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.