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, 744305 and 361638 candidate SSRs were identified from the genomes of S. offcinarum and S. spontaneum, respectively. We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including S. spontaneum, S. offcinarum, S. robustum, 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 S. spontaneum accessions), group Ⅱ(two S. offcinarum accessions), group Ⅲ(18 modern sugarcane hybrid accessions), and group Ⅳ (five S. robustum 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.

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

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 350002,P.R.China;State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources&Guangxi Key Laboratory for Sugarcane Biology,Guangxi University,Nanning 530004,P.R.China;College of Life Sciences,Fujian Normal University,Fuzhou 350007,P.R.China

农业科学学报（英文）

[1]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-.Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum)[J].农业科学学报（英文）,2022(11):3230-3244

offcinarum,robustum

Genome,wide,development,interspecific,microsatellite,markers,Saccharum,officinarum,spontaneum,Sugarcane,has,large,complex,polyploid,that,hindered,progress,genomic,research,molecular,assisted,selection,user,friendly,have,attracted,considerable,attention,owing,their,ideal,genetic,attributes,However,these,were,not,characterized,developed,scale,due,previously,lacking,high,quality,chromosome,level,assembled,sugarcane,genomes,In,this,study,candidate,SSRs,identified,from,respectively,We,verified,reliability,predicted,by,using,pairs,detect,polymorphisms,among,representative,accessions,including,modern,hybrid,results,showed,displayed,Furthermore,randomly,selected,diversity,total,alleles,generated,polymorphic,primers,each,ranging,two,seven,analysis,revealed,distributed,four,main,groups,five,Experimental,verification,supported,predictions,number,wet,experiments,valuable,studies,linkage,maps,comparative,association

0.47364