Welcome to Chinese Journal of Tropical Crops,

Chinese Journal of Tropical Crops ›› 2020, Vol. 41 ›› Issue (4): 722-729.DOI: 10.3969/j.issn.1000-2561.2020.04.013

• Biotechnology and Tissue Culture • Previous Articles     Next Articles

Development, Characterization and Speciality of Microsatellite Markers in AP85-441 and R570 Genomic Reference Sequences

XU Zhijun1,2,3,ZHAO Sheng4,HU Xiaowen1,2,3,KONG Ran1,2,3,SU Junbo1,2,3,LIU Yang1,2,3,*()   

  1. 1. South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524091, China
    2. Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524013, China
    3. Guangdong Engineering Technology Research Center for Dryland Water-saving Agriculture, Zhanjiang, Guangodong 524013, China
    4. Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
  • Received:2019-06-06 Revised:2019-09-16 Online:2020-04-25 Published:2020-05-09
  • Contact: LIU Yang


Lacking of molecular markers is an important factor restricting the development of marker-based genetic and breeding research. In this study, 512 835 and 97 839 microsatellite sequence, which accounted for 0.32% and 0.35% of the genome, were identified based AP85-441 and R570 genomic reference sequences respectively, using the MISA software. In the genomes, the dominant repeat units were single nucleotide, dinucleotide and trinucleotide, and each repeat unit was dominated by AT-enriched elements. 472 117 and 89 748 loci of the genomes could be used to develop SSR markers. 16 691 and 13 271 homologous genes corresponding to sorghum chromosome 1-10 were identified by homology analysis on the genes of Saccharum spontaneum, sugarcane and sorghum, and 13 224 and 7624 pairs of SSR primers were developed by the gene sequence. In silico PCR analysis of these SSR markers revealed that the markers were mostly multilocus amplified in Saccharum spontaneum genome, and the effective markers in the two genomes were 79.35% and 36.13%, 79.01% and 93.36%, respectively. Part of the SSR markers showed specific amplification in the genomes. 1368 and 1420 SSR were specific single-locus amplification in AP85-441 and R570, respectively. 752 SSR were single-locus amplification in the two genomes, and the amplification sites and source genes of these SSR were distributed on all chromosomes in the genome. In this study, the SSR loci identified would be conducive to enriching the molecular markers of sugarcane, and the 3540 pairs of SSR primers developed will provide support for the determination of homologous linkage groups and group genetic origin in the construction of sugarcane genetic map.

Key words: sugarcane, microsatellite sequence, homologous gene, SSR marker, specific amplification

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