing an association panel of 150 accessions ofS. tuberosumGroup Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain from 13.7% to 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively.In silicoanalysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candi...
Cassava,Crantz, has been positioned as one of the most promising crops world-wide representing th... more Cassava,Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused bypv. manihotis (), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB. An F1 mapping population of 117 full sibs was tested for resistance to twostrains (318 and681) at two locations in Colombia: La Vega, Cundinamarca and Arauca. The evaluation was conducted in rainy and dry seasons and additional tests were carried out under controlled greenhouse conditions. The phenotypic evaluation of the response torevealed continuous variation. Based on composite interval mapping analysis, 5 strain-specific QTL for resistance toexplaining between 15.8 and 22.1% of ph...
Background The transition from vegetative to floral phase is the result of complex crosstalk of e... more Background The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. Results In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL int...
Background The frequency of droughts has dramatically increased over the last 50 years, causing y... more Background The frequency of droughts has dramatically increased over the last 50 years, causing yield declines in cereals, including wheat. Crop varieties with efficient root systems show great potential for plant adaptation to drought stress, however; genetic control of root systems in wheat under field conditions is not yet well understood. Results Natural variation in root architecture plasticity (phenotypic alteration due to changing environments) was dissected under field-based control (well-irrigated) and drought (rain-out shelter) conditions by a genome-wide association study using 200 diverse wheat cultivars. Our results revealed root architecture and plasticity traits were differentially responded to drought stress. A total of 25 marker-trait associations (MTAs) underlying natural variations in root architectural plasticity were identified in response to drought stress. They were abundantly distributed on chromosomes 1 A, 1B, 2 A, 2B, 3 A, 3B, 4B, 5 A, 5D, 7 A and 7B of the...
Organic farming has the potential to tackle the imminent task of sustainable food production, if ... more Organic farming has the potential to tackle the imminent task of sustainable food production, if the yields could be raised. Here, the benefits of additional exotic alleles, the necessity of increased genetic heterogeneity in organically farmed systems and the buffering capacities by the pronounced plasticity of root traits are demonstrated. Two barley populations, naturally adapted for more than two decades to organic and conventional farming systems, were compared by a novel strategy of whole genome resequencing of pooled samples. Substantial allele frequency deviations between the farming systems were uncovered (for various agronomically relevant chromosomal regions) by testing multiple generations. In contrast to the organic adapted population, an early equilibrium in the conventional population was observed, accompanied reduced genetic diversity. Differences between the populations were revealed in root morphology, developmental processes and abiotic stress responses. These fin...
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...
Developing stress tolerant plants continues to be the goal of breeders due to their realized yiel... more Developing stress tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought in particular have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation are not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This particular ability could enable training of plants to face future challenges that increase in frequency and intensity in changing climates. A better understanding of stress memory and the associated mechanisms is required to breed stress tolerant genotypes. Contrary to the use of genetic modification tools that has brought controversial hype, misinformation and fear among consumers, epigenetic technology is a powerful tool capable of offering potential benefits. In this perspective, this review discuss...
Key message The genetic response to changing climatic factors selects consistent across the teste... more Key message The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Abstract Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays...
BackgroundIn addition to heterogeneity and artificial selection, natural selection is one of the ... more BackgroundIn addition to heterogeneity and artificial selection, natural selection is one of the forces used to combat climate change and improve agrobiodiversity in evolutionary plant breeding. Accurate identification of the specific genomic effects of natural selection will likely accelerate transfer between populations. Thus, insights into changes in allele frequency, adequate population size, gene flow and drift are essential. However, observing such effects often involves a trade-off between costs and resolution when a large sample of genotypes for many loci is analysed. Pool genotyping approaches achieve high resolution and precision in estimating allele frequency when sequence coverage is high. Nevertheless, high-coverage pool sequencing of large genomes is expensive.ResultsThree pool samples (n = 300, 300, 288) from a barley backcross population were generated to assess the population's allele frequency. The tested population (BC2F21) has undergone 18 generations of natu...
A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore... more A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore, it is critically important to evaluate the root system variation for breeding crop plants towards stress adaptation. We phenotyped root architectural traits of naturally adapted populations from organic and conventional cropping systems under hydroponic and field trails. Long-term natural selection under these two cropping systems resulted a microevolution in root morphological and anatomical traits. Barley lines developed under organic system possessed longer roots with narrow root angle, larger surface area, increased root mass density, and a thinner root diameter with an increased number of metaxylem vessels. In contrast, lines adapted to the conventional system tend to have a shorter and wider root system which possess a larger root volume with thicker diameter, but has fewer metaxylem vessels. Allometry analysis established a relationship between root traits and plant size among b...
Water deficit, which is increasing with climate change, is a serious threat to agricultural susta... more Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain...
Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under diff... more Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under different soil available N. Knowing how wheat responds to or interacts with N to produce grains is essential in the selection of N use efficient cultivars. We assessed in this study variations among wheat genotypes for productivity-related traits under three cropping systems (CS), high-nitrogen with fungicide (HN-WF), high-nitrogen without fungicide (HN-NF) and low-nitrogen without fungicide (LN-NF) in the 2015, 2016 and 2017 seasons. ANOVA results showed genotypes, CS, and their interactions significantly affected agronomic traits. Grain yield (GY) increased with higher leaf chlorophyll content, importantly under CS without N and fungicide supply. Yellow rust disease reduced the GY by 20% and 28% in 2015 and 2016, respectively. Moreover, averaged over growing seasons, GY was increased by 23.78% under CS with N supply, while it was greatly increased, by 52.84%, under CS with both N and fungi...
Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultiva... more Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, “Cardos” (registered in 1998) which was the first among the panel to contain this transloc...
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...
BackgroundBread wheat is one of the most important crops for the human diet, but the increasing s... more BackgroundBread 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.ResultsAmong the over-represented salt...
Flowering time is a complex trait and has a key role in crop yield and adaptation to environmenta... more Flowering time is a complex trait and has a key role in crop yield and adaptation to environmental stressors such as heat and drought. This study aimed to better understand the interconnected dynamics of epistasis and environment and look for novel regulators. We investigated 534 spring barley MAGIC DH lines for flowering time at various environments. Analysis of quantitative trait loci (QTLs), epistatic interactions, QTL × environment (Q×E) interactions, and epistasis × environment (E×E) interactions were performed with single SNP and haplotype approaches. In total, 18 QTLs and 2420 epistatic interactions were detected, including intervals harboring major genes such as Ppd-H1, Vrn-H1, Vrn-H3, and denso/sdw1. Epistatic interactions found in field and semi-controlled conditions were distinctive. Q×E and E×E interactions revealed that temperature influenced flowering time by triggering different interactions between known and newly detected regulators. A novel flowering-delaying QTL a...
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 ...
Potato,Solanum tuberosum, is one of the highest consumed food in the world, being the basis of th... more Potato,Solanum tuberosum, is one of the highest consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused byPhytophtora infestans. Here, we present a multi-environmental analysis of the response toP. infestansusing an association panel of 150 accessions ofS. tuberosumGroup Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain from 13.7% to 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively.In silicoanalysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candi...
Cassava,Crantz, has been positioned as one of the most promising crops world-wide representing th... more Cassava,Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused bypv. manihotis (), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB. An F1 mapping population of 117 full sibs was tested for resistance to twostrains (318 and681) at two locations in Colombia: La Vega, Cundinamarca and Arauca. The evaluation was conducted in rainy and dry seasons and additional tests were carried out under controlled greenhouse conditions. The phenotypic evaluation of the response torevealed continuous variation. Based on composite interval mapping analysis, 5 strain-specific QTL for resistance toexplaining between 15.8 and 22.1% of ph...
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Papers by Agim Ballvora