Uncovering QTLs for uppermost internode length and panicle exsertion in rice (Oryza sativa L.)

Uppermost internode length (UIL) and panicle exsertion are two important traits that contribute significantly to increased yield in rice. The present study was conducted using recombinant inbred lines (RILs) comprising 201 lines derived from RTN10B and IRG213. These RILs were evaluated at three different locations— Delhi, Karnal, and Aduthurai. We report the mapping of quantitative trait loci (QTLs) for uppermost internode length and the panicle exsertion ratio (PER), as well as QTLs for plant height (PH), tiller number, length of the second internode, length of the third internode, length from the flag leaf to the panicle tip (PFL), and panicle length (PL). Mapping was performed using a custom microsatellite linkage map constructed for the population, having a total span of 2077.1 cM with 104 markers. A total of 22 QTLs were identified for various traits, among which 19 were found distributed in four hotspots. A total of 11 major effect QTLs and 11 minor effect QTLs were identified for various internode length-related traits. Among the four QTLs identified for PFL, three QTLs— qPFL1.1 , qPFL1.2, and qPFL2.1 —co-localized with previously reported QTLs, while qPFL8.1 was a novel QTL. A major QTL hotspot was identified on chromosome 1, located at the marker interval of RM12055-RM320. The size of the major QTL hotspot on chromosome 1 was 1.4 Mb and contained a total of seven HEs for PER, PFL, PH, PL, UIL, SIL, and TIL. Based on the in-silico analysis of the major QTL hotspot on chromosome 1, we identified 15 putative candidate genes associated with internode length- and panicle-related traits. Furthermore, narrowing the genomic region through the fine mapping of the marker intervals facilitated the identification of candidate genes to enable more precise marker-assisted selection for uppermost internode length and panicle exsertion.