Fast X-ray fluorescence microscopy provides high-throughput phenotyping of element distribution in seeds.

The concentration, chemical speciation, and spatial distribution of essential and toxic mineral elements in cereal seeds have important implications for human health. To identify genes responsible for element uptake, translocation, and storage, high-throughput phenotyping methods are needed to visualize element distribution and concentration in seeds. Here, we used X-ray fluorescence microscopy (µ-XRF) as a method for rapid and high-throughput phenotyping of seed libraries and developed an ImageJ-based pipeline to analyze the spatial distribution of elements. Using this method, we nondestructively scanned 4,190 ethyl methanesulfonate (EMS)-mutagenized M1 rice (Oryza sativa) seeds and 533 diverse rice accessions in a genome-wide association study (GWAS) panel to simultaneously measure concentrations and spatial distribution of elements in the embryo, endosperm, and aleurone layer. A total of 692 putative mutants and 65 loci associated with the spatial distribution of elements in rice seed were identified. This powerful method provides a basis for investigating the genetics and molecular mechanisms controlling the accumulation and spatial variations of mineral elements in plant seeds.

Comprehensive sequence and whole-life-cycle expression profile analysis of the phosphate transporter gene family in rice.

Plant phosphate transporter (PT) genes comprise a large family with important roles in various physiological and biochemical processes. In this study, a database search yielded 26 potential PT family genes in rice (Oryza sativa). Analysis of these genes led to identification of eight conserved motifs and 5-12 trans-membrane segments, most of them conserved. A total of 237 putative cis elements were found in the 2-kb upstream region of these genes. Of these, a majority were Pi-response and other stress-related cis regulatory elements, such as PHO-like, TATA-box-like, PHR1, or Helix-loop-helix elements, and WRKY1 and ABRE elements, suggesting gene regulation by these signals. Comprehensive expression analysis of these genes was performed using data from microarrays hybridized with RNA from 27 tissues covering the entire lifecycle from three rice genotypes: Minghui 63, Zhenshan 97, and Shanyou 63. Real-time PCR analysis confirmed that three rice PT genes are preferentially expressed in stamen at 1 d before flowering, two in panicle at the heading stage, and two in flag leaf at 14 d after the heading stage. Hormone-treatment experiments revealed differential up-regulation or down-regulation of 11 rice PT genes in seedlings exposed to five hormones, respectively. These results will be useful for elucidating the roles of these genes in the growth, development, and stress response of the rice plant.