Genome-Wide Analysis of mineral concentrations in Wheat Grains

Dalia Z. Alomari; Marion S. Röder

 ** Plant breeding department /Gene and genome mapping, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.

alomari@ipk-gatersleben.de

Abstract

After the green revolution and improving crops yield production, the nutritional qualities were dropped down. Therefore, improving the nutritional quality became an imperative need particularly in the developing countries where malnutrition is spreading and one of the important crops in the world is wheat. Discovering the genetic factors underlying the natural variation of minerals in wheat (Triticum aestivum L.) is the main goal of the project.  A genome-wide association study (GWAS) of calcium (Ca) iron (Fe) and zinc (Zn) concentrations in wheat  grains using a European wheat diversity panel of 369 varieties and phenotypic data based on three years of field experiments has been used. Inductively coupled plasma optical emission spectrometry (ICP-OES) was used to measure the mineral concentrations in wheat grains. High genotyping densities of single-nucleotide polymorphism (SNP) markers were obtained from the application of the 90k iSELECT ILLUMINA array and 35k Affymetrix array resulting in 15,523 polymorphic markers and additionally, a subpanel of 183 genotypes was analyzed with a novel 135k Affymetrix marker array including 28,710 polymorphic SNPs. Best linear unbiased estimates (BLUEs) for Ca, Fe and Zn were calculated across the years and ranged from 288.20 to 647.50 μg·g−1, 24.42 to 52.42 μg·g−1 and 25.05 to 52.67 μg·g−1  respectively with a high heritability value for Ca and moderate value for both of Fe and Zn. A total of 485 SNP marker–trait associations (MTAs) were detected in complete panel data obtained from grains cultivated in both of the two years and BLUE values by considering associations with a -log10 (P-value) ≥3.0. The most significant association was located on chromosome 5A (114.5 cM) and was linked to a gene encoding cation/sugar symporter activity as a potential candidate gene. GWAS revealed 41 and 40 significant SNPs for Fe and Zn respectively in the complete panel whereas the number of significant SNPs was increased to 137 and 161 in the subpanel. The most significant association were located on chromosome 2A (763,689,738-765,710,113 bp) and within this region we detected candidate genes that associated with Fe uptake or transportation such as NAC transcription factors and transmembrane proteins. The most significant and consistent associations for Zn were located on chromosomes 3B (723,504,241-723,611,488 bp) and 5A (462,763,758-466,582,184 bp) and within this genomic region we found candidate genes  involved in Zn uptake and transport or represent bZIP and mitogen-activated protein kinase genes. These findings provide insight into the genetic basis for understanding the background of mineral accumulations in wheat grains by highlighting potential candidate genes that in turn may help breeders to select high Ca, Fe and Zn-containing genotypes to improve human health and grain quality.

 

Key words: wheat, calcium, iron, zinc, GWAS, SNP, MTAs, candidate genes.