Harnessing Crop Biodiversity and Genomics Assisted Pre-Breeding Approaches for Next Generation Climate-Smart Varieties
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ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE250611 | GEO | 2024/01/31
REPOSITORIES: GEO
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Project description:Most business-as-usual scenarios for farming under changing climate regimes project that the agriculture sector will be significantly impacted from increased temperatures and shifting precipitation patterns. Perhaps ironically, agricultural production contributes substantially to the problem with yearly greenhouse gas (GHG) emissions of about 11% of total anthropogenic GHG emissions, not including land use change. It is partly because of this tension that Climate Smart Agriculture (CSA) has attracted interest given its promise to increase agricultural productivity under a changing climate while reducing emissions. Considerable resources have been mobilized to promote CSA globally even though the potential effects of its widespread adoption have not yet been studied. Here we show that a subset of agronomic practices that are often included under the rubric of CSA can contribute to increasing agricultural production under unfavorable climate regimes while contributing to the reduction of GHG. However, for CSA to make a significant impact important investments and coordination are required and its principles must be implemented widely across the entire sector.
| S-EPMC7190105 | biostudies-literature
Project description:IntroductionBeing one of the "big three" most cultivated cereals in the world, wheat plays a crucial role in ensuring global food/nutrition security, supplying close to 20% of the global needs for calories and proteins. However, the increasingly large fluctuations between years in temperatures and precipitation due to climate change cause important variations in wheat production worldwide. This fact makes wheat breeding programs a tool that, far from going out of fashion, is becoming the most important solution to develop varieties that can provide humanity with the sufficient amount of food it demands without forgetting the objective of quality.Material and methodsThe National Institute of Agricultural and Veterinary Research in Portugal has carried out a long-term experiment (9 years) in different locations to test four different bread-making wheat cultivars, each representing important variations in germplasm. Wheat yield and quality traits obtained by official methods were recorded in 18 different environments regarding temperature and precipitation.Results and discussionAccording to the ANOVA and PCA, protein content, wet gluten, dough tenacity, and extensibility were found to be highly affected by the environment. Paiva cultivar presented a higher yield in almost all the tested environments, but its quality traits varied enormously. Contrary behavior was recorded for Valbona cultivar. Antequera cultivar, with a production ranging between 4.7 and 9.3 tons/ha and a protein content between 11 and 16.8%, seems to be the most resilient cultivar regarding both productivity and quality of the flour with reference to changes in the main climate traits. The most ancient cultivar, Roxo, released in 1996, showed the worst results in this experiment, supporting the need to continue working in wheat breeding to meet the unavoidable changes in the environment.
| S-EPMC11335553 | biostudies-literature
Project description:Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.
2020-03-19 | GSE129220 | GEO
Project description:Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
| S-EPMC5454074 | biostudies-literature
Project description:Seed of 4 lines of S. tuberosum var andigena were sown and, after transplanting, grown in 3 gal nursery containers in a greenhouse with natural daylight. The seeds were sown in July and the drought stress experiment began in September. Drought stress was administered by withholding water and monitored by measuring the rate of photosynthesis (PS; LiCor 6400). We found that loss of photosynthetic capability (ie a PS rate of 0-2 mM CO2/m2/sec) correlated with a severe drought stress. Control plants were watered normally and maintained a PS rate of 18-20 mM CO2/m2/sec. After drought stress, the treated plants were re-watered and PS measurements taken again. After the first cycles of stress, control and treated plants were harvested and roots, tubers and shoots were stored at –80°C for RNA extractions. The drought experiment was then repeated for the remaining plants such that they were exposed to a second cycle of stress. For each line of S. andigena, there were 2 control and 2 treated plants per cycle of stress. RNA was extracted following the acid phenol protocol of TIGR. Keywords: Direct comparison, loop design
2007-09-01 | GSE8207 | GEO
Project description:Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.
| S-EPMC4330709 | biostudies-literature
Project description:The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
| S-EPMC10750425 | biostudies-literature
Project description:Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
| S-EPMC9523482 | biostudies-literature
Project description:BackgroundClimate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY1.1, qDTY2.1, qDTY3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal.ResultsGrain yield advantage of the NILs with qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 and qDTY2.1 + qDTY3.1 + Sub1 ranged from 76 to 2479 kg ha- 1 and 396 to 2376 kg ha- 1 under non-stress (NS) respectively and 292 to 1118 kg ha- 1 and 284 to 2086 kg ha- 1 under reproductive drought stress (RS), respectively. The NIL, IR96322-34-223-B-1-1-1-1 having qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321-1447-651-B-1-1-2 having qDTY1.1 + qDTY3.1 + Sub 1 and IR 94391-131-358-19-B-1-1-1 having qDTY3.1 + Sub1 have been released as varieties Bahuguni dhan-1' and 'Bahuguni dhan-2' respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322-34-223-B-1-1-1-1, IR 96321-1447-651-B-1-1-2 and IR 94391-131-358-19-B-1-1-1 respectively on 6 K SNP Infinium chip.ConclusionThe drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha- 1 under reproductive stage drought stress and 0.1 to 1.0 t ha- 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.
| S-EPMC6379507 | biostudies-literature
Project description:Prairie cordgrass (Spartina pectinata Bosc ex Link) is an indigenous, perennial grass of North America that is being developed into a cellulosic biomass crop suitable for biofuel production. Limited research has been performed into the breeding of prairie cordgrass; this research details an initial investigation into the development of a breeding program for this species. Genomic libraries enriched for four simple sequence repeat (SSR) motifs were developed, 25 clones from each library were sequenced, identifying 70?SSR regions, and primers were developed for these regions, 35 of which were amplified under standard PCR conditions. These SSR markers were used to validate the crossing methodology of prairie cordgrass and it was found that crosses between two plants occurred without the need for emasculation. The successful cross between two clones of prairie cordgrass indicates that this species is not self-incompatible. The results from this research will be used to instigate the production of a molecular map of prairie cordgrass which can be used to incorporate marker-assisted selection (MAS) protocols into a breeding program to improve this species for cellulosic biomass production.
| S-EPMC3513731 | biostudies-literature