Oryza sativa cultivar:Dongnong422 and Kongyu131 Raw sequence reads. Oryza sativa cultivar:Dongnong422 and Kongyu131

An evaluation of cold tolerance was performed on the experimental farm of Northeast Agricultural University, Harbin, China (47°98′N, 128°08′E) in 2014, 2015 and 2016. The parents and RIL populations were grown in a randomized block design with two replications of double row plots, a 2-m row length, a 30-cm row spacing and a 10-cm hill spacing. The 190 RILs were divided into three groups, early maturing, middle-maturing and late-maturing groups, according to their heading dates. DN422 belongs to the late-maturing group, and KY131 belongs to the early maturing group. For the evaluation of cold tolerance, each group was irrigated with 17°C water in an irrigated pool (25 m × 5 m) independently from the panicle initiation stage (approximately 35 days after transplanting for the early maturing group, approximately 40 days after transplanting for the middle-maturing group, and approximately 45 days after transplanting for the late-maturing group) to the full heading stage. When the auricle of the flag leaf is approximately 5 cm below the auricle of the penultimate leaf on each plant, the pollen should have undergone meiosis, which was indicative of panicle initiation stage (Satake and Hayase 1970). Water at 17°C was prepared in a storage pool with a cool and warm water mixture measured by the temperature sensors. Flood irrigation was performed from the inlet to the outlet (5 m) of the irrigated pool. The depth of the irrigated water was 18-20 cm, and the irrigated time was from 8 a.m to 16 p.m every day.The percent seed set under the cold-water treatment (PSST), the ratio of the number of fertile seeds in the number of total seeds, was used as the index of cold tolerance. A basic statistical analysis was implemented by the SPSS16.0 software (SPSS Inc., Chicago, IL, USA). The extreme cold-tolerant and sensitive plants in the RIL population used for Seq-BSA were selected according to the mean data of F7, F8 and F9 RILs.