Fine mapping of cisc(t), a gene for cold-induced seedling chlorosis, and identification of its candidate in rice

The seedlings of indica rice cultivar Dular are susceptible to chlorosis under low temperature conditions. Our previous studies indicated that low temperature-induced seedling chlorosis is controlled by a recessive gene, located between SSR markers RM257 and RM242, on the long arm of chromosome 9. We temporarily named the gene cisc(t). Using a large F₂ population derived from a cross between Dular and the japonica cultivar Lemont, which displays a normal green color at low temperatures, cisc(t) was fine mapped to within a 12-kb interval. There is only one annotated gene in this interval, which encodes a pentatricopeptide repeat (PPR) protein. Sequence analysis indicated that 8 bases were deleted at the 60th base in the Dular allele, resulting in a frame-shift mutation and loss of function of the gene. This is consistent with the chlorosis mutant phenotype of Dular. In addition, previous studies have shown that many chlorosis mutants of seedlings are related to PPR proteins. Hence, we presume that the PPR gene is the candidate for cisc(t).