Restriction-associated DNA Sequencing Research Articles

First Evidence of Thalassochory in the Ficus Genus: Seed Dispersal Using the Kuroshio Oceanic Current.

Plants distributed between southern Taiwan and the north of the Philippines are spread among numerous small islands in an area crossed by the powerful Kuroshio current. Oceanic currents can be effective seed-dispersal agents for coastal plant species. Moreover, the Luzon Strait is an area prone to tropical cyclones. The aim of this study is to look at the dispersal capability of an endangered coastal plant species, the Mearns fig (Ficus pedunculosa var. mearnsii), using both experimental and population genetics methods. Southern Taiwan, the Philippines, and the islands between Luzon and Taiwan Island. This study combined two types of analysis, i.e., buoyancy experiments on syconia and double digest restriction-associated DNA sequencing (ddRAD), to analyze the population genetics of the Mearns fig. We first discovered that mature Mearns fig syconia could float in seawater. They have a mean float duration of 10 days to a maximum of 21 days. Germination rates varied significantly between Mearns fig seeds that had undergone different durations of flotation treatment. Population genetic analysis shows a high degree of inbreeding among various Mearns fig populations. Moreover, no isolation by distance was found between the populations and individuals. From our analysis of the genetic structure of the Mearns fig populations, we can clearly highlight the effect of the Kuroshio oceanic current on the seed dispersal of this fig tree. Comprehensive analysis has shown that Mearns fig seeds are still viable before the mature syconium sinks into the seawater, and so they could use the Kuroshio Current to float to the current population locations in Taiwan.

The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis.

The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme-substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.

Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye.

Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST ) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP-EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP-EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3-1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.

A survey of the genome-wide genetic variation of &lt;i&gt;Hibiscus hamabo&lt;/i&gt; (Malvaceae)

&lt;i&gt;Hibiscus hamabo&lt;/i&gt; (Malvaceae) is a deciduous shrub mainly found in northeast Asia, including China, Japan, and Korea. Due to its limited distribution on Jejudo Island and at several sites in Jeollanam-do in Korea, &lt;i&gt;H. hamabo&lt;/i&gt; has been designated as an endangered species by the Ministry of the Environment and has been the subject of several restoration programs. In this study, we quantified genetic variations using double-digestion restrictionassociated DNA sequencing technology in 96 individuals of &lt;i&gt;H. hamabo&lt;/i&gt; from 13 distinct populations in Korea. We determined 3,352 genome-wide single nucleotide polymorphism loci after stringent filtering processes and analyzed the level of genetic variation within and among populations as well as the population differentiation and genetic ancestry with various assumptions pertaining to the population origin. Our results indicated weak differentiations among populations surveyed in this study but clearly suggested that most of the &lt;i&gt;H. hamabo&lt;/i&gt; populations maintain a relatively high level of genetic diversity as evidence of frequent genetic exchanges among populations via outcrossing or sequential gene flows. For a more detailed analysis of the origin of Korean &lt;i&gt;H. hamabo&lt;/i&gt; and its demographic history, it will be necessary to expand sampling in China and Japan.

Weak range-wide population structure in the blackfin tuna (Thunnus atlanticus) revealed by analysis of genome-wide SNPs

Abstract Blackfin tuna (Thunnus atlanticus) is a small tuna distributed in the western Atlantic Ocean where it is exploited by growing recreational and commercial regional fisheries. In this work, genome-wide genetic variation was analysed to investigate the occurrence of stock subdivision. A de novo assembly of the blackfin tuna genome was generated using Illumina paired-end sequencing data and applied as a reference for population genomic analysis of specimens from nine localities (average sample size per locality n = 72) spanning most of the blackfin tuna distribution range. A total of 2139 single-nucleotide polymorphisms were discovered and genotyped using the double-digest restriction associated DNA sequencing. Pairwise exact homogeneity tests were significant in 24 out of 36 population pairs and significant spatial autocorrelation of genotypes was observed for specimens collected within 2250 km of each other. However, divergence among locality samples was very low (pairwise FST range 0.0002–0.0025) and significant temporal variations were detected in localities sampled multiple times. Approaches to detect cryptic groups de novo were unsuccessful. Additional sampling is warranted to determine if multiple stocks need to be defined for management and assess temporal and spatial patterns of gene flow connecting them.

Population genomics and phylogeography of four Australasian waterfowl

ABSTRACT Biogeographic barriers can restrict gene flow, but variation in ecological drivers of dispersal influences the effectiveness of these barriers among different species. Detailed information about the genetic connectivity and movement of waterfowl across biogeographic barriers in northern Australia and Papua New Guinea is limited. We compared genetic connectivity for four species of Australasian waterfowl that vary in their capacity and predisposition for dispersal: Radjah Shelduck (Radjah radjah), Wandering Whistling Duck (Dendrocygna arcuata), Green Pygmy Goose (Nettapus pulchellus), and Pacific Black Duck (Anas superciliosa). We obtained >3,700 loci from double-digest restriction-associated DNA sequencing for 15 to 40 individuals per species and found idiosyncratic patterns of population structure among the four species. The mostly sedentary Radjah Shelduck exhibited clear genetic differences between New Guinea and Australia as well as among locations within Australia. Although the population structure was consistent with isolation by distance, the Torres Strait and Carpentaria Barrier contributed more to genetic differences than geographic distance alone. In contrast, the presumed sedentary Green Pygmy Goose did not show obvious structure. Likewise, populations of the more dispersive Wandering Whistling Duck and Pacific Black Duck were unstructured and genetically indistinguishable between southern New Guinea and northern Australia. Our data suggest that some Australo-Papuan biogeographical barriers are insufficient to impede gene flow in waterfowl species capable of dispersing great distances. In sedentary species like the Radjah Shelduck, these barriers, perhaps coupled with its ecology and natural history, restrict gene flow. Our findings bring new insight into the population ecology of Australo-Papuan waterfowl.

How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree.

Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas such as the Loky-Manambato region (north) raise questions regarding the causes and age of forest fragmentation. The Loky-Manambato region also harbours a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamics in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction-associated DNA sequencing data and chloroplast microsatellites. Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across these antique mosaic habitats, calling for the study of organismal interactions that promote gene flow.

&lt;i&gt;Corrigendum to&lt;/i&gt;: Phylogenetics of the skyhoppers (&lt;i&gt;Kosciuscola&lt;/i&gt;) of the Australian Alps: evolutionary and conservation implications

The true biodiversity of Australia&amp;#x2019;s alpine and subalpine endemics is unknown. Genetic studies to date have focused on sub-regions and restricted taxa, but even so, indicate deep divergences across small geographic scales and therefore that the bulk of biodiversity remains to be discovered. We aimed to study the phylogeography of the Australian Alps by focusing on the skyhoppers (&lt;italic&gt;Kosciuscola&lt;/italic&gt;), a genus of five species of flightless grasshoppers whose combined distributions both span the region and are almost exclusively contained within it. Our sampling covered 650&amp;#x2009;km on the mainland and several sites in Tasmania with total of 260 specimens used to reconstruct a robust phylogeny of &lt;italic&gt;Koscisucola&lt;/italic&gt;. Phylogenies were based on single nucleotide polymorphism data generated from double-digested restriction-associated DNA sequencing. Skyhoppers diverged around 2 million years ago and have since undergone complex diversification seemingly driven by climatic oscillations throughout the Pleistocene. We recovered not 5 but 14 clades indicating the presence of many unknown species. Our results support conspicuous geographic features as genetic breaks; e.g. the Murray Valley, and inconspicuous ones; e.g. between the Bogong High Plains and Mt Hotham. Climate change is progressing quickly in the region and its impact, particularly on snow, could have severe consequences for the skyhoppers&amp;#x2019; overwinter survival. The true diversity of skyhoppers highlights that biodiversity loss in the Alps as a result of climate change is likely to be far greater than what can be estimated based on current species numbers and that management including small geographical scales is key.

Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises.

Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive‐bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low‐coverage and double‐digest restriction‐associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5426 variant sites within the tortoise genome, we detected patterns of within‐island population structure, but no differentiation between the islands. These unexpected results highlight the importance of using genome‐wide genetic markers to capture higher‐resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low‐coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non‐model species with large genomes.

Hybridization between two introduced, invasive crayfish species in the upper Juniata River system, Pennsylvania, USA

Abstract Hybridization of non-native crayfishes with native crayfishes can facilitate invasion success of the non-native. We report novel genetic evidence of hybridization between rusty crayfish, Faxonius rusticus (Girard, 1852), and Allegheny crayfish, F. obscurus (Hagen, 1870), two non-native species in the upper Juniata River basin of central Pennsylvania. We used double-digest restriction-associated DNA sequencing, which yielded 28,031 single nucleotide polymorphisms, to characterize the extent of hybridization. Two of eight individuals with mixed character traits were identified as the progeny of hybrids backcrossed into rusty crayfish. One individual, presumed to be a rusty crayfish in the field, was genetically identified as a hybrid backcross to rusty crayfish. The three crayfish taxa (rusty, Allegheny, and intermediates) are virtually indistinguishable based on typical morphological characters. Key character traits that distinguish rusty and Allegheny crayfishes can be mixed atypically in certain individuals (i.e., intermediates). Our results indicate that introgressive hybridization has occurred between rusty and Allegheny crayfishes, and that at least some of the character-trait intermediate individuals have hybrid ancestry. Hybridization may be an additional means by which invasive rusty crayfish increase their fitness and dominance at the expense of existing species and their habitat.

Neither connectivity nor genetic diversity matter in the conservation of a rare fern and a moss on insular erratic boulders

Erratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands for the regionally critically endangered fern Asplenium septentrionale, about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of A. septentrionale and the moss Hedwigia ciliata on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid A. septentrionale, abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of A. septentrionale mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of H. ciliata were identified, and populations consisting of a single multilocus genotype were less common than in A. septentrionale. For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of A. septentrionale seems to be rare, while colonisation by H. ciliata appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.

Fungus-bacterium associations are widespread in fungal cultures isolated from a semi-arid natural grassland in Germany.

We report on a study that aimed at establishing a large soil-fungal culture collection spanning a wide taxonomic diversity and systematically screening the collection for bacterial associations. Fungal cultures were isolated from soil samples obtained from a natural grassland in eastern Germany and bacterial associations were assessed by PCR-amplification and sequencing of bacterial 16S rRNA. In addition, intraspecies genetic diversities of a subset of the isolated species were estimated by double-digest restriction associated DNA sequencing. A total of 688 fungal cultures, representing at least 106 fungal species from 36 different families, were obtained and even though clonal isolates were identified in almost all fungal species subjected to ddRAD-seq, relatively high genetic diversities could be observed in some of the isolated species. A total of 69% of the fungal isolates in our collection were found to be associated with bacteria and the most commonly identified bacterial genera were Pelomonas, Enterobacter and Burkholderia. Our results indicate that bacterial associations commonly occur in soil fungi, even if antibiotics are being applied during the isolation process, and provide a basis for the use of our culture collection in ecological experiments that want to acknowledge the importance of intraspecies genetic diversity.

Reduced metagenome sequencing for strain-resolution taxonomic profiles

BackgroundStudies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data.ResultsWe suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time.ConclusionWe find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.1VZ3xwdVv3tXqsbKN3Vx-QVideo abstract

Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino.

Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.

Phylogenetics of the skyhoppers (

The true biodiversity of Australia’s alpine and subalpine endemics is unknown. Genetic studies to date have focused on sub-regions and restricted taxa, but even so, indicate deep divergences across small geographic scales and therefore that the bulk of biodiversity remains to be discovered. We aimed to study the phylogeography of the Australian Alps by focusing on the skyhoppers (Kosciuscola), a genus of five species of flightless grasshoppers whose combined distributions both span the region and are almost exclusively contained within it. Our sampling covered 650 km on the mainland and several sites in Tasmania with total of 260 specimens used to reconstruct a robust phylogeny of Koscisucola. Phylogenies were based on single nucleotide polymorphism data generated from double-digested restriction-associated DNA sequencing. Skyhoppers diverged around 2 million years ago and have since undergone complex diversification seemingly driven by climatic oscillations throughout the Pleistocene. We recovered not 5 but 14 clades indicating the presence of many unknown species. Our results support conspicuous geographic features as genetic breaks; e.g. the Murray Valley, and inconspicuous ones; e.g. between the Bogong High Plains and Mt Hotham. Climate change is progressing quickly in the region and its impact, particularly on snow, could have severe consequences for the skyhoppers’ overwinter survival. The true diversity of skyhoppers highlights that biodiversity loss in the Alps as a result of climate change is likely to be far greater than what can be estimated based on current species numbers and that management including small geographical scales is key.

Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus).

Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.

Genetic map and heritability of Aspergillus flavus

The carcinogenic aflatoxins are a human health concern as well as an economic burden to corn, peanut and other crops grown within the United States and globally. Aflatoxins are produced by fungi species in Aspergillus section Flavi, primarily Aspergillus flavus. Though previously thought of as only asexual, A. flavus has recently been found to undergo sexual reproduction both in laboratory crosses and in the field. To elucidate the consequences of genetic exchange through a single generation of the sexual cycle within A. flavus, we constructed genetic maps based on three mapping populations, each composed of the parental strains and approximately 70 F1 progeny. Genome-wide data using double digest Restriction Associated DNA sequencing identified 496, 811, and 576 significant polymorphisms differentiating parents across eight linkage groups; these polymorphisms served as markers. Average spacing between marker loci was 3.1, 2.1, and 3.5 map units and overall map length was 1504.4, 1669.2, and 2001.3 cM. Recombination was non-randomly distributed across chromosomes with an average rate of recombination of about 46.81 cM per Mbp. We showed inheritance of mitochondrial loci from the sclerotial (female) parent in crosses, whereas nuclear loci showed a 1:1 segregation ratio from both parents. The linkage map will be useful in QTL analyses to identify traits that increase sexual fertility in A. flavus and modulate aflatoxin production, both of which have significant implications for sustainable reduction of aflatoxin contamination using biological control agents.

Development of new SNP and INDEL loci for the valuable African timber species Lophira alata

The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes.

Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia.

In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.

Genomic selection for parasitic ciliate Cryptocaryon irritans resistance in large yellow croaker

Large yellow croaker is an important marine aquaculture species in the southeast coast of China. It suffers serious diseases caused by Cryptocaryon irritans, a parasitic cilliate which causes huge economic losses to the aquaculture industry of large yellow croaker. This study aims to apply genomic selection (GS) technology to the selection breeding of large yellow croaker with resistance to C. irritans. The resistant phenotype was measured as a binary trait, survival or death, in challenge experiments using reference population. Double-digest restriction-associated DNA (ddRAD) sequencing approach was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for reference population and selection candidates. A database of 811 individuals and 16,515 SNPs was constructed and used for GS analysis. The GS model containing the top 600 SNP markers with the smallest P value possessed highest predictability and was used to calculate genetic estimated breeding value (GEBV) in selection candidates. The individuals with high GEBV in selection candidates was selected as broodstocks for the breeding of resistant strain (RS), and the remaining individuals for the control strain (CS). Significant resistance difference between RS and CS was detected in a C. irritans challenge test. After 96-h, the survival rate of RS and CS were 59.2% and 9.9%, respectively. Moreover, 120-h survival rate of RS declined to 40.8%, while CS had no surviving individuals. The results confirmed that GS was effective genetic breeding techniques in resistant breeding against C. irritans in large yellow croaker.