Decoding multi-QTL networks and candidate genes for rice grain size qGW5 using chromosomal segment substitution line Z525

Grain size is difficult to research due to its complex inheritance, which is usually controlled by multiple genes in traditional populations. Single segment substitution lines (SSSLs) are ideal materials for the genetic studying of these complex traits and breeding by design owing to their favorable quantitative trait loci (QTL) in the uniform genetic background. Here, we constructed a new rice (Oryza sativa L.) short-wide grain chromosomal segment substitution line Z525 with four substitution segments from R232 in the genetic background of Xihui18. Then, an F₂ population from Xihui18/Z525 was used as a segregation population to map QTL for grain size by mixed linear model method. In total, four QTL were detected, and four SSSLs (S1–S4) and five dual-segment substitution lines (DSSLs, D1–D5) were developed, and within them 15 QTL (qGL5, qGW5, qRLW5, qGWT5, qGW3, qRLW3, qGWT3, qGL4, qGW4, qRLW4, qGWT4, qGL7, qGW7, qRLW7, and qGWT7) were associated with grain size. Again, the genetic models of various QTL for grain size were revealed. Interaction of qGW3 (a = 0.09 mm) and qGW4 (a = 0.04 mm) in D1 produced −0.04 mm of epistatic effect; qGW3 (a = 0.09 mm) and qGW5 (a = 0.16 mm) belonged to independent inheritance in D2. Finally, by overlapping substitution mapping and DNA sequencing, we identified a novel qGW5, different from the reported GW5 (5.73 Mb), within an estimated interval of 1.10 Mb of Chr.5. LOC_Os05g12260, LOC_Os05g12570, and LOC_Os05g13950 are possible candidates for qGW5.