Plant Breeding is an essential agricultural practice that has shaped the food we eat today. By selectively crossing plants with desirable traits, breeders have developed varieties that can withstand environmental stressors, such as pests, diseases, and extreme weather. For example, modern wheat varieties are bred for resistance to stem rust whereas rice can be engineered to survive floods. Nutritional enhancements are also a focus, with ‘Golden Rice’ being fortified with Vitamin A. High-yielding crop varieties, hypoallergenic foods, and plants that can grow in saline or cooler climates further exemplify the achievements of plant breeding. These advancements not only improve crop resilience and yields but also address global challenges like food security and climate change.

Objectives of Plant Breeding

The objectives of plant breeding are diverse, each targeting specific needs and challenges in agriculture.

Here’s an in-depth look at each of the primary goals:

1. Enhancing Yield

• The most fundamental objective is to increase the amount of produce that can be harvested per unit area. This is achieved by selecting traits that contribute to yield, such as the number of grains per plant, the size of the fruits, or the number of pods per plant. Higher yield is crucial for feeding an ever-growing global population.

2. Improving Quality

• Quality improvement can refer to various attributes depending on the crop and its use. For food crops, this might include taste, texture, color, nutritional content (like protein or vitamin levels), and cooking properties. For industrial crops like cotton or flax, quality might mean fiber strength, length, and fineness.

3. Stress Resistance

Plants face numerous stresses that can significantly reduce yield.

a. Biotic Stresses

• These include resistance to pests like insects and mites, pathogens like fungi, bacteria, and viruses, and competition from weeds. Breeding for resistance involves promoting traits that allow plants to either avoid these stresses or survive them with minimal impact.

b. Abiotic Stresses

• These are non-living factors such as drought, flood, salinity, high or low temperatures, and poor soil nutrition. Developing crops that can tolerate these conditions is essential for maintaining yields in less-than-ideal farming environments.

4. Adaptability

• Some regions have unique climatic and soil conditions that require specially adapted varieties. Plant breeders aim to develop crops that can thrive in diverse environmental conditions, ensuring food production is possible in a wide range of geographical locations.

5. Reducing Dependence on Chemicals

• There is an increasing push to minimize the use of agricultural chemicals like fertilizers, herbicides, and pesticides due to their environmental and health impacts. Breeding can help by developing varieties that grow well with less fertilizer or that are more competitive with weeds, reducing the need for herbicides. Disease and pest-resistant varieties can similarly diminish the need for pesticides.

6. Maturation Time

• The breeding of varieties with shorter growing seasons means that farmers can either grow more crops in a year or reduce the risk of crop failure due to late-season environmental stresses.

7. Storage and Transportability

• Traits that improve a crop’s shelf life and durability during transport are highly valuable, particularly for fruits and vegetables. This reduces post-harvest losses and extends the availability of fresh produce.

8. Biofortification

• This is a relatively new objective in plant breeding that aims to improve the nutritional profile of crops to combat nutrient deficiencies in populations. An example is the development of crops with enhanced levels of vitamins, minerals, and amino acids.

9. Energy Efficiency

• Some crops are bred specifically for bioenergy production. The goal here is to maximize the amount of biomass or the energy content per unit area.

10. Aesthetic Qualities

• For ornamental plants, breeders often focus on improving the aesthetic qualities such as the size, color, and shape of flowers and foliage.

The underlying theme across all these objectives is sustainability and resilience: producing more with less, in a way that is sustainable for the environment and can cope with the unpredictable challenges posed by climate change. Plant breeders must balance these objectives, as progress in one area can sometimes come at the cost of another. For example, a variety that yields more might be less resistant to disease or might require more water. Therefore, a major part of plant breeding is finding the right combination of traits that will meet the needs of farmers, markets, and consumers in a particular region.

Techniques in Plant Breeding

1. Conventional or Classical Breeding

a. Mass Selection

• Breeders select the best-looking plants from a field, harvest them collectively, and use their seed for the next planting.

b. Pure-Line Selection

• From a mixed population, breeders select individual plants that show desirable traits and self-pollinate them over successive generations to produce a genetically uniform line.

c. Backcross Breeding

• A desirable gene from one plant variety is introduced into an established variety by repeated crossing and selection.

2. Hybrid Breeding

• Breeders cross two genetically different parent plants to produce a hybrid that possesses the best traits of both parents, a phenomenon known as heterosis or hybrid vigor.

3. Molecular Breeding

a. Marker-Assisted Selection (MAS)

• DNA markers linked to desirable traits are used to screen plants at the seedling stage, allowing breeders to select those most likely to carry the traits without having to grow them to maturity.

b. Genomic Selection

• Breeders use the genetic data from a plant to predict its performance and select the best candidates early in the breeding cycle.

4. Genetic Engineering

a. Transgenic Techniques

• Genes from one organism (not necessarily a plant) are inserted into a plant’s genome to express a particular trait such as herbicide resistance or nutritional enhancement.

b. Cisgenic Techniques

• Unlike transgenic, cisgenesis involves transferring genes between plants that are sexually compatible.

5. Genome Editing

a. CRISPR-Cas9

• This technology allows for precise ‘cutting and pasting’ of DNA sequences within the plant’s genome, enabling the removal of undesirable traits or the enhancement of desired ones.

6. Polyploid Breeding

• Breeders create plants with more than two sets of chromosomes. Polyploids often have increased size and vigor and may combine the traits of two different species.

7. Mutation Breeding

• Plants are exposed to chemicals or radiation to induce mutations, with the hope that some will result in beneficial traits that can then be bred into commercial varieties.

8. Haploid and Doubled Haploid Breeding

• Haploid plants, which have only one set of chromosomes, are produced to achieve homozygosity quickly. These haploids are then treated to double their chromosome number, creating doubled haploids which are genetically uniform and true-breeding.

9. Bioinformatics and Computational Breeding

• Advanced computational tools are used to analyze genetic information and simulate breeding outcomes, which can save time and resources in the breeding process.

10. Speed Breeding

• Techniques like extended photoperiods (long-light regimes) and controlled environments are used to accelerate plant growth, allowing more generations of a plant to be grown in a year.

Each of these techniques has specific applications and is chosen based on the breeding objectives, the species of plant, and the traits of interest. Together, they represent a toolkit that plant breeders can draw from to address the ever-evolving challenges of agriculture, food security, and sustainability.

Classical Plant Breeding

Classical plant breeding, also known as traditional or conventional breeding, refers to the methods used to improve plant species through selective breeding before the advent of molecular biology techniques. It relies on the genetic variation naturally present within a species or between closely related species.

Here are the key approaches and methods within classical plant breeding:

1. Mass Selection

• In mass selection, a large number of individuals from a population that show desirable traits are selected, and their seeds are mixed to produce the next generation. Over time, the population improves for the selected traits.

2. Pure-Line Selection

• This involves selecting the best individual plants based on their performance and phenotype and self-pollinating them over several generations to produce a genetically uniform line. The resulting pure lines are true breeding for the selected traits.

3. Hybrid Breeding

• Hybrid breeding involves crossing two genetically different parent lines to produce offspring (F1 generation) that often show superior traits due to heterosis, or hybrid vigor. These hybrids may be more vigorous, higher yielding, or more resistant to diseases than either parent.

4. Backcross Breeding

• A desirable trait found in one plant (donor) is introduced into another plant (recipient), which has the overall better genotype. After the initial cross, offspring are repeatedly crossed (backcrossed) to the recipient parent to recover the recipient’s traits, while retaining the desired trait from the donor.

5. Pedigree Method

• This method involves crossing two genotypes and then self-pollinating the offspring for several generations. In each generation, selections are made for improved performance and desirable traits. Detailed records are kept for each plant lineage or “pedigree.”

6. Bulk Method

• The bulk method involves interbreeding selected individuals without selection for several generations. After several seasons, the seeds from the bulk population are harvested and sown separately and selection is applied.

7. Single Seed Descent

• A single seed is chosen from each plant to carry on to the next generation, often in a greenhouse or controlled environment, which allows for rapid advancement of generations.

8. Recurrent Selection

• Recurrent selection is used to improve populations by selecting the best individuals to be intercrossed to produce a new generation, which is then used for further selection. This method is often used for traits that are expressed differently in different environments or for improving multiple traits.

9. Clonal Selection

• In species that are propagated vegetatively (like potatoes or apples), clonal selection is used. Desirable traits from natural or induced mutations are selected and vegetatively propagated to maintain the genetic identity of the variety.

10. In Situ and Ex Situ Conservation

• This involves maintaining genetic diversity through the conservation of plants in their natural environments (in situ) or preserving their genetic material in gene banks (ex situ), which can be a source of genetic variation for future breeding.

Classical breeding has been and continues to be of immense importance in the development of new crop varieties. It has led to significant increases in yield, quality, and disease resistance in numerous crops essential for human consumption. Despite the rise of molecular breeding techniques, classical plant breeding remains a cornerstone of crop improvement programs around the world due to its simplicity, cost-effectiveness, and the fact that it does not involve genetic modification which can be subject to regulatory and public acceptance issues.

Modern Plant Breeding

Modern plant breeding is an advanced form of agriculture that incorporates a multitude of scientific disciplines and technologies. It builds upon the principles of classical breeding but leverages genetic knowledge and tools to improve efficiency and precision.

Here’s an overview of some key techniques and concepts in modern plant breeding:

1. Molecular Breeding

a. Marker-Assisted Selection (MAS)

• Utilizes molecular markers, which are DNA sequences associated with desirable traits, to select plants that carry those traits without having to grow them to maturity.

b. Quantitative Trait Loci (QTL) Mapping

• Identifies the locations of genes associated with quantitative traits, such as yield or drought tolerance.

c. Genome-Wide Association Studies (GWAS)

• Uses a whole-genome approach to associate specific genetic variations with particular traits.

2. Genetic Engineering

a. Transgenic Crops

• Introduces genes from different species into plants to confer new characteristics, such as pest resistance or increased nutritional value.

b. Cisgenesis

• Involves transferring genes between plants that could be conventionally bred, i.e., they are within the same species or closely related species.

3. Genome Editing

a. CRISPR-Cas9

• A precise method of making specific changes to the DNA of a plant, such as knocking out genes or introducing small changes, without introducing foreign DNA.

b. TALENs and ZFNs

• Older genome editing tools that use engineered proteins to cut DNA at specific locations, allowing for targeted mutations.

4. Genomic Selection

• Plants are selected based on their genomic information. Predictive models are used to estimate the breeding value of an individual, considering all marker information across the genome.

5. High-Throughput Phenotyping

• Advanced imaging and sensors are used to measure plant characteristics quickly and accurately. This allows breeders to collect data on plant traits more efficiently.

6. Bioinformatics

• Utilizes computational tools to manage and analyze large sets of biological data, facilitating the understanding of gene function and improving selection processes.

7. Speed Breeding

• Techniques such as extended daylight hours and controlled environmental conditions to accelerate plant growth, enabling more generations to be produced in a shorter period.

8. Tissue Culture and Micropropagation

• Plant cells or tissues are grown in sterile, controlled environments, allowing for the rapid production of plantlets with desired traits.

9. Synthetic Biology

• Designing and constructing new biological parts, devices, and systems, or re-designing existing natural biological systems for useful purposes, which can include developing new traits in plants.

10. EcoTilling

• A variation of TILLING (Targeting Induced Local Lesions IN Genomes), which is a way to find natural genetic variations that can be used in breeding programs.

11. Omics Technologies

a. Genomics

• The study of the entire genetic makeup of plants.

b. Transcriptomics

• Analysis of the complete set of RNA transcripts produced by the genome.

c. Proteomics

• Study of the entire protein set (proteome) encoded by the genome.

d. Metabolomics

• The study of chemical processes involving metabolites, providing data on chemical composition and potential traits.

Modern plant breeding is reshaping the way we approach crop improvement, offering greater precision and the potential to tackle complex traits that were previously difficult to breed for, such as stress tolerance, efficiency in nutrient use, and quality traits. These advances are particularly crucial in the face of global challenges such as climate change, population growth, and the need for sustainable agricultural practices.

Participatory Plant Breeding

Participatory plant breeding (PPB) is an approach that involves collaboration between plant breeders and farmers in the plant breeding process. Unlike conventional plant breeding methods, which are often conducted in research stations and may not always address the specific needs of farmers, PPB seeks to directly involve the end users — the farmers — to ensure that the breeding objectives are closely aligned with their needs and preferences. This approach is especially relevant in developing countries and for crops that are less commercially focused.

1. Key Features of Participatory Plant Breeding

a. Inclusion of Farmers

• Farmers are involved in decision-making throughout the breeding process, from defining breeding goals to selecting and evaluating varieties.

b. On-Farm Selection and Breeding

• Much of the selection work is carried out under the farmers’ own field conditions rather than in a research environment. This ensures that the selected varieties are well-suited to local conditions.

c. Empowerment and Capacity Building

• Farmers gain knowledge about plant breeding and genetics, which empowers them to make informed decisions and could lead to farmer-led breeding initiatives.

d. Diversity of Selection Environments

• Because PPB is conducted in a variety of real-world conditions, it may result in varieties that perform well across a wider range of environments.

e. Attention to Local Needs

• PPB can focus on traits that are important to local communities but may be overlooked by commercial breeding programs such as specific cooking qualities or cultural preferences.

f. Increased Genetic Diversity

• PPB often utilizes local landraces and traditional varieties as breeding material, which can help maintain and utilize genetic diversity.

g. Integration of Traditional Knowledge

• Farmers’ traditional knowledge about local crops and environments can guide breeding efforts leading to more relevant and sustainable agricultural practices.

h. Enhanced Adoption Rates

• Varieties developed through PPB are more likely to be adopted by farmers, as they have been involved in the development process and the varieties are tailored to their needs.

i. Social and Community Development

• PPB fosters a sense of community and collective responsibility for agricultural improvement.

2. Steps in Participatory Plant Breeding

a. Goal Setting

• Plant breeders and farmers discuss and agree upon the goals of the breeding program.

b. Genetic Material Selection

• Based on the agreed goals, appropriate genetic material (seeds of different varieties) is selected for testing.

c. On-Farm Trials

• Farmers grow the selected varieties in their own fields, alongside their traditional crops.

d. Assessment and Feedback

• Farmers evaluate the performance of these varieties and provide feedback to the breeders.

e. Selection and Refinement

• Based on the farmers’ evaluations, certain varieties are selected for further breeding or direct use.

f. Seed Multiplication and Distribution

• Selected varieties are multiplied and distributed to other farmers, often through community-based seed production systems.

PPB is considered particularly useful for marginalized areas where farming conditions are highly variable and where it is crucial that crops are adapted to local conditions. It also serves as a way to conserve agrobiodiversity and support sustainable agriculture by developing crops that are resilient and well-suited to local ecosystems and cultural practices.

Evolutionary Plant Breeding

Evolutionary plant breeding, also known as composite cross-breeding or evolutionary participatory breeding, is an approach that harnesses the natural process of evolution to create robust and adaptable crop varieties. This method is distinct in that it promotes genetic diversity within a crop population, as opposed to selecting for uniformity as in conventional breeding programs.

Here’s how evolutionary plant breeding works:

1. Concept of Evolutionary Plant Breeding

• The core idea is to allow a population of several different genotypes to grow together, intercross, and evolve under specific environmental conditions or stresses. Over time, this population may develop traits that enable it to thrive in the environment it’s exposed to, much like natural plant populations evolve over generations.

2. Key Features of Evolutionary Plant Breeding

a. Genetic Diversity

• A diverse gene pool is created by mixing seeds from many different varieties or by using a genetically diverse landrace.

b. Natural Selection

• The mixed population is allowed to grow under the local environmental conditions with natural selection favoring the plants best suited to those conditions.

c. Farmer Involvement

• Similar to participatory plant breeding, farmers often play a key role in managing the crop population and selecting seeds for future plantings.

d. Adaptation to Local Conditions

• Over time, the population becomes increasingly well-adapted to the local environment including climate, soil, and biotic factors such as pests and diseases.

e. Resilience to Change

• The high level of genetic variation within the population provides a buffer against changes and stresses, potentially offering greater resilience to climate change and variability.

3. Steps in Evolutionary Plant Breeding

a. Creation of the Initial Population

• Seeds from various sources are mixed to create a population with high genetic diversity.

b. Planting and Growth

• This population is sown in an environment where the plants are intended to grow and produce.

c. Natural Selection

• Plants are allowed to grow with minimal intervention, allowing natural selection to occur.

d. Harvesting

• Seeds from the surviving, and presumably well-adapted, plants are harvested either randomly or with some degree of selection by farmers.

e. Repetition

• The cycle is repeated, with the harvested seeds sown in the next season, allowing the population to continue evolving.

4. Advantages of Evolutionary Plant Breeding

• Can produce varieties that are highly adapted to local conditions, including low-input or organic systems.

• Increases the resilience of crops to stresses and diseases without the need for extensive external inputs.

• Helps maintain agricultural biodiversity which is crucial for food security and ecosystem health.

• Can be a low-cost alternative to conventional breeding, especially in regions where resources are limited.

5. Challenges and Considerations

• The resulting varieties are not genetically uniform, which can be less desirable in modern agricultural systems where uniformity is often preferred for mechanical harvesting and processing.

• It may take many generations for the population to become optimally adapted to the local conditions.

• The approach might not be suitable for all crops, especially those with long breeding cycles or complex genetics.

Evolutionary plant breeding is considered a promising approach to develop crops that are resilient to climate change and sustainable for future generations. It is particularly relevant for smallholder farmers in diverse and challenging growing conditions and for maintaining genetic diversity in agricultural systems.

Challenges in Plant Breeding