Genetic Diversity and Domestication of Rice Species

The genetic diversity and domestication of rice species encompass the evolutionary processes and human interventions that transformed wild Oryza relatives into high‐yielding crops. Two principal domesticated species, Asian rice (Oryza sativa) and African rice (Oryza glaberrima), emerged through distinct domestication events and selective pressures, leading to independent bottlenecks and unique allelic signatures. Wild progenitors contributed a wealth of natural variation—including single nucleotide polymorphisms, structural variants and presence–absence polymorphisms—that underpin key agronomic traits such as grain size, panicle architecture and stress tolerance. Global efforts to characterise this diversity have revealed complex patterns of subpopulation structure, introgression between indica, japonica and aus groups, and selective sweeps around domestication genes. Advances in high‐throughput sequencing, phenotyping platforms and analytical frameworks now enable fine‐scale mapping of quantitative trait loci and the assembly of comprehensive variation maps. These insights are crucial for breeding programmes aimed at enhancing yield stability, resource use efficiency and resilience to biotic and abiotic stresses in the face of climate change and growing food demand.

Research from Nature Portfolio

Recent studies have delivered high‐density germplasm resources and analytical tools for genome‐wide association mapping in rice. One platform integrates a diverse immortal collection with a high‐density single nucleotide polymorphism array, enabling the detection of both major and minor effect loci for grain length and other domestication traits with unprecedented resolution. Another investigation employed high‐resolution phenotyping of 49 panicle traits across tropical rice accessions, combined with genome‐wide association analyses, to uncover numerous subpopulation‐specific quantitative trait loci clusters; this work delineated a panicle morphocline from wild to modern varieties and proposed genetic models underlying complex inflorescence architecture. In parallel, the de novo assembly and comparison of the African rice genome with its wild progenitor revealed evidence for a single‐region independent domestication, identifying unique loci under selection and highlighting the distinct evolutionary trajectories of O. glaberrima.

Genetic Diversity and Domestication of Rice Species publication trend

The graph below shows the total number of articles in genetic diversity and domestication of rice species across all publications each year (not limited to Nature Index journals).

Technical terms

Single nucleotide polymorphism (SNP): A variation at a single base position in the DNA sequence among individuals, used as a marker for genetic diversity and trait mapping.

Genome‐wide association study (GWAS): A methodology that scans the genome for statistical associations between genetic variants and phenotypic traits in a diverse population.

Quantitative trait locus (QTL): A genomic region harbouring one or more genes that contribute to variation in a quantitative trait, such as grain yield or flowering time.

Introgression: The incorporation of genetic material from one population or species into another through hybridisation and repeated backcrossing.

Haplotype: A set of alleles or sequence variants at multiple neighbouring loci that are inherited together from a single parent and used to trace genealogical or breeding histories.

References

1. Open access resources for genome-wide association mapping in rice. Nature Communications (2016).
2. Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters. Nature Communications (2016).
3. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics (2014).
4. A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants. Nucleic Acids Research (2023).
5. Genomic decoding of breeding history to guide breeding-by-design in rice. National Science Review (2023).
6. The 3,000 rice genomes project. GigaScience (2014).