Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.)

Abstract

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.

Genome-Wide Association Study Reveals Genomic Regions Associated With Molybdenum Accumulation in Wheat Grains

“… Yang et al (2018) analyzed the Mo concentration in rice grains by GWAS and demonstrated that variations of Mo concentration in rice grains can be attributed to variable expression of OsMOT1;1 . Furthermore, Cobb et al (2021) also found strong genetic signals for Mo concentration in the shoot in the genomic region of the OsMOT1;1 gene on rice chromosome 8 by GWAS analysis. In wheat, GWAS has been employed to analyze the concentrations of several minerals in the grains, such as zinc ( Alomari et al, 2018 ; Velu et al, 2018 ; Cu et al, 2020 ; Zhou et al, 2020 ), iron ( Alomari et al, 2019 ; Cu et al, 2020 ), and calcium ( Alomari et al, 2017 ).…”

Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines

“…Variation in the elemental composition of plant tissue is governed by genetics, the local environment, and their interaction (GxE). Numerous studies have shown that elemental accumulation is under quantitative genetic control within a given environment (Cobb et al, 2021 ; Fikas et al, 2019 ; Liu et al, 2020 ; Ziegler et al, 2018 ); however, this effect varies across different environments. For example, in seeds of Sorghum bicolor , most of the 20 elements assayed showed significant variation explained by the interaction of genotype and environment, but the strength of the GxE effect varied by element (Shakoor et al, 2016 ).…”

Global Geographical Variation in Elemental and Arsenic Species Concentration in Paddy Rice Grain Identifies a Close Association of Essential Elements Copper, Selenium and Molybdenum with Cadmium

“…This is nowhere so prominent than in subsistence diets that rely on polished grains, where milling grains, unfortunately, removes a substantial portion of nutrients present in wholegrain (Rahman et al 2019). Grain mineral nutrition varies due to soil conditions and cultivation and fertilization practice (Nyachoti et al 2021;Gashu et al 2021;Welsh and Graham 2004;White and Broadley 2005), and to crop genetics (Cobb et al 2021;Huang et al 2015;Norton et al 2014). Maximizing grain nutrient density, to deliver as great a quantity of each essential element as feasible, given that bioavailability in the gut is also an issue for elements such as iron (Hoekenga et al 2011), is a major goal for those wishing to improve human health (Gashu et al 2021;Rahman et al 2019).…”

“…Phosphorus, an essential but generally poorly available in soils, undergoes both these storage strategies under luxury uptake, though plants rapidly downregulate phosphate assimilation if leaf tissue becomes too high (Chiou et al 2006). Quantitative trait loci analysis, also indicates for some elements, notably cadmium, lead, selenium, zinc, that grain accumulation is under genetic control in rice (Cobb et al 2021;Huang et al 2015;Norton et al 2014). Given these complexities, for food security and safety mitigation strategies, it is important to know how elemental concentrations vary regionally for foods, Deficiency or toxicity mitigation for a specific region may include soil fertilization, water management, food supplementation or high grain nutrient directed breed strategies, i.e.…”