Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

Molecular insights into the genetic diversity and population structure of Artemisia annua L. as revealed by insertional polymorphisms

The knowledge about the level of genetic diversity and population structure in natural populations of Artemisia annua L. is a primary step in breeding programs for development of new cultivars with higher artemisinin level and better quality of secondary metabolites composition. We used PCR-based "retrotransposon-microsatellite amplified polymorphisms" (REMAPs) to study insertional polymorphism in A. annua genome to assess genetic variability and population structure in a collection of 118 accessions collected from north and northwest of Iran. Twenty-five primer combinations of 10 retrotransposon and seven ISSR primers amplified a total of 693 clear and unambiguous fragments in the studied accessions. The average number of bands, polymorphic bands, polymorphism, effective number of alleles, Shannon's information index and expected heterozygosity were 27.72, 24.76, 88.14%, 1.47, 0.42 and 0.28, respectively. The analysis of molecular variance revealed high genetic variation present within sampled geographical regions. Distance-based cluster analysis assigned the studied accessions into four clusters according to their geographical origin, which were also confirmed by principal coordinate analysis. In model-based Bayesian clustering, the maximum value of Δk was obtained when the collection of 118 assayed A. annua accessions assigned into two subgroups (K = 2). The results showed the high genetic variation in the collection of Iranian sweet wormwood which revealed by REMAP markers indicating the reliability and efficiency of this marker system for analysis of genetic diversity and population structure of A. annua.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40415-022-00860-x.

Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer

Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.

Comparative population genetics of swimming crab host (Portunus pelagicus) and common symbiotic barnacle (Octolasmis angulata) in Vietnam

Background

By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms.

Methods

Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages.

Results

Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R² = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).

Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity

Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The "copy-out and paste-in" life cycle of replicative transposition in these dispersive and ubiquitous RTEs leads to new genome insertions without excision of the original element. RTEs are important drivers of species diversity; they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative components in genome evolution. Accordingly, various applications have been developed to explore the polymorphisms in RTE insertion patterns. These applications include conventional or anchored polymerase chain reaction (PCR) and quantitative or digital PCR with primers designed for the 5' or 3' junction. Marker systems exploiting these PCR methods can be easily developed and are inexpensively used in the absence of extensive genome sequence data. The main inter-repeat amplification polymorphism techniques include inter-retrotransposon amplified polymorphism (IRAP), retrotransposon microsatellite amplified polymorphism (REMAP), and Inter-Primer Binding Site (iPBS) for PCR amplification with a single or two primers.

Current Situation, Global Potential Distribution and Evolution of Six Almond Species in China

Almond resources are widely distributed in Central Asia; its distribution has not been studied in detail. Based on the first-hand data of field investigation, climate variables and chloroplast genome data, climatic characteristics of six almond species in China were analyzed, and the global distribution and evolutionary relationship were predicted. The six almond species are concentrated between 27.99°N and 60.47°N. Different almond species have different climatic characteristics. The climate of the almond species distribution has its characteristics, and the distribution of almond species was consistent with the fatty acid cluster analysis. All the test AUC (area under curve) values of MaxEnt model were larger than 0.92. The seven continents except for Antarctica contain suitable areas for the six almond species, and such areas account for approximately 8.08% of the total area of these six continents. Based on the analysis of chloroplast DNA and the distribution characteristics, the evolutionary relationship of the six almond species was proposed, which indicated that China was not the origin of almond. In this study, the construction of a phylogenetic tree based on the chloroplast genome and the characteristics of geographical distribution were constructed. The six almond species in China may have evolved from "Unknown almond species" through two routes. The MaxEnt model for each almond species provided satisfactory results. The prediction results can provide the important reference for Prunus dulcis cultivation, wild almond species development and protection.

Mitochondrial relationships between various chamomile accessions

Matricaria chamomilla L. (GRIN; The Plant List 2013) is an important medicinal plant and one of the most frequently consumed tea plants. In order to assess mitochondrial genome variation of different cultivated chamomile accessions, 36 mitochondrial SNP markers were used in a HRM (high resolution melting) approach. In thirteen accessions of chamomile (n = 155), twenty mitochondrial haplotypes (genetic distances 0.028–0.693) were identified. Three of the accessions (‘Camoflora’, ‘Mat19’ and ‘Manzana’) were monomorphic. The highest genotypic variability was found for the Croatian accession ‘PG029’ with nine mitochondrial haplotypes (mitotypes) and the Argentinian ‘Argenmilla’ with seven mitotypes. However, most of the mitotypes detected in these accessions were infrequent in our sample set, thus disclosing an unusual high amount of substitutions within the mitochondrial genome of these accessions. The mitotypes with the highest frequency in the examined dataset were MT1 (n = 27), MT9 (n = 23) and MT17 (n = 20). All of the frequent mitochondrial lines are distributed not only over several accessions but also over several geographical origins. The origins often build a triplet with on average two to three concurrent lines. The most distantly related accessions were ‘Mat19’ and ‘Camoflora’ (0.539), while ‘PNOS’ and ‘Margaritar’ (0.007) showed the lowest genetic distance.

Advances in biotechnology and propagation of nut trees in Iran

As one of the main origin centers of nut trees, Iran is the fourth leading nut crops producer in the world (6% of total nut production). Due to the high genetic diversity, development of new varieties and rootstocks with desirable characteristics have been highly considered by fruit breeders in Iran. In this regard, molecular breeders concentrate on filling the gaps in the conventional breeding with the aim of accelerating breeding programs. Recent advancements in molecular breeding such as next-generation sequencing (NGS) techniques, high-throughput genotyping platforms and genomics-based approaches including genome wide association studies (GWAS), and genomic selection (GS) have opened up new avenues to enhance the efficiency of nut trees breeding. Over the past decades, Iranian nut crops breeders have successfully used advanced molecular and genomic tools such as molecular markers, genetic transformations and high-throughput genotyping to explore the genetic basis of the desired traits and eventually to develop new varieties and rootstocks. Due to a broad international cooperation, a clear perspective is envisaged for the nut breeding programs in Iran, especially based on new biotechnology techniques. The propagation of nut trees in Iran have also been dramatically improved. Different types of grafting and tissue culture (micropropagation or somatic embryogenesis) techniques for propagation of nut crops have been studied intensively in the last 30 years in Iran and the successful techniques have been commercialized. Several certified nurseries are producing grafted and micropropagation plants of walnut, pistachio and other nut crops commercially. A part of the grafted and micropropagaited plants of nut crops in Iran is being exported to the other countries. Establishing modern orchards of nut crops using new cultivars and rootsocks is presently being advised by professional consultants.

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.)

As a source of genetic variation, almond germplasm resources are of great significance in breeding. To better reveal the mutation characteristics and evolution patterns of the almond chloroplast (cp) genome, the complete cp genomes from six almond species were analyzed. The lengths of the chloroplast genome of the six almond species ranged from 157,783 bp to 158,073 bp. For repeat sequence analysis, 53 pairs of repeats (30 bp or longer) were identified. A total of 117 SSR loci were observed, including 96 polymorphic SSR loci. Nine highly variable regions with a nucleotide variability (Pi) higher than 0.08, including rps16, rps16-psbK, atpF-atpH, rpoB, ycf3-rps4, rps4-ndhJ, accD-psaI and rps7-orf42 (two highly variable regions) were located. Based on the chloroplast genome evolution analysis, three species (P. tenella, P. pedunculata and P. triloba) and wild cherry (P. tomentosa) were grouped into clade I. Clade II consisted of two species (P. mongolica and P. tangutica) and wild peach (P. davidiana). Clade III included the common almond (P. dulcis), cultivated peach (P. persica) and GanSu peach (P. kansuensis). This result expands the researchers' vision of almond plant diversity and promotes an understanding of the evolutionary relationship among almond species. In brief, this study provides abundant resources for the study of the almond chloroplast genome, and has an important reference value for study of the evolution and species identification of almond.

Developing Transposable Element Marker System for Molecular Breeding

Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

Background

Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C. finetiana obtained using the Illumina paired-end sequencing technology.

Results

Sequences on a total of 71,900 high-quality unigenes with the mean length of 865 bp were produced in this study. There were 6192unigenes annotated and classified into 49 functional sub-groups in three main ontology categories in GO (Gen Ontology) database,14,022 unigenes mapped to COGs (Clusters of Orthologous Groups) database and classified into 25 functional categories, and 21,494 unigenes obtained and divided into 128 pathways of KEGG (Kyoto Encyclopedia of Genes) Database. A total of 7532 SSRs were discovered from 6337 unigenes. We randomly tested 210 primer pairs, of which 52 primer pairs were able to generate specific products, and 19 possessed polymorphism in the 13 wild populations of six species from Clematis, which were used as a test material.

Conclusions

The dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis.

Electronic supplementary material

The online version of this article (10.1186/s41065-018-0060-x) contains supplementary material, which is available to authorized users.

Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F₁ progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F₁ progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The 'copy and paste' lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5' or 3' junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants' genetic diversity.

Characterizing the transcriptome and microsatellite markers for almond (Amygdalus communis L.) using the Illumina sequencing platform

BACKGROUND

The almond tree (Prunus amygdalus Batsch) is an important nut tree grown in subtropical regions that produces nutrient-rich nuts. However, a paucity of genomic information and DNA markers has restricted the development of modern breeding technologies for almond trees.

RESULTS

In this study, almonds were sequenced with Illumina paired-end sequencing technology to obtain transcriptome data and develop simple sequence repeats (SSR) markers. We generated approximately 64 million clean reads from the various tissues of mixed almonds, and a total of 42,135 unigenes with an average length of 988 bp were obtained in the present study. A total of 27,586 unigenes (57.7% of all unigenes generated) were annotated using several databases. A total of 112,812 unigenes were annotated with the Gene Ontology (GO) database and assigned to 82 functional sub-groups, and 29,075 unigenes were assigned to the KOG database and classified into 25 function classifications. There were 9470 unigenes assigned to 129 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways from five categories in the KEGG pathway database. We further identified 8641 SSR markers from 48,012 unigenes. A total of 100 SSR markers were randomly selected to validate quality, and 82 markers could amplify the specific products of A. communis L., whereas 70 markers were successfully transferable to five species (A. ledebouriana, A. mongolica, A. pedunculata, A. tangutica, and A. triloba).

CONCLUSIONS

Our study was the first to produce public transcriptome data from almonds. The development of SSR markers will promote genetics research and breeding programmes for almonds.