Engineering the lodging resistance mechanism of post-Green Revolution rice to meet future demands.
Ontology highlight
ABSTRACT:
SUBMITTER: Hirano K
PROVIDER: S-EPMC5489430 | biostudies-other | 2017
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Lodging reduces grain yield in cereal crops. Understanding the genetic basis of lodging resistance (LR) benefits LR breeding. In the study, 524 accessions from a rice germplasm collection and 193 recombinant inbred lines were phenotyped for 17 LR-related traits. Height and culm strength (the magnitude of applied force necessary to break the culm) were two major factors affecting LR. We conducted genome-wide association study (GWAS) and identified 127 LR-associated loci. Significant phenotypic correlations between culm-strength traits and yield-related traits were observed. To reveal the genetic relationship between them, we conducted GWAS of culm-strength traits with adding yield-related trait as a covariate and detected 63 loci linking culm strength and yield. As a proof, a near-isogenic line for an association locus on chromosome 7 showed enhanced LR and yield. Strikingly, 58 additional loci were identified in the covariate-added GWAS. Several LR-associated loci had undergone divergent selection. Linkage analysis supported the GWAS results. We propose that introgression of alleles beneficial for both culm strength and panicle weight without negative effects on panicle number or pyramiding high-yielding alleles and lodging-resistant alleles without effects on yield can be employed for the post-Green-Revolution breeding.
| S-EPMC8051602 | biostudies-literature
Project description:The human population is expected to reach ?9 billion by 2050. The ensuing demands for water, food and energy would intensify land-use conflicts and exacerbate environmental impacts. Therefore we urgently need to reconcile our growing consumptive needs with environmental protection. Here, we explore the potential of a land-use optimisation strategy to increase global agricultural production on two major groups of crops: cereals and oilseeds. We implemented a spatially-explicit computer simulation model across 173 countries based on the following algorithm: on any cropland, always produce the most productive crop given all other crops currently being produced locally and the site-specific biophysical, economic and technological constraints to production. Globally, this strategy resulted in net increases in annual production of cereal and oilseed crops from 1.9 billion to 2.9 billion tons (46%), and from 427 million to 481 million tons (13%), respectively, without any change in total land area harvested for cereals or oilseeds. This thought experiment demonstrates that, in theory, more optimal use of existing farmlands could help meet future crop demands. In practice there might be cultural, social and institutional barriers that limit the full realisation of this theoretical potential. Nevertheless, these constraints have to be weighed against the consequences of not producing enough food, particularly in regions already facing food shortages.
| S-EPMC3817586 | biostudies-literature
Project description:Sustainable food systems aim to provide sufficient and nutritious food, while maximizing climate resilience and minimizing resource demands as well as negative environmental impacts. Historical practices, notably the Green Revolution, prioritized the single objective to maximize production over other nutritional and environmental dimensions. We quantitatively assess outcomes of alternative production decisions across multiple objectives using India's rice-dominated monsoon cereal production as an example. We perform a series of optimizations to maximize nutrient production (i.e., protein and iron), minimize greenhouse gas (GHG) emissions and resource use (i.e., water and energy), or maximize resilience to climate extremes. We find that increasing the area under coarse cereals (i.e., millets, sorghum) improves nutritional supply (on average, +1% to +5% protein and +5% to +49% iron), increases climate resilience (1% to 13% fewer calories lost during an extreme dry year), and reduces GHGs (-2% to -13%) and demand for irrigation water (-3% to -21%) and energy (-2% to -12%) while maintaining calorie production and cropped area. The extent of these benefits partly depends on the feasibility of switching cropped area from rice to coarse cereals. Based on current production practices in 2 states, supporting these cobenefits could require greater manure and draft power but similar or less labor, fertilizer, and machinery. National- and state-level strategies considering multiple objectives in decisions about cereal production can move beyond many shortcomings of the Green Revolution while reinforcing the benefits. This ability to realistically incorporate multiple dimensions into intervention planning and implementation is the crux of sustainable food production systems worldwide.
| S-EPMC6911172 | biostudies-literature
Project description:The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene, semi-dwarf1 (sd1), which encodes a gibberellin biosynthesis enzyme, made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution, but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica, along with their wild ancestor O. rufipogon Griff, revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace, not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication, suggesting that ancient humans already used the green revolution gene.
| S-EPMC3131315 | biostudies-literature
Project description:The National Science Foundation estimates that 80% of the jobs available during the next decade will require math and science skills, dictating that programs in biochemistry and molecular biology must be transformative and use new pedagogical approaches and experiential learning for careers in industry, research, education, engineering, health-care professions, and other interdisciplinary fields. These efforts require an environment that values the individual student and integrates recent advances from the primary literature in the discipline, experimentally directed research, data collection and analysis, and scientific writing. Current trends shaping these efforts must include critical thinking, experimental testing, computational modeling, and inferential logic. In essence, modern biochemistry and molecular biology education must be informed by, and integrated with, cutting-edge research. This environment relies on sustained research support, commitment to providing the requisite mentoring, access to instrumentation, and state-of-the-art facilities. The academic environment must establish a culture of excellence and faculty engagement, leading to innovation in the classroom and laboratory. These efforts must not lose sight of the importance of multidimensional programs that enrich science literacy in all facets of the population, students and teachers in K-12 schools, nonbiochemistry and molecular biology students, and other stakeholders. As biochemistry and molecular biology educators, we have an obligation to provide students with the skills that allow them to be innovative and self-reliant. The next generation of biochemistry and molecular biology students must be taught proficiencies in scientific and technological literacy, the importance of the scientific discourse, and skills required for problem solvers of the 21st century.
| S-EPMC7397093 | biostudies-literature
Project description:The introduction of semidwarf rice (Oryza sativa L.) led to record yield increases throughout Asia in the 1960s. The major semidwarfing allele, sd-1, is still extensively used in modern rice cultivars. The phenotype of sd-1 is consistent with dwarfism that results from a deficiency in gibberellin (GA) plant growth hormones. We propose that the semidwarf (sd-1) phenotype is the result of a deficiency of active GAs in the elongating stem arising from a defective 20-oxidase GA biosynthetic enzyme. Sequence data from the rice genome was combined with previous mapping studies to locate a putative GA 20-oxidase gene (Os20ox2) at the predicted map location of sd-1 on chromosome 1. Two independent sd-1 alleles contained alterations within Os20ox2: a deletion of 280 bp within the coding region of Os20ox2 was predicted to encode a nonfunctional protein in an indica type semidwarf (Doongara), whereas a substitution in an amino acid residue (Leu-266) that is highly conserved among dioxygenases could explain loss of function of Os20ox2 in a japonica semidwarf (Calrose76). The quantification of GAs in elongating stems by GC-MS showed that the initial substrate of GA 20-oxidase activity (GA53) accumulated, whereas the content of the major product (GA20) and of bioactive GA1 was lower in semidwarf compared with tall lines. We propose that the Os20ox2 gene corresponds to the sd-1 locus.
| S-EPMC124420 | biostudies-literature
Project description:BACKGROUND:Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the 'Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. RESULTS:A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition. CONCLUSIONS:Tongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome.
| S-EPMC4883996 | biostudies-literature
Project description:The impact of modern agriculture on the evolutionary trajectory of plant pathogens is a central question for crop sustainability. The Green Revolution replaced traditional rice landraces with high-yielding varieties, creating a uniform selection pressure that allows measuring the effect of such intervention. In this study, we analyzed a unique historical pathogen record to assess the impact of a major resistance gene, Xa4, in the population structure of Xanthomonas oryzae pv. oryzae (Xoo) collected in the Philippines in a span of 40 years. After the deployment of Xa4 in the early 1960s, the emergence of virulent pathogen groups was associated with the increasing adoption of rice varieties carrying Xa4, which reached 80% of the total planted area. Whole genomes analysis of a representative sample suggested six major pathogen groups with distinctive signatures of selection in genes related to secretion system, cell-wall degradation, lipopolysaccharide production, and detoxification of host defense components. Association genetics also suggested that each population might evolve different mechanisms to adapt to Xa4. Interestingly, we found evidence of strong selective sweep affecting several populations in the mid-1980s, suggesting a major bottleneck that coincides with the peak of Xa4 deployment in the archipelago. Our study highlights how modern agricultural practices facilitate the adaptation of pathogens to overcome the effects of standard crop improvement efforts.
| S-EPMC6976662 | biostudies-literature
Project description:Mitochondria are the power houses of the cell, but unlike the static structures portrayed in textbooks, they are dynamic organelles that move about the cell to deliver energy to locations in need. These organelles fuse with each other then split apart; some appear anchored and others more free to move around, and when damaged they are engulfed by autophagosomes. Together, these processes-mitochondrial trafficking, fusion and fission, and mitophagy-are best described by the term "mitochondrial dynamics". The molecular machineries behind these events are relatively well known yet the precise dynamics in neurons remains under debate. Neurons pose a peculiar logistical challenge to mitochondria; how do these energy suppliers manage to traffic down long axons to deliver the requisite energy supply to distant parts of the cell? To date, the majority of neuronal mitochondrial dynamics studies have used cultured neurons, Drosophila larvae, zebrafish embryos, with occasional experiments in resting mouse nerves. However, a new study in this issue of PLOS Biology from Marija Sajic and colleagues provides an in vivo look at mitochondrial dynamics along resting and electrically active neurons of live anaesthetized mice.
| S-EPMC3876985 | biostudies-literature
Project description:Changes in expression patterns may occur when organisms are presented with new environmental challenges, for example following migration or genetic changes. To elucidate the mechanisms by which the translational machinery adapts to such changes, we perturbed the tRNA pool of Saccharomyces cerevisiae by tRNA gene deletion. We then evolved the deletion strain and observed that the genetic adaptation was recurrently based on a strategic mutation that changed the anticodon of other tRNA genes to match that of the deleted one. Strikingly, a systematic search in hundreds of genomes revealed that anticodon mutations occur throughout the tree of life. We further show that the evolution of the tRNA pool also depends on the need to properly couple translation to protein folding. Together, our observations shed light on the evolution of the tRNA pool, demonstrating that mutation in the anticodons of tRNA genes is a common adaptive mechanism when meeting new translational demands. DOI: http://dx.doi.org/10.7554/eLife.01339.001.
| S-EPMC3868979 | biostudies-literature