Identification of Manganese Use Efficiency Candidate Genes in Winter Barley (Hordeum vulgare): GWAS on Chlorophyll a Fluorescence and ICP-OES

Besides yield, disease resistances, and economical traits, nutrient use efficiency has become of major interest. On top of the macronutrient use efficiency, crop production faces nowadays problems of micronutrients depleted soil. Manganese (Mn) deficiency is a major plant nutritional disorder in winter cereals resulting in yield reduction and increasing winter kill. Mn deficiency is difficult to diagnose due to the lack of visual symptoms. Identification of genes controlling Mn use efficiency has been fruitless so far.

This abiotic stress affects specifically the plant photosystem. Therefore Mn use efficiency of 248 winter barley varieties was phenotyped by chlorophyll a fluorescence in Mn deficient conditions in field and greenhouse for three years. Mn quantification in leaves was carried out by Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES). Using 9k SNP iSelect array, Genome Wide Association Study (GWAS) was performed to identify genetic variants governing this trait.

Combining association genetics with straightforward phenotyping methods, several significant SNP were detected. Associations were found to be environment-specific. Recent genome barley sequence allows identification of candidate genes playing a role in Mn plant metabolism. This trait shows a very dynamic, environmental dependency characterization. It involves many putative genes among which oxalate oxidase, Mn superoxide dismutase and photosystem II subunit proteins.

Genome location of SNPs provides and very useful information for plant breeding purposes. The use of plant nutrition tools with GWAS approach offer a better understanding of Mn use efficiency and shows promising perspectives for breeding more efficient barley varieties for complex polygenic traits.