Using Spectral Reflectance Indices as Proxy Phenotypes for Genome‐Wide Association Studies of Yield and Yield Stability in Pacific Northwest Winter Wheat

Abstract

Spectral reflectance technology has recently opened up new possibilities to characterize traits that are resource intensive or difficult to measure directly in large germplasm collections. We have previously reported various spectral reflectance indices that have selectable genetic variations, strong associations with yield, and moderate to high efficiency of indirect selection in winter wheat (Triticum aestivum L.) adapted to the US Pacific Northwest. The objective of this study was to identify genomic regions of agronomic importance by using these indices as surrogates in genome‐wide association studies. Yield plots were evaluated for agronomic traits, canopy spectral reflectance, and canopy temperature under rainfed and irrigated conditions for 3 yr (2012–2014). Eight spectral reflectance indices were used for the association mapping study: green normalized difference vegetation index, normalized chlorophyll‐pigment ratio index, normalized difference vegetation index, normalized water index, plant nitrogen content index, photochemical reflectance index, simple ratio index, and xanthophyll epoxidation state. Marker‐based population structure explained 8 to 20% of phenotypic variation in these indices. Association mapping was conducted using 3653 single‐nucleotide polymorphism markers, two population subgroups, and reduced kinship matrices. We identified 80 quantitative trait loci for these indices across 16 chromosomes, most of which showed significant pleiotropic effect and positional proximity to grain yield, grain number per spike, thousand‐kernel weight, volume weight, plant height, and heading date. The study demonstrated the impending possibility of using canopy spectral reflectance in identifying novel and previously known loci that contribute to yield and yield stability under variable environments.