Dataset Information

Identification of genomic region(s) responsible for high iron and zinc content in rice.

ABSTRACT: Micronutrient especially iron and zinc-enriched rice hold immense promise for sustainable and cost-effective solutions to overcome malnutrition. In this context, BC₂F₅ 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).

SUBMITTER: Dixit S

PROVIDER: S-EPMC6544658 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Identification of genomic region(s) responsible for high iron and zinc content in rice.

Dixit Shilpi S Singh Uma Maheshwar UM Abbai Ragavendran R Ram T T Singh Vikas Kumar VK Paul Amitava A Virk P S PS Kumar Arvind A

Scientific reports 20190531 1

Micronutrient especially iron and zinc-enriched rice hold immense promise for sustainable and cost-effective solutions to overcome malnutrition. In this context, BC<sub>2</sub>F<sub>5</sub> 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 ...[more]

PMID: 31148549

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Project description:Micronutrient malnutrition, especially deficiency of two mineral elements, iron [Fe] and zinc [Zn] in the developing world needs urgent attention. Pearl millet is one of the best crops with many nutritional properties and is accessible to the poor. We report findings of the first attempt to mine favorable alleles for grain iron and zinc content through association mapping in pearl millet. An association mapping panel of 130 diverse lines was evaluated at Delhi, Jodhpur and Dharwad, representing all the three pearl millet growing agro-climatic zones of India, during 2014 and 2015. Wide range of variation was observed for grain iron (32.3-111.9 ppm) and zinc (26.6-73.7 ppm) content. Genotyping with 114 representative polymorphic SSRs revealed 0.35 mean gene diversity. STRUCTURE analysis revealed presence of three sub-populations which was further supported by Neighbor-Joining method of clustering and principal coordinate analysis (PCoA). Marker-trait associations (MTAs) were analyzed with 267 markers (250 SSRs and 17 genic markers) in both general linear model (GLM) and mixed linear model (MLM), however, MTAs resulting from MLM were considered for more robustness of the associations. After appropriate Bonferroni correction, Xpsmp 2261 (13.34% R2-value), Xipes 0180 (R2-value of 11.40%) and Xipes 0096 (R2-value of 11.38%) were consistently associated with grain iron and zinc content for all the three locations. Favorable alleles and promising lines were identified for across and specific environments. PPMI 1102 had highest number (7) of favorable alleles, followed by four each for PPMFeZMP 199 and PPMI 708 for across the environment performance for both grain Fe and Zn content, while PPMI 1104 had alleles specific to Dharwad for grain Fe and Zn content. When compared with the reference genome Tift 23D2B1-P1-P5, Xpsmp 2261 amplicon was identified in intergenic region on pseudomolecule 5, while the other marker, Xipes 0810 was observed to be overlapping with aspartic proteinase (Asp) gene on pseudomolecule 3. Thus, this study can help in breeding new lines with enhanced micronutrient content using marker-assisted selection (MAS) in pearl millet leading to improved well-being especially for women and children.

Project description:Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha-1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34-19.52%) and enriched the Zn content of polished rice (1.40-20.05%). Specifically, redundancy analysis (RDA) and Mantel's test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil-microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Project description:BackgroundThe B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now.Methodology/principal findingsIn this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern.Conclusions/significanceThe combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes.

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Identification of genomic region(s) responsible for high iron and zinc content in rice.

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Identification of genomic region(s) responsible for high iron and zinc content in rice.

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