Jiang Shukun, Sun Shichen, Bai Liangming, Ding Guohua, Wang Tongtong, Xia Tianshu, Jiang Hui, Zhang Xijuan, Zhang Fengming
Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China.
PLoS One. 2017 Jul 17;12(7):e0181037. doi: 10.1371/journal.pone.0181037. eCollection 2017.
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.
粳稻主要分布在中国北方，占中国粳稻种植总面积的一半以上。高产、优质和早熟是该地区粳稻的主要育种性状和商业特性。我们利用Illumina测序技术对一个典型的北方粳稻品种龙稻24及其亲本（龙稻5和吉粳83）进行了重测序和全基因组变异分析。共产生了53.17 G的clean碱基，超过96.8%的reads被映射到基因组参考序列上。实现了平均有效深度为43.67×的覆盖。以粳稻品种日本晴的基因组序列为参考，我们在龙稻24基因组中鉴定出420,475个单核苷酸多态性（SNP）、95,624个插入缺失（InDel）和14,112个结构变异（SV）。我们在龙稻24基因组和龙稻5基因组之间鉴定出361,117个SNP和81,488个InDel。我们还在龙稻24基因组和吉粳83基因组之间检测到428,908个SNP和97,209个InDel。对龙稻24中的22个产量相关基因、22个品质相关基因和39个抽穗期基因进行了分析。Gn1a、EP3、SCM2、Wx、ALK、OsLF和Hd17的等位基因来自母本龙稻5。qGW8、SSIVa、SBE3、SSIIIb、SSIIc、DTH2、Ehd3和OsMADS56的其他等位基因来自父本吉粳83。这些结果将有助于我们研究中国北方水稻产量、品质和早熟的遗传基础。
