Two New Genes That Shorten Rice Stems Could Help Breed Lodging-Proof Crops

Rice feeds more than half of humanity, and the height of its stalks quietly determines whether a harvest survives a storm. Tall plants with long internodes—the hollow segments between the nodes of the stem—are prone to lodging, the catastrophic flattening of crops that ruins yields and complicates harvesting. Ever since the Green Revolution showed that semi-dwarf varieties carrying the famous sd1 gene could dramatically boost grain output, breeders have hunted for additional height-controlling genes to build sturdier, more resilient plants. A new study published in Theoretical and Applied Genetics by Bingxian Li, Jinghan Sun, Erbao Liu and colleagues at Anhui Agricultural University, together with collaborators at the International Rice Research Institute, the Rice Research Institute of Uzbekistan, the Anhui Academy of Agricultural Sciences and the Chinese Academy of Agricultural Sciences, now adds two promising names to that list: INL1 and INL2.

The team set out to dissect the genetic architecture of internode number and internode length, the two traits that together define plant height in rice. Rather than relying on classical crosses between two parents, the researchers deployed a genome-wide association study, or GWAS, across a remarkably diverse panel of 429 rice accessions. This population-scale approach exploits the natural historical recombination of the rice genome: if a particular DNA variant consistently tracks with shorter internodes across hundreds of unrelated varieties, that variant likely sits near a gene genuinely involved in the trait. The scale of the genotyping was impressive in its own right—3.16 million high-quality single nucleotide polymorphisms were used to scan the twelve rice chromosomes for statistical associations with each measured trait.

The scan paid off. The analysis identified 34 significant marker-trait associations linking specific genomic regions to internode characteristics, and among these the researchers pinpointed four quantitative trait loci, or QTLs, that had not been described before. Within the most compelling regions, two candidate genes emerged and were christened Internode number and length 1 (INL1) and INL2. Functional annotations suggested that INL1 encodes a cytochrome P450 enzyme, while INL2 encodes a zinc finger protein transcription factor. Both gene families are heavyweight players in plant biology: cytochrome P450s catalyze an enormous range of biochemical reactions, including steps in hormone synthesis, and zinc finger transcription factors act as molecular switches that regulate suites of downstream genes.

The choice of these two gene families is particularly intriguing given what is already known about stem elongation. Gibberellins, a class of phytohormones, are the principal drivers of internode elongation, and the Green Revolution sd1 gene itself encodes a gibberellin biosynthesis enzyme. Cytochrome P450 enzymes have repeatedly surfaced in this arena—EUI1, another rice P450 monooxygenase, modulates gibberellin responses to control internode elongation, and several P450s participate in brassinosteroid biosynthesis, a hormone pathway that crosstalks extensively with gibberellins. Similarly, Cys2/His2 zinc finger proteins in rice have been shown to repress SD1/OsGA20ox2, tying transcriptional control directly to gibberellin production. INL1 and INL2 therefore fit neatly into an emerging picture of height regulation as a multi-layered network combining hormone metabolism and transcriptional governance.

Correlation, however, is not causation, and the team moved to functional validation using CRISPR/Cas9 genome editing. By knocking out INL1 and INL2 in rice, the researchers created plants in which these genes no longer function. The result was unambiguous: the knockout lines displayed shorter internodes and reduced overall plant height compared with wild-type plants. This loss-of-function phenotype provides strong experimental evidence that both genes act as positive regulators of internode elongation—when they are disabled, stems grow shorter. For breeders, genes that reduce height when knocked out are exactly the kind of raw material needed for dwarf breeding programs aimed at improving lodging resistance.

To understand how the knockouts produce their dwarfed stature, the researchers turned to transcriptomics, measuring genome-wide gene expression changes in the edited plants. The analysis revealed that loss of INL1 and INL2 differentially modulates gibberellin metabolism, ultimately leading to the dwarf phenotype. In other words, disrupting these genes perturbs the hormonal machinery that normally drives cell elongation in the stem, choking back the growth of internodes. This places the two new genes upstream of, or within, the gibberellin pathway and suggests that they coordinate the metabolic flux that fuels stem extension.

Beyond gene function, the study explored natural allelic variation in INL1 and INL2 through haplotype analysis. Haplotypes are characteristic combinations of DNA variants inherited together at a locus, and different haplotypes often produce different trait values. The researchers found that accessions carrying the HapA type of the two genes had shorter internodes than those carrying other haplotypes. This means that favorable, height-reducing alleles of OsINL1 and OsINL2 already exist within the rice gene pool, circulating among natural and cultivated varieties. Rather than waiting for new mutations, breeders can in principle track these haplotypes with DNA markers and introgress them into elite cultivars through marker-assisted selection.

The practical implications extend well beyond plant architecture trivia. Lodging is a chronic threat to rice production worldwide, particularly as extreme weather events intensify and high-yielding varieties carry heavier panicles atop their stems. Lodged crops suffer reduced photosynthesis, impaired grain filling, greater disease pressure and harvest losses. Because plant height is determined by the number and length of individual internodes, genes that fine-tune each segment offer breeders granular control: reducing the length of specific internodes can lower the center of gravity and strengthen the culm without necessarily sacrificing the biomass or yield potential that taller plants sometimes confer. The authors note that the favorable alleles of INL1 and INL2 reduce height and can be further used in rice dwarf breeding to improve lodging resistance.

There is also a broader scientific payoff. Most dwarfing work in rice has centered on sd1 and a handful of related loci, and researchers have increasingly argued that additional dwarfing or semi-dwarfing genes are needed to diversify the genetic basis of height control and avoid the vulnerabilities of over-reliance on a single locus. By combining a large, diverse association panel, dense SNP coverage, new QTL discovery, CRISPR validation and transcriptomic profiling, this study demonstrates a full pipeline from statistical signal to mechanistic hypothesis to breeding-ready allele. The finding that a cytochrome P450 and a zinc finger transcription factor converge on gibberellin metabolism enriches the known regulatory map of stem growth and may illuminate how gibberellin homeostasis is tuned in other cereal crops such as wheat and barley, where similar architecture principles apply.

As global demand for rice continues to climb against a backdrop of shrinking arable land and volatile weather, the genetics of stem architecture has become a frontline topic in crop science. The identification of INL1 and INL2 shows how modern genomics—millions of SNPs, hundreds of accessions, precision gene editing and hormone-level transcriptomics—can convert a field-measurable trait like internode length into molecular tools that breeders can deploy. If the favorable haplotypes of these two genes perform as hoped when pyramided into elite backgrounds, the humble rice stalk may soon stand a little shorter, and a great deal steadier, in the fields that feed the world.

Subject of Research: Genetic basis of internode length and plant height regulation in rice

Article Title: Candidate genes identification for internode length in rice via genome-wide association studies

Article References: Li, B., Sun, J., Yao, Q., Ding, Y., Geng, Y., Bao, Y., Ang, Y., Jiang, H., Yang, Z., Shi, Y., Jiang, J., Dang, X., Zhang, C., Ergashev, M. A., Li, M., Ali, J., Li, Z., & Liu, E. (2026). Candidate genes identification for internode length in rice via genome-wide association studies. Theoretical and Applied Genetics, 139(10), Article 294. https://doi.org/10.1007/s00122-026-05395-3

Image Credits: AI Generated

DOI: 10.1007/s00122-026-05395-3

Keywords: rice, genome-wide association study, internode length, plant height, INL1, INL2, gibberellin, CRISPR/Cas9, lodging resistance, dwarf breeding, cytochrome P450, zinc finger transcription factor