Identification of QTLs associated with tillering and root biomass that are robust across different developmental stages and environments in rice

Authors: Barnaby, Jinyoung; McClung, Anna; Edwards, Jeremy; Jackson, Aaron; Pinson, Shannon

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2022
Publication Date: 8/3/2022
Citation: Barnaby, J.Y., McClung, A.M., Edwards, J., Jackson, A.K., Pinson, S.R. 2022. Identification of QTLs associated with tillering and root biomass that are robust across different developmental stages and environments in rice. Scientific Reports. https://doi.org/10.1038/s41598-022-17109-y.
DOI: https://doi.org/10.1038/s41598-022-17109-y

Interpretive Summary: Rice is a major agronomic crop for more than half the world's population. Tillering is a key determinant of grain yield and biomass in small grain crops. Another important agronomic trait is the root system which is responsible for water and mineral uptake, competition with weeds, and tolerance to some biological pests. Exploring the interrelationship of tillering, shoot biomass and root biomass is integral to understanding productivity in rice as well as the interaction of the rice plant with the environment. Although progress on identifying quantitative trait loci (QTL) and genes important in production of tillers and root volume in rice has been made, exploring more QTLs using different genetic backgrounds and environments is of importance as these traits are regulated by a complex network driven by genetic and environmental factors. In this study, we evaluated a population of offspring derived from a cross of a high yielding indica cultivar originating from China, Rondo, and the US tropical japonica cultivar, Francis, to determine if novel indica-derived QTL could be determined that would be useful in improving productivity in US rice germplasm. Some 260 progeny were evaluated in two greenhouse studies at the six week old vegetative tillering stage and in one field study with plants evaluated at maturity. The offspring progeny were evaluated for tiller number (TN), root biomass (RB), and shoot biomass (SB) and were genotyped using 7000 genetic markers resulting in eleven QTL being identified for these traits. The robustness of QTLs across the two different plant developmental stages was determined and genes were identified that may be directly related to these chromosomal regions associated with TN, RB, and SB. The detected QTL provide an understanding of the genetic and physiological mechanisms underlying these traits, and can be used by breeders to develop high yielding rice varieties.

Technical Abstract: 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 qTN, two qRB, and three qSB. 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 QTL 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.