Abstract
The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH1.1 and Zn7.1 were consistently identified in all the four environments, ten QTLs qDF3.1, qDF6.2 qDF9.1 qPH5.1 qGL3.1, qGW3.1, qGW11.1, and qZn6.2 were detected in two environments, while two major loci qBLB11.1 and qBLB5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.
Highlights
Micronutrient deficiencies and their associated health risks have become a major global health burden
Breeding rice varieties with enhanced nutrition, especially for Fe and zinc concentration (Zn) along with a suite of desirable agronomic and diseases resistance traits is a major priority of rice research (Bouis, 2003; Swamy et al, 2016)
There were many positive correlations among different agronomic traits but yield per hectare (YLD) was negatively correlated with Fe and Zn; while Fe and Zn were always strongly positively correlated irrespective of the environments and populations
Summary
Micronutrient deficiencies and their associated health risks have become a major global health burden. Various agencies have made significant efforts on a global scale to combat micronutrient deficiencies through preventive supplementation, fortification, and biofortification approaches (Dalmiya and Schultink, 2003). Biofortification of major staple crops is considered as the most cost-effective and sustainable approach to tackle hidden hunger. The successful effort by HarvestPlus to biofortify sweet potato with vitamin A targeted to Africa and Latin America was awarded the World Food Prize for the year 2016. Recognition of this significant feat has provided an added impetus to expedite the development and release of biofortified staple crops targeted to different regions of the world to make a global impact on health and nutrition
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