Mapping quantitative trait loci associated with callus browning in Dongxiang common wild rice (Oryza rufipogon Griff.)

Abstract Background: The genetic transformation of indicarice (Oryza sativa ssp. indica) is limited by its poor in vitro tissue culturability, especially callus browning. Elucidating the common wild rice (Oryza rufipogon Griff.) genes controlling callus browning is a literally fundamental method for improving the tissue culturability of indica rice varieties. Methods and results: In the present study, we used a population of 129 O. rufipogon (Dongxiang common wild rice; DXCWR) introgression lines in the elite cultivar GC2 (Oryza sativa ssp. indica) background and 159 simple sequence repeat (SSR) markers to identify quantitative trait loci (QTLs) associated with callus browning in rice. The callus browning phenotype was evaluated using the indices of the callus browning rate (CBR), callus browning index (CBI), and standard callus browning index (SCBI). Conclusions: We detected 30 QTLs associated with callus browning across the genotypes, which were located on chromosomes 1, 2, 3, 4, 8, 9, and 12. These were repeatedly associated with differences in CBR, CBI, and SCBI. The alleles from DXCWR had an additive effect in reducing callus browning. Especially, we identified new QTLs near RM247 an RM7003 on chromosome 12, indicating the QTLs were unique in DXCWR. Furthermore, we identified six introgression lines with significantly reduced callus browning, which is expected that these lines will be useful materials for the genetic transformation and fine mapping of the culturability trait.