Genetic dissection for zinc deficiency tolerance in rice using bi-parental mapping and association analysis
- 16 June 2017
- journal article
- research article
- Published by Springer Science and Business Media LLC in Theoretical and Applied Genetics
- Vol. 130 (9), 1903-1914
- https://doi.org/10.1007/s00122-017-2932-2
Abstract
Key message Zinc deficiency is a widespread soil constraint in rice production. Here, we present QTL/candidate genes associated with Zn deficiency tolerance identified through bi-parental QTL mapping and genome-wide association analysis. Abstract Zinc (Zn) deficiency is a widespread soil constraint in rice production. Despite several physiological studies elucidating Zn deficiency tolerance mechanisms, little is known about genetic factors conferring tolerance. To identify QTL associated with root development, biomass accumulation, and grain yield under Zn deficiency, we combined bi-parental QTL mapping in a population of 200 backcross inbred (BC1F6) lines and genome-wide association analysis using 247 k SNP markers across 140 accessions of an indica diversity panel. Three QTLs for Zn deficiency tolerance on chromosomes 3, 6, and 12 co-localized in both approaches and the association analysis detected two additional strong QTL on chromosomes 1 and 9 not present in the bi-parental population. Based on haplotype analysis of the indica panel, biomass consistently increased due to the minor ‘tolerance’ haplotypes, which had frequencies between 13 and 34%. By utilizing the previous transcript data collected from the same Zn-deficient field, we identified one putative candidate gene within the chromosome 6-QTL, which was associated with all traits in both analyses. Gene Os06g44220 was barely expressed under +Zn conditions but strongly upregulated in both root and shoot under stress and consistently more so in the tolerant genotype. Os06g44220 is an uncharacterized gene with expression previously detected only under salinity stress. Four SNP alterations within the promoter region distinguish the two alleles identified and a genotype tolerant to Zn deficiency shares the same allele as salinity tolerant varieties, lending support to the hypothesis that this gene may confer tolerance to both stresses.Funding Information
- The UK’s Biotechnology and Biological Sciences Research Council (BBSRC) (BB/J011584/1)
This publication has 29 references indexed in Scilit:
- Enhancing phosphorus and zinc acquisition efficiency in rice: a critical review of root traits and their potential utility in rice breedingAnnals of Botany, 2012
- Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL MappingPLoS Genetics, 2011
- Evidence for the mechanisms of zinc uptake by rice using isotope fractionationPlant, Cell & Environment, 2010
- Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicolaBMC Genomics, 2010
- Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc‐transporter activityNew Phytologist, 2010
- Malate Exudation by Six Aerobic Rice Genotypes Varying in Zinc Uptake EfficiencyJournal of Environmental Quality, 2009
- Genetic Identification of Quantitative Trait Loci for Contents of Mineral Nutrients in Rice GrainJournal of Integrative Plant Biology, 2008
- Gene Nomenclature System for RiceRice, 2008
- Effects of Zinc Deficiency on Rice Growth and Genetic Factors Contributing to TolerancePlant Physiology, 2006
- An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic conceptsEuphytica, 2005