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Japonica  rice mainly distributes in north of China, which accounts for more than half of the total  japonica  rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern  japonica  rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the  japonica  cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of  Gn1a ,  EP3 ,  SCM2 ,  Wx ,  ALK ,  OsLF  and  Hd17  came from the female parent Longdao5. The other alleles of  qGW8 ,  SSIVa ,  SBE3 ,  SSIIIb ,  SSIIc ,  DTH2 ,  Ehd3  and  OsMADS56  came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China.

Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield