Joshua N. Cobb, Chen Chen, Yuxin Shi, Lyza G. Maron, Danni Liu, Mike Rutzke, Anthony Greenberg, Eric Craft, Jon Shaff, Edyth Paul, Kazi Akther, Shaokui Wang, Leon V. Kochian, Dabao Zhang, Min Zhang & Susan R. McCouch

Theoretical and Applied Genetics August 2021; vol. 134:2613–2637

Key message

Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants.

Abstract

Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

See: https://link.springer.com/article/10.1007/s00122-021-03848-5

Figure: Six-week-old rice plants grown under hydroponics conditions. Rice plants grown from pre-germinated seedlings under hydroponic growth conditions to 6 weeks of age.