scholarly journals Application of Genomics and Phenomics in Plant Breeding for Climate Resilience

2020 ◽  
pp. 53-66
Author(s):  
Noel Ndlovu
Keyword(s):  
Plant Breeding ◽  
Crop Improvement ◽  
Cost Effective ◽  
Breeding Systems ◽  
Plant Performance ◽  
Biological Study ◽  
Interdisciplinary Field ◽  
Climate Resilience ◽  
Next Generation Sequencing Ngs ◽  
Evolution Of Genomes

Advances in the fields of genomics and phenomics are currently creating significant foundations for the sustainable intensification of plant breeding initiatives targeting climate resilience. Genomics is a biological study that focuses on architecture, function, editing, mapping, and evolution of genomes. It can be applied extensively in climate resilience breeding for cost-effective, rapid, and high-through put genotyping, phenotyping, and trait mapping. The efficacy of genomics-assisted breeding (GAB) is strongly hinged on the high resolution and robustness of Next Generation Sequencing (NGS) and CRISPR/Cas9-based Gene Editing systems. The integration of genomics and phenomics in crop improvement can upscale the efficiency of breeding systems targeting climate resilience and hasten cultivar release cycle. Phenomics is an interdisciplinary field that focuses on the enhanced measurement of plant performance, growth, and composition. Similarly, phenomics has revolutionized the efficacy of plant breeding off-trial initiatives established to phenotypically characterize and study diversity levels of collected germplasm. Field phenomics tools such as the phenonet, phenomobile, and phenonetwork have proven to be efficient in capturing large sums of multiscale and multidimensional experimental data. The main purpose of this review article is to present a summarized account of the probable applications of integrated systems of genomics and phenomics in plant breeding for climate resilience in major crops.

New and novel genetic tools for improving crops.

2021 ◽  
Vol 16 (028) ◽  
Author(s):  
Penna Suprasanna
Keyword(s):  
Plant Breeding ◽  
Agronomic Traits ◽  
Plant Traits ◽  
Crop Improvement ◽  
Genetically Modified Crops ◽  
Climate Resilience ◽  
Crop Varieties ◽  
New Novel ◽  
High Throughput Phenotyping ◽  
Sequencing Platforms

Abstract The basic tenet of crop improvement is the novel genetic variability that is achieved through selection, hybridization, mutation and recombination. The new technological innovations of plant breeding offer scope for transforming crop improvement with more precision and resolution. Advances in genomic-based tools and high-throughput phenotyping have enabled the analysis of genetic variation and identification of molecular signatures of agronomic traits. Molecular markers and molecular-marker-assisted breeding have facilitated the speedy selection of new, novel genetic combinations in breeding for high-yielding, stress-tolerant and nutritionally enriched crops. Transgenic methods have revolutionized modification for stress tolerance and higher productivity, and several genetically modified crops are under cultivation. Availability of genome sequencing platforms and genomic resources has significantly contributed to accessing novel genes and validating their functions. Genome-editing tools and recent advances of prime editing are now accessible for precise genetic alteration of plant traits. The new plant breeding tools will certainly foster development of highly productive, improved crop varieties for achieving food security and climate resilience.

Farmer Participatory Crop Improvement. I. Varietal Selection and Breeding Methods and Their Impact on Biodiversity

1996 ◽  
Vol 32 (4) ◽  
pp. 445-460 ◽  
Author(s):  
J. R. Witcombe ◽  
A. Joshi ◽  
K. D. Joshi ◽  
B. R. Sthapit
Keyword(s):  
Plant Breeding ◽  
Crop Improvement ◽  
Cost Effective ◽  
Participatory Plant Breeding ◽  
Participatory Varietal Selection ◽  
Farmer Participatory Research ◽  
Long Term Effect ◽  
Impact On Biodiversity ◽  
The Impact

SUMMARYFarmer participatory approaches for the identification or breeding of improved crop cultivars can be usefully categorized into participatory varietal selection (PVS) and participatory plant breeding (PPB). Various PVS and PPB methods are reviewed. PVS is a more rapid and cost-effective way of identifying farmer-preferred cultivars if a suitable choice of cultivars exists. If this is impossible, then the more resource-consuming PPB is required. PPB can use, as parents, cultivars that were identified in successful PVS programmes. Compared with conventional plant breeding, PPB is more likely to produce farmer-acceptable products, particularly for marginal environments. The impact of farmer participatory research on biodiversity is considered. The long-term effect of PVS is to increase biodiversity, but where indigenous variability is high it can also reduce it. PPB has a greater effect on increasing biodiversity although its impact may be limited to smaller areas. PPB can be a dynamic form of in situ genetic conservation.

scholarly journals Rewiring Meiosis for Crop Improvement

2021 ◽  
Vol 12 ◽  
Author(s):  
Pallas Kuo ◽  
Olivier Da Ines ◽  
Christophe Lambing
Keyword(s):  
Plant Breeding ◽  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Meiotic Chromosome ◽  
Crop Improvement ◽  
Plant Performance ◽  
Dna Double Strand Breaks ◽  
Chromosome Engineering ◽  
Division Process ◽  
New Varieties

Meiosis is a specialized cell division that contributes to halve the genome content and reshuffle allelic combinations between generations in sexually reproducing eukaryotes. During meiosis, a large number of programmed DNA double-strand breaks (DSBs) are formed throughout the genome. Repair of meiotic DSBs facilitates the pairing of homologs and forms crossovers which are the reciprocal exchange of genetic information between chromosomes. Meiotic recombination also influences centromere organization and is essential for proper chromosome segregation. Accordingly, meiotic recombination drives genome evolution and is a powerful tool for breeders to create new varieties important to food security. Modifying meiotic recombination has the potential to accelerate plant breeding but it can also have detrimental effects on plant performance by breaking beneficial genetic linkages. Therefore, it is essential to gain a better understanding of these processes in order to develop novel strategies to facilitate plant breeding. Recent progress in targeted recombination technologies, chromosome engineering, and an increasing knowledge in the control of meiotic chromosome segregation has significantly increased our ability to manipulate meiosis. In this review, we summarize the latest findings and technologies on meiosis in plants. We also highlight recent attempts and future directions to manipulate crossover events and control the meiotic division process in a breeding perspective.

Farmer Participatory Crop Improvement. I. Varietal Selection and Breeding Methods and Their Impact on Biodiversity

1996 ◽  
Vol 32 (4) ◽  
pp. 445-460 ◽  
Author(s):  
J. R. Witcombe ◽  
A. Joshi ◽  
K. D. Joshi ◽  
B. R. Sthapit
Keyword(s):  
Plant Breeding ◽  
Crop Improvement ◽  
Cost Effective ◽  
Participatory Plant Breeding ◽  
Participatory Varietal Selection ◽  
Farmer Participatory Research ◽  
Long Term Effect ◽  
Impact On Biodiversity ◽  
The Impact

SUMMARYFarmer participatory approaches for the identification or breeding of improved crop cultivars can be usefully categorized into participatory varietal selection (PVS) and participatory plant breeding (PPB). Various PVS and PPB methods are reviewed. PVS is a more rapid and cost-effective way of identifying farmer-preferred cultivars if a suitable choice of cultivars exists. If this is impossible, then the more resource-consuming PPB is required. PPB can use, as parents, cultivars that were identified in successful PVS programmes. Compared with conventional plant breeding, PPB is more likely to produce farmer-acceptable products, particularly for marginal environments. The impact of farmer participatory research on biodiversity is considered. The long-term effect of PVS is to increase biodiversity, but where indigenous variability is high it can also reduce it. PPB has a greater effect on increasing biodiversity although its impact may be limited to smaller areas. PPB can be a dynamic form of in situ genetic conservation.

scholarly journals Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits

2021 ◽  
Author(s):  
Pallavi Sinha ◽  
Vikas K. Singh ◽  
Abhishek Bohra ◽  
Arvind Kumar ◽  
Jochen C. Reif ◽  
...  
Keyword(s):  
Statistical Methods ◽  
Genetic Gain ◽  
Crop Improvement ◽  
Breeding Population ◽  
Breeding Cycle ◽  
Climate Resilience ◽  
Heritability Estimation ◽  
Improvement Programs ◽  
Statistical Designs ◽  
Novel Alleles

Abstract Key message Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Abstract Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.

scholarly journals Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

2021 ◽  
Vol 22 (11) ◽  
pp. 5585
Author(s):  
Sajid Fiaz ◽  
Sunny Ahmar ◽  
Sajjad Saeed ◽  
Aamir Riaz ◽  
Freddy Mora-Poblete ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Food Security ◽  
Plant Breeding ◽  
Genome Editing ◽  
Crop Improvement ◽  
Hybrid Seed Production ◽  
Biotic And Abiotic Stress ◽  
Transcription Activator ◽  
Protein System ◽  
Breeding Techniques

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

Efficient High-throughput Techniques for the Analysis of Disease-Resistant Plant Varieties and Detection of Food Adulteration

2021 ◽  
Vol 23 ◽  
Author(s):  
Romesh Kumar Salgotra ◽  
Rafiq Ahmad Bhat ◽  
Deyue Yu ◽  
Javaid Akhter Bhat
Keyword(s):  
Multiplex Pcr ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Crop Improvement ◽  
Small Sample ◽  
Food Crops ◽  
Genomic Resources ◽  
Breeding Programmes ◽  
Next Generation Sequencing Ngs

Abstract: Over the past two decades, the advances in the next generation sequencing (NGS) platforms have led to the identification of numerous genes/QTLs at high-resolution for their potential use in crop improvement. The genomic resources generated through these high-throughput sequencing techniques have been efficiently used in screening of particular gene of interest particularly for numerous types of plant stresses and quality traits. Subsequently, the identified-markers linked to a particular trait have been used in marker-assisted backcross breeding (MABB) activities. Besides, these markers are also being used to catalogue the food crops for detection of adulteration to improve the quality of food. With the advancement of technologies, the genomic resources are originating with new markers; however, to use these markers efficiently in crop breeding, high-throughput techniques (HTT) such as multiplex PCR and capillary electrophoresis (CE) can be exploited. Robustness, ease of operation, good reproducibility and low cost are the main advantages of multiplex PCR and CE. The CE is capable of separating and characterizing proteins with simplicity, speed and small sample requirements. Keeping in view the availability of vast data generated through NGS techniques and development of numerous markers, there is a need to use these resources efficiently in crop improvement programmes. In summary, this review describes the use of molecular markers in the screening of resistance genes in breeding programmes and detection of adulterations in food crops using high-throughput techniques.

scholarly journals Association Mapping for Improvement of Quantitative Traits in Plant Breeding Populations

1970 ◽  
Vol 2 (1) ◽  
pp. 72-89
Author(s):  
Umesh R Rosyara ◽  
Bal K Joshi
Keyword(s):  
Association Mapping ◽  
Plant Breeding ◽  
Fine Mapping ◽  
Quantitative Trait ◽  
Human Genetics ◽  
Crop Improvement ◽  
Nucleotide Polymorphisms ◽  
Breeding Populations ◽  
Validation Of Results ◽  
Mapping Populations

DNA-based molecular markers have been extensively utilized for mapping of genes and quantitative trait loci (QTL) of interest based on linkage analysis in mapping populations. This is in contrast to human genetics that use of linkage disequilibrium (LD)-based mapping for fine mapping of QTLs using single nucleotide polymorphisms. LD based association mapping (AM) has promise to be used in plants. Possible use of such approach may be for fine mapping of genes / QTLs, identifying favorable alleles for marker aided selection and cross validation of results from linkage mapping for precise location of genes / QTLs of interest. In the present review, we discuss different mapping populations, approaches, prospects and limitations of using association mapping in plant breeding populations. This is expected to create awareness in plant breeders in use of AM in crop improvement activities.Key words: Association mapping; plant breeding; DNA marker; quantitative trait lociDOI: http://dx.doi.org/10.3126/njb.v2i1.5686  Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 72-89

scholarly journals Shotguns Vs Lasers: Identifying Barriers and Facilitators to Scaling-Up Plant Molecular Farming for High-Value Health Products

2019 ◽  
Author(s):  
Jonathan Menary ◽  
Matthew Hobbs ◽  
Sara Mesquita de Albuqurque ◽  
Agata Pacho ◽  
Pascal M. W. Drake ◽  
...  
Keyword(s):  
Social Acceptance ◽  
Molecular Farming ◽  
Qualitative Interviews ◽  
Crop Improvement ◽  
Cost Effective ◽  
Scaling Up ◽  
Barriers And Facilitators ◽  
Horizon 2020 ◽  
Plant Molecular Farming ◽  
Health Products

Plant molecular farming (PMF) is a convenient and cost-effective way to produce high-value recombinant proteins that can be used in the production of a range of health products, from pharmaceutical therapeutics to cosmetic products. New plant breeding techniques (NPBTs) provide a means to enhance PMF systems more quickly and with greater precision than ever before, and have the potential to produce health and health-related products that are superior to current mammalian systems. However, the feasibility, regulatory standing and social acceptability of both PMF and NPBTs are in question. This paper qualitatively explores the perceptions of key stakeholders on two European Union (EU) Horizon 2020 programmes – Pharma-Factory and Newcotiana – towards the barriers and facilitators of PMF and NPBTs in Europe. One-on-one qualitative interviews were undertaken with N=20 individuals involved in one or both of the two projects at 16 institutions in seven countries (Belgium, France, Germany, Italy, Israel, Spain and the UK). The findings indicate that the current EU regulatory environment and the perception of the public towards biotechnology are seen as the main barriers to scaling-up PMF and NPBTs. Competition from existing systems and the lack of plant-specific regulations likewise present challenges for PMF developing beyond its current niche. However, respondents felt that the communication of the benefits and purpose of NPBT PMF could provide a platform for improving the social acceptance of genetic modification. The importance of the media in this process was highlighted. This article explores the justifications used by scientists for the use of NPBTs for crop improvement and suggests that the multi-level perspective framework is a useful tool for understanding the systemic factors that have shaped the development of PMF up until today.

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