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Journal of Integrative Agriculture  2022, Vol. 21 Issue (11): 3230-3244    DOI: 10.1016/j.jia.2022.08.129
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum
LIU Lei1, WANG Heng-bo1, LI Yi-han1,2, CHEN Shu-qi1, WU Ming-xing1, DOU Mei-jie1, QI Yi-yin1, FANG Jing-ping3, ZHANG Ji-sen1,2
1 Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R.China

2 State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, P.R.China

3 College of Life Sciences, Fujian Normal University, Fuzhou 350007, P.R.China

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Sugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection.  The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes.  However, these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes.  In this present study, 744 305 and 361 638 candidate SSRs were identified from the genomes of Sofficinarum and Sspontaneum, respectively.  We verified the reliability of the predicted SSRs by using 1 200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including Sspontaneum, Sofficinarum, Srobustum, and modern sugarcane hybrid.  The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions.  Furthermore, 100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.  A total of 320 alleles were generated using 100 polymorphic primers, with each marker ranging from two to seven alleles.  The genetic diversity analysis revealed that these accessions were distributed in four main groups, including group I (14 Sspontaneum accessions), group II (two Sofficinarum accessions), group III (18 modern sugarcane hybrid accessions), and group IV (five Srobustum accessions).  Experimental verification supported the reliability of the SSR markers based on genome-wide predictions.  The development of a large number of SSR markers based on wet experiments is valuable for genetic studies, including genetic linkage maps, comparative genome analysis, genome-wide association studies, and marker-assisted selection in Saccharum.

Keywords:  Saccharum        genome-wide        simple repeat sequences (SSR)        microsatellite        molecular markers  
Received: 28 January 2022   Accepted: 14 July 2022
Fund: This work was supported by the National Key Research and Development Program of China (2021YFF1000101-5), the Science and Technology Planting Project of Guangdong Province, China (2019B020238001), the Natural Science Foundation of Fujian Province, China (2019J05066), the National Natural Science Foundation of China (41906096), and the Guangdong Laboratory for Lingnan Modern Agriculture and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, China.  
About author:  Correspondence FANG Jing-ping,; ZHANG Ji-sen, E-mail:

Cite this article: 

LIU Lei, WANG Heng-bo, LI Yi-han, CHEN Shu-qi, WU Ming-xing, DOU Mei-jie, QI Yi-yin, FANG Jing-ping, ZHANG Ji-sen. 2022. Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum. Journal of Integrative Agriculture, 21(11): 3230-3244.

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