Gene pyramiding stacks resistance genes to shield rice from devastating diseases

Rice feeds more people than almost any other crop on Earth, yet its harvest is under relentless attack. Bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae, can strip away 20 to 80 percent of yield. Rice blast, a fungal disease driven by Pyricularia oryzae, has recorded losses exceeding 50 percent, while sheath blight from Rhizoctonia solani and sheath rot from Sarocladium oryzae add further damage that can reach 85 percent in severe seasons. A comprehensive review published in Innovations in Agriculture now examines how breeders are answering this threat with gene pyramiding, a strategy that stacks multiple resistance genes into a single rice genotype to build resistance that pathogens cannot easily overcome.

The logic behind pyramiding is rooted in a concept outlined as early as 1953 by Watson and Singh: deliberately incorporating desirable genes from different parent plants into one genotype so that several resistance mechanisms are expressed simultaneously. When a variety carries only one resistance gene, a pathogen population can evolve to defeat it within a few seasons. Stacking genes changes that calculus dramatically. Research cited in the review shows that combining additional dominant genes with the xa5 gene produces enhanced, long-lasting resistance against bacterial blight compared with plants possessing only a single resistance gene. The approach also strengthens the genetic foundation of resistance in ways that reduce the burden of pesticide residues in the food chain, a growing concern for consumers and regulators alike.

The case for moving away from chemical control is stark. Pesticides remain the most popular disease management tool among farming communities, but they are expensive for small-scale farmers who must apply many sprays, and their repeated use invites pathogen resurgence and residue problems. The review highlights a telling example: in May 2011, a rice shipment from India containing tricyclazole levels exceeding 0.1 ppm was slated for return from the American shore, and throughout the preceding decade roughly 90 percent of shipments were declined because of tricyclazole contamination. Host plant resistance, the review argues, is one of the most crucial, affordable, and environmentally beneficial elements of integrated disease management in rice, and pyramiding is its most advanced expression.

Technically, gene pyramiding proceeds in two broad phases. When more than three founding parents carry the desired genes, the first phase, known as the pedigree phase, aims to accumulate all target genes into a single genotype called the root genotype. A cross between two parents produces a hybrid carrying two desirable genes, and by the F3 generation a root genotype containing all the desirable genes can be developed. The second phase, the fixation step, establishes the target genes in a homozygous state to attain the desired genotype. Doubled haploid techniques, including tissue culture methods and artificial induction of haploids, can accelerate this fixation. Conventional routes such as pedigree crossing, backcross breeding, cumulative hybridization, and repeated selection have long been used, but molecular marker genotyping now allows breeders to evaluate fewer generations while finding the appropriate gene combination, streamlining the entire process.

The review catalogs the resistance genes already deployed in pyramided rice lines with impressive specificity. For bacterial leaf blight, breeders have combined Xa4, xa5, xa13, Xa21, and Xa38. For blast, the stacked arsenal includes Pi1, Pi2, Pi9, Pi54, Pi46, and Pita. For sheath blight, the quantitative resistance loci qSBR7-1, qSBR11-1, and qSBR11-2 have been pyramided. These lines, carrying either single genes or combinations, are instrumental in disease-resistant genetic improvement programs and serve as parents for developing profitable varieties that resist multiple diseases at once.

Marker-assisted selection sits at the heart of the molecular approach. A molecular marker functions as a genetic tag, a identifiable site in the genome that regulates a certain phenotypic trait, allowing breeders to select plants carrying target genes without waiting for disease symptoms to appear. The documented successes are striking. Using MAS, the blast resistance genes Pi2 and Pi9 were added to the elite rice variety Improved Tapaswini, which already carried four bacterial blight resistance genes; the resulting pyramids ITGP2 and ITGP5 demonstrated resistance to blast with disease scores of zero, and lesion lengths against bacterial blight ranged from 0.70 to 2.50 centimeters. In another program, pyramided line BL-40-21-86-28-208 showed blast resistance with a disease scale of 1 to 2 and recovery of 95.50 percent of the recurrent parent genome, with grain yield slightly higher than the recurrent parent itself.

Marker-assisted backcrossing extends these gains by repeatedly crossing a donor genotype carrying the target gene with a popular cultivar, recovering the elite genome while retaining the resistance trait. Near-isogenic lines R1791, R1792, and R1793, developed by introducing the blast genes Pi46 and Pita into HH179, recorded resistance spectra of 64.7 to 97.1 percent against 34 pathogen isolates, far exceeding the recurrent parent’s 23.5 percent. The major dominant bacterial blight gene Xa38 was successfully incorporated into APMS 6B through MABB, with backcross-derived lines showing lesion lengths of 1.63 to 4.27 centimeters against all Xoo strains. In Italy, the renowned Japonica variety was enhanced against blast by integrating four Pi genes, Piz, Pib, Pita, and Pik, producing lines with broad resistance patterns. Three distinct MABB strategies exist: stepwise transfer, which targets individual genes with heightened accuracy but takes longer; simultaneous transfer, which is faster but risks losing pyramided genes when donor parents differ; and the combined simultaneous and stepwise approach, which streamlines the timeframe while guaranteeing full gene fixation and is considered the most widely accepted and dependable.

Transgenic methods offer a complementary route, moving engineered genes between plants through natural Agrobacterium-mediated transformation or artificial techniques such as gene guns and particle bombardment. The successful cloning of the rice Xa21 gene, which confers resistance against diverse isolates of the blight pathogen, demonstrated robust field performance, and stacking Pi genes through transgenesis is described as a promising strategy against Magnaporthe oryzae. Notably, when transgenic plants expressing Xa21 were compared with MAS-derived lines carrying the same gene, both proved almost identical at the molecular level. Transgenes also function as markers for molecular selection and early detection, enabling the creation of stable homozygous lines while substantially reducing the time and effort required for recurrent backcrossing.

The advantages over conventional breeding are quantifiable. Molecular techniques can introduce desired genes from various parents into a single genotype in merely two to three generations, compared with at least six generations needed conventionally to recover 99.2 percent of the recurrent parent genome. Selecting individual plants at the seedling stage through DNA marker tests replaces extensive field trials with large populations, saves field area, lowers germplasm maintenance costs, and remains dependable because it accounts for environmental variations that confound phenotypic screening. The technique also manages linkage drag, the transmission of unwanted genes alongside target genes that degrades performance of supplementary characters, a persistent problem that repeated backcrossing alone struggles to overcome.

Challenges remain, and the review is candid about them. Establishing and maintaining a molecular marker laboratory demands significant initial investment in equipment, consumables, and constant-temperature storage dependent on electricity supply. Marker reliability in predicting phenotype is generally low, sampling bias can affect small populations, and an extended gap between a marker and its major gene compounds recombination difficulties. Success also hinges on well-defined functional characteristics of the genes being pyramided, the reproductive potential of the crop, available operating capital, and the breeder’s ability to recognize appropriate genotypes. Yet the trajectory is clear: pyramided lines carrying stacked resistance genes for bacterial leaf blight, blast, and sheath blight are already flowing into varietal development pipelines, and their integration with other disease management strategies positions gene pyramiding as a competent method for augmenting the genetic basis of resistance in one of the world’s most vital staple crops.

Subject of Research: Gene pyramiding as a molecular breeding strategy for durable disease resistance in rice

Article Title: Gene pyramiding an advanced approach for disease management in rice: A review

Article References: Thorat, S., Gangwar, R. K., & Sisodiya, D. (2024). Gene pyramiding an advanced approach for disease management in rice: A review. Innovations in Agriculture, 7, 1-12. https://doi.org/10.3897/ia.2024.125404

Image Credits: AI Generated

DOI: 10.3897/ia.2024.125404

Keywords: rice, gene pyramiding, disease resistance, marker-assisted selection, bacterial leaf blight, rice blast, plant breeding, food security, Gene, pyramiding, advanced, approach