Extensive phenotyping and genome-wide analysis of grain number-related traits in a diverse wheat core collection

Bread wheat (Triticum aestivum L.) is one of the most important staple crops globally. Grain number per spikelet (GPS) is an important yield component in wheat. It is influenced by floret number per spikelet (FPS) and floret fertility. Through three consecutive years of observation of FPS, GPS, and floret fertility per spikelet (FFPS) in a globally collected hexaploid wheat core collection and using an improved genotyping dataset, we identified 42 marker-trait associations (MTA) for spikelet-related traits through the single-nucleotide polymorphism and the k-mer-based genome-wide association studies. Those MTA explain 4.45%-24.45% phenotypic variations for the FFPS and GPS traits, indicating a substantial effect on spikelet-related traits. We found significant negative associations between days to heading (DTH) and spikelet-related traits, suggesting that DTH and spikelet-related traits are subject to a certain degree of common genetic control. We identified several potential candidate gene models in the associated regions, including TraesCS2A03G0815500, which encodes a protein with a sterile alpha motif domain, and TraesCS2A03G0780600, which encodes a plastid-targeted lipoxygenase. These genes may facilitate wheat breeding and help elucidate the mechanisms of wheat grain set.