Identification of QTLs Associated With Tillering and Biomass in Rice That Are Robust Across Different Developmental Stages and Environments

Tillering and plant biomass are key determinants of rice crop productivity. In this study, quantitative trait loci (QTLs) associated with tiller number (qTN), root biomass (qRB), and shoot biomass (qSB) were mapped with ~260 recombinant inbred lines derived from a ‘Francis’ by ‘Rondo’ cross using data collected at the 6-week-old maximum tillering stage from 2 years of greenhouse study, and at the harvest stage from 1 year of field study. We discovered six qTNs, two qRBs, and three qSBs. Multiple linear regression further indicated that qTN1-2, qTN3-3, qTN4, qRB3, and qRB5 were robust at the maximum tillering stage while qTN3-2 was detected only at the harvest stage. Moreover, qTN3-1 was consistently significant across different developmental stages and growing environments. 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. Two genes in the qRB peak target regions included an expressed protein and a WRKY gene. These detected QTLs provide an understanding of the genetic and physiological mechanisms underlying these traits and can be used in breeding for rice varieties with increased plant productivity.