Previous studies indicated that several TN-QTL were more strongly detected at the 5- to 6-week-old seedling stage than at or after heading 18, 28, 29, 30, and further study showed that selection for increased tillering at 5- to 6-week-old vegetative stage resulted in increases in tillering at maturity, panicle number, and grain yield under drill-seeded field conditions 11. Studies using indica x japonica mapping populations have demonstrated high yield attributed to increases in tiller number (TN) coming from the indica parent 10, 18, 24, 25, 27, 28.
In general, japonica rice cultivars have fewer tillers compared to indica cultivars 9, 10, 24, 25, 26. Therefore, identifying QTLs that are robust across different genetic backgrounds and environments is of importance. However, although QTLs have been widely identified, studies have shown that tiller development is regulated by a complex network driven by genetic and hormonal factors (e.g., auxins, cytokinins, abscisic acid, gibberelins, and strigolactones) that are sensitive to environmental fluctuations 19, 20, 21, 22, 23. Progress has been made in identifying quantitative trait loci (QTLs) and genes important in production of tillers in rice that can be used in varietal improvement programs 9, 10, 11, 12, 13, 14, 15, 16, 17, 18. Tillering is a key determinant of grain yield and biomass in rice and tillering at an early vegetative stage is important for weed competition 8. However, because the indica sub-population has been demonstrated to have greater allelic diversity, it has been proposed as a means of improving tropical and temperate japonica based varieties 4, 5, 6, 7. rice breeding efforts have focused on these two genetic sub-populations with very limited utilization of germplasm from other gene pools 3. Cultivars grown in these two regions are derived from the Japonica sub-species primarily, tropical japonica, long grain cultivars in the Mid-south and temperate japonica-derived medium grain cultivars in the West 2. rice acreage is located in the Mid-south with the remainder in California 1. This knowledge of the QTLs, associated markers, candidate genes, and germplasm resources with high TN, RB and SB is of value to rice cultivar improvement programs. Two genes in the qRB peak target regions included an expressed protein and a WRKY gene. The genes identified from the peak target qTN regions included a carotenoid metabolism enzyme, a MYB transcription factor, a CBS domain-containing protein, a SAC3/GANP family protein, a TIFY motif containing protein, and an ABC transporter protein. Moreover, qTN3-1 was consistently significant across different developmental stages and growing environments. Multiple linear regression further indicated that qTN1-2, qTN3-3, qTN4-1, qRB3-1, and qRB5-1 were significant at the maximum tillering stage while qTN3-2 was detected only at the harvest stage. Across these three studies, we discovered six qTNs, two qRBs, and three qSBs. Here, we mapped tiller and biomass QTLs with ~ 250 recombinant inbred lines derived from a ‘Francis’ by ‘Rondo’ cross using data collected at the maximum tillering stage from two years of greenhouse study, and further compared these QTLs with those mapped at the harvest stage from a field study. However, little information is available on quantitative trait loci (QTLs) associated with tiller number ( qTN), root biomass ( qRB), and shoot biomass ( qSB) at the active tillering stage which occurs approximately 6 weeks after planting. Tillering at the vegetative stage is associated with weed competition, nutrient uptake, and methane emissions. Tillering and plant biomass are key determinants of rice crop productivity.