biostudies-literatureYun PNational Key R&D Program of China11https://www.ebi.ac.uk/biostudies/studies/S-EPMC10828150biostudies-literatureUnknown44(2)Grain size is an important appearance quality trait in rice, which also affects grain yield. In this study, a recombinant inbred line (RIL) population derived from a cross between <i>indica</i> variety 9311 and <i>japonica</i> variety Cypress was constructed. And 181 out of 600 RILs were sequenced, and a high-density genetic map containing 2842 bin markers was constructed, with a total map length of 1500.6 cM. A total of 10 quantitative trait loci (QTL) related to grain length (GL), grain width (GW), grain length-to-width ratio (LWR), and 1000-grain weight (TGW) were detected under two environments. The genetic effect of <i>qGL4</i>, a minor QTL for GL and TGW, was validated using three heterogeneous inbred family (HIF) segregation populations. It was further dissected into two closed linkMolecular breeding : new strategies in plant improvementIdentification of <i>qGL4.1</i> and <i>qGL4.2</i>, two closely linked QTL controlling grain length in rice.PMC108281502021YFD1200500Xia JLi ZZhang CMa TWang YYun PZhou KfalseIdentification of <i>qGL4.1</i> and <i>qGL4.2</i>, two closely linked QTL controlling grain length in rice.Grain size is an important appearance quality trait in rice, which also affects grain yield. In this study, a recombinant inbred line (RIL) population derived from a cross between <i>indica</i> variety 9311 and <i>japonica</i> variety Cypress was constructed. And 181 out of 600 RILs were sequenced, and a high-density genetic map containing 2842 bin markers was constructed, with a total map length of 1500.6 cM. A total of 10 quantitative trait loci (QTL) related to grain length (GL), grain width (GW), grain length-to-width ratio (LWR), and 1000-grain weight (TGW) were detected under two environments. The genetic effect of <i>qGL4</i>, a minor QTL for GL and TGW, was validated using three heterogeneous inbred family (HIF) segregation populations. It was further dissected into two closed link2024-01-01T00:00:00Z2024 Feb2025-04-04T14:05:39.948Z2025-04-04T14:05:39.948ZS-EPMC108281503830438210.1007/s11032-024-01447-y