Identification of QTLs controlling low-temperature germination of the East European rice (Oryza sativa L.) variety Maratteli

Germinability under low temperature is one of the most important traits in seedling establishment in direct-sowing culture of rice. The objective of this study was the identification of genes responsible for higher and faster germination under low temperature, with the aim of breeding new rice varieties for direct-sowing culture. We identified four quantitative trait loci (QTLs) responsible for germination properties under low temperature in an East European rice variety, Maratteli. Maratteli-derived alleles at qLTG3-1 and qLTG3-2 on chromosome 3 and qLTG11-1 on chromosome 11 increased germination rate under low temperature. In contrast, the Maratteli allele at qLTG1-1 on chromosome 1 reduced the rate. Near-isogenic lines (NILs) with the Akitakomachi genetic background harboring qLTG3-1 and qLTG11-1 alleles from Maratteli accelerated germination and a NIL with qLTG1-1 delayed germination under low temperature, resulting in enhanced or suppressed germination rates, respectively. These QTLs altered the germination profile of Akitakomachi. Hence, Maratteli is a better source of genes for the improvement of germination under low temperature. We conclude that the low temperature germinability of various Japanese varieties inferior in this character can be improved by marker-assisted selection without modification of other superior traits. These NILs may also contribute to uncovering the molecular mechanisms of cold tolerance at the germination stage.