Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

Abstract

Recently-developed molecular markers are becoming powerful tools, with applications in crop genetics and improvement. Microsatellites, or simple sequence repeats (SSRs), are widely used in genetic fingerprinting, kinship analysis, and population genetics, because of the advantages of high variability from co-dominant and multi-allelic polymorphisms, and accurate and rapid detection. However, more recent evidence suggests they may play an important role in genome evolution and provide hotspots of recombination. This review describes the development of SSR markers through different techniques, and the detection of SSR markers and applications for sugarcane genetic research and breeding, such as cultivar identification, genetic diversity, genome mapping, quantitative trait loci (QTL) analysis, paternity analysis, cross-species transferability, segregation analysis, phylogenetic relationships, and identification of wild cross hybrids. We also discuss the advantages and disadvantages of SSR markers and highlight some future perspectives.

Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid Biosynthesis Genes

“…SSR markers (microsatellites) are widely used in genetic diversity studies, QTL and genetic mapping, molecular-assisted selection (MAS), and cultivar identification, because they are multi-allelic, co-dominant, highly informative, relatively accurate and easily detected [33]. SSR markers have been often used to map different types of Rubus [9,13], fingerprinting germplasm [34], and in studies of the genetic diversity and population structure within [28] and among [29] Rubus species.…”

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

“…Of the many available DNA markers, simple sequence repeats (SSRs) are commonly used for investigating plant genetics and breeding because they are widely distributed and abundant in plant genomes. They are also genetically codominant, highly reproducible, multi-allelic, and perfectly suitable for high-throughput genotyping [21][22][23][24][25]. Expressed sequence tag (EST)-derived markers in the genomic coding regions have an advantage over genomic DNA-derived markers, and can be efficiently amplified to reveal conserved sequences among related species [26].…”

Complete chloroplast genome of a rare and endangered plant species Osteomeles subrotunda: genomic features and phylogenetic relationships with other Rosaceae plants

“…SSR markers are tandemly repeated nucleotide sequence consisting copies of mono-, di-, tri-, or tetranucleotide motifs flanked by unique sequences (McCouch et al 1997). SSR sequences distribute in nuclear genomes, and they are widely used in genetic diversity analysis, linkage mapping studies, and marker-assisted breeding (Kaur et al 2015;Almontero and Espino 2016;Tian et al 2017;Ahmad et al 2018;Chao et al 2018). Likewise, CP genome sequences have been found to contain SSRs, and they have been increasingly used in both population genetic structure and evolutionary studies for their high polymorphism (Kikuchi et al 2013;Wheeler et al 2014;Fu et al 2016;Takahashi et al 2018).…”