Wild rice: unlocking the future of rice breeding

Genus-Wide Pan-Genome Analysis of Oryza Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics

The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement.

Analysis of Coix Seed Oil Biosynthesis Facilitates the Identification of Lysophosphatidic Acid Acyltransferase

Coix seed oil (CSO) is a natural substance with significant anticancer potential. However, the molecular mechanism and the gene regulatory network of lipid biosynthesis were not identified in Coix seed. Here, a comprehensive transcriptome analysis was conducted on two Coix varieties with different lipid contents. The results revealed that a total of 48,110 genes were generated by de novo assembly, of which 84.45% genes were successfully annotated by the database. Based on functional annotation and gene expression, the metabolic network of crucial genes for oil accumulation and fatty acid (FA) synthesis in Coix seed has been successfully established, and it has been confirmed that lysophosphatidic acid acyltransferase (LPAT) in triacylglycerol (TAG) biosynthesis contributed to the changes in the content of FAs and had a significant selective binding ability to unsaturated fatty acids (UFAs) by the heterologous expression of yeast. Our data provides valuable references for subsequent gene function characterization and biosynthesis pathway optimization.

Fine mapping of qROL1 for root length at early seedling stage from wild rice (Oryza nivara)

Root is an important tissue to absorb water and nutrients from soil in plant and root architecture is one of critical traits influencing grain yield in crop. However, the genetic basis of root architecture remains unclear. In the present study, we identified a wild rice (Oryza nivara) introgression line Ra33 with longer seedling root length compared with the recipient parent 9311, an indica variety. Observation of longitudinal sections of root showed that the meristem length of Ra33 was significantly longer than that of 9311. Using an F2 secondary segregating population derived from a cross between introgression line Ra33 and the recipient parent 9311, we detected a major QTL for root length at early seedling stage, qROL1, between the molecular markers M3 and M5 on chromosome 1, and the O. nivara-derived allele at qROL1 increased root length under the background of 9311. In addition, the near-isogenic line NIL-ROL1 showed a significant increase in root length compared with the recipient parent 9311, further demonstrating the genetic effect of qROL1. And then, a total of 159 recombinant individuals were screened from 3355 F2 individuals and the QTL qROL1 was narrowed down to an approximate 78 kb interval between markers M4 and RM3, including 12 predicted genes. Further sequence comparison and expression analysis of the predicted genes in the fine-mapping region indicated that eight genes might be the interesting candidates of qROL1. The findings will provide new clues to reveal the genetic basis of root length and genetic resources for root architecture improvement in rice.

Supplementary information

The online version contains supplementary material available at 10.1007/s11032-025-01564-2.

Revisiting development and physiology of wild rice relatives for crop improvement and climate resilience

KEY MESSAGE

The review summarizes developmental and physiologic traits of wild rice relatives that can be targeted in mainstream rice-improvement programs for yield increases under changing climate. Increasing rice yield and productivity under changing climatic conditions is imperative for sustainable food security, given rice is a major staple crop around the world. Natural variation in crop plants, including wild relatives, offers remarkable genetic variability to explore the desirable developmental and physiologic traits for crop improvement. Wild relatives of rice, with distinct developmental and physiologic features compared to cultivated varieties, are the potential genetic and genomic resource for rice yield increases under changing climate. A thorough genetic basis of rice developmental and architectural changes during domestication is now established with the identification and characterization of domestication genes. Photosynthetically efficient wild rice accessions, with desirable developmental, physiologic, and metabolic traits, have been identified in recent years that could be instrumental for rice improvement. While several abiotic and biotic stress-tolerant wild relatives of rice along with the associated genetic loci have been identified over the years, a comprehensive insight into the desirable developmental and physiologic attributes of the wild rice is limited. Moreover, the usage of wild rice is not streamlined in rice-improvement programs due to genetic and genomic constraints. In this review, we summarize the desirable developmental and physiologic features of wild rice species that can be exploited for combining yield increases with climate resilience in rice-improvement programs.

African Cultivated, Wild and Weedy Rice (Oryza spp.): Anticipating Further Genomic Studies

Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima's population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop-wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts.