Characterization of the Root Transcriptome for Iron and Zinc Homeostasis-related Genes in Indica rice (Oryza sativa L) (original) (raw)
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Identification of genomic region(s) responsible for high iron and zinc content in rice
Scientific Reports
Micronutrient especially iron and zinc-enriched rice hold immense promise for sustainable and costeffective solutions to overcome malnutrition. In this context, BC 2 F 5 population derived from cross between RP-Bio226 and Sampada was used to localize genomic region(s)/QTL(s) for grain Fe (iron) and Zn (zinc) content together with yield and yield-related traits. Genotyping of mapping population with 108 SSR markers resulted in a genetic map of 2317.5 cM with an average marker distance of 21.5 cM. Mean grain mineral content in the mapping population across the two seasons ranged from 10.5-17.5 ppm for Fe and 11.3-22.1 ppm for Zn. Based on the multi-season phenotypic data together with genotypic data, a total of two major QTLs for Fe (PVE upto 17.1%) and three for Zn (PVE upto 34.2%) were identified. Comparative analysis across the two seasons has revealed four consistent QTLs for Fe (qFe 1.1 , qFe 1.2 , qFe 6.1 and qFe 6.2) and two QTL for Zn content (qZn 1.1 and qZn 6.2). Additionally, based on the previous and current studies three meta-QTLs for grain Fe and two for grain Zn have been identified. In-silico analysis of the identified QTL regions revealed the presence of potential candidate gene(s) such as, OsPOT, OsZIP4, OsFDR3, OsIAA5 etc., that were previously reported to influence grain Fe and Zn content. The identified QTLs could be utilized in developing high yielding, Fe and Zn denser varieties by marker assisted selection (MAS).
Journal of Plant Molecular Biology and …, 2011
Expression of twenty five metal transport related genes was analyzed in root and leaf tissue of twelve diverse rice genotypes at maximum tillering (MTS) and mid-grain fill (MGF) stages to understand their role in iron/zinc uptake and transport and remobilization. Well-nourished rice plants grown with sufficient supply of iron (Fe) and zinc (Zn) were used for expression analysis. Differential expression of metal homeostasis related candidate genes was observed among genotypes, tissue types and developmental stages. Maximum number of genes (twenty four) genes expressed in flag leaf tissue (MGF) showing variation in level of expression among genotypes. Root transcriptome profiling revealed that nine genes (OsZIP4,
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Micronutrient deficiencies, particularly of iron (Fe) and zinc (Zn), in the diet contribute to health issues and hidden hunger. Enhancing the Fe and Zn content in globally staple food crops like rice is necessary to address food malnutrition. A Genome-Wide Association Study (GWAS) was conducted using 85 diverse rice accessions from the Democratic Republic of Congo (DRC) to identify genomic regions associated with grain Fe and Zn content. The Fe content ranged from 0.95 to 8.68 mg/100 g on a dry weight basis (dwb) while Zn content ranged from 0.87 to 3.8 mg/100 g (dwb). Using MLM and FarmCPU models, we found 10 significant SNPs out of which one SNP on chromosome 11 was associated with the variation in Fe content and one SNP on chromosome 4 was associated with the Zn content, and both were commonly detected by the two models. Candidate genes belonging to transcription regulator activities, including the bZIP family genes and MYB family genes, as well as transporter activities involved...
Identifying QTLs/genes for iron and zinc in rice grains can help in biofortification programs. 168 F 7 RILs derived from Madhukar × Swarna were used to map QTLs for iron and zinc concentrations in unpolished rice grains. Iron ranged from 0.2 to 224 ppm and zinc ranged from 0.4 to 104 ppm. Genome wide mapping using 101 SSRs and 9 gene specific markers showed 5 QTLs on chromosomes 1, 3, 5, 7 and 12 significantly linked to iron, zinc or both. In all, 14 QTLs were identified for these two traits. QTLs for iron were co-located with QTLs for zinc on chromosomes 7 and 12. In all, ten candidate genes known for iron and zinc homeostasis underlie 12 of the 14 QTLs. Another 6 candidate genes were close to QTLs on chromosomes 3, 5 and 7. Thus the high priority candidate genes for high Fe and Zn in seeds are OsYSL1 and OsMTP1 for iron, OsARD2, OsIRT1, OsNAS1, OsNAS2 for zinc and OsNAS3, OsNRAMP1, Heavy metal ion transport and APRT for both iron and zinc together based on our genetic mapping studies as these genes strictly underlie QTLs. Several elite lines with high Fe, high Zn and both were identified.
Transcriptomic analysis of rice in response to iron deficiency and excess
Background: Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe. Results: We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots. Conclusion: These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.
Iron homeostasis related genes in rice
Genetics and Molecular Biology, 2003
Iron is essential for plants. However, excess iron is toxic, leading to oxidative stress and decreased productivity. Therefore, plants must use finely tuned mechanisms to keep iron homeostasis in each of their organs, tissues, cells and organelles. A few of the genes involved in iron homeostasis in plants have been identified recently, and we used some of their protein sequences as queries to look for corresponding genes in the rice (Oryza sativa) genome. We have assigned possible functions to thirty-nine new rice genes. Together with four previously reported sequences, we analyzed a total of forty-three genes belonging to five known protein families: eighteen YS (Yellow Stripe), two FRO (Fe 3+-chelate reductase oxidase), thirteen ZIP (Zinc regulated transporter / Iron regulated transporter Protein), eight NRAMP (Natural Resistance-Associated Macrophage Protein), and two Ferritin proteins. The possible cellular localization and number of potential transmembrane domains were evaluated, and phylogenetic analysis performed for each gene family. Annotation of genomic sequences was performed. The presence and number of homologues in each gene family in rice and Arabidopsis is discussed in light of the established iron acquisition strategies used by each one of these two plants.
Current Science, 2015
To understand the role of metal homeostasis-related genes in rice, micronutrient levels of different tissue types were analysed at mid grain-filling stage followed by the expression analysis of candidate genes in these tissues. Subsequently, the association between the gene expression pattern and micronutrient level in tissues as well as mature grains was analysed. Out of 11 candidate genes used for gene expression analysis utilizing bulked cDNA based RT-PCR, 8 genes showed high level of expression in flag leaf and second leaf tissues. Four genes showed poor level of expression in immature grains and low to negligible expression in stem tissues. Further, six candidate genes were selected based on differential response of cDNA bulk analysis for the expression studies of individual rice genotypes, including four high-zinc rice genotypes, namely R-RHZ-LI-25, IR92970-111-1-2, R-RHZ-SM-3, R-RHZ-SM-4 which showed higher level of expression for genes OsVIT1, OsFER1, OsYSL2 and OsYSL9. Whereas low or negligible level gene expression in stem tissue of five genes, except OsFER1 shows that rice stem tissue could be involved in the uptake of micronutrients. The characterization of genes in this study provides deeper insight into the tightly regulated mechanism of metal homeostasis with respect to different tissue types and understanding of sourcesink relationship of mineral acquisition and remobilization.
Background: Identifying QTLs/genes for iron and zinc in rice grains can help in biofortification programs. Genome wide mapping showed 14 QTLs for iron and zinc concentration in unpolished rice grains of F7 RILs derived from Madhukar × Swarna. One line (HL) with high Fe and Zn and one line (LL) with low Fe and Zn in unpolished rice were compared with each other for gene expression using qPCR. 7 day old seedlings were grown in Fe+ and Fe− medium for 10 days and RNA extracted from roots and shoots to determine the response of 15 genes in Fe− conditions. Results: HL showed higher upregulation than LL in shoots but LL showed higher upregulation than HL in roots. YSL2 was upregulated only in HL roots and YSL15 only in HL shoots and both up to 60 fold under Fe− condition. IRT2 and DMAS1 were upregulated 100 fold and NAS2 1000 fold in HL shoot. NAS2, IRT1, IRT2 and DMAS1 were upregulated 40 to 100 fold in LL roots. OsZIP8, OsNAS3, OsYSL1 and OsNRAMP1 which underlie major Fe QTL showed clear allelic differences between HL and LL for markers flanking QTL. The presence of iron increasing QTL allele in HL was clearly correlated with high expression of the underlying gene. OsZIP8 and OsNAS3 which were within major QTL with increasing effect from Madhukar were 8 fold and 4 fold more expressed in HL shoot than in LL shoot. OsNAS1, OsNAS2, OsNAS3, OsYSL2 and OsYSL15 showed 1.5 to 2.5 fold upregulation in flag leaf of HL when compared with flag leaf of Swarna. Conclusion: HL and LL differed in root length, Fe concentration and expression of several genes under Fe deficiency. The major distinguishing genes were NAS2, IRT2, DMAS1, and YSL15 in shoot and NAS2, IRT1, IRT2, YSL2, and ZIP8 in roots. The presence of iron increasing QTL allele in HL at marker locus close to genes also increased upregulation in HL.
Rice (Oryza sativa L.) is a “Global Grain” cultivated widely across the world feeding millions of mankind. As the humankind faces nutrient deficit in cultivated crops, rice supplemented with micronutrients is an important substitute to overcome such malnutrition. Several QTLs for the grain micronutrient contents have been identified and mapped on rice chromosome but their refinement and genetic dissection are yet underway to truly understand the quantitative variation and genes contributing to them. Further the availability of rice genome sequence has opened up the possibility of identifying candidate genes involved in Fe/ Zn accumulation in grains. In this study we have selected and characterized five known QTLs, two (QTL qFE-1 and qFE-9) governing Fe content and three (QTLs qZN-5, qZN-7 and qZN-11) governing Zn content in rice. Scanning the selected QTLs revealed that QTL qFE-1 and qFE-9 comprises 8 and 12 BAC/PAC clones whereas QTLs qZN-5, qZN-7 and qZN-11 comprises 6, 8, and 12 BAC/PAC clones respectively. This also resulted in the identification of eight candidate genes predicted to be involved in the activities of uptake, transport and accumulation iron and zinc in rice which were further analyzed for transmembrane domains, localization of proteins and expression. In silico spatial and temporal expression of the candidate genes by ESTs and MPSS signature tags showed prominent expression in diverse tissue libraries including meristematic tissues, developing seeds and in pathogen infected leaves suggesting putative role of genes in loading of Fe/ Zn to grains as well as in other activities related to virulence and defense mechanism. Further we analyzed the abundance of microsatellites or SSRs in the genomic, cDNA, exon, intron and UTR regions underlying candidate genes. A total of 255 SSRs including 164 SSRs in the genomic region, 46 in the cDNA sequences and 45 SSRs in the exon, intron and UTR sequences were identified. According to repeat motif, trinucleotide repeats and according to sequence length, Class II SSRs were the most commonly found microsatellites. Twenty six novel candidate gene based microsatellite markers have been developed from the genomic, cDNA, exon, intron and UTR regions. The identification putative candidate genes related to Fe/ Zn contents in rice and their specific novel microsatellite markers in this study will help in the development of gene specific DNA markers for marker-assisted mapping as well as in the discovery of novel Fe/ Zn related genes in rice.
GENE EXPRESSION ANALYSIS IN ROOTS OF RICE (ORYZA SATIVA L.) UNDER VARIED ZINC CONDITION
Zinc (Zn), is an important element essential to both plant and humans which play key role in gene expression, cell development and replication processes. Zinc deficiency is prevalent and widespread in rice consuming countries which causes delayed plant development and decreased crop yield. Many studies have investigated the response of rice plants to Zn deficiency using high and low zinc accumulating genotypes at physiological and biochemical level. However, little information is available about mechanisms at molecular level. Therefore, an attempt was made to understand the Zn deficiency in the roots of rice seedlings through transcriptome analysis. The results revealed that a diverse set of differentially expressed genes (DEGs) with distinct functions were altered under zinc deficient condition as compared to zinc supplemented condition. DEGs were majorly involved in primary metabolism such as carbohydrate, lipid, protein and secondary metabolism. KEGG pathway analysis revealed that majority of DEGs were upregulated and down regulated in biosynthesis of terpenoids and steroids, oxidative phosphorylation, nitrogen metabolism, citrate cycle pathways. The present result reveal that zinc deficiency leads to activation of several genes and gene networks, indicating how plants cope with the micronutrient deficiency at different developmental stages of rice.