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

Background Genetic transformation of indica rice ( Oryza sativa ssp. indica ) is limited by callus browning, which results in poor in vitro tissue culturability. Elucidating the genes in common wild rice ( Oryza rufipogon Griff.) that control callus browning is fundamental for improving the tissue culturability of indica rice varieties. Methods and results 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. We evaluated callus browning based on the indices of callus browning rate (CBR), callus browning index (CBI), and standard callus browning index (SCBI). Conclusions We detected 30 QTLs associated with callus browning across all lines, mapping to chromosomes 1, 2, 3, 4, 8, 9, and 12. These genomic regions were repeatedly associated with differences in CBR, CBI, and SCBI. The alleles from DXCWR showed additive effects in reducing callus browning. We identified new QTLs near the markers RM247 and RM7003 on chromosome 12, indicating that these QTLs are unique to DXCWR. Furthermore, we identified six introgression lines with significantly lower callus browning. These lines will be useful germplasms for genetic transformation and fine-mapping of the culturability trait.