The Multiline Concept in Plant Breeding.

1. Introduction

Crop diseases caused by fungi, bacteria, viruses and nematodes are among the most important biotic constraints to agricultural productivity worldwide. Historically, breeders deployed single major resistance genes (often called R genes) into popular cultivars to provide strong and rapid control of disease. However, pathogens are highly plastic, reproduce quickly, and can evolve virulent races that break single-gene resistances — producing the well-known boom-and-bust cycles.

The multiline concept was proposed to blunt these cycles by creating a population-level defense: a crop variety that is agronomically uniform but genetically heterogeneous for resistance genes. Instead of one genotype facing the pathogen, the population is a mosaic of near-isogenic lines, each carrying different resistance genes. This chapter explores the concept fully — from genetics and breeding steps to epidemiology, examples and modern enhancements.

2. Definition

The Multiline Concept in plant breeding is the deliberate cultivation of a mixture of near-isogenic lines (NILs) that are identical in agronomic traits (yield, maturity, grain quality, plant type) but differ in genes for resistance to a target pathogen. When combined and sown as a single seed lot, the multiline behaves like a single variety in farmers' fields while providing population-level diversity in resistance.

3. Historical Development

The idea of multilines traces to mid-20th century plant breeding. Important milestones include:

• Jensen (1952) — conceptualized the multiline idea to slow epidemics and increase durability of resistance.
• 1960s–1970s — Breeders such as Norman Borlaug applied concepts of genetic diversity and resistance deployment during wheat improvement, integrating the principle into rust-resistance strategies.
• Subsequent applications — barley multilines for powdery mildew in Europe; experimental rice multilines for blast control; practical use in plantation crops by mixing resistant clones.

Although multilines were not universally adopted due to seed production and policy challenges, they influenced how breeders think about durable resistance and population-level strategies.

4. Objectives

The main objectives of creating and deploying multiline populations are:

• Provide durable resistance and extend the useful life of resistance genes
• Reduce the probability and intensity of epidemics
• Stabilize yields across seasons and environments
• Retain a uniform appearance and agronomic performance to meet farmer and market needs
• Lower dependence on chemical controls (fungicides)
• Allow dynamic updating of resistance composition over time

5. Genetic Basis

Multiline populations are built from Near-Isogenic Lines (NILs). The genetic steps are:

1. Select an elite recurrent parent (a widely-grown variety with superior agronomic traits).
2. Identify donor sources of distinct resistance genes from germplasm collections, landraces, or wild relatives.
3. Introgress a single resistance gene into the recurrent parent through repeated backcrossing (commonly 6–7 generations).
4. Confirm that each NIL differs from the recurrent parent only at the resistance gene locus (molecular markers are useful here).
5. Assemble a set of NILs, each carrying different resistance genes against the same pathogen.

Example: If wheat variety A is recurrent parent then NILs might be A_Sr31, A_Sr24, A_Sr36, A_Sr9e etc., where each NIL carries a different stem-rust resistance gene.

6. Steps in Developing a Multiline Variety

Developing a multiline variety requires careful breeding and seed-production planning. Key steps include:

6.1 Selection of Recurrent Parent

Choose an elite, widely adapted variety with high yield, acceptable quality, and farmer preference. This ensures acceptance of the multiline because its agronomic performance remains unchanged.

6.2 Identification of Resistance Sources

Screen germplasm, landraces, and gene banks for resistance genes that act against diverse races of the target pathogen. Document gene action (major gene vs partial resistance), spectrum of effectiveness, and potential gene interactions.

6.3 Introgression (Backcrossing)

Perform repeated backcrosses with selection for the resistance gene and for recovery of the recurrent parent's background. Marker-assisted selection (MAS) drastically reduces time by allowing early and accurate selection of desired genotypes.

6.4 Development and Testing of NILs

Advance lines to homozygosity, confirm uniform agronomic traits, and test for differential response to pathogen races under controlled and field conditions.

6.5 Assembly and Seed Multiplication

Decide on the number and proportion of NILs to include (common practice: 4–10 NILs). Mix seed in the target proportions and multiply carefully to maintain the composition. Seed producers must avoid contamination and maintain accurate records of proportions at every generation.

6.6 Release and Management

Release the multiline as a single variety. Monitor pathogen populations regionally and update the mixture composition when necessary by substituting NILs.

7. Mechanism of Disease Resistance in Multiline Populations

The epidemiological and evolutionary mechanisms that give multilines their advantage include:

• Barrier effect: When a pathogen infects plants carrying a matching virulence, adjacent resistant plants limit secondary spread.
• Dilution of susceptible hosts: Because susceptible genotypes are not ubiquitous, pathogen reproduction is reduced.
• Slower evolution: Selection for virulence alleles that overcome particular resistance genes is weaker because those alleles provide little advantage in a mixed host population.
• Local extinction of pathogen foci: Infected foci often fail to expand if surrounded by resistant NILs.

Analogy: This is similar to the concept of herd immunity in human populations — some individuals are resistant and prevent large-scale epidemics.

8. Advantages

Key benefits of multilines include:

• Durable and broad-spectrum control — difficult for a pathogen to simultaneously overcome multiple genes.
• Yield stability — buffered against variable disease pressure across seasons.
• Reduced agrochemical use — fewer fungicide applications needed in many cases.
• Farmer-friendly performance — retains the appearance, quality, and management profile of a single popular variety.
• Dynamic management — the mixture composition can be updated as new virulent races appear.

9. Limitations

Despite advantages, multilines have practical constraints:

• Time and resources: Developing multiple NILs and maintaining seed lots is time-consuming and costly.
• Seed-production complexity: Maintaining precise proportions requires high-quality seed systems and careful quality control.
• Farmer and market acceptance: In some systems, farmers prefer perfectly uniform crops for mechanical harvesting and market standards.
• Not universally applicable: Cross-pollinated crops pose additional challenges for maintaining multiline composition.
• Risk of partial breakdown: If multiple NILs are overcome, protection drops and the multiline will need replacement.

10. Examples of Multiline Use

Practical and experimental uses include:

• Wheat: Multilines against stem rust and leaf rust in Mexico, the United States and India.
• Barley: Multilines for powdery mildew control in parts of Europe.
• Rice: Experimental mixtures for blast disease control in Asia.
• Perennial crops: Coffee and tea plantations sometimes plant mixtures of resistant clones as functional multilines.

11. Modern Applications and Future Prospects

Biotechnology and modern breeding tools have revitalized the multiline concept:

• Marker-Assisted Selection (MAS): Allows rapid, accurate selection of introgressed resistance genes and confirms background recovery.
• Gene pyramiding: Molecular tools enable stacking multiple genes into single NILs when appropriate.
• Genome editing (e.g., CRISPR): Offers the potential for precise and rapid modification of resistance loci to create new NILs.
• Dynamic multilines: Programmes can maintain a rotating composition of NILs to respond to evolving pathogen populations.
• Cultivar mixtures: Broader mixtures combining whole cultivars (not only NILs) can give similar epidemiological benefits when chosen carefully.

Together, these approaches allow breeders to design resilient cropping systems that combine genetic resistance with integrated disease management practices.