Development of SSR markers and database based on genomes of sugarcane and its relatives
Sugarcane (Saccharum spp.hybrid) is an important crop for both sugar production and bioenergy.However,due to the complexity of the sugarcane genome,research in its population genetics has lagged behind other crops.Currently,the reference genome for sugarcane still requires significant improvements.The development of SSR (Simple Sequence Repeat) markers and databases based on the genomes of sugarcane and its relatives will be instrumental in advancing population genetics research.In this study,we identified SSRs from the genomes of three sugarcane species (Saccharum spontaneum,Saccharum officinarum,and Saccharum spp.hybrid) and two related species (Miscanthus sinensis and Sorghum bicolor).We quantified and categorized the SSRs for each genome,selecting those with high polymorphism for the genetic diversity analysis of 104 sugarcane-related mate-rials.A total of 1,860,645 SSRs were identified across the five genomes,with mononucleotide,dinucleotide,and trinucleotide repeats being the most common.Synteny analysis of SSRs across the genomes revealed the evolutionary relationships among species,with the kinship order from closest to most distant being:R570,Saccharum officinarum,Saccharum spontaneum,Miscanthus sinensis,and Sorghum bicolor.Genetic diversity analysis using SSR and InDel markers showed that Banmao 92-105 was the first to diverge from other samples,with Saccharum spontaneum forming a distinct group,Saccharum robustum and Sac-charum officinarum clustering together,and Saccharum spp.hybrid forming its own separate group.Additionally,we developed a web-based database for sugarcane SSRs,which includes the identified SSRs from the five genomes,along with corresponding primers and other related information.This study provides a valuable molecular tool for sugarcane research and breeding efforts.
万方数据
维普
