Research Article: Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification

Date Published: February 2, 2018

Publisher: Public Library of Science

Author(s): C. N. Neeraja, Kalyani S. Kulkarni, P. Madhu Babu, D. Sanjeeva Rao, K. Surekha, V Ravindra Babu, Jin-Song Zhang.

http://doi.org/10.1371/journal.pone.0192362

Abstract

Polished rice is poor source of micronutrients, however wide genotypic variability exists for zinc uptake and remobilization and zinc content in brown and polished grains in rice. Two landraces (Chittimutyalu and Kala Jeera Joha) and one popular improved variety (BPT 5204) were grown under zinc sufficient soil and their analyses showed high zinc in straw of improved variety, but high zinc in polished rice in landraces suggesting better translocation ability of zinc into the grain in landraces. Transcriptome analyses of the panicle tissue showed 41182 novel transcripts across three samples. Out of 1011 differentially expressed exclusive transcripts by two landraces, 311 were up regulated and 534 were down regulated. Phosphate transporter-exporter (PHO), proton-coupled peptide transporters (POT) and vacuolar iron transporter (VIT) showed enhanced and significant differential expression in landraces. Out of 24 genes subjected to quantitative real time analyses for confirmation, eight genes showed significant differential expression in landraces. Through mapping, six rice microsatellite markers spanning the genomic regions of six differentially expressed genes were validated for their association with zinc in brown and polished rice using recombinant inbred lines (RIL) of BPT 5204/Chittimutyalu. Thus, this study reports repertoire of genes associated with high zinc in polished rice and a proof concept for deployment of transcriptome information for validation in mapping population and its use in marker assisted selection for biofortification of rice with zinc.

Partial Text

Rice (Oryza sativa L.) is the staple food crop of 50% of the world and a major energy source especially in the developing countries. Polished rice, the most preferred form for consumption, is a poor source of micronutrients especially iron and zinc [1–3]. The excess dependence on polished rice in the Asian countries was reported to be responsible for malnutrition whose daily caloric intake is mainly confined to rice [4–6].

Transcriptomics analyses of developing panicles of three genotypes comprising two landraces with high zinc content (>20 ppm) and one improved variety with zinc content (~12 ppm) in polished rice grown under normal conditions revealed a set of differential expressed genes comprising several families associated with mineral homeostasis and other activities of cell metabolism.

Biofortification of rice for high zinc in rice appears to be promising strategy for addressing the some of the malnutrition issues in developing countries, especially for those whose major diet is polished rice with poor micronutrients. The development of varieties with high zinc would be relevant to alleviate malnutrition, but the lack of information on translocation of nutrients from vegetative tissues to grains is one of the barriers to rice biofortification [40, 66, 67]. Several donors for high zinc in polished rice have been identified through the evaluation of landraces and are being used in development of high zinc breeding lines [18–21, 68]. In parallel, several studies are being conducted on mechanism of zinc uptake and its translocation into the grain [41, 42, 69–73]. However, the information on genes associated with zinc uptake and its translocation are very limited in rice, but for reports on zinc transporters and ZIP genes [27, 74–76]. Some transgenics of rice with metal chelating molecules like nicotianamine, IRT, 2’-deoxymugineic acid (DMA) targeted for the enhanced iron content also showed increased zinc content in grain, thus role of a few candidate genes in zinc homeostasis is available [27, 77–83]. Since, physiological studies of zinc in rice have shown transfer of zinc from the vegetative tissues to reproductive tissues to be constraint for achieving high zinc in rice grain, we attempted to characterize a set of genes expressed in developing panicles of two landraces (CTM and KJJ) with high zinc in the polished rice in comparison with a popular improved high yielding rice variety with low zinc content in polished rice (BPT) grown under sufficient zinc soil conditions. Most of the work on zinc nutrition in plants has concentrated on genes and pathways related to extreme phenotypes, such as zinc deficiency and zinc excess-derived changes in growth and/or bulk concentrations in shoots or roots [35, 39, 84]. In general, to identify the differential expressed genes associated with nutrients, excess or deficient conditions are studied along with control [46, 48, 50]. However, to identify the set of genes responsible for high zinc under general irrigated rice cultivation conditions as practiced by the farmers with fertilization of zinc or native soil zinc, the genotypes were grown under regular soil with sufficient zinc. The two rice landraces of the present study appeared to be promising donors for the high zinc content in polished rice reiterating the fact that the landraces to be the source of novel genes/alleles for traits of interest as observed for stress tolerance and other traits in rice [85,86].

Our study provided an overview of the panicle transcriptome of three rice genotypes with differential zinc content in polished rice and highlighted putative candidate genes associated with high zinc in polished rice. Several novel transcripts have been identified along with the significant differentially expressed specific transporters viz., NRAMP, VIT, POT, PHO and MATE. The association of six differential expressed genes with zinc in polished rice is validated through expression and mapping analyses. We have demonstrated the generated transcriptome information for validation of associated genes in mapping population as a proof of concept. Overall, the resource generated in this study can be used to identify the suitable candidate genes for association and validation for high zinc in polished rice.

 

Source:

http://doi.org/10.1371/journal.pone.0192362

 

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