A Genome-Wide Association Study Reveals the Genetic Mechanisms of Nutrient Accumulation in Spinach

Abstract

Spinach is a significant source of vitamins, minerals, and antioxidants. These nutrients make it delicious and beneficial for human health. However, the genetic mechanism underlying the accumulation of nutrients in spinach remains unclear. In this study, we analyzed the content of chlorophyll a, chlorophyll b, oxalate, nitrate, crude fiber, soluble sugars, manganese, copper, and iron in 62 different spinach accessions. Additionally, 3,356,182 high-quality, single-nucleotide polymorphisms were found using resequencing and used in a genome-wide association study. A total of 2077 loci were discovered that significantly correlated with the concentrations of the nutritional elements. Data mining identified key genes in these intervals for four traits: chlorophyll, oxalate, soluble sugar, and Fe. Our study provides insights into the genetic architecture of nutrient variation and facilitates spinach breeding for good nutrition.

Keywords: candidate genes; genome-wide association study; nutrients; single-nucleotide polymorphism; spinach.

Figure 1

Correlation analysis of different nutritional elements in spinach.

Figure 2

Distribution of 3,356,182 single-nucleotide polymorphisms (SNPs) among the six chromosomes of spinach within 1 Mb.

Figure 3

Linkage disequilibrium (LD) decay in the genome-wide association study (GWAS) population. The red dotted lines indicate the attenuation distance when the r-squared value of 0.35.

Figure 4

Manhattan plot for genome-wide association study (GWAS) of oxalate content in spinach using GLM and FarmCPU models. The horizontal and vertical axes represent the genomic position of the SNP and the association power for each SNP, respectively, with the trait expressed as −log₁₀(p). The dashed line shows the Bonferroni-corrected genome-wide threshold.