Lam Thi Dinh, Yoshiaki Ueda, Daniel Gonzalez, Juan Pariasca Tanaka, Hideki Takanashi and Matthias Wissuwa.

Rice (2023) 16:37; doi.org/10.1186/s12284-023-00654-z

Abstract

The rice root system consists of two types of lateral roots, indeterminate larger L-types capable of further branching, and determinate, short, unbranched S-types. L-type laterals correspond to the typical lateral roots of cereals whereas S-type laterals are unique to rice. Both types contribute to nutrient and water uptake and genotypic variation for density and length of these laterals could be exploited in rice improvement to enhance adaptations to nutrient and water-limited environments. Our objectives were to determine how best to screen for lateral root density and length and to identify markers linked to genotypic variation for these traits. Using diferent growing media showed that screening in nutrient solution exposed genotypic variation for S-type and L-type density, but only the lateral roots of soil-grown plants varied for their lengths. A QTL mapping population developed from parents contrasting for lateral root traits was grown in a low-P feld, roots were sampled, scanned and density and length of lateral roots measured. One QTL each was detected for L-type density (LDC), S-type density on crown root (SDC), S-type density on L-type (SDL), S-type length on L-type (SLL), and crown root number (RNO). The QTL for LDC on chromosome 5 had a major efect, accounting for 46% of the phenotypic variation. This strong positive efect was confrmed in additional feld experiments, showing that lines with the donor parent allele at qLDC5 had 50% higher LDC. Investigating the contribution of lateral root traits to P uptake using stepwise regressions indicated LDC and RNO were most infuential, followed by SDL. Simulating efects of root trait diferences conferred by the main QTL in a P uptake model confrmed that qLDC5 was most efective in improving P uptake followed by qRNO9 for RNO and qSDL9 for S-type lateral density on L-type laterals. Pyramiding qLDC5 with qRNO9 and qSDL9 would be possible given that trade-ofs between traits were not detected. Phenotypic selection for the RNO trait during variety development would be feasible, however, the costs of doing so reliably for lateral root density traits is prohibitive and markers identifed here therefore provide the frst opportunity to incorporate such traits into a breeding program.

See https://thericejournal.springeropen.com/articles/10.1186/s12284-023-00654-z

Figure 4: Confirmation of allelic effects at qLDC5 in the BC1F6 generation by measuring L-type lateral root density on root samples excavated from the low-P field in Tsukuba in 2022. Different letters indicate significant differences and “n” indicates the number of lines classified into each allelic group