Characterization of a major QTL for manganese accumulation in rice grain

Guang Chen,Kai Hong,Bin Zhang,Zhenyu Gao,Anpeng Zhang,Youlin Peng,Chaolei Liu,Qian Qian,Shenglong Yang,Yuanyuan Li,Hongzhen Jiang,Banpu Ruan

doi:10.1038/s41598-017-18090-7

Abstract

Some diets lack sufficient manganese (Mn), an essential mineral. Increasing Mn in grain by biofortification could prevent Mn deficiency, but may increase levels of the toxic element cadmium (Cd). Here, we investigated Mn in rice (Oryza sativa) grains in recombinant inbred lines (RILs) from the cross of 93–11 (low grain Mn) with PA64s (high grain Mn). Quantitative trait locus (QTL) analysis to identify loci controlling grain Mn identified a major QTL, qGMN7.1, on the short arm of chromosome 7; qGMN7.1 explained 15.6% and 22.8% of the phenotypic variation in the RIL populations grown in two distinct environments. We validated the QTL with a chromosome segment substitution line (CSSL), CSSL-qGMN7.1, in the 93–11 background harboring qGMN7.1 from PA64s. Compared to 93–11, CSSL-qGMN7.1 grain had increased Mn and decreased Cd concentrations; CSSL-qGMN7.1 roots also showed enhanced Mn uptake. Fine mapping delimited qGMN7.1 to a 49.3-kb region containing OsNRAMP5, a gene responsible for Mn and Cd uptake. Sequence variations in the OsNRAMP5 promoter caused changes in its transcript level, and in grain Mn levels. Our study thus cloned a major QTL for grain Mn concentration in rice, and identified materials for breeding rice for high Mn and low Cd concentrations in the grain.

Highlights

Manganese (Mn) is an essential trace element for plants, domestic animals, and humans[1]
Using the high-resolution single-nucleotide polymorphism (SNP) map, we detected 12 Quantitative trait locus (QTL) for grain Mn concentration distributed on all chromosomes except for chromosomes [10, 11], and 12 (Fig. S2 and Table S2)
Among those QTLs, 5 were identified in the recombinant inbred lines (RILs) populations grown in both Hainan and Hangzhou, and 8 had additive effects coming from PA64s

Summary

Introduction

Manganese (Mn) is an essential trace element for plants, domestic animals, and humans[1]. As rice is the staple food for over half of the world’s population, production of rice with adequate levels of Mn and low levels of Cd would benefit human health. Mn accumulation in rice grains occurs via root uptake, vascular transport, and transfer into the developing grain. The hybrid cultivar Liang-You-Pei-Jiu (LYPJ) was produced by a cross between the paternal parent [93–11] (an indica variety widely grown in China), and the maternal parent PA64s (with a mixed genetic background of indica and japonica). We performed a QTL analysis for grain Mn concentration based on the previously developed genetic map and characterized a major QTL controlling Mn accumulation in rice grains

Methods

Results

Conclusion