Research Article: Resequencing and variation identification of whole genome of the japonica rice variety “Longdao24” with high yield

Date Published: July 17, 2017

Publisher: Public Library of Science

Author(s): Shukun Jiang, Shichen Sun, Liangming Bai, Guohua Ding, Tongtong Wang, Tianshu Xia, Hui Jiang, Xijuan Zhang, Fengming Zhang, Aimin Zhang.


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.

Partial Text

Given continuing population growth and increasing competition for arable land between food and energy crops, the next century may witness serious global food shortage problems. Thus, there is a need for an increase in rice yield, because rice is the world’s most important staple food crop. To substantially increase rice yield, Japan initiated a super high-yielding rice breeding program in 1981 that was targeted to raise rice yield 50% within 15 years. However, this target has not yet been realized [1, 2]. Next, the International Rice Research Institute (IRRI) launched a new plant-type breeding program to develop super rice in 1989, with the target of developing a super rice. However, this target was not reached either [1–3]. In order to meet the food demand required by the Chinese people in the 21st century, a program to breed super rice through combining morphological improvement and the utilization of inter-subspecific heterosis was set up by the Ministry of Agriculture and the Ministry of Science and Technology in 1996 and 1997, respectively [1, 2, 4]. Today, nearly 80 super rice varieties have been released and some of them show high grain yields of 12–21 t/hm2 in field experiments [4]. The core of super rice breeding is an effective use of germ plasma resources and favorable genes. For example, most of the northern japonica super rice varieties have DEP1 gene, which controlled large erect panicle [5, 6]. Although a large progress about the genetic basis for yield, grain quality and heading date of super rice had achieved [5–7], but the molecular mechanism is still poorly understood.




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