A domestication-selected enhancer coordinates source-sink balance to improve harvest index and yield in maize

Crop yield is fundamentally determined by the harvest index, the proportion of photosynthates allocated to grain. However, its genetic and evolutionary basis remains elusive. Here, we show that the maize harvest index increased by 81% during domestication. A major locus, Harvest Index1 (HI1), contributes to this divergence and is controlled by a 9.1-kb presence/absence variation. This insertion acts as a distant enhancer to boost the expression of the downstream B-type response regulator BRR1 and was fixed by selection. Mechanistically, the transcription factor CONZ1 binds to both the HI1 enhancer and the BRR1 promoter, recruiting the acetyltransferase General Control Nonrepressed 5 (GCN5) to form a chromatin loop that enhances BRR1 expression. BRR1 directly activates genes involved in carbon and nitrogen metabolism and transport, promoting source-to-sink allocation to increase harvest index and grain yield even under nitrogen-limiting conditions. Our findings elucidate a key domestication-selected regulatory module that coordinates resource allocation, providing a strategic target for sustainable crop improvement.