Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

Abstract

The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.

Progress update: Crop development of biofortified staple food crops under HarvestPlus

“…Positive correlation between iron and zinc allows for simultaneous improvement of both minerals. Quantitative trait loci (QTLs) associated with Zn enhancement in rice have been reported, but none of them with an effect larger than 30% phenotypic variation [105,106,107,108,109]. Research efforts continue to identify major QTLs associated with grain zinc content and better understand zinc uptake, transport, and remobilization into the grain [110,111].…”

Genetic Control of Plasticity in Root Morphology and Anatomy of Rice in Response to Water Deficit

“…Most of the root traits are complex polygenic in nature, and we expected that the effect of the individual underlying loci would be small. Therefore, we chose a suggestive threshold of P # 1.00E-04 to detect significant associations, as followed recently for the same population (Rebolledo et al, 2016) and in many other rice GWAS (Zhao et al, 2011;Norton et al, 2014;Dimkpa et al, 2016). The similar threshold also was used in another GWAS for rice root traits (Courtois et al, 2013 …”

Genetic Improvement of Iron Toxicity Tolerance in Rice-Progress, Challenges and Prospects in West Africa

“…This approach has been successfully applied to map genes/loci for aluminum tolerance (Famoso et al, 2010) and grain arsenic, copper, molybdenum, and zinc (Norton et al, 2014). Currently application of molecular markers in breeding for tolerance to Fe toxicity (by marker-assisted selection; MAS) is seriously limited by the fact that most QTLs reported are for small effects and even for the few major ones, large confidence intervals and/or lack of validation in other genetic backgrounds and environments (actual field testing) constitute a drawback to their use.…”