Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq

Abstract

Background Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants. Results In this study, a mutant displaying extremely low Cd accumulation ( lcd1 ) in rice plant and grain was generated by EMS mutagenesis from indica rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the lcd1 mutant were identified by MutMap and the transcriptome changes between lcd1 and WT under Cd exposure were analyzed by RNA-seq. The lcd1 mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that lcd1 was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the lcd1 mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of OsNRAMP5 . This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the lcd1 mutant. A total of 1208 genes were differentially expressed between lcd1 and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased OsHMA3 expression probably adds to the effect of OsNRAMP5 mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the lcd1 mutant. Conclusions An extremely low Cd mutant lcd1 was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the lcd1 mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding. Electronic supplementary material The online version of this article (10.1186/s12870-019-1867-y) contains supplementary material, which is available to authorized users.

Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns

“…Cd contamination in rice grains has become a problem in China and other countries in Asia, mainly due to water and soil contamination 38 . It has been reported that knockout of OsNramp5 via CRISPR/Cas9 targeting exons 1, 7, and 9 or alteration of OsNramp5 on exon 7 via ethyl methanesulfonate drastically decreases Cd accumulation in rice grains, roots, and shoots, with or without significantly lowering the yield 39 – 42 . Our gene PAV analysis results revealed a 408-kb deletion on chromosome 7 that spans the entire OsNramp5 region in accessions Luohong3A and Luohong4A (Fig.…”

Cadmium isotope fractionation reveals genetic variation in Cd uptake and translocation by Theobroma cacao and role of natural resistance-associated macrophage protein 5 and heavy metal ATPase-family transporters

“…Such work has particularly focused on genes that encode either transporters, such as natural resistanceassociated macrophage proteins (NRAMPs) [18][19][20][21][22][23][24][25] , which mediate the entry of Cd from the rhizosphere, or those such as heavy metal ATPases (HMAs) [26][27][28][29][30][31][32] , which determine the deposition of Cd in vacuoles or its translocation in the plant. Significant findings include (i) that the level of NRAMP5 in rice may be linked to the higher uptake of Cd in this species than in maize 21 , (ii) combining knockout of one homeologous HMA4 gene (nonsense mutation) and reduction of the other (missense mutation) reduced Cd levels in tobacco, while maintaining plant vigour 27 , and (iii) the identification in wheat of HMA3 variants linked to reduced Cd accumulation 26 .…”

Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves

“…3000, which is also in agreement with other transcriptome projects in rice, where ca. 1000-3000 DEGs have been reported (e.g., Li et al, 2018;Cao et al, 2019;Chen et al, 2019;Sun et al, 2019). The response of the rice transcriptome is quite variable, depending on the organ, cultivar, and environmental conditions.…”