Macaronesia Acts as a Museum of Genetic Diversity of Relict Ferns: The Case of Diplazium caudatum (Athyriaceae)

Macaronesia has been considered a refuge region of the formerly widespread subtropical lauroid flora that lived in Southern Europe during the Tertiary. The study of relict angiosperms has shown that Macaronesian relict taxa preserve genetic variation and revealed general patterns of colonization and dispersal. However, information on the conservation of genetic diversity and range dynamics rapidly diminishes when referring to pteridophytes, despite their dominance of the herbaceous stratum in the European tropical palaeoflora. Here we aim to elucidate the pattern of genetic diversity and phylogeography of Diplazium caudatum, a hypothesized species of the Tertiary Palaeotropical flora and currently with its populations restricted across Macaronesia and disjunctly in the Sierras de Algeciras (Andalusia, southern Iberian Peninsula). We analysed 12 populations across the species range using eight microsatellite loci, sequences of a region of plastid DNA, and carry out species-distribution modelling analyses. Our dating results confirm the Tertiary origin of this species. The Macaronesian archipelagos served as a refuge during at least the Quaternary glacial cycles, where populations of D. caudatum preserved higher levels of genetic variation than mainland populations. Our data suggest the disappearance of the species in the continent and the subsequent recolonization from Macaronesia. The results of the AMOVA analysis and the indices of clonal diversity and linkage disequilibrium suggest that D. caudatum is a species in which inter-gametophytic outcrossing predominates, and that in the Andalusian populations there was a shift in mating system toward increased inbreeding and/or clonality. The model that best explains the genetic diversity distribution pattern observed in Macaronesia is, the initial and recurrent colonization between islands and archipelagos and the relatively recent diversification of restricted area lineages, probably due to the decrease of favorable habitats and competition with lineages previously established. This study extends to ferns the concept of Macaronesia archipelagos as refugia for genetic variation.

Genetic diversity analysis of the invasive gall pest Leptocybe invasa (Hymenoptera: Apodemidae) from China

Leptocybe invasa Fisher et LaSalle is a global invasive pest that seriously damages Eucalyptus plants. Studying the genetic diversity, genetic structure and introgression hybridization of L. invasa in China is of great significance for clarifying the breeding strategy, future invasion and diffusion trends of L. invasa in China and developing scientific prevention and control measures. Genetic diversity and phylogenetic analyses of 320 L. invasa female adults from 14 geographic populations in China were conducted using 10 polymorphic microsatellite loci (SSRs) and mitochondrial DNA cytochrome oxidase I gene sequences (COIs). (1) The Bayesian phylogenetic tree and haplotype network diagram showed that only haplotype Hap3 existed in L. invasa lineage B in China, while haplotypes Hap1 and Hap2 existed in lineage A, among which haplotype Hap2 was found for the first time. The nucleotide and haplotype diversities of lineage A were higher than those of lineage B. (2) The SSR genetic diversity of the Wuzhou Guangxi, Ganzhou Jiangxi and Panzhihua Sichuan populations was higher than that of the other 11 populations, and the SSR genetic diversity of lineage A was higher than that of lineage B. (3) The AMOVA analysis of mitochondrial COI data showed that 75.55% of the variation was among populations, and 99.86% of the variation was between lineages, while the AMOVA analysis of nuclear SSR data showed that 35.26% of the variation was among populations, and 47.04% of the variation was between lineages. There were obvious differences in the sources of variation between the COI and SSR data. (4) The optimal K value of COI and SSR data in structure analysis was 2, and PCoA analysis also divided the dataset into two obvious categories. The UPMGA phylogenetic tree based on SSR data clustered 14 geographic species into two groups. The results of genetic structure analysis supported the existence of two lineages, A and B, in China. (5) Structural analysis showed that there was obvious introgressive hybridization in Wuzhou Guangxi, Ganzhou Jiangxi, Panzhihua Sichuan and other populations. These results suggest that lineage introgressive hybridization has occurred in the L. invasa population in China. The introgressive hybridization degree and genetic diversity of lineage A are obviously higher than those of lineage B. Lineage introgressive hybridization may be the driving force for further L. invasa invasion and diffusion in China in the future.

Spatial Scale Patterns of Genetic Diversity and Gene Flow in Populations of Sweet Detar (Detarium microcarpum Guill. & Perr.; Fabaceae)

The main objective of this study is to investigate the patterns of genetic diversity and phylogenetic relationships within populations of Detarium microcarpum (Fabaceae) relative to different spatial conditions. Seventy-eight (78) accessions of D. microcarpum belonging to six populations (Phytogeographic districts) were sampled. In order to have very good quality DNA for molecular analysis, an optimization of the DNA isolation protocol was made. The molecular analysis of the accessions was carried out using 7 chloroplast microsatellite markers. The polymorphism rate (P) is 85.71% and the Polymorphism Information Content (PIC) was in the range of 0.43 (Ntcp_9) to 0.73 (Ccmp_2) with an average of 0.59. Allelic richness (A) ranged from 1.41 to 2.85 with an average of 2.04. The observed heterozygosity (Ho) ranged from 0.23 to 0.60 with an average of 0.39. The expected heterozygosity (He) ranged from 0.43 to 0.60 with a mean of 0.50. Wright's fixation index (FIS) ranged from − 0.17 to 0.47. The effective allele (Ae) is between 1.77 and 2.53 with an average of 2.02. Wright differentiation index (FST) was 0.024. Phylogenetic analysis revealed that the NST value was significantly higher than the GST value (NST = 0.452; GST = 0.190; P < 0.05). A relatively low hd haplotype diversity is obtained (Hd = 0.320). AMOVA analysis showed that 17.35% of the variation existed within populations but 45.80% among populations within the species. Neighbor-Joining phylogenetic tree of D. microcarpum revealed three non-distinct clusters haplotypes showing the existence of gene flow between populations of the species. Our findings of genetic structure and gene flow of D. microcarpum populations based on different spatial conditions is caused by evolutionary forces such as scattering and pollination.

Molecular Insights Into the Genetic Diversity and Population Structure of Artemisia Annua L. As Revealed by Insertional Polymorphisms

BackgroundRetrotransposons-RTNs, are main source of variations in plant genomes that copying and pasting themselves into different transposon and work by changing RNA back into DNA via reverse transcription. For that reason, they are largely utilized in plants as optimum molecular markers to determine DNA fingerprinting, genetic mapping, and genetic variability. ResultsInter-retrotransposon amplified polymorphisms (IRAPs) were used to measure genetic variability and structure in a collection of 118 sweet wormwood (A. annua) accessions identifying and amplifying 849 loci using 32 IRAP primers, derived from Rosaceae, Gramineae, and Solanaceae retroelements. Single IRAP primer Tnt1.OL16 based on RTN produced the maximum count of markers. Percentage of polymorphic loci (PPL), mean expected heterozygosity (He), number of effective alleles (Ne) and information index (I) of Shannon, in the studied collection were 95.80%, 0.30, 1.48 and 0.46, in the same order. AMOVA analysis showed nonexistence of significant genetic structures during structure analysis, however, the 4 populations had three clusters based on the NJ dendrogram that depicted a relatively higher level of genetic variation within each population. These clusters were approximately congruent with corresponding geographical distributions. ConclusionsIn conclusion, low genetic diversity of Iranian Sweet wormwood was detected that could be reduced through introduction of appropriate exotic or improved germplasm to reduce the effects of inbreeding depression.

Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide

White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover.

Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 94.04% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 76.07% polymorphism rate, and Nei's distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting the average Shannon's information index (ISSR:0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (%96). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distance matrices was 0.88. The results of the study put forward resources for advanced breeding techniques, and contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

Polyphenolic and molecular variation in Thymus species using HPLC and SRAP analyses

In the present research, inter and intra genetic variability of 77 accessions belonging to 11 Thymus species were assessed using eight SRAP primer combinations. High polymorphism (98.3%) was observed in the studied species. The cluster analysis classified Thymus species into five main groups. According to molecular variance (AMOVA) analysis, 63.14% of total genetic variation was obtained within the species, while 36.86% of variation was observed among species. STRUCTURE analysis was also performed to estimate the admixture of species. For instance, T. carmanicus and T. transcaspicus revealed high admixtures. HPLC analysis also demonstrated the presence of rosmarinic acid (32.3–150.7 mg/100 g DW), salvianolic acid (8–90 mg/100 g DW), and cinnamic acid (1.7–32.3 mg/100 g DW) as major phenolic acids, as well as apigenin, epicatechin, and naringenin as the major flavonoids. The highest phenolic and flavonoid contents were detected in T. transcaspicus (37.62 mg gallic acid equivalents (GAE) g−1 DW) and T. vulgaris (8.72 mg quercetin equivalents (QE) g−1 DW), respectively. The antioxidant properties and total phenolic of Thymus species were examined using DPPH and β-carotene-linoleic acid model systems and consequently T. vulgaris and T. pubescens were detected with the highest and the lowest antioxidant activities respectively. Cluster and principal Components Analysis (PCA) of the components classified the species in to three groups. Finally, similarity within some species was observed comparing molecular and phytochemical markers. For instance, T. vulgaris separated from other species according to major polyphenolic profiles and molecular analyses, as well as T. transcaspicus, T. carmanicus, and T. fedtschenkoi that were clustered in the same groups.

The study of genetic distinctions of brown Swiss cattle breed with using STR-markers

The study of allele pool condition and genetic diversity of Brown Swiss cattle breed was conducted with using STR-markers. Sample collection included samples (n=347) of five breeds: Russian selection Brown Swiss (BSH1), German selection Brown Swiss (BSH2), Jersey (DJ), Simmental (SIM), Kostromskaya(KOS) and Holstein (HOLSH). Polymorphism of 11 microsatellite loci was studied on 16-channell genetic analyzer ABI3130xl. A total of 393 allales with minimal number in DJ group (54) and maximal in SIM group (84) were founded. The number of alleles per locus ranged from 25 (BM1824) to 50 (TGLA122) and average number of alleles per locus ranged from 4.33 (TGLA126) to 8.33 (TGLA122) with a mean of 5.95. Effective number of alleles per locus varied from 2.88 (DJ) to 3.76 (BSH2). Maximal (4.64) and minimal (3.73) numbers of informative alleles were found in BSH2 and BSH1 groups, respectively. Observed heterozygosity range exceeded 0.70 in all groups, except DJ. A total of 23 private alleles were detected ranged from 0,005 (SIM) to 0,385 (DJ). AMOVA analysis showed that 80.068% of variation was observed within populations while 5.186% of variability was intergroup differences. The population structure analysis showed a high level of belonging of all groups to their own cluster. The FCA method revealed an overlapping of multilocus genotypes of BSH1, BSH2 иKOS groups. The results we obtained reveal a high level of genetic diversity in Russian population of Brown Swiss cattle breed.

Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers

A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.

Struktur Populasi Ikan Tuna Mata Besar (Thunnus obesus) Dengan Analisis DNA Mikrosatelit Di Perairan Samudera Hindia

Tuna mata besar (Thunnus obesus) merupakan salah satu komoditi ekspor perikanan tuna utama di Indonesia akibatnya intensitas penangkapan tuna mata besar mengalami peningkatan di Samudera Hindia sehingga perlu adanya pengelolaan dan pemanfaatan secara berkesinambungan dalam waktu jangka panjang maka diperlukan pemahaman tentang struktur populasi. Sebanyak 30 sampel jaringan sirip dari tuna mata besar dikumpulkan dari 2 (dua) populasi di Samudera Hindia (barat Sumatera dan selatan Nusa Tenggara) selama Desember 2015 sampai dengan Mei 2016. Penelitian ini bertujuan untuk mendapatkan informasi struktur populasi tuna mata besar di Samudera Hindia dengan analisis mikrosatelit. Analisis DNA di lakukan di laboratorium Balai Penelitian dan Pengembangan Budidaya Laut, Gondol dan 1st Base - Singapura. Manfaat penelitian ini adalah memberikan data dan informasi mengenai struktur populasi. Hasil penelitian dengan analisis AMOVA (Analysis of Moleculer Varians) menunjukkan bahwa populasi tuna mata besar di Samudera Hindia barat Sumatera serta selatan Nusa Tenggara masih satu populasi