Two Novel QTLs for the Harvest Index that Contribute to High-Yield Production in Rice (Oryza sativa L.)

BACKGROUND: The harvest index (HI) is a measure of the biological success of forming harvestable products. However, our understanding of the genetic basis of HI in rice (Oryza sativa L.) is limited, because it is a complex trait consisting of various yield-related traits and physiological attributes. YTH183 is a high-yielding line with large panicles and high HI derived from a cross between the Indica Group variety IR 64 and the NPT line IR 69093-41-2-3-2 (YP5). RESULTS: Here, we detected two novel QTLs for HI, designated qHI5.1 on chromosome 5 and qHI8.1 on chromosome 8, by using 155 recombinant inbred lines (RILs) derived from the cross between IR 64 and YTH183. The YTH183 allele at qHI5.1 contributed to a wide grain, resulting in heavy grain weight and panicle weight, and was consistently effective under the different environmental conditions of subtropical (Ishigaki) and temperate (Tsukuba) regions. Genetic polymorphism revealed that qHI5.1 was identical to GSE5/GW5, which is known to control the grain weight. On the other hand, although qHI8.1 functioned additively with qHI5.1 for higher HI, it did not show any significant effect on grain or panicle weight. In addition, its effects on HI were shown only in the first seasons at Ishigaki but not at Tsukuba or in the second season at Ishigaki. CONCLUSION: Our results indicate that qHI5.1 controls the grain size, regardless of whether environmental conditions are of subtropical or temperate regions, while qHI8.1 might be involved in controlling the physiological processes of source ability or the translocation of photosynthesis products from vegetative organs to grains depending on environmental conditions during the maturing stage. These QTLs will be useful genetic resources for future breeding programs to break through the ceiling of maximum yield in Indica Group varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-021-00456-1.