Univariate and Multivariate QTL Analyses Reveal Covariance Among Mineral Elements in the Rice Ionome.

Huan Liu,Mary Lou Guerinot,Zhong Tang,Su-Xian Long,Fang-Jie Zhao,Xin-Yuan Huang,David E Salt,Shannon R M Pinson

doi:10.3389/fgene.2021.638555

Abstract

Rice provides more than one fifth of daily calories for half of the world’s human population, and is a major dietary source of both essential mineral nutrients and toxic elements. Rice grains are generally poor in some essential nutrients but may contain unsafe levels of some toxic elements under certain conditions. Identification of quantitative trait loci (QTLs) controlling the concentrations of mineral nutrients and toxic trace metals (the ionome) in rice will facilitate development of nutritionally improved rice varieties. However, QTL analyses have traditionally considered each element separately without considering their interrelatedness. In this study, we performed principal component analysis (PCA) and multivariate QTL analyses to identify the genetic loci controlling the covariance among mineral elements in the rice ionome. We resequenced the whole genomes of a rice recombinant inbred line (RIL) population, and performed univariate and multivariate QTL analyses for the concentrations of 16 elements in grains, shoots and roots of the RIL population grown in different conditions. We identified a total of 167 unique elemental QTLs based on analyses of individual elemental concentrations as separate traits, 53 QTLs controlling covariance among elemental concentrations within a single environment/tissue (PC-QTLs), and 152 QTLs which determined covariation among elements across environments/tissues (aPC-QTLs). The candidate genes underlying the QTL clusters with elemental QTLs, PC-QTLs and aPC-QTLs co-localized were identified, including OsHMA4 and OsNRAMP5. The identification of both elemental QTLs and PC QTLs will facilitate the cloning of underlying causal genes and the dissection of the complex regulation of the ionome in rice.

Highlights

Rice provides more than one fifth of daily calories for half of the world’s human population, making it a staple food crop of primary global importance
A total of 241.84 Gb of sequencing data were generated for the two parents and 257 recombinant inbred line (RIL) with more than 96% of clean reads being mapped to the Nipponbare reference genome (Supplementary Table 1)
LM and TQ were sequenced at 65 × and 57 × coverage, respectively, while the population was sequenced at 2 × coverage on average for each RIL

Summary

Introduction

Rice provides more than one fifth of daily calories for half of the world’s human population, making it a staple food crop of primary global importance. In addition to being the main calorie source, rice can be a major dietary source of both essential mineral nutrients and toxic elements. Hidden hunger, caused by diets deficient for essential vitamins and mineral nutrients, has become a global challenge. Rice can be a major dietary source of toxic heavy metals, especially for persons consuming rice as their staple food. Rice was found to contribute as much as 56 and 60% of total dietary intake of two toxic elements cadmium (Cd) and arsenic (As), respectively, for the general population in China (Li et al, 2011; Song et al, 2017). It is desirable to increase the levels of healthbeneficial elements and to decrease the accumulation of toxic elements in rice grains to ensure the production of nutritious and safe rice

Methods

Results

Conclusion