Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes

This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.

A Study on the Clustering of Extra Virgin Olive Oils Extracted from Cultivars Growing in Four Ionian Islands (Greece) by Multivariate Analysis of Their Phenolic Profile, Antioxidant Activity and Genetic Markers

Background: The phenolic fraction of extra virgin olive oil (EVOO) has disease preventive and health-promoting properties which are supported by numerous studies. As such, EVOO is defined as a functional food. The aim of the present study was to characterize the phenolic profile of olive oil from cultivars farmed in the Ionian Islands (Zakynthos, Kefalonia, Lefkada, and Kerkyra) and to investigate the association of phenols to antioxidant activity, which is central to its functionality. Furthermore, the study investigates whether multivariate analyses on the concentration of individual biophenolic compounds and genetic population diversity could classify the olive oil samples based on their geographic origin. Methods: Phenols were determined in 103 samples from different Ionian Island tree populations by 1H nuclear magnetic resonance (NMR), and sample antioxidant activity was measured by their capacity to reduce the free radical 2,2-diphenyl-1-picrylhydrazyl) (DPPH). Genetic diversity was measured by estimating Nei’s population genetic distance using 15 reproducible bands from random amplified polymorphic DNA (RAPD) genotyping. Results: Principal component analysis (PCA) of the secoiridoid concentrations clustered samples according to cultivar. Clustering based on genetic distances is not concordant with phenolic clustering. A cultivar effect was also demonstrated in the association between the concentration of individual phenols with DPPH reducing activity. Conclusions: Taken together, the study shows that the olive oil phenolic content defines “cultivar-specific phenolic profiles” and that environmental factors other than agronomic conditions contribute more to phenotype variance than genetics.

Development and characterization of Simple Sequence Repeats (SSRs) markers in durian kura-kura (Durio testudinarius Becc.) using NGS data

Durian Kura-kura (Durio testudinarius Becc.) belongs to the Malvaceae family and is an endemic species of Borneo. Recently, genomic-based next-generation sequencing (NGS) approaches have been carried out for germplasm conservation and plant breeding programs. The NGS technologies allow plant genomes to be sequenced quickly and inexpensively and enable the efficient development of SSR markers through the in-silico approaches. This study aimed to develop and characterize simple sequence repeats (SSRs) from the assembled genome. The 1203929 scaffolds of the assembled genome were produced from the Ray assembler. The SSRs were identified and extracted using the MISA program produced 4315 sequences containing SSRs. The six motif repeats of SSRs were identified; consist of 431 sequences of dinucleotide (the most motif is AT), 3257 sequences of trinucleotide (the most motif is TTA), 516 sequences of tetranucleotide (the most motif is AAAT), 89 sequences of pentanucleotide (the most motif is ATTTT), 18 sequences of hexanucleotide and four sequences of heptanucleotide. The new SSRs markers will be used in further studies of genetic population of D. testudinarius and plant breeding programs.

Genetic population of Plasmodium knowlesi during pre-malaria elimination in Thailand

Background Thailand is committed to eliminating malaria by 2024. From 2013 to 2020, the total number of malaria cases have decreased, from 37,741 to 4474 (an 88.1% reduction). However, infections with Plasmodium knowlesi, a monkey malarial pathogen that can also infect humans, have been increasingly observed. This study focused on the molecular analysis of P. knowlesi parasites causing malaria in Thailand. Methods Under Thailand’s integrated Drug Efficacy Surveillance (iDES), which includes drug-resistance monitoring as part of routine case-based surveillance and responses, specimens were collected from malaria patients (n = 966) between 2018 and 2020. Thirty-one mono P. knowlesi infections (3.1%), most of which were from eastern and southern Thailand, were observed and confirmed by nested PCR assay and DNA sequencing. To evaluate whether these pathogens were from different lineages, cluster analysis based on seven microsatellite genotyping markers and the merozoite surface protein 1 (pkmsp1) gene was carried out. The P. knowlesi pyrimethamine resistance gene dihydrofolate reductase (pkdhfr) was sequenced and homology modelling was constructed. Results The results of analysing the seven microsatellite markers and pkmsp1 sequence demonstrated that P. knowlesi parasites from eastern Thailand were of the same lineage as those isolated in Cambodia, while the parasites causing malaria in southern Thailand were the same lineage as those isolated from Malaysia. The sequencing results for the pkdhfr genes indicated the presence of two mutations, Arg34Leu and a deletion at position 105. On analysis with homology modelling, the two mutations were not associated with anti-malarial drug resistance. Conclusions This report compared the genetic populations of P. knowlesi parasites in Thailand from 2018 to 2020 and have shown similar lineages as those isolated in Cambodia and Malaysia of P. knowlesi infection in Thailand and demonstrated that the P. knowlesi parasites were of the same lineages as those isolated in Cambodia and Malaysia. The parasites were also shown to be sensitive to pyrimethamine.

Primer design of D-loop region for wild population genetics of Rusa timorensis in Indonesia

Rusa timorensis (Javan deer) is endemic wildlife in Indonesia and is estimated at less than 10.000 individuals with continuously declining populations due to habitat loss and illegal hunting in the wild. This declining low population indicates a greater risk of extinction. Unfortunately, the genetic information of the wild Javan deer population for conservation management strategies still lacks data due to challenging sampling in the wild. Most recent studies were analysing the breeding populations outside Indonesia. Here, we propose the primer design of the D-loop genetic marker to determine the genetic population of wild Javan deer. We used metadata analysis of genetic sequences and new samples from five wild populations to design the specific primer of the D-loop region of the wild Javan deer in Indonesia. We used software, i.e.., Primer3 to design the primers, BLAST for specificity and Oligo Analyzer™ Tool for efficiency of the primer. The Annealing temperature optimisation started with pre-denaturation at 94 °C followed by 35 cycles of denaturation at 95°C; 51-56°C annealing for each one degree’s different per PCR treatment; and 72°C extensions. We successfully designed a specific primer (RL-3.1a) to amplify 235 bp of the D-loop region at 52°C annealing’s temperature.

Host genotype structures the microbiome of a globally dispersed marine phytoplankton

Phytoplankton support complex bacterial microbiomes that rely on phytoplankton-derived extracellular compounds and perform functions necessary for algal growth. Recent work has revealed sophisticated interactions and exchanges of molecules between specific phytoplankton–bacteria pairs, but the role of host genotype in regulating those interactions is unknown. Here, we show how phytoplankton microbiomes are shaped by intraspecific genetic variation in the host using global environmental isolates of the model phytoplankton host Thalassiosira rotula and a laboratory common garden experiment. A set of 81 environmental T. rotula genotypes from three ocean basins and eight genetically distinct populations did not reveal a core microbiome. While no single bacterial phylotype was shared across all genotypes, we found strong genotypic influence of T. rotula, with microbiomes associating more strongly with host genetic population than with environmental factors. The microbiome association with host genetic population persisted across different ocean basins, suggesting that microbiomes may be associated with host populations for decades. To isolate the impact of host genotype on microbiomes, a common garden experiment using eight genotypes from three distinct host populations again found that host genotype influenced microbial community composition, suggesting that a process we describe as genotypic filtering, analogous to environmental filtering, shapes phytoplankton microbiomes. In both the environmental and laboratory studies, microbiome variation between genotypes suggests that other factors influenced microbiome composition but did not swamp the dominant signal of host genetic background. The long-term association of microbiomes with specific host genotypes reveals a possible mechanism explaining the evolution and maintenance of complex phytoplankton–bacteria chemical exchanges.

Population genetics and connectivity in Paphies subtriangulata and Paphies australis (Bivalvia: Mesodesmatidae)

<p>Understanding the different types of genetic population structure that characterise marine species, and the processes driving such patterns, is crucial for establishing links between the ecology and evolution of a species. This knowledge is vital for management and conservation of marine species. Genetic approaches are a powerful tool for revealing ecologically relevant insights to marine population dynamics. Geographic patterns of genetic population structure are largely determined by the rate at which individuals are exchanged among populations (termed ‘population connectivity’), which in turn is influenced by conditions in the physical environment. The complexity of the New Zealand marine environment makes it difficult to predict how physical oceanographic and environmental processes will influence connectivity in coastal marine organisms and hence the type of genetic structure that will form. This complexity presents a challenge for management of marine resources but also makes the New Zealand region an interesting model system to investigate how and why population structure develops and evolves over time. Paphies subtriangulata (tuatua) and P. australis (pipi) are endemic bivalve ‘surf clams’ commonly found on New Zealand surf beaches and harbour/estuary environments, respectively. They form important recreational, customary and commercial fisheries, yet little is known about the stock structure of these species. This study aimed to use genetic techniques to determine population structure, levels of connectivity and ‘seascape’ genetic patterns in P. subtriangulata and P. australis, and to gain further knowledge of common population genetic processes operating in the New Zealand coastal marine environment. Eleven and 14 novel microsatellite markers were developed for P. subtriangulata and P. australis, respectively. Samples were collected from 10 locations for P. subtriangulata and 13 locations for P. australis (35-57 samples per location; total sample size of 517 for P. subtriangulata and 674 for P. australis). Geographic patterns of genetic variation were measured and rates of migration among locations were estimated on recent and historic time scales. Both species were characterised by genetic population structure that was consistent with their habitat. For P. subtriangulata, the Chatham Island population was strongly differentiated from the rest of the sampled locations. The majority of mainland locations were undifferentiated and estimated rates of migration among locations were high on both time scales investigated, although differentiation among some populations was observed. For P. australis, an overall isolation by distance (IBD) pattern was likely to be driven by distance between discrete estuary habitats. However, it was difficult to distinguish IBD from hierarchical structure as populations could be further subdivided into three significantly differentiated groups (Northern, South Eastern and South Western), providing evidence for barriers to dispersal. Further small scale patterns of genetic differentiation were observed in some locations, suggesting that complex current patterns and high self-recruitment drive small scale genetic population structure in both P. subtriangulata and P. australis. These patterns of genetic variation were used in seascape genetic analyses to test for associations with environmental variables, with the purpose of understanding the processes that might shape genetic population structure in these two species. Although genetic population structure varied between the two species, common physical and environmental variables (geographic distance, sea surface temperature, bed slope, tidal currents) are likely to be involved in the structuring of populations. Results suggest that local adaptation, in combination with restricted dispersal, could play a role in driving the small scale patterns of genetic differentiation seen among some localities. Overall, the outcomes of this research fill a gap in our knowledge about the rates and routes by which populations are connected and the environmental factors influencing such patterns in the New Zealand marine environment. Other studies have highlighted the importance of using multi-faceted approaches to understand complex processes operating in the marine environment. The present study is an important first step in this direction as these methods are yet to be widely applied to New Zealand marine species. Importantly, this study used a comparative approach, applying standardised methodology to compare genetic population structure and migration across species. Such an approach is necessary if we wish to build a robust understanding of the spatial and temporal complexities of population dynamics in the New Zealand coastal marine environment, and to develop effective management strategies for our unique marine species.</p>