17 research outputs found
Integration of GWAS and transcriptome analyses to identify SNPs and candidate genes for aluminum tolerance in rapeseed (Brassica napus L.)
The exchangeable aluminum (Al), released from the acid soils, is another addition to the environmental stress factors in the form of Al toxicity stress. Al stress affects the normal crop development and reduces the overall yield of rapeseed (Brassica napus L.). The response mechanism of plants to Al toxicity is complicated and difficult to understand with few QTL related studies in rapeseed under Al toxicity stress
Mapping aluminum tolerance loci in cereals: A tool available for crop breeding
Aluminum (Al) toxicity is the main factor limiting crop productivity in
acidic soils around the world. In cereals, this problem reduces crop
yields by 30-40%. The use of DNA-based markers linked to phenotypic
traits is an interesting alternative approach. Strategies such as
molecular marker-assisted selection (MAS) in conjunction with
bioinformatics-based tools such as graphical genotypes (GGT) have been
important for confirming introgression of genes or genomic regions in
cereals but also to reduce the time and cost of identifying them
through genetic selection. These biotechnologies also make it possible
to identify target genes or quantitative trait loci (QTL) that can be
potentially used in similar crops to increase their productivity. This
review presents the main advances in the genetic improvement of cereals
for Al-tolerance
Expressão de OsFRDL1, um membro da família MATE, indica seu envolvimento na resposta ao alumínio em arroz
In soils under acidic conditions, Aluminum (Al) is solubilized to its ionic form, which is toxic to plants. Al rapidly inhibits root elongation, water and nutrient uptake, resulting in crop yield reduction. Members of the MATE family are responsible for citrate transport and Al detoxification in different species. In rice, the OsFRDL1 gene (MATE family) is homologous to the HvAACT1 and SbMATE, which are involved in Al tolerance in barley and sorghum, respectively. Silencing OsFRDL1 showed that it is not involved in Al tolerance in rice. However, the OsFRDL1 expression was not accessed in rice genotypes contrasting for Al tolerance. Thus, in this study, four Brazilian rice genotypes were evaluated in response to Al treatment in different time of exposition and OsFRDL1 expression was analyzed. The analyzed cultivars displayed different responses to Al dose x time. Al affected root growth in all analyzed genotypes, however, a minor negative effect that only occurred after 72 and 48 hours of exposure was detected in Farroupilha and BRS Curinga cultivars, respectively. In contrast, BR-IRGA 410 and IAS 12-9 showed a negative effect in root growth from the first hours of exposure to Al. Two cultivars differing in Al tolerance were used for gene expression analysis. The expression of OsFRDL1 was highly increased in Al-tolerant cultivar Farroupilha than in the Al-sensitive cultivar BR IRGA 410. This results indicates that OsFRDL1 is regulated by Al. This finding suggests that OsFRDL1 is involved in Al stress response, however seems to be insufficient in controlling Al tolerance.Em solos em condições de acidez, o alumínio (Al) é solubilizado em sua forma iônica, a qual é tóxica para as plantas. O Al rapidamente inibe o crescimento radicular e a obtenção de água e nutrientes, resultando na redução da produtividade. Membros da família MATE são responsáveis pelo transporte do citrato e detoxificação do Al em diferentes espécies. Em arroz, o gene OsFRDL1 (da família MATE) é homólogo aos genes HvAACT1 e SbMATE, os quais são envolvidos na tolerância ao Al em cevada e sorgo, respectivamente. O silenciamento de OsFRDL1 demonstrou que este gene não é envolvido com a tolerância ao Al em arroz. No entanto, a expressão de OsFRDL1 não foi acessada em genótipos de arroz contrastantes quanto à tolerância ao Al. Assim, neste estudo, quatro genótipos de arroz brasileiros foram avaliados em resposta ao tratamento com Al em diferentes tempos de exposição e a expressão do gene OsFRDL1 também foi avaliada. Os genótipos analisados apresentaram diferentes respostas ao Al dose x tempo. O Al afetou o crescimento radicular em todos os genótipos avaliados, no entanto, um pequeno efeito negativo que ocorreu após 72 e 48 horas de exposição foi identificado nos genótipos Farroupilha e BRS Curinga, respectivamente. Por outro lado, BR-IRGA 410 e IAS 12-9 apresentaram um efeito negativo no crescimento radicular a partir das primeiras horas de exposição ao Al. Dois genótipos foram utilizados para as análises de expressão gênica. A expressão do gene OsFRDL1 foi aumentada no genótipo Farroupilha, tolerante ao Al, em relação ao genótipo BR IRGA 410, sensível ao Al. Estes resultados indicam que o gene OsFRDL1 está envolvido na resposta ao estresse por Al, no entanto, parece que este gene não é suficiente para controlar a tolerância ao Al
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress
Background: Wheat is a major staple crop with broad adaptability to a wide range of environmental conditions.This adaptability involves several stress and developmentally responsive genes, in which microRNAs (miRNAs) have emerged as important regulatory factors. However, the currently used approaches to identify miRNAs in this\ud
polyploid complex system focus on conserved and highly expressed miRNAs avoiding regularly those that are often lineage-specific, condition-specific, or appeared recently in evolution. In addition, many environmental and biological factors affecting miRNA expression were not yet considered, resulting still in an incomplete repertoire of wheat miRNAs.\ud
Results: We developed a conservation-independent technique based on an integrative approach that combines machine learning, bioinformatic tools, biological insights of known miRNA expression profiles and universal criteria of plant miRNAs to identify miRNAs with more confidence. The developed pipeline can potentially identify novel wheat miRNAs that share features common to several species or that are species specific or clade specific. It allowed the discovery of 199 miRNA candidates associated with different abiotic stresses and development stages. We also highlight from the raw data 267 miRNAs conserved with 43 miRBase families. The predicted miRNAs are highly associated with abiotic stress responses, tolerance and development. GO enrichment analysis showed that they may play biological and physiological roles associated with cold, salt and aluminum (Al) through auxin signaling pathways, regulation of gene expression, ubiquitination, transport, carbohydrates, gibberellins, lipid, glutathione and secondary metabolism, photosynthesis, as well as floral transition and flowering.\ud
Conclusion: This approach provides a broad repertoire of hexaploid wheat miRNAs associated with abiotic stress responses, tolerance and development. These valuable resources of expressed wheat miRNAs will help in elucidating the regulatory mechanisms involved in freezing and Al responses and tolerance mechanisms as well as for development and flowering. In the long term, it may help in breeding stress tolerant plants
Suppression of Phospholipase Dγs Confers Increased Aluminum Resistance in Arabidopsis thaliana
Aluminum (Al) toxicity is the major stress in acidic soil that comprises about 50% of the world's arable land. The complex molecular mechanisms of Al toxicity have yet to be fully determined. As a barrier to Al entrance, plant cell membranes play essential roles in plant interaction with Al, and lipid composition and membrane integrity change significantly under Al stress. Here, we show that phospholipase Dγs (PLDγs) are induced by Al stress and contribute to Al-induced membrane lipid alterations. RNAi suppression of PLDγ resulted in a decrease in both PLDγ1 and PLDγ2 expression and an increase in Al resistance. Genetic disruption of PLDγ1 also led to an increased tolerance to Al while knockout of PLDγ2 did not. Both RNAi-suppressed and pldγ1-1 mutants displayed better root growth than wild-type under Al stress conditions, and PLDγ1-deficient plants had less accumulation of callose, less oxidative damage, and less lipid peroxidation compared to wild-type plants. Most phospholipids and glycolipids were altered in response to Al treatment of wild-type plants, whereas fewer changes in lipids occurred in response to Al stress in PLDγ mutant lines. Our results suggest that PLDγs play a role in membrane lipid modulation under Al stress and that high activities of PLDγs negatively modulate plant tolerance to Al
Plant Proteomic Research
Plants, being sessile in nature, are constantly exposed to environmental challenges resulting in substantial yield loss. To cope with harsh environments, plants have developed a wide range of adaptation strategies involving morpho-anatomical, physiological, and biochemical traits. In recent years, there has been phenomenal progress in the understanding of plant responses to environmental cues at the protein level. This progress has been fueled by the advancement in mass spectrometry techniques, complemented with genome-sequence data and modern bioinformatics analysis with improved sample preparation and fractionation strategies. As proteins ultimately regulate cellular functions, it is perhaps of greater importance to understand the changes that occur at the protein-abundance level, rather than the modulation of mRNA expression. This Special Issue on "Plant Proteomic Research" brings together a selection of insightful papers that address some of these issues related to applications of proteomic techniques in elucidating master regulator proteins and the pathways associated with plant development and stress responses. This Issue includes four reviews and 13 original articles primarily on environmental proteomic studies
Pre-breeding of tef [Eragrostic tef (Zucc.) trotter] for tolerance to aluminium toxicity.
Doctor of Philosophy in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg 2015.Tef [Eragrostis tef (Zucc.) Trotter] is the most widely grown cereal crop in Ethiopia. Its grain is used for human consumption and the straw is an important and highly valued livestock feed. Soil acidity and Al toxicity are among the major production constraints affecting tef in Ethiopia. Utilization of lime and other non-genetic acid soil management options is constrained by various socio-economic factors. Development of cultivars with tolerance to Al-toxicity is a complementary approach to liming in the production of globally important crops such as wheat, rice, maize, barley, sorghum and rye. However, no breeding for tolerance to Al toxicity in tef had been undertaken previously. Hence, this research project was initiated in order to address the following objectives:
1. To assess the perceptions, challenges and coping mechanisms of farmers dealing with soil acidity and Al-toxicity in problem areas of north western Ethiopia;
2. To characterize the reactions of released tef varieties to soil acidity and the associated Al-toxicity;
3. To determine the extent of genetic diversity among tef germplasm collected from areas of Ethiopia with acid soil;
4. To isolate and characterize EMS-induced mutants of tef for tolerance to Al-toxicity and other important agronomic traits;
5. To evaluate the use of hydroponics system as a phenotyping platform to screen for Al-tolerance in tef, using root measurement and haematoxylin assay methods.
There is no information on breeding for Al-tolerance in tef. Therefore, relational background literature was collated on other cereals on their mechanisms of Al-toxicity, tolerance mechanisms, genetic control, screening methods and marker assisted breeding. The information obtained from such sources was used to develop and undertake the subsequent breeding activities on tef.
In order to meet the set objectives, several laboratory, greenhouse, and field experiments were conducted at the Amhara Regional Agricultural Research Institute (ARARI), Ethiopia, from December 2012 to June 2015.
A Participatory Rural Appraisal (PRA) study was conducted in three Districts of north western Ethiopia that are affected by acid soils, in order to assess the state of soil acidity, and to determine its perceived causes and indicators, and to document the coping strategies of the farmers. Semi-structured interviews, group discussions and
soil analyses were the main techniques used to generate data in this background study. Farmers’ perceived the causes of soil acidity to include: soil erosion; poor nutrient recycling; the abandoning of traditional fertility management practices; the unbalanced and/or minimal use of external inputs; and the exclusive use of acid-forming, inorganic fertilizers. Soil erosion, soil acidity, the high cost of mineral fertilizers and lime, cash shortages, and a lack of acid tolerant crop varieties were ranked as the top constraints. Species tolerance to soil acidity was found to be one of the major factors that influenced crop choice by farmers. A decline in genetic diversity and the rapid expansions of newly introduced, acid tolerant crops such as oat and triticale were noticed. The pH (H2O) of most of the soils in the study sites was in a strongly acidic range (4.6–5.5). Gashena Akayita of Banja District was the most acidic of all and had high levels of exchangeable Al. The limitations of the current coping strategies suggested the need to introduce compatible technologies that would ensure the sustainable management of the soils in the region, by the small-scale farmers there.
Thirty three Released Varieties and selected accessions of tef were evaluated for their tolerance to soil acidity in pot trials. Twenty eight of these were then evaluated under field conditions. The results revealed the presence of significant genetic variability within the test genotypes. Nearly all the test genotypes were highly sensitive to soil acidity and Al-toxicity. However, a local landrace that is widely grown in Banja, a District severely affect by soil acidity, consistently outperformed the other genotypes both under pot and field conditions. There were changes in the ranking of the tef genotypes tested under pot and field conditions, which suggested the need to consider other edaphic and climatic factors when breeding for Al-tolerance. Overall, the grain yield of the test genotypes and the tolerant local landrace were less than the national mean yield of tef, identifying the need to develop varieties with better tolerance of acid soils and the associated Al-toxicity, aiming for superior agronomic performances in acid soils.
Twenty-seven tef accessions collected from three regions of Ethiopia that are affected by acid soils were evaluated, together with released breeders’ varieties, and selected breeding materials for genetic diversity, using 16 selected and highly polymorphic SSR markers. Analysis of molecular variance (AMOVA) showed highly significant differences (P<0.001) among and within populations. Despite the wide geographical separation of the collection sites, 88.5% of the accessions from acid soils were
grouped into two clusters (Clusters II and III) while 90% of the breeding materials and the Released Varieties were grouped into Cluster I. A significant degree of genetic differentiation was observed among the populations. Accessions from the north western Ethiopia exhibited a significant level of variation for most of the genetic diversity parameters. The number of private alleles was significantly higher for tef plants from acid soils than the Released Varieties and the breeding materials the Pair-wise estimates of genetic identity and gene flow showed higher values existed between the Released Varieties and breeding materials.
About 15,000 M2 seeds were screened under acid soil conditions along with the M0 mutagenized seeds of the parent variety Tsedey and an Al-tolerant local landrace, Dabo banja. Twenty one M2 plants with root lengths of greater than the mean plus standard deviation of the tolerant check were selected and their M3 progenies were characterized for Al-tolerance and morpho-agronomic traits under greenhouse and field conditions, respectively. There were highly significant differences for Al-tolerance between the M3 mutant lines and the parent (P<0.001); and between the M3 mutant lines and the sensitive check (P<0.001). However, there was no significant difference between the M3 mutant lines and the tolerant check. The result of the morpho-agronomic characterization revealed the presence of significant differences between the M3 mutants for 16 of the 20 quantitative traits measured.
Five levels of AlK(SO4)2.12H2O were evaluated (0, 150, 250,350, 450, 550 μM) in order to select the optimal concentration of Al that can most efficiently discriminate between sensitive and tolerant tef genotypes, using a hydroponic growing facility and measuring root lengths. The haematoxylin staining method was also assessed as a tool for the visual evaluation of tef varieties for Al-tolerance using selected test genotypes. There were highly significant differences (P<0.001) between the treatments, both for dose of Al and for genotype sensitivity to Al. The maximum differences in relative root length (RRL) (%) and root length (RL) (mm) between the sensitive and the tolerant genotypes were observed at the Al level of 150 μM Al. This concentration efficiently discriminated between 28 test genotypes with different levels of sensitivity to Al-toxicity. A visual assessment of the reactions of two sensitive and two tolerant genotypes to haematoxylin staining using 0, 150 and 250 μM of AlK(SO4)2.12H2O showed differential staining reactions in their roots that were consistent with their prior root growth measurements
Uncovering the transcriptional response of popcorn (Zea mays L. var. everta) under long-term aluminum toxicity.
To date, the investigation of genes involved in Al resistance has focused mainly on microarrays and short periods of Al exposure. We investigated genes involved in the global response under Al stress by tracking the expression profile of two inbred popcorn lines with different Al sensitivity during 72 h of Al stress. A total of 1003 differentially expressed genes were identified in the Al-sensitive line, and 1751 were identified in the Al-resistant line, of which 273 were shared in both lines. Genes in the category of ?response to abiotic stress? were present in both lines, but there was a higher number in the Al-resistant line. Transcription factors, genes involved in fatty acid biosynthesis, and genes involved in cell wall modifications were also detected. In the Al-resistant line, GST6 was identified as one of the key hub genes by co-expression network analysis, and ABC6 may play a role in the downstream regulation of CASP-like 5. In addition, we suggest a class of SWEET transporters that might be involved in the regulation of vacuolar sugar storage and may serve as mechanisms for Al resistance. The results and conclusions expand our understanding of the complex mechanisms involved in Al toxicity and provide a platform for future functional analyses and genomic studies of Al stress in popcorn
Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants
Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants’ demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production