New and Advanced Technology in Plant Breeding

 New and Advanced Technology in Plant Breeding: How They Can Boost Crop Production and Resilience

Plant breeding is the science and art of improving crop varieties for human use. It has been practiced for thousands of years by farmers and gardeners, who selected and propagated plants with desirable traits such as yield, quality, disease resistance, and adaptation to local conditions. However, traditional plant breeding methods are often slow, labor-intensive, and limited by the available genetic diversity within a species.

In recent decades, new technologies have emerged that can accelerate plant breeding and expand the genetic potential of crops. These technologies include genomic-assisted breeding (GAB), genome editing, speed breeding, high-throughput phenotyping, and artificial intelligence (AI). These technologies can help breeders to create novel crop varieties that can cope with the challenges of climate change, pests, diseases, and food security.

Genomic-Assisted Breeding (GAB)

GAB is the use of molecular markers and genomic information to select plants with desirable traits. Molecular markers are DNA sequences that are associated with specific genes or traits. By screening plants for these markers, breeders can identify and select plants that carry the desired genes or traits without having to wait for them to express in the field. This can save time, resources, and increase the accuracy and efficiency of breeding.

GAB also allows breeders to access the full landscape of genetic diversity within a species by constructing pan-genomes. Pan-genomes are collections of all the genes and genetic variations found in different individuals or populations of a species. By comparing pan-genomes, breeders can identify rare or lost genes or variations that can be used to improve crop performance or introduce new traits.

 

Genome Editing

Genome editing is the precise modification of DNA sequences in living cells using engineered nucleases or enzymes that can cut and paste DNA. Genome editing can be used to introduce, delete, or replace specific genes or DNA segments in plants. This can create new variations or traits that are not possible or difficult to achieve by conventional breeding or genetic modification.

One of the most widely used genome editing tools is CRISPR/Cas, which stands for clustered regularly interspaced short palindromic repeats/CRISPR-associated. CRISPR/Cas is a system that consists of a guide RNA that recognizes a target DNA sequence and a Cas enzyme that cuts the DNA at that site. By providing different guide RNAs and Cas enzymes, breeders can edit multiple genes or sites in a plant genome.

Genome editing has numerous applications in crop improvement, such as creating resistance to abiotic and biotic stress, enhancing nutritional quality, modifying plant architecture, and facilitating domestication. Genome editing can also be combined with other techniques such as base editing, prime editing, Cisgenesis, intragenesis, oligonucleotide-directed mutagenesis, reverse breeding, and agro-infiltration to create more precise and diverse changes in plant genomes.

Speed Breeding

Speed breeding is the use of controlled environmental conditions such as light, temperature, humidity, and nutrition to shorten the life cycle of plants and increase the number of generations per year. Speed breeding can accelerate the development and evaluation of new crop varieties by reducing the time required for flowering, seed production, and seed germination.

Speed breeding can be applied to various crops such as cereals, legumes, oilseeds, vegetables, and ornamentals. Speed breeding can also be integrated with GAB and genome editing to rapidly introduce and test new traits in plants. Speed breeding can also enable breeders to exploit the natural variations in underutilized crops that have potential for adaptation to changing climates.

 

High-Throughput Phenotyping

High-throughput phenotyping is the use of automated or semi-automated methods to measure plant traits such as growth, morphology, physiology, biochemistry, and yield. High-throughput phenotyping can generate large amounts of data on plant performance under different environmental conditions. This data can help breeders to identify and select plants with superior traits or stress tolerance.

High-throughput phenotyping can be performed at different scales such as laboratory, greenhouse, field, or aerial platforms. High-throughput phenotyping can also employ various sensors or imaging techniques such as cameras, spectrometers, lidars, radars, thermometers, fluorometers, chlorophyll meters, gas analyzers, etc. High-throughput phenotyping can also be coupled with AI and machine learning to analyze and interpret the data and provide insights for breeding decisions.

Artificial Intelligence (AI)

Artificial intelligence refers to the simulation of human intelligence processes by machines. In plant breeding, AI can optimize breeding programs by utilizing tools such as data mining, pattern recognition, prediction modeling, optimization algorithms, simulation modeling, and decision support systems. AI helps breeders integrate and analyze large and complex datasets from genomics, Phenomics, environment, and management. It also aids in designing and executing more efficient experiments and trials. AI can discover new genes, traits, or interactions that enhance crop performance and resilience.

AI can help breeders to integrate and analyze large and complex data sets from various sources such as genomics, Phenomics, environment, and management. AI can also help breeders to design and execute more efficient and effective experiments and trials. AI can also help breeders to discover new genes, traits, or interactions that can improve crop performance or resilience.

 Conclusion

New and advanced technologies in plant breeding can offer great opportunities for creating novel and improved crop varieties that can meet the current and future demands of agriculture and food security. These technologies can also help breeders to overcome the limitations and challenges of traditional plant breeding methods. However, these technologies also pose some challenges such as ethical, social, legal, regulatory, and economic issues that need to be addressed by stakeholders and policymakers. Therefore, it is important to foster a constructive dialogue and collaboration among researchers, breeders, farmers, consumers, regulators, and society to ensure the safe and responsible use of these technologies for the benefit of humanity and the environment.

Some examples of crops that have been improved using these technologies are:

Corn: Bayer has used precision breeding and artificial intelligence to create corn varieties that are tailored to specific field conditions and customer needs. Bayer has also used genome editing to create corn varieties that are resistant to drought and herbicides.

Wheat: Researchers have used speed breeding and genome editing to create wheat varieties that are resistant to diseases, pests, and heat stress. They have also used genome editing to modify the gluten content and quality of wheat.

Rice: Researchers have used genomic-assisted breeding and high-throughput phenotyping to create rice varieties that are tolerant to salinity, drought, flooding, and cold stress. They have also used genome editing to create rice varieties that are resistant to bacterial blight and have enhanced nutritional value⁴⁵.

Tomato: Researchers have used genome editing and morphogenic factors to create tomato varieties that have improved fruit size, shape, color, flavor, and shelf life. They have also used genome editing to create tomato varieties that are resistant to viruses and nematodes .

Potato: Researchers have used Cisgenesis and intragenesis to create potato varieties that are resistant to late blight, a devastating fungal disease. They have also used oligonucleotide-directed mutagenesis to create potato varieties that have reduced acrylamide content, a potential carcinogen .

Source: 

(1) New Technologies Driving the Future of Plant Breeding - Bayer. https://www.bayer.com/en/agriculture/new-technologies-driving-future-plant-breeding.

(2) Recent advances in crop transformation technologies - Nature. https://www.nature.com/articles/s41477-022-01295-8.

(3) Advances in Crop Breeding Through Precision Genome Editing. https://www.frontiersin.org/articles/10.3389/fgene.2022.880195/full.

(4) (PDF) Biotechnology: An Advanced Tool for Crop Improvement - ResearchGate. https://www.researchgate.net/publication/331540922_Biotechnology_An_Advanced_Tool_for_Crop_Improvement.

(5) Next-Generation Breeding Strategies for Climate-Ready Crops. https://www.frontiersin.org/articles/10.3389/fpls.2021.620420/full.

 

(1) New Plant-Breeding Techniques: What are we talking about?. https://www.farm-europe.eu/travaux/new-plant-breeding-techniques-what-are-we-talking-about/.

(2) New Technologies Driving the Future of Plant Breeding - Bayer. https://www.bayer.com/en/agriculture/new-technologies-driving-future-plant-breeding.

(3) Next-Generation Breeding Strategies for Climate-Ready Crops. https://www.frontiersin.org/articles/10.3389/fpls.2021.620420/full.

(4) New plant breeding techniques and their regulatory ... - PubMed. https://pubmed.ncbi.nlm.nih.gov/33631493/.

(5) Accelerated Breeding of Plants: Methods and Applications. https://link.springer.com/chapter/10.1007/978-3-030-41866-3_1.

(6) Role of New Plant Breeding Technologies for Food Security and .... https://onlinelibrary.wiley.com/doi/10.1002/aepp.13044.

 CRISPR: Transforming Plant Research and Revolutionizing Agriculture

Introduction

In the realm of scientific innovation, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) has emerged as a game-changing tool, enabling precise gene editing and holding immense potential for plant research and agriculture. This revolutionary technology has opened up new avenues for developing crops with improved traits, disease resistance, and enhanced nutritional value. In this blog, we will explore the latest research in plant CRISPR applications and the transformative impact it has on agriculture.

                                                                      Fig.1

Precision Genome Editing: Tailoring Plants to Perfection

CRISPR-Cas9 technology has revolutionized plant research by enabling precise modifications to the plant genome. Scientists can target specific genes responsible for traits such as yield, stress tolerance, and nutritional content, and introduce desired changes. By leveraging CRISPR, researchers have been able to develop plants with enhanced qualities, such as disease resistance in crops like rice, wheat, and maize. This precision genome editing offers immense potential for addressing global challenges, including food security and sustainable agriculture.

Improving Nutritional Content: Biofortification through CRISPR

One of the key areas of focus in plant research is biofortification, enhancing the nutritional value of crops to combat malnutrition and dietary deficiencies. CRISPR has been instrumental in this field by enabling targeted modifications in plant genes responsible for nutrient production. For example, scientists have used CRISPR to enhance the iron and zinc content in staple crops like rice, wheat, and cassava. This breakthrough offers a sustainable solution to address micronutrient deficiencies and improve human health on a global scale.

                                                                           Fig.2

Disease Resistance: Enhancing Plant Immunity

Crop diseases can cause significant losses in agricultural productivity. CRISPR technology has the potential to develop crops with enhanced disease resistance, reducing the reliance on chemical pesticides and promoting sustainable farming practices. Researchers have successfully used CRISPR to confer resistance to devastating plant diseases such as citrus greening in oranges, late blight in potatoes, and bacterial blight in rice. By editing specific genes involved in disease susceptibility, scientists can create crops that are better equipped to withstand pathogen attacks, leading to increased crop yields and reduced environmental impact.

Climate Adaptation: Developing Resilient Crops

Climate change poses a significant threat to global agriculture, with rising temperatures, droughts, and extreme weather events impacting crop productivity. CRISPR technology offers a powerful tool for developing climate-resilient crops. By modifying genes associated with stress responses, such as those involved in drought tolerance or heat resistance, researchers can create plants better suited to withstand changing environmental conditions. This research can contribute to the development of climate-smart agriculture, ensuring food security in the face of a changing climate.

Gene Regulation: Beyond DNA Editing

In addition to precise DNA editing, CRISPR has opened up new possibilities in gene regulation. Researchers are exploring CRISPR-based technologies like CRISPRi (interference) and CRISPRa (activation) to modulate gene expression in plants. This approach allows for fine-tuning of gene activity without making changes to the DNA sequence. By selectively activating or repressing specific genes, scientists can influence traits such as flowering time, fruit ripening, and hormone responses. This innovative use of CRISPR expands the toolkit available for plant researchers and offers exciting prospects for crop improvement.

                                                                        Fig.3

Conclusion

CRISPR technology has ushered in a new era of plant research and agricultural advancement. With its precision genome editing capabilities, CRISPR holds the potential to revolutionize crop breeding, improve nutritional content, enhance disease resistance, and develop climate-resilient varieties. By harnessing the power of CRISPR, scientists and researchers can pave the way for sustainable agriculture, food security, and a healthier future. As we continue to explore the possibilities of this transformative technology, it is crucial to uphold ethical considerations, promote responsible use, and engage in open dialogue to maximize its positive impact on plants, agriculture, and society as a whole.

Genome editing technology

What is Genome Editing? 

•Genome modifying, or genome engineering, or gene modifying, may be a quite hereditary designing where DNA is embedded, erased, changed or supplanted within the genome of a living organic structure.

•Unlike early hereditary building methods that arbitrarily embeds hereditary material into a bunch genome, genome altering focuses on the additions to site specific locations.

Genome editiors 

As of 2015 four groups of built nucleases were utilized: meganucleases, zinc finger nucleases (ZFNs), interpretation activator-like effector-based nucleases (TALEN), and therefore the bunched routinely interspaced short palindromic rehashes (CRISPR/Cas9) framework.

•Nine genome editors were accessible starting at 2017. 

•All three significant classes of those compounds—zinc finger nucleases (ZFNs), interpretation activator-like effector nucleases (TALENs) and designed meganucleases—were chosen naturally Methods because the 2011 Method of the Year.

•The CRISPR-Cas9 framework was chosen by Science as 2015 Breakthrough of the Year. 

• The nucleases create specific double-strand breaks (DSBs) at desired locations within the genome and harness the cell’s endogenous mechanisms to repair the induced break by natural processes of homologous recombination (HR) and non-homologous end- joining (NHEJ).

 

Utilizations:  

Gene knock out

Gene tagging 

Unique mutation (insertion/deletion study) 

Gene knock in 

Promoter have a glance at

Strategies for plant genome control 

Classical breeding 

Transgenic technique 

Targeted genome enhancing

Meganucleases 

•Meganucleases, found within the late 1980s, are catalysts within the endonuclease family which are portrayed by their ability to perceive and cut huge DNA successions (from 14 to 40 base sets).

•The maximum widespread and excellent acknowledged meganucleases are the proteins within the LAGLIDADG own family, which owe their call to a conserved amino acid collection.

•Meganucleases have the advantage of inflicting less toxicity in cells than methods inclusive of Zinc finger nuclease (ZFN), in all likelihood because of extra stringent DNA series recognition.

•One fundamental disadvantage is the construction of sequence-specific enzymes for all possible sequences is steeply-priced and time consuming, as one is not benefiting from combinatorial possibilities that methods including ZFNs and TALEN- based totally fusions utilize. 

 

Crop in which it is used 

Maize : Herbicide obstruction ( Gao et al, 2010 ) 

Cotton : Herbicide obstruction and and bug opposition ( D'Halluin et al., 2013 ) 

Impediment 

Hard to regulate the DNA restricting site 

Little recognition site

What is ZFN innovation?  

Zinc fingers were first found within the African pawed amphibian (Xenopus laevis) in 1985.

A class of designed DNA-restricting proteins. 

Encourage targated altering of the genome by making double strand breaks inside the DNA at specific places. 

Double strand breaks are important for site-explicit mutagenesis. 

Invigorate the cell’s natural DNA repair methods i.e, HR and NHEJ  

Generate exactly targeted genomic editing leading to cell strains with targated gene deletions, integrations, or modifications.

 

What are zinc finger nuclease 

Extraordinarily particular genomic scissor 

Consists of two practical domains 

• A DNA – binding domain 

•  A DNA- cleaving domain accommodates of nuclease area of FoK I ( FokI could be a obviously going down type IIS restrict enzyme and is found in Flavobacterium okeanokoites.

Crop in which it turned into used

Maize : Herbicide resistance ( Shukla et al., 2009 ) 

Soybean : Physiological quality ( Curtin et al., 2011 ) 

Tomato : Towards TYLCV  ( Takenaka et al., 2007 ) 

Impediment  

Off objective impact  

Development is lumbering and tedious 

Uses of ZFN 

•Repairing mutations 

•Insertion of gene or DNA piece at explicit site 

•Repair or supplant distorted genes 

•Disabiling an allele 

•Allele altering 

•Applications in clinical segment 

• a) Gene treatment 

• b)Treatment of HIV

TALENs ( Transcription activator-like effector nucleases )

Transcription activator-like effector nucleases TALENs are the restriction nuclease engineered to scale back precise sequences of DNA . They're made by means of fusing: DNA-binding domain (TAL effector) DNA-cleavage area ( the catalytic domain of RE FoK I).

TALENs may be designed to tie any ideal DNA succession to chop at explicit areas in DNA. First time revealed by Ulla Bonas in Xanthomonas oryzae (1989).

 

TALEN constructs are utilized in a very comparable manner to designed zinc finger nucleases and have three blessings in focused mutagenesis

1. DNA binding specificity is higher.

2. Off-target impacts are lower, and 

3. 3. Development of DNA-binding domain names is less complicated.

Primarily based on the most theoretical distance between DNA binding and nuclease hobby, TALEN methods lead to the best precision.

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats)

 

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) are hereditary components that microorganisms use as a kind of gained insusceptibility to secure against infections. They comprise of short arrangements that begin from viral genomes and are fused into the bacterial genome.

Cas (CRISPR associated proteins) manner these sequences and reduce matching viral DNA sequences.

With the help of introducing plasmids containing Cas genes and explicitly developed CRISPRs into eukaryotic cells, the eukaryotic genome are often reduce at any desired position. some organizations, including Cellectis and Editas are attempting to adapt the CRISPR technique while creating gene explicit treatments.

Parts of CRISPR 

Proto spacer adjacent motif (PAM) could be a DNA arrangement promptly following the DNA succession focused by the Cas9 nuclease within the CRISPR bacterial versatile resistant framework.

PAM may be a component of the invading virus or plasmid, however isn't a thing of the bacterial CRISPR locus. Cas9 won't efficiently bind to or cleave the target DNA sequence if it's not followed by way of the PAM sequence.

CRISPR RNA (crRNA) may be a trans-encoded small RNA with 24 nucleotide complementarity to the repeat regions of crRNA precursor transcripts.

Trans activating crRNA (tracr RNA ) is formed of of a more drawn out stretch of bases that are consistent and provides the "stem circle" structure limited by the CRISPR nuclease.

 At the point when these RNA parts hybridize they structure a guide RNA which "programmably" targets CRISPR nucleases to DNA arrangements relying upon the complementarity of the crRNA and therefore the presence of various DNA capabilities (PAM collection identified by the nuclease).

 

Examples of plants changed with CRISPR innovation 

Corn : Targeted mutagenesis ( Liang et al. 2014 ) 

Rice : Targeted mutagenesis ( Belhaj et al. 2013 ) 

Sorghum : Targeted gene alteration ( Jiang et al. 2013b ) 

Sweet orange : Targeted genome altering ( Jia and Wang 2014 ) 

Tobacco : Targeted mutagenesis ( Belhaj et al. 2013 ) 

Utility in Agriculture

1. Can be utilized to make serious extent of hereditary inconstancy at exact locus in the genome of the crop plants.

2. Capacity device for multiplexed converse and forward hereditary study. 

3. Exact transgene joining at explicit loci.  

4. Developing biotic and abiotic safe attributes in crop plants.  

5. Potential tool for growing virus resistant crop types.

6. Can be utilized to eliminate  undesirable species like herbicide resistant weeds, insect pest.

7. Ability device for improving polyploid crops like potato and wheat.

References

Jasin M (June 1996). "Genetic manipulation of genomes with rare-cutting endonucleases". Trends in Genetics. 12 (6): 224–8. doi:10.1016/0168-9525(96)10019-6.

 Science News Staff (17 December 2015). "Breakthrough of the Year: CRISPR makes the cut.

Tan WS, Carlson DF, Walton MW, Fahrenkrug SC, Hackett PB (2012). Precision editing of large animal genomes. Advances in Genetics. 80. pp. 37–97. doi:10.1016/B978-0-12-404742-6.00002-8.

Cheong, Kang Hao; Koh, Jin Ming; Jones, Michael C. (2019). "Black Swans of CRISPR: Stochasticity and Complexity of Genetic Regulation". BioEssays. 0 (7): 1900032. doi:10.1002/bies.201900032.