Harnessing neo-domestication of wild pigmented rice for enhanced nutrition and sustainable agriculture

Ray Singh Rathore, Wenjun Jiang, Khalid Sedeek & Magdy Mahfouz

Theoretical and Applied Genetics; May 3 2025; vol.138; article 108

Advances in precision gene editing have enabled the rapid domestication of wild crop relatives, a process known as neo-domestication. During domestication, breeding rice for maximum productivity under optimal growth conditions reduced genetic diversity, eliminating variants for stress tolerance and grain nutrients. Wild rice varieties have rich genetic diversity, including variants for disease resistance, stress tolerance, and grain nutritional quality. For example, the grain of pigmented wild rice has abundant antioxidants (anthocyanins, proanthocyanidins, and flavonoids), but low yield, poor plant architecture, and long life cycle limit its cultivation. In this review, we address the neo-domestication of wild pigmented rice, focusing on recent progress, CRISPR-Cas editing toolboxes, selection of key candidate genes for domestication, identifying species with superior potential via generating genomic and multi-omics resources, efficient crop transformation methods and highlight strategies for the promotion and application pigmented rice. We also address critical outstanding questions and potential solutions to enable efficient neo-domestication of wild pigmented rice and thus enhance food security and nutrition.

See https://link.springer.com/article/10.1007/s00122-025-04896-x

Figure 1: Strategies for traditional and neo-domestication approaches for the domestication of wild vs. pigmented rice. a Representation of the domestication process and subsequent loss of genetic variation. This illustration depicts the domestication process, highlighting the gradual loss of useful genetic variation that has resulted from selective breeding and the selection of a limited number of alleles. Over time, as humans have selected specific desirable traits such as increased yield or uniformity, the genetic diversity in cultivated rice populations has decreased, leading to a reduction in the pool of available alleles. b Neo-domestication approaches for wild pigmented rice. This illustration depicts the proposed and currently practiced neo-domestication approaches for wild pigmented rice, aimed at addressing future agricultural challenges. These approaches focus on expediting the selection and domestication of elite pigmented rice varieties, while retaining genetic diversity and the associated elite traits. By leveraging advanced breeding techniques and genomic tools, these neo-domestication strategies offer promising avenues for developing improved pigmented rice varieties capable of both meeting evolving agricultural needs and preserving genetic diversity