Revealing the complex genetic structure of cultivated amaryllis (Hippeastrum hybridum) using transcriptome-derived microsatellite markers

Abstract

Although amaryllis (Hippeastrum hybridum) plants are commonly used in physiological and ecological research, the extent of their genomic and genetic resources remains limited. The development of molecular markers is therefore of great importance to accelerate genetic improvements in Hippeastrum species. In this study, a total of 269 unique genes were defined that might regulate the flower spathe development of amaryllis. In addition, 2000 simple sequence repeats (SSRs) were detected based on 171,462 de novo assembled unigenes from transcriptome data, and 66,4091 single nucleotide polymorphisms (SNPs) were also detected as putative molecular markers. Twenty-one SSR markers were screened to evaluate the genetic diversity and population structure of 104 amaryllis accessions. A total of 98 SSR loci were amplified for all accessions. The results reveal that Nei’s gene diversity (H) values of these markers ranged between 0.055 and 0.394, whereas the average values of Shannon’s Information index (I) ranged between 0.172 and 0.567. Genetic tree analysis further demonstrates that all accessions can be grouped into three main clusters, which can be further divided into two subgroups. STRUCTURE-based analysis revealed that the highest ΔK values were observed when K = 5, K = 6, K = 7 and K = 8. The results of this study enable large-scale transcriptomics and classification of Hippeastrum genetic polymorphisms and will be useful in the future for resource conservation and production.

Assessment of genetic diversity and identification of core germplasm in single-flowered amaryllis (Hippeastrum hybridum) using SRAP markers

“…Except for Me03/Em11 and Me06/Em07, all primer combinations showed 100% polymorphism across the accessions. In previous studies, RAPD, ISSRs and SSRs have been used to analyze the genetic variation in 25, 62 and 104 amaryllis hybrids [7][8][9][10]. However, the percentage of polymorphic fragments found in the RAPD (72.6%), ISSRs (92.4%) and SSRs (93.9%) was lower than that in the SRAPs (99.5%) in our study.…”

“…The average values of H and I for all SRAP primer combinations were 0.344 and 0.513, respectively. In the SSR study with more germplasm, the average H and I values in 104 cultivated amaryllis were 0.264 and 0.407, respectively [10]. Overall, these results confirmed that SRAP markers can be powerful and effective tools for clarifying genetic diversity in cultivated amaryllis.…”

“…Fresh young leaves were collected in the spring and immediately frozen in liquid nitrogen and stored at À80 C until DNA isolation. The total genomic DNA was extracted using a modified CTAB procedure as described by Wang et al [10]. The final DNA concentration was adjusted to optimum using an Epoch microplate spectrophotometer (BioTek, Winooski, VT, USA).…”

“…Molecular markers are very powerful tools for accelerating ornamental flower breeding [6]. In the case of amaryllis, random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSRs) and simple sequence repeats (SSRs) have been successfully applied to construct DNA fingerprints and assess genetic diversity [7][8][9][10]. Similar to the use of RAPD, ISSRs and SSRs, the use of sequence-related amplified polymorphisms (SRAPs) is also a developed polymerase chain reaction (PCR)-based molecular marker technique.…”

Morphological traits and genetic parameters of Hippeastrum hybridum

“…Amaryllis is a genus from the family Amarylidaceae and the order Asparagales. The genus contains 75 species South America (Wang et al, 2018), and its endemic species are found in Brazil. It is a bulbous plant among the top 20 popular flowers in the world.…”