Photoperiod-insensitive E1–E4 alleles prolong the reproductive phase and enhance yield in short-season soybean grown in subtropical regions

Photoperiod sensitivity regulates the latitudinal adaptation of short-day soybean. In sub-tropical regions, monsoon sowing under progressively shortening day lengths often restricts growth, necessitating long juvenile photoperiod-sensitive cultivars. However, the role of major photoperiod-regulating maturity genes in determining flowering behaviour and reproductive duration across latitudinal gradients remains insufficiently understood. To address this gap, near-isogenic lines (NILs) carrying recessive alleles at the E1, E2, E3, and E4 loci were developed in the genetic background of the highly photosensitive soybean variety SL 958 (E1E2E3E4). Multi-location trials across latitudes showed that recessive alleles at these loci reduced days to flowering (R1) without affecting maturity (R8) at higher latitudes, thereby extending the mean reproductive period by 17%. Early flowering in NILs did not reduce vegetative biomass, as vegetative growth continued into the reproductive phase, resulting in greater reproductive development and 27–126% higher grain yield per plant compared with SL 958. A photothermal sensitivity index (PTSI) based on average photoperiod and growing degree days (GDD) across latitudes showed that e1- and e3-NILs were the least sensitive to environmental variation, with PTSI values 30.4% (688.6) and 52.3% (472.2) lower than the recurrent parent SL 958 (988.9), respectively. These results demonstrate that extending the reproductive period through modification of photoperiod genes can improve yield potential in short-season rainfed soybean systems of sub-tropical regions.