Characterization of Simple Sequence Repeat (SSR) Markers Mined in Whole Grape Genomes

Abstract

SSR (simple sequence repeat) DNA markers are widely used for genotype DNA identification, QTL mapping, and analyzing genetic biodiversity. However, SSRs in grapes are still in their early stages, with a few primer pairs accessible. With the whole-genome sequencing (WGS) of several grape varieties, characterization of grape SSR changed to be necessary not only to genomics but to also help SSR development and utility. Based on this, we identified the whole-genome SSR of nine grape cultivars (‘PN40024’, ‘Cabernet Sauvignon’, ‘Carménère’, ‘Chardonnay’, ‘Merlot’, ‘Riesling’, ‘Zinfandel’, ‘Shine Muscat’, and ‘Muscat Hamburg’) with whole-genome sequences released publicly and found that there are great differences in the distribution of SSR loci in different varieties. According to the difference in genome size, the number of SSRs ranged from 267,385 (Cabernet Sauvignon) to 627,429 (Carménère), the density of the SSR locus in the genome of nine cultivars was generally 1 per Kb. SSR motif distribution characteristic analysis of these grape cultivars showed that the distribution patterns among grape cultivars were conservative, mainly enriched in A/T. However, there are some differences in motif types (especially tetranucleotides, pentanucleotides, and hexanucleotides), quantity, total length, and average length in different varieties, which might be related to the size of the assembled genome or the specificity of variety domestication. The distribution characteristics of SSRs were revealed by whole-genome analysis of simple repeats of grape varieties. In this study, 32 pairs of primers with lower polymorphism have been screened, which provided an important research foundation for the development of molecular markers of grape variety identification and the construction of linkage maps of important agronomic traits for crop improvement.

Profile microsatellite mining of whole genome sequencing and transcriptomic assembly in dwarf and tall areca nut (Areca catechu) in Indonesia

“…NGS can be used for microsatellite isolation by Whole Genome Sequencing (WGS) and transcriptome assembly. SSR isolation using WGS has been carried out on cultivated spinach (Spinacia oleracea) (Bhattarai et al 2021) and grape (Vitis vinifera) (Pei et al 2023). SSR isolation for transcriptome assembly has been carried out in crispa (Luctuca sativa) (Zhang et al 2021), oil palm (Zhou et al 2020), red ginger (Alpinia purpurata) (Vidya et al 2021), and golden saxifrage (Chrysosplenium alternifolium) (Xiang et al 2023).…”