Identification of a novel QTL for grain number per panicle employing NGS-based QTL-seq approach in rice (Oryza sativa L.)

The grain number is one of the highly complex and crucial traits determining the grain yield in rice. To identify grain number QTLs in rice, we employed the QTL-seq approach in the 297 F population derived from the cross between BPT5204 and NLR33892. In this investigation, five regions viz., qGN1, qGN3, qGN7, qGN9, and qGN12 on chromosomes 1,3,7,9, and 12, respectively, were identified as QTLs governing grain number per panicle in rice. To verify the QTLs identified in the present study, traditional QTL mapping was carried out using InDel markers and previously reported SSRs in the QTL region. From qGN12 QTL, RM6953 showed a significant association with the number of grains per panicle with a phenotypic variance of 24.58, 22.10, and 17.20% in F, F and BCF populations, respectively, at < 0.0001 P value, indicating major QTL. From genome resequencing data, a missense variance was observed in the exonic region of LOC_Os12g39330 gene controlling AP2 domain-containing protein which plays an important role in seed development in rice. Hence, this QTL can be a potential target for map-based cloning and marker-assisted transfer to enhance the grain number in rice.