The taxonomic significance of ddRADseq based microsatellite markers in the closely related species of Heracleum (Apiaceae)

Abstract

Many studies on Heracleum have shown poor correspondence between observed molecular clusters and established taxonomic classification amongst closely related species. This might reflect both unresolved taxonomy but perhaps also a lack of good genetic markers. This lack of appropriate and cost effective species-specific genetic markers hinders a resolved relationship for the species complex, and this in turn causes profound management challenges for a genus that contains both endemic species, with important ecological roles, and species with an invasive potential. Microsatellites are traditionally considered markers of choice for comprehensive, yet inexpensive, analyses of genetic variation, including examination of population structure, species identity, linkage map construction and cryptic speciation. In this study, we have used double digest restriction site associated DNA sequencing (ddRADseq) to develop microsatellite markers in Heracleum rechingeri. Genomic DNA from three individuals were digested with Sbf1 and Nde1 and size selected for library construction. The size-selected fragments were sequenced on an Ion Torrent sequencer and a total of 54 microsatellite sequences were bioinformatically confirmed. Twenty five loci were then tested for amplification, resulting in 19 of these being successfully amplified across eight species, comprising both the so-called thick-stemmed species (H. persicum, H. rechingeri, H. gorganicum and H. lasiopetalum), and thin-stemmed species (H. anisactis, H. pastinasifolium and H. transcaucasicum). Both Bayesian and distance-based clustering, and principal coordinate analyses clearly separated these into two groups. Surprisingly, three H. pastinacifolium populations were not separated from populations of the morphologically similar endemic species, H. anisactis, suggesting lack of genetic differentiation. Likewise, high genetic similarity was found between H. persicum and H. rechingeri populations, questioning taxonomic separation at the species level between these taxa. Further analyses are needed to re-evaluate the taxonomic significance of observed morphological variability currently applied to distinguish these sister taxa. Nevertheless, our results represent progress in the effort to develop cost-efficient molecular tools for species discrimination in this genus.

Genetic variation and structure of endemic and endangered wild celery (Kelussia odoratissima Mozaff.) quantified using novel microsatellite markers developed by next-generation sequencing

“…Ex Fleming, and Heracleum sp. revealed that AT/AT, GA/TC, AAG/CTT, and TGA/TCA were the most predominant motifs among dinucleotide and trinucleotide motifs ( Fu et al., 2013 ; Bharti et al., 2018 ; Jia et al., 2019 ; Daemi-Saeidabad et al., 2020 ; Kumar et al., 2020 ). These discrepancies could be explained by the difference in genomic content and structure of the investigated species, marker development techniques, and mining principles ( Liu et al., 2019 ; Lopez et al., 2015 ; Zhang et al., 2017 ; Zhang et al., 2022 ).…”

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

“…Among them, biotinylated SSR primers were used for Arracacia xanthorrhiza [ 82 ], I-SSR in Bupleurum chinense [ 83 ], ddRAD-seq in Heracleum spp. [ 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 ].…”