Discovering genetic loci associated with rate of vegetative index gain using UAV-based phenomics in spring wheat

In wheat, the pre-heading stage determines spikelet formation, floret fertility, and canopy development, making it a critical window for early stress detection and yield potential. The genetic basis of pre-heading canopy development in wheat has remained constrained by the conventional phenotyping due to the low temporal resolution. Here, we quantified the rate of vegetation index gain (RVIs) during tillering to heading stages using UAV-mounted multispectral sensor in 196 spring wheat cultivars representing 112 years of breeding history. RVIs were calculated using six vegetation indices for consecutive two growing seasons, and genome wide association study (GWAS) was performed on RVIs, grain yield (GY) and thousand grain weight (TGW) using a wheat 37K SNP array. RVIs showed significant positive correlations with grain yield (r=0.28-0.43; p<0.001) and consistently increased in the modern cultivars compared to old cultivars. This indicated that resource remobilization during pre-heading canopy development significantly contributed to GY during modern wheat breeding. GWAS identified 67 loci, including 12 Group-I loci associated only with RVIs, and 18 Group-II loci associated with both RVIs and yield traits. Two stable loci on chr1B and chr5D consistently increased GY and RVIs across environments, and the tag SNPs were converted to selectable KASP markers. The allelic distribution on global wheat collection of [~]3000 accessions showcased that favorable alleles on both loci were dominant in cultivars compared to landraces. Similarly, favorable alleles showed more frequency in winter type than spring type. Across breeding eras both alleles showed increasing trend with chr5D reaching near fixation and chr1B remaining partially enriched in modern cultivars. Our work on capturing pre-heading canopy development, discovery of two stable loci underpinning yield and RVIs, and development of KASP markers provided a strong foundation to HTP assisted genetic dissection of GY and facilitated the understanding of canopy dynamics and yield formation.