Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

Abstract

Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites.

Genome-wide characterization of simple sequence repeats in Palmae genomes

“…Of dinucleotide SSRs, the (AT) n motif was the most frequent in all examined genomes except for P. dactylifera, and this trend was similar in dicots (Sonah et al 2011), pineapple (Fang et al 2016), cucumber (Cavagnaro et al 2010), and sweet orange (Biswas et al 2014). The most abundant dinucleotide repeat in P. dactylifera was (AG) n , which is consistent with previous findings in Brachypodium distachyon (Sonah et al 2011), wheat (Deng et al 2016), and garden asparagus (Li et al 2016). Among trinucleotide SSRs, the (AAT) n motif was the most predominant in C. nucifera, C. simplicifolius, and E. guineensis, and consistent with reports from garden asparagus (Li et al 2016), cucumber (Cavagnaro et al 2010), pineapple (Fang et al 2016), and Medicago truncatula and Populus trichocarpa (Sonah et al 2011).…”

“…However, in plants, grass genomes are known to have high GC content compared to other angiosperm families (Barow and Meister 2002;Šmarda and Bureš 2012). This study found the five palm genomes analyzed had lower GC content (28.12-39.65%) than do grasses (43.57-46.90%) (Singh et al 2016), a number of Poaceae species (Deng et al 2016), five monocots (43.57-46.14%), and two green algae (55.70 and 63.45%) (Zhao et al 2014). In addition, GC content was not evenly distributed in three of the species, the exceptions being C. nucifera and E. guineensis ( ∼ 32%).…”

“…The high mutation rates of SSRs make them highly informative and useful for a wide range of applications such as evolutionary research, population genotyping, and markerassisted breeding. Recent studies have utilized genomewide approaches for the development of SSR markers in plants (Shi et al 2014;Deng et al 2016;Kumari et al 2019). Perhaps the main advantage of this strategy is to produce a large number of SSR markers distributed evenly throughout the genome.…”

Detection and application of genome-wide variations in peach for association and genetic relationship analysis

“…Therefore, the discovery and distribution analysis of SVs will accelerate our rapid identification of candidate genes within the previous location using linkage analysis and GWAS. Furthermore, the density of SSRs (634.43 per Mb) identified in this study was higher than that in cucumber (552 SSR/Mb) [24], watermelon (111 SSR/Mb) [8], and most species of Triticeae (96~668 SSRs/Mb) [25]. The abundance of SSRs in peach can facilitate the genetic research of this species.…”

Fingerprint analysis of Bombyx mori local variety resources based on SSR markers

“…SSR is widespread throughout various eukaryotic genomes, and there are many reports [25][26][27] on the use of SSR to research species revolution and classification. As can be seen from dozens of species of animals and plants concerned, the SSR technique can quicken material classification and identification accurately.…”