Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Abstract

Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A . dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A . dahurica . We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A . dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A . dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.

Development and Transferability of EST-SSR Markers for Pinus koraiensis from Cold-Stressed Transcriptome through Illumina Sequencing

“…Identifying and developing a large number of molecular marker loci and their highly polymorphic primers using whole-genome and transcriptome data, are crucial for the protection and utilization of germplasm resources. Compared to other DNA molecular markers, such as the amplified fragment length polymorphism (AFLP), single nucleotide polymorphism (SNP), random amplified polymorphic DNA (RAPD), and restriction fragment length polymorphism (RFLP), SSRs are useful and efficient molecular markers with a high level of polymorphic information, low cost, and codominant characteristics; thus, they are considered a powerful tool to study genetic diversity, determine genetic structure, construct genetic maps, and identify relationships between many non-model species, especially endangered species [15][16][17]. Previous studies of SSR development, including chloroplast microsatellites (cpSSRs) and expressed sequence tag-simple sequence repeats (EST-SSRs) of P. koraiensis, were mainly based on multi-omics data such as the chloroplast genome and transcriptome [12,18,19].…”

Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers

“…SSR markers are based on microsatellites and are considered the most efficient and abundant molecular markers with a high ratio of genome coverage. They are highly reproducible and can be used to study codominant inheritance ( Chen et al, 2019 ). Moreover, SSR polymorphisms are employed to identify and characterize germplasm resources in terms of affiliation ( Tuler et al, 2015 ), and the development and characterization of genomic SSRs in hemp are important to enable genetic research and marker-assisted selection.…”

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

“…[ 84 ] and data mining from EST-databases in Centella asiatica [ 85 ]. Moreover, RNA-seq analyses were used for microsatellite development in Coriandrum sativum , Notopterygium incisum , Foeniculum vulgare , Oenanthe javanica , Apium graveolens , Angelica biserrata and Angelica dahurica [ 75 , 86 , 87 , 88 , 89 , 90 , 91 ]; whereas DNA-seq runs were performed with the same goal in Notopterygium oviforme , Anethum sowa , Cuminum cyminum , Scaligeria lazica , Foeniculum vulgare [ 46 , 92 , 93 , 94 , 95 ]. In Table 2 , we sum up what was described so far by reporting the main SSR-set developed in the Apiaceae family.…”