QTL identification for yield components using single segment substitution lines dissected by rice CSSL-Z799

As one of the world’s most important cereals, rice ( Oryza sativa L.) demands sustained yield improvement. However, this goal is challenging because yield components are complex quantitative traits governed by numerous minor-effect genes. To reveal this genetic complexity, Single Segment Substitution Lines (SSSLs) provide an ideal platform for gene identification and designed breeding. Here, we report on a Chromosome Segment Substitution Line (CSSL), Z799, containing 10 substitution segments from the restorer line R225 in the genetic background of Nipponbare. These substitution located on eight different chromosomes, with an average substitution length of 3.0 Mb. Z799 exhibited a complex yield-related phenotype relative to Nipponbare, with several traits being significantly altered. Genetic mapping in a secondary F 2 population of Nipponbare/Z799 uncovered 27 QTL, but a more efficient SSSL-based approach, which yielded five lines (S1-S5), detected a total of 35 QTL. All five SSSLs significantly enhanced grain length through distinct QTL ( qGL1 , qGL3 , qGL12-1 , qGL12-2 , qGL12-3 ) without compromising grain width. Mechanistically, microscopic observation of lemma cells revealed two divergent pathways: four QTL ( qGL1 , qGL3 , qGL12-1 , qGL12-2 ) increased grain length by promoting cell division, whereas qGL12–3 achieved the same effect by stimulating cell expansion. Our study thus not only identifies critical QTL for yield components but also elucidates their underlying cellular mechanisms, offering a platform for future gene cloning and designed breeding strategies.