Dissection of Two QTL for Grain Size Linked on the Long Arm of Chromosome 5 in Rice

Abstract Background: Most agronomical traits of crops are complex traits controlled by several major quantitative trait locus (QTL) and many minor QTL. Grain size determines grain weight and influences rice appearance quality. Identification of minor QTL is important for understanding the genetic and molecular network regulating grain size in rice. Following previous identification of QTL for grain weight and size using populations derived from the Teqing/IRBB52 indica rice cross, one QTL, qTGW5/qGL5 having significant effects on grain weight and length, was targeted for validation, dissection and fine-mapping.Result: Firstly, the effect of qTGW5/qGL5 was validated using two near isogenic line (NIL) F2 populations. Then, qTGW5/qGL5 was dissected into two closely linked QTL for grain size using four sets of NILs with sequential segregating regions. One of them, qTGW5 with the IRBB52 alleles increased grain weight, length and width with the same allelic direction, was located within an 1896.4-kb region flanked by RM18865 and Fi25273. The other one, qGL5 controlling grain length, was further delimited into a 68.8-kb region using seven NIL-F2 populations. Six annotated genes were found in the qGL5 region, of which five showed nucleotide polymorphisms between the two parental lines. In three of the six annotated genes, significant expression differences were detected between qGL5-NILs.Conclusions: Two closely-linked QTL having small effects for grain size in rice were separated using NIL-derived populations. One of them, qGL5 was fine-mapped into a 68.8-kb region containing six annotated genes. Our work lays a foundation for cloning minor QTL for grain size and offers potential targets for marker-assisted breeding in rice.