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1.
Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach.
Mirdar Mansuri, R, Shobbar, ZS, Babaeian Jelodar, N, Ghaffari, M, Mohammadi, SM, Daryani, P
BMC plant biology. 2020;(1):452
Abstract
BACKGROUND Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. RESULTS A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. CONCLUSIONS The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.
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2.
A scoping review of adoption of climate-resilient crops by small-scale producers in low- and middle-income countries.
Acevedo, M, Pixley, K, Zinyengere, N, Meng, S, Tufan, H, Cichy, K, Bizikova, L, Isaacs, K, Ghezzi-Kopel, K, Porciello, J
Nature plants. 2020;(10):1231-1241
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Abstract
Climate-resilient crops and crop varieties have been recommended as a way for farmers to cope with or adapt to climate change, but despite the apparent benefits, rates of adoption by smallholder farmers are highly variable. Here we present a scoping review, using PRISMA-P (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols), examining the conditions that have led to the adoption of climate-resilient crops over the past 30 years in lower- and middle-income countries. The descriptive analysis performed on 202 papers shows that small-scale producers adopted climate-resilient crops and varieties to cope with abiotic stresses such as drought, heat, flooding and salinity. The most prevalent trait in our dataset was drought tolerance, followed by water-use efficiency. Our analysis found that the most important determinants of adoption of climate-resilient crops were the availability and effectiveness of extension services and outreach, followed by education levels of heads of households, farmers' access to inputs-especially seeds and fertilizers-and socio-economic status of farming families. About 53% of studies reported that social differences such as sex, age, marital status and ethnicity affected the adoption of varieties or crops as climate change-adaptation strategies. On the basis of the collected evidence, this study presents a series of pathways and interventions that could contribute to higher adoption rates of climate-resilient crops and reduce dis-adoption.
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The impact of crop residue biochars on silicon and nutrient cycles in croplands.
Li, Z, Song, Z, Singh, BP, Wang, H
The Science of the total environment. 2019;:673-680
Abstract
Croplands are subjected to nutrient loss mainly due to agricultural harvest. Silicon has beneficial effect on alleviating nutrient imbalance-induced stress. Addition of crop residue biochars to cropland can import both silicon (Si) and nutrients (e.g. nitrogen, phosphorus and potassium) directly and enhance their availability. Nevertheless, how the concentrations of Si and nutrients vary among the biochars derived from different feedstocks, and how crop Si and nutrients respond to addition of biochars to croplands have not yet been clarified comprehensively and quantitatively. Total and essentially available Si and nutrients in crop residue biochars and their relationships with crop Si and nutrient uptake were investigated by using data collected from peer reviewed papers. Biochars derived from rice husk, rice straw, corn stover, sugarcane residues, and wheat straw, which were produced by thermal pyrolysis at 150-900 °C under oxygen-limited conditions, averagely contained 20.03% (n = 10), 12.39% (n = 16), 10.25% (n = 7), 7.40% (n = 9), and 3.34% (n = 3) of total Si, respectively. By contrast, crop residue biochars contained, on average, 1.23% nitrogen (n = 461), 0.32% phosphorus (n = 209), 0.56% sulfur (n = 187), 2.73% potassium (n = 197), 1.17% calcium (n = 123), and 0.54% magnesium (n = 111), which largely depended on and varied widely with their feedstocks and pyrolysis conditions. On average, 32.6%-54.9% of the total Si and nutrients (excluding nitrogen) in crop residue biochars were essentially available. Hence, addition of crop residue biochars to croplands may contribute a considerable amount of total and available Si and nutrients, except available inorganic nitrogen. The increasing amounts of Si and nutrient input with addition of biochars had positive and statistically significant (p < 0.05) relationships with the increment of crop Si and nutrient uptake, respectively. In conclusion, addition of crop residue biochars can be beneficial to sustainable agriculture system through concerting Si and nutrient cycling in croplands.
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Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data.
Benny, J, Pisciotta, A, Caruso, T, Martinelli, F
BMC plant biology. 2019;(1):194
Abstract
BACKGROUND Our study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different crops. The aim was to identify and map which genes play a key role in drought response on leaves across different crops. Forty-two RNA-seq samples were analyzed from 9 published studies in 7 plant species (Arabidopsis thaliana, Solanum lycopersicum, Zea mays, Vitis vinifera, Malus X domestica, Solanum tuberosum, Triticum aestivum). RESULTS Twenty-seven (16 up-regulated and 11 down-regulated) drought-regulated genes were commonly present in at least 7 of 9 studies, while 351 (147 up-regulated and 204 down-regulated) were commonly drought-regulated in 6 of 9 studies. Across all kind of leaves, the drought repressed gene-ontologies were related to the cell wall and membrane re-structuring such as wax biosynthesis, cell wall organization, fatty acid biosynthesis. On the other hand, drought-up-regulated biological processes were related to responses to osmotic stress, abscisic acid, water deprivation, abscisic-activated signalling pathway, salt stress, hydrogen peroxide treatment. A common metabolic feature linked to drought response in leaves is the repression of terpenoid pathways. There was an induction of AL1 (alfin-like), UGKYAH (trihelix), WRKY20, homeobox genes and members of the SET domain family in 6 of 9 studies. Several genes involved in detoxifying and antioxidant reactions, signalling pathways and cell protection were commonly modulated by drought across the 7 species. The chromosome (Chr) mapping of these key abiotic stress genes highlighted that Chr 4 in Arabidopsis thaliana, Chr 1 in Zea mays, Chr 2 and Chr 5 in Triticum aestivum contained a higher presence of drought-related genes compared to the other remaining chromosomes. In seedling studies, it is worth notice the up-regulation of ERF4 and ESE3 (ethylene), HVA22 (abscisic acid), TIR1 (auxin) and some transcription factors (MYB3, MYB94, MYB1, WRKY53 and WRKY20). In mature leaves, ERF1 and Alfin-like 1 were induced by drought while other transcription factors (YABBY5, ARR2, TRFL2) and genes involved phospholipid biosynthesis were repressed. CONCLUSIONS The identified and mapped genes might be potential targets of molecular breeding activities to develop cultivars with enhanced drought resistance and tolerance across different crops.
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A meta-analysis of crop response patterns to nitrogen limitation for improved model representation.
Seufert, V, Granath, G, Müller, C
PloS one. 2019;(10):e0223508
Abstract
The representation of carbon-nitrogen (N) interactions in global models of the natural or managed land surface remains an important knowledge gap. To improve global process-based models we require a better understanding of how N limitation affects photosynthesis and plant growth. Here we present the findings of a meta-analysis to quantitatively assess the impact of N limitation on source (photosynthate production) versus sink (photosynthate use) activity, based on 77 highly controlled experimental N availability studies on 11 crop species. Using meta-regressions, we find that it can be insufficient to represent N limitation in models merely as inhibiting carbon assimilation, because in crops complete N limitation more strongly influences leaf area expansion (-50%) than photosynthesis (-34%), while leaf starch is accumulating (+83%). Our analysis thus offers support for the hypothesis of sink limitation of photosynthesis and encourages the exploration of more sink-driven crop modelling approaches. We also show that leaf N concentration changes with N availability and that the allocation of N to Rubisco is reduced more strongly compared to other photosynthetic proteins at low N availability. Furthermore, our results suggest that different crop species show generally similar response patterns to N limitation, with the exception of leguminous crops, which respond differently. Our meta-analysis offers lessons for the improved depiction of N limitation in global terrestrial ecosystem models, as well as highlights knowledge gaps that need to be filled by future experimental studies on crop N limitation response.
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Methods matter: a meta-regression on the determinants of willingness-to-pay studies on biofortified foods.
De Steur, H, Wesana, J, Blancquaert, D, Van Der Straeten, D, Gellynck, X
Annals of the New York Academy of Sciences. 2017;(1):34-46
Abstract
Following the growing evidence on biofortification as a cost-effective micronutrient strategy, various researchers have elicited consumers' willingness to pay (WTP) for biofortified crops in an effort to justify and determine their adoption. This review presents a meta-analysis of WTP studies on biofortified foods, either developed through conventional breeding or using genetic modification technology. On the basis of 122 estimates from 23 studies (9507 respondents), consumers are generally willing to pay 21.3% more for biofortified crops. Because WTP estimates are often determined through different valuation methods and procedures, a meta-regression was carried out to examine the role of potential determinants. Aside from contextual factors, such as type of food crop, target nutrient, and region (but not breeding technique), various methodological factors significantly influence premiums, including the type of respondent, nature of the study, study environment, participation fee, and provided information. The findings allow researchers to better anticipate potential methodological biases when examining WTP for (biofortified) foods, while it gives policy makers a broad understanding of the potential demand for different biofortified crops in various settings.
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Rates of return to sorghum and millet research investments: A meta-analysis.
Zereyesus, YA, Dalton, TJ
PloS one. 2017;(7):e0180414
Abstract
Sorghum and millet grow in some of the most heterogeneous and austere agroecologies around the world. These crops are amongst the top five cereal sources of food and feed. Yet, few studies document the impact of sorghum and millet genetic enhancement. The Internal Rate of Return (ROR) is one of the most popular metrics used to measure the economic return on investment on agricultural research and development (R&D). This study conducted a meta-analysis of 59 sorghum and millet ROR estimates obtained from 25 sources published between 1958 and 2015. The average rate of return to sorghum and millet R&D investment is between 54-76 percent per year. All studies computed social rather than private RORs because the technologies were developed using public funds originating from host country National Agricultural Research Systems (NARS) and international organizations such as the INTSORMIL CRSP, ICRISAT and others. Nearly three quarter of the studies focused only on sorghum (72 percent) and around one tenth of the studies (8 percent) on millet. Regression models analyzed the determinants of variation in the reported RORs. Results show that ex-ante type and self-evaluated type of analyses are positively and significantly associated with the ROR estimates. Compared to estimates conducted by a university, results from international institutions and other mixed organizations provided significantly smaller estimates. Estimates conducted at national level also are significantly lower than those conducted at sub-national levels. The ROR is higher for studies conducted in the United States and for those conducted more recently. The study also reconstructed modified internal rate of return (MIRR) for a sub-sample of the reported RORs following recent methods from the literature. These results show that the MIRR estimates are significantly smaller than the reported ROR estimates. Both results indicate that investment in sorghum and millet research generates high social rates of return.
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Reduction of transpiration and altered nutrient allocation contribute to nutrient decline of crops grown in elevated CO(2) concentrations.
McGrath, JM, Lobell, DB
Plant, cell & environment. 2013;(3):697-705
Abstract
Plants grown in elevated [CO(2) ] have lower protein and mineral concentrations compared with plants grown in ambient [CO(2) ]. Dilution by enhanced production of carbohydrates is a likely cause, but it cannot explain all of the reductions. Two proposed, but untested, hypotheses are that (1) reduced canopy transpiration reduces mass flow of nutrients to the roots thus reducing nutrient uptake and (2) changes in metabolite or enzyme concentrations caused by physiological changes alter requirements for minerals as protein cofactors or in other organic complexes, shifting allocation between tissues and possibly altering uptake. Here, we use the meta-analysis of previous studies in crops to test these hypotheses. Nutrients acquired mostly by mass flow were decreased significantly more by elevated [CO(2) ] than nutrients acquired by diffusion to the roots through the soil, supporting the first hypothesis. Similarly, Mg showed large concentration declines in leaves and wheat stems, but smaller decreases in other tissues. Because chlorophyll requires a large fraction of total plant Mg, and chlorophyll concentration is reduced by growth in elevated [CO(2) ], this supports the second hypothesis. Understanding these mechanisms may guide efforts to improve nutrient content, and allow modeling of nutrient changes and health impacts under future climate change scenarios.