Genetic Characterization of Spring Wheat Cultivars from a High-Altitude Region in China Using a 100K Single-Nucleotide Polymorphism Panel

Abstract

Uncovering the genetic characteristics of important traits in wheat cultivars is essential for targeted wheat breeding. Here, a liquid 100K single-nucleotide polymorphism (SNP) chip panel, integrating markers of known function, was selected and used to analyze genetic characteristics for 115 spring wheat cultivars from a high-altitude region of China. A total of 102 reported functional markers closely related to important traits were identified, including 54 related to yield and grain quality and 33 associated with disease resistance and stress tolerance. Of the cultivars, 58.2% of cultivars contained excellent marker genes in the range of 20 to 29. Genetic structure analysis revealed that the cultivars were grouped into five subgroups. Genome-wide association studies identified 218 significant loci on 20 chromosomes, with the exception of chromosome 3D, associated with nine traits and which explained 14.15–29% of phenotypic variance, with 199 potential candidate genes being annotated for the nine traits studied. Notably, 21 previously unidentified candidate genes, with associated SNPs, were closely associated with seven traits, explaining 14.26–19.86% of the phenotypic variance. The current study revealed the genetic characteristics of spring wheat cultivars from a high-altitude region of China. This will provide a reference for spring wheat breeding for high-altitude regions and promote the fine-mapping of new genetic loci controlling important traits.

Keywords

• wheat germplasm
• functional genes
• phenotype
• gene chip
• genome-wide association studies