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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (2): 316-321.doi: 10.3724/SP.J.1006.2019.82037

• RESEARCH NOTES • Previous Articles    

Development of molecular markers polymorphic between Dongxiang wild rice and Geng rice cultivar ‘Nipponbare’

Xiao-Ding MA1,Jiang-Hong TANG2,Jia-Ni ZHANG2,Di CUI1,Hui LI3,Mao-Mao LI3,*(),Long-Zhi HAN1,*()   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
    2 Chongqing Normal University, Chongqing 401331, China
    3 Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
  • Received:2018-07-09 Accepted:2018-10-08 Online:2019-02-12 Published:2018-11-06
  • Contact: Mao-Mao LI,Long-Zhi HAN E-mail:lmm3056@163.com;hanlongzhi@caas.cn
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0100101);This study was supported by the National Key Research and Development Program of China(2016YFD0100301);the National Natural Science Foundation of China(31501287);the National Natural Science Foundation of China(31671664);the National Key Technology Support Program of China(2015BAD01B01-1);the Agricultural Science and Technology Innovation Program of CAAS;the National Crop Germplasm Conservation Project(2017NWB036-01);the National Crop Germplasm Conservation Project(2017NWB036-12-2);and the National Crop Germplasm Resources Platform Project(NICGR2017-001)


Dongxiang wild rice is a type of common wild rice (Oryza rufipogon) that has the northernmost natural distribution of any wild rice species. The genome of Dongxiang wild rice differs from that of modern cultivated rice varieties (Oryza sativa). At present, a set of molecular markers that covers the entire genome of Dongxiang wild rice is lacking. In this study, we used Dongxiang wild rice and the Geng rice variety “Nipponbare” as research materials. By screening the existing collection of 1017 SSR and InDel markers and the 217 InDel markers which were designed using Dongxiang wild rice genome resequencing information, we obtained a set of 203 markers polymorphic between Dongxiang wild rice and ‘Nipponbare’, which were relatively uniformly distributed on the 12 rice chromosomes, and basically covered the entire genome, with an average inter-locus distance of 1.9 Mb. Through the genotyping of five Xian and five Geng varieties, we concluded that those 203 polymorphic molecular markers have a high application value in genotype analysis of Dongxiang wild rice and Geng rice offspring population. These results provide a powerful tool for exploring beneficial genes from Dongxiang wild rice as well as marker-assisted breeding and selection.

Key words: InDel marker, genome re-sequencing, Geng rice

Fig. 1

Screening of polymorphic molecular markers 1: Dongxiang wild rice; 2: Nipponbare; 3: artificial F1 hybrid between Dongxiang wild rice and Nipponbare; M: DNA size marker."

Table 1

Distribution of polymorphic molecular marker loci on 12 rice chromosomes"

Chromosome length (kb)
Number of marker
Mean interval
1 43270 23 1881
2 35937 22 1633
3 36413 30 1213
4 35502 17 2088
5 29958 16 1872
6 31248 18 1736
7 29697 16 1856
8 28443 13 2187
9 23012 14 1643
10 23207 9 2578
11 29021 13 2232
12 27531 12 2294

Fig. 2

Distribution of polymorphic molecular marker loci on rice chromosomes The numbers to the left of each chromosome indicate the physical locations of the marker loci in Mb."

Fig. 3

Genotyping of Xian and Geng cultivars by polymorphic molecular markers 1: Dongxiang wild rice; 2: Nipponbare; 3: Liaoyan 241; 4: Songgeng 8; 5: Jigeng 88; 6: Huaidao 9; 7: Hexi 6; 8: Huanghuazhan; 9: Baiyusimiao; 10: Yangdao 6; 11: Xiangwanxian 12; 12: Ezhong 5."

Table 2

Consensus analysis of genotype identification of Xian and Geng cultivars using the polymorphic molecular markers"

Number of
Number of Dongxiang wild rice genotype
Number of Nipponbare genotype
Number of heterozygous genotype
Number of others
295 (5×59) 34 (11.6%) 250 (84.7%) 6 (2.0%) 5 (1.7%)
295 (5×59) 218 (73.9%) 40 (13.5%) 5 (1.7%) 32 (10.9%)
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