Flowering time regulator qFT13‐3 involved in soybean adaptation to high latitudes

Summary Soybean is a short‐day plant that typically flowers earlier when exposed to short‐day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome‐wide association studies (GWAS) using two re‐sequencing datasets that included 113 wild soybeans ( G. soja ) and 1192 cultivated soybeans ( G. max ), respectively, and simultaneously identified a candidate flowering gene, qFT13‐3 , which encodes a protein homologous to the pseudo‐response regulator ( PRR ) transcription factor. We identified four major haplotypes of qFT13‐3 in the natural population, with haplotype H4 ( qFT13‐3 H4 ) being lost during domestication, while qFT13‐3 H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13‐3 H1 were located in high‐latitude regions. Knockout of qFT13‐3 accelerated flowering and maturity time under long‐day conditions, indicating that qFT13‐3 functions as a flowering inhibitor. Our results also showed that qFT13‐3 directly downregulates the expression of GmELF3b‐2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13‐3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13‐3 can be utilized for the breeding of high‐yield cultivars with a short maturity time suitable for high latitudes.