Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach

Abstract

Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.

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Fig. 1: Grain Mn distributions in all rice accessions.
Fig. 2: Distribution of grain Mn concentration in rice in four subpopulations in four-field experiments.
Fig. 3: Genome-wide association-mapping results for grain Mn concentration in rice using single-trait analysis in all accessions grown in Arkansas under flooded condition in 2006.
Fig. 4: Genome-wide association-mapping results for grain Mn concentration in the temperate japonica subpopulation based on the 5.2 M SNP dataset, as well as local linkage disequilibrium analysis and SNP allele effects.
Fig. 5: Genome-wide association-mapping results for grain Mn concentration in rice based on the 5.2 M SNP dataset using multi-experiment analysis.

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Acknowledgements

This research was partly supported by the US National Science Foundation, Plant Genome Research Program (grant #IOS 0701119 to DES, MLG and SRMP) and The US National Institutes of Health (grant 2P4ES007373 to MLG and DES). PR is a PhD student funded by the Thai Government Scholarship.

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Ruang-areerate, P., Travis, A.J., Pinson, S.R.M. et al. Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach. Heredity (2020). https://doi.org/10.1038/s41437-020-00390-w

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