Genome-wide association analysis of lodging-related basal internode traits in spring wheat (Triticum aestivum L.)

Morphological traits of lowest basal internodes of wheat stem play critical roles in conferring resistance to stem lodging, which significantly impacts wheat yield and quality worldwide. However, the genetic mechanisms underlying morphological traits of lowest basal internodes of wheat are not fully elucidated. To identify molecular markers/genomic loci and putative candidate genes regulating basal internode morphological traits that are key to lodging resistance, this study conducted a genome-wide association study (GWAS) using a mapping panel consisting of 181 diverse spring wheat genotypes grown in four environments. Genotypes in the mapping panel exhibited significant variation in morphological traits of lowest basal internodes across all trial environments. Using multiple statistical models and a threshold of -log 10 ( P ) ≥ 3.5, our marker trait association analysis identified a total of 50 significant SNPs representing 31 QTLs linked to lowest basal internode morphological traits considered in this study, and these QTLs are distributed over 13 chromosomes of bread wheat. Genes involved in signal transduction, and cytokinin and cell wall macro molecule metabolic processes are among putative candidate genes associated with the significant SNPs linked to the traits studied. Haplotype analysis of the marker data in QTLs represented by three or more significant SNPs led to the identification of 18 ​ haplotypes with unique phenotypic effects. The study identified genomic regions/SNP markers and putative candidate genes that regulate different morphological traits of lowest basal internodes in wheat, which are crucial for enhanced resistance to stem lodging.