Identification of qTGW2, a Minor-Effect QTL Controlling Grain Weight in Rice

Grain weight and grain shape are key traits affecting grain yield and quality in rice. In this research, a quantitative trait locus (QTL), qTGW2, that controls 1000-grain weight (TGW), grain length (GL), and grain width (GW) in rice, was fine-mapped within an 84.7 kb region on chromosome 2 using three sets of near isogenic lines (NILs) originated from the indica rice cross, Teqing (TQ)/IRBB52. In the NIL populations, the TGW, GL, and GW of the IRBB52 homozygous lines increased by 0.22 g, 0.020 mm, and 0.009 mm compared with the TQ homozygous lines. Four annotated genes showed nucleotide polymorphisms between the two parental lines in the qTGW2 region. Only one annotated gene, LOC_Os02g57660, exhibited significant expression differences between NILTQ and NILIRBB52 in the young panicles performed by RNA sequencing and the quantitative real-time polymerase chain reaction. These results indicated that LOC_Os02g57660, which encodes phosphatidylinositol-4-phosphate 5-kinase (PIP5K), was the candidate gene of qTGW2. Then, one insertion-deletion (InDel) was found in the LOC_Os02g57660 coding region. The haplotype analysis was performed based on the phenotypic data of 4720 rice accessions from RiceVarMap V2.0. Two haplotypes, Hap1 (TQ-type) and Hap2 (IRBB52-type), were classified according to one InDel. Significant differences in grain weight traits were identified between Hap1 and Hap2. Hap2 has greater GL and RLW but lower GW, thus exhibiting potential to simultaneously improve grain yield and quality.