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Genome-Wide Association Study of Calcium Accumulation in Grains of European Wheat Cultivars.

ABSTRACT: Mineral concentrations in cereals are important for human health, especially for people who depend mainly on consuming cereal diet. In this study, we carried out a genome-wide association study (GWAS) of calcium concentrations in wheat (Triticum aestivum L.) grains using a European wheat diversity panel of 353 varieties [339 winter wheat (WW) plus 14 of spring wheat (SW)] and phenotypic data based on two field seasons. High genotyping densities of single-nucleotide polymorphism (SNP) markers were obtained from the application of the 90k iSELECT ILLUMINA chip and a 35k Affymetrix chip. Inductively coupled plasma optical emission spectrometry (ICP-OES) was used to measure the calcium concentrations of the wheat grains. Best linear unbiased estimates (BLUEs) for calcium were calculated across the seasons and ranged from 288.20 to 647.50 among the varieties (μg g-1 DW) with a mean equaling 438.102 (μg g-1 DW), and the heritability was 0.73. A total of 485 SNP marker-trait associations (MTAs) were detected in data obtained from grains cultivated in both of the two seasons and BLUE values by considering associations with a -log10 (P-value) ≥3.0. Among these SNP markers, we detected 276 markers with a positive allele effect and 209 markers with a negative allele effect. These MTAs were found on all chromosomes except chromosomes 3D, 4B, and 4D. 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. Additionally, a number of candidate genes for the uptake or transport of calcium were located near significantly associated SNPs. 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 genetically highly diverse variety panels. The research demonstrates the feasibility of the GWAS approach for illuminating the genetic architecture of calcium-concentration in wheat grains and for identifying putative candidate genes underlying this trait.

SUBMITTER: Alomari DZ

PROVIDER: S-EPMC5663994 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundHexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood.ResultsHere, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61-26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain.ConclusionTo identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.

Project description:BackgroundThe analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins.ResultsProteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different.ConclusionsWheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.

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Genome-Wide Association Study of Calcium Accumulation in Grains of European Wheat Cultivars.

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