Morpho-Colorimetric Diversity and Genome-Wide Association Study of Wheat Spike Architecture Based on Image Processing Under Well-Watered and Rain-Fed Conditions

Rapid and efficient evaluation of morpho-colorimetric characteristics of wheat spike remains challenging, and thus the development of new methods is necessary. In this study, spike images of 298 bread wheat genotypes were processed to obtain different morpho-colorimetric traits under well-watered and rain-fed conditions. For this purpose, scripts were prepared in Python programming language. In addition, for the genetic dissection of spike system architecture, genome-wide association studies were performed by two models (MLM and FarmCPU) with 43,823 single-nucleotide polymorphism (SNP) markers. The results indicated wide diversity among wheat landraces and cultivars in terms of all traits in both well-watered and rain-fed conditions. Under rain-fed conditions, the yellowness and color intensity of spikes increased, while their whiteness represented a decrease. Colorimetric characteristics of the spike, compared to morphometric traits, had almost high heritability. However, no correlation was found between spike color and grain color. Cluster analysis based on these traits almost led to the separation of cultivars from landraces. The marker-trait associations (MTAs) identified for these traits were spread over various chromosomes. The number of identified markers in the MLM model was significantly higher than that of the FarmCPU model. Chromosomes 1A, 1B, 2A, 3D, and 6B had the most MTAs for spike colorimetric traits, while chromosomes 2B, 3A, 3B, 6B, and 7A contained the highest number of MTAs for spike morphometric traits. Some of these SNPs were environmental stable and model stable, and had pleiotropic effects. Gene annotation results demonstrated that some significant SNPs are linked with genes that are highly important in plant growth regulation. These genes were mainly involved in drought stress tolerance pathways. Metabolic, mitogen-activated protein kinases signaling, endocytosis, ATP-binding cassette transporters, plant hormone signal transmission, ubiquitin-mediated proteolysis, and biosynthesis of various plant secondary metabolites were identified as part of the Kyoto Encyclopedia of Genes and Genome pathways. In this study, a new approach was presented to the rapid phenotyping of spike traits, and our findings provide good insight into spike morpho-colorimetric characteristics that can be considered in future research.