Two-year QTL dissecting of high harvest index and related traits in a novel rice variety Yuenongsimaio

High harvest index (HI), defined as the grain yield-to-biomass ratio (≥ 0.55), reflects a well-balanced source-sink relationship. It is a key trait in rice high-HI breeding programs, which has proven to be a successful strategy for developing super high-yield rice varieties. However, its genetic basis remains elusive. This study conducted QTL analysis for HI-related traits using a recombinant inbred line (RIL) population derived from a cross between a geng / japonica cultivar, Lijiangxintuanheigu (LTH), and a high HI xian / indica variety, Yuenongsimiao (YNSM). A high‑density genetic map with 6674 bin markers identified 97 QTLs across 12 HI-related traits, forming 13 QTL clusters that affect the source-sink related traits in rice. These bin markers were converted from 1,009,324 high-quality SNPs sourced from the sequenced RIL population. Notably, qRSC1 (QTL cluster of rice source capacity 1 ), which included qFLL1 , qSTW1 , qBM1.2 , and qHI1 , was tightly linked to the semi-dwarf gene sd1 and collectively shaped the high HI plant architecture of YNSM. In contrast, qRSC3 ( qFLL3 / qFLW3 / qSTW3 / qBM3.1 / qHI3.1 ) exhibited an opposite effect and positively regulated source-related traits. Among nine QTLs associated with yield per plant (YPP), only qYPP2.2 , part of qRSS2 (QTL cluster of rice sink size 2 ), was consistently detected over two consecutive years. qRSS2 governed sink size by integrating multiple yield-related QTLs, including qYPP2.2 . Overall, qRSC1 , qRSC3 , and qRSS2 collectively optimized source-sink balance, enabling YNSM’s high HI and high yields. These findings provide insights into the genetic basis of high HI in YNSM and may facilitate breeding high-yielding rice with superior HI. • YNSM, a novel high HI rice with large source/sink organs, has 97 QTLs forming 13 clusters affecting source-sink traits. • Notably, qRSC1 (source capacity QTL cluster), tightly linked to semi-dwarf gene sd1 , determines YNSM's plant architecture with high HI. • In contrast, qRSC3 exhibited an entirely opposite effects, positively impacting source-related traits. • qRSC3 and sink size QTL cluster qRSS2 act as key determinants for expanding source capacity and sink size, respectively, enabling YNSM to achieve high yield and maintain high HI. • Collectively, these three loci function synergistically to optimize source-sink balance, underpinning the high-yielding and high-HI plant architecture of YNSM.