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.
Highlights
Sugarcane (Saccharum spp.) is a major global crop, required for the production of biofuels such as ethanol, but it produces 80% of total dietary sugar globally [1], and 92% of the sugar consumed in China [2]
We describe the development of and applications for simple sequence repeats (SSRs) in sugarcane genetic research and breeding, which we believe could be useful for future crop improvement programs
The presence of minor and non-specific products increases the difficulty of the identification of legitimate alleles; accurately calculating the size of an allele is difficult because of differences in migration between gel lanes, when size markers are in the outer lanes
Summary
Sugarcane (Saccharum spp.) is a major global crop, required for the production of biofuels such as ethanol, but it produces 80% of total dietary sugar globally [1], and 92% of the sugar consumed in China [2]. All commercial sugarcane breeding populations in the world share a narrow genetic base, due to their ancient origins from a small number of popular hybrids, such as POJ2878, Co419, and NCo310, which were developed in the early 1900s. These varieties were developed from complex interspecific hybridization through the Nobilization breeding process among wild clones of S. spontaneum and S. officinarum. Alternative approaches have been designed to reduce the time for SSR isolation and to substantially increase the number of SSR loci produced [24,25] These methods include: (i) Next-generation sequencing or high throughput sequencing, (ii) EST libraries search, and (iii) enriched-genomic libraries search. CTTTAACTTTAACTTTAA (B) Based on the arrangement of nucleotides in the repeat motifs: Perfect repeat
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