Mapping QTLs controlling low-temperature germinability in rice by using single segment substitution lines derived from 4 AA-genome species of wild rice

Rice growth is sensitive to low temperature. Chilling injury is one of the main natural disasters in rice cultivation, and is damaging to rice growth at all developmental stages. Low-temperature germinability (LTG) is an important trait for seedling establishment, especially in rice direct-sowing practice. However, the genetic mechanism of LTG remains elusive. Here, we report the mapping of QTLs controlling LTG in rice using 586 single segment substitution lines (SSSL) derived from 4 AA-genome wild rice species. 21 SSSLs with the highest germination rate at low temperature in both of the two tested seasons were selected, from them 10 QTLs controlling LTG were identified by substitution mapping to locate on 6 chromosomes: chromosome 1, 3, 5, 7, 8 and 11, with an interval length of 3.45 to 20.15 cM. Five QTLs were detected from Niv-SSSls: qLTGn3-1 , qLTGn5-1 , qLTGn5-3 , qLTGn7-1 and qLTGn7-2 , their additive effects ranged from 3.72% to 19.74% in late season 2018. qLTGb1-1 and qLTGb8-2 were detected in the SSSLs with O. barthii as the donor and they accounted for at least 9.51% of the total phenotypic variation. Two QTLs, qLTGg5-2 and qLTGg8-1 , were derived from O. glumaepatula, and their average additive effects were 4.28% and 20.39% in late seasons 2018, respectively. qLTGm11-1 on chromosome 11 was the only QTL identified from O. meridionalis . All QTLs derived from wild rice species improved low-temperature germination significantly. The SSSL library with wild rice species as donor is therefore a valuable resource for rice germplasm innovation and the breeding of chilling-resistant varieties.