High Level Of Genetic Diversity Research Articles

Exploring the Agronomic Performance and Molecular Characterization of Diverse Spring Durum Wheat Germplasm in Kazakhstan

Spring durum wheat occupies over 0.5 M ha in Kazakhstan and represents an important domestic and export commodity. This study aimed to characterize 151 durum wheat cultivars and advanced lines originating from eight breeding programs of the Kazakhstan–Siberia Spring Wheat Improvement Network (KASIB) between 2003 and 2018. The phenotypic characterization was performed in two contracting evaluation sites more than 1000 km apart (Almaty in the Southeast and Shortandy in the North) for two years and a total of 11 agronomic traits were recorded. Field trials at both locations followed regional agronomy practices, including sowing, harvesting, and genotype evaluation using a randomized complete block design (RCBD). The growing season was longer in Almaty, resulting in a higher number of grains per spike. Though grains are smaller in size with an overall higher yield, 243 g/m2 versus 170 g/m2, there was no correlation between germplasm performance at the two sites. Molecular characterization was performed with 10 iPBS-retrotransposons primers that resulted in a total of 345 bands and showed a mean polymorphism of 91.9%. Mean values of gene diversity (0.251), Shannon’s information index (0.388), and expected heterozygosity (0.233) revealed a relatively high level of genetic diversity in the KASIB set. AMOVA revealed higher genetic variations due to differences within the populations. Marker-based cluster analysis, including STRUCTURE and neighbor-joining algorithms, divided the material into two populations with clear differences in geographic origin. Superiors and diverse germplasm identified in the study are recommended for marker assisted selection and breeding.

Genetic Diversity and Population Structure of African Sorghum (Sorghum bicolor L. Moench) Accessions Assessed through Single Nucleotide Polymorphisms Markers.

Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs.

Genetic Variation in Sexual Size Dimorphism Is Associated with Variation in Sex-Specific Plasticity in Drosophila.

AbstractThe difference in body size between females and males, or sexual size dimorphism (SSD), is ubiquitous, yet we have a poor understanding of the developmental genetic mechanisms that generate it and how these mechanisms may vary within and among species. Such an understanding of the genetic architecture of SSD is important if we are to evaluate alternative models of SSD evolution, but the genetic architecture is difficult to describe because SSD is a characteristic of populations, not individuals. Here, we overcome this challenge by using isogenic lineages of Drosophila to measure SSD for 196 genotypes. We demonstrate extensive genetic variation for SSD, primarily driven by higher levels of genetic variation for body size among females than among males. While we observe a general increase in SSD with sex-averaged body size (pooling for sex) among lineages, most of the variation in SSD is independent of sex-averaged body size and shows a strong genetic correlation with sex-specific plasticity, such that increased female-biased SSD is associated with increased body size plasticity in females. Our data are consistent with the condition dependence hypothesis of sexual dimorphism and suggest that SSD in Drosophila is a consequence of selection on the developmental genetic mechanisms that regulate the plasticity of body size.

Immigration and seasonal bottlenecks: high inbreeding despite high genetic diversity in an oscillating population of Culicoides sonorensis (Diptera: Ceratopogonidae).

Most population genetic studies concern spatial genetic differentiation, but far fewer aim at analyzing the temporal genetic changes that occur within populations. Vector species, including mosquitoes and biting midges, are often characterized by oscillating adult population densities, which may affect their dispersal, selection, and genetic diversity over time. Here, we used a population of Culicoides sonorensis from a single site in California to investigate short-term (intra-annual) and long-term (inter-annual) temporal variation in genetic diversity over a 3 yr period. This biting midge species is the primary vector of several viruses affecting both wildlife and livestock, thus a better understanding of the population dynamics of this species can help inform epidemiological studies. We found no significant genetic differentiation between months or years, and no correlation between adult populations and the inbreeding coefficient (FIS). However, we show that repeated periods of low adult abundance during cooler winter months resulted in recurring bottleneck events. Interestingly, we also found a high number of private and rare alleles, which suggests both a large, stable population, as well as a constant influx of migrants from nearby populations. Overall, we showed that the high number of migrants maintains a high level of genetic diversity by introducing new alleles, while this increased diversity is counterbalanced by recurrent bottleneck events potentially purging unfit alleles each year. These results highlight the temporal influences on population structure and genetic diversity in C. sonorensis and provide insight into factors effecting genetic variation that may occur in other vector species with fluctuating populations.

Genetic and cultural evidence suggests a refugium for killer whales off Japan during the Last Glacial Maximum

AbstractDuring glacial periods, highly mobile species were able to shift their ranges to warmer regions that remained ice‐free—so‐called “glacial refugia.” Glacial refugia often preserved higher levels of genetic diversity than areas that were colonized after the retreat of glaciers. In this study, we examined genetic and vocal variation in R‐type (“resident”) killer whales,Orcinus orca, from Nemuro Strait in the western North Pacific to test the hypothesis that environmentally stable marine regions may have preserved refugial populations of the killer whale that retained historical genetic and cultural diversity. We found three distinct mtDNA control region haplotypes and stereotyped calls that differed significantly from the repertoire of a population further north off Kamchatka and the adjacent western North Pacific. Therefore, both genetic and cultural evidence suggest that at least some killer whales from Nemuro Strait represent a separate maternal lineage. The control region haplotype diversity for Nemuro Strait is comparable to that for the rest of the North Pacific. The data presented here are consistent with the existence of the southwestern glacial refugium for killer whales in the waters off northern Japan during the Last Glacial Maximum.

Optimizing targeted gene flow to maximize local genetic diversity: when and how to act under various scenarios of environmental change

Targeted gene flow is an emerging conservation approach which involves introducing a cohort of individuals with particular traits to locations where they can produce a conservation benefit. This technique is being proposed to adapt recipient populations to a known threat, but questions remain surrounding how best to maximize conservation outcomes during periods of continuous directional environmental change. Here we introduce a new management objective—to keep the recipient population extant and with maximum diversity of local alleles—and we explore how varying the timing and size of an introduction can maximise this objective. Our results reveal a trade-off between keeping a population extant and maintaining a high level of genetic diversity, but management levers can often optimize this so that nearly 100% of the allelic diversity is preserved. These optimum outcomes sets are highly sensitive to the predicted rate of environmental shift, as well as the level of outbreeding depression in the system.

A survey of the genome-wide genetic variation of <i>Hibiscus hamabo</i> (Malvaceae)

<i>Hibiscus hamabo</i> (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, <i>H. hamabo</i> 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 <i>H. hamabo</i> 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 <i>H. hamabo</i> 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 <i>H. hamabo</i> and its demographic history, it will be necessary to expand sampling in China and Japan.

Genetic diversity of the stag beetle, Lucanus cervus (Insecta, Coleoptera) in Romania based on ND1 mitochondrial sequences

Lucanus cervus (Linnaeus, 1758) is one of the largest Coleoptera species in Europe and one of the most recognizable. It is a saproxylic species living in woodlands and wooded urban habitats and spending its larval stages inside tree trunks below or near soil level, feeding on decaying wood. The stag beetle has a wide distribution covering the entire Europe up to the Ural Mountains. In this paper, we attempted to describe the diversity and genetic structure of L. cervus populations in Romania using the NADH mitochondrial molecular marker. We identified 36 haplotypes arranged in a star-shaped structure with a central haplotype shared by many samples and linked by one or two mutational steps with other 35, represented by 1–3 samples. This pattern is frequently attributed to populations that have undergone recent range expansion, a phenomenon which is also sustained by the mismatch analysis. The analyzed populations revealed various degrees of genetic diversity. Many populations with relatively high levels of genetic diversity were found outside the Natura 2000 Network Special Areas of Conservation, while some populations included in protected areas proved to have low values of genetic variability. This underlines the need to review the designated protection sites for this species in Romania.

Genetic and epigenetic variation of Trapa bispinosa under slope gradient: A case study in a subtropical freshwater lake

Dynamic environmental factors can influence the genetic diversity and epigenetic variation of aquatic plants, thus accelerate the rate of species adaptations. Trapa bispinosa is an aquatic crop which is widely distributed in China and worldwide, yet little is known about the genetic and epigenetic variations of T. bispinosa in fishery and nature habitats. By using AFLP and MSAP, we analyzed the genetic and epigenetic variations of 27 T. bispinasa populations in a subtropical freshwater lake. A relative high level of genetic diversity (mean HE = 0.312, I = 0.480, PPL = 54.90%) and epigenetic variation (mean eHE = 0.351, eI = 0.531, ePPL = 67.84%) were detected. Besides, fishery habitats maintained relative higher epigenetic variations of T. bispinosa (HE = 0.254, eI = 0.378, ePPL = 68.28%) than nature habitats (eHE = 0.253, eI = 0.376, ePPL = 67.77%). Overall variations were basically distributed within populations (ØST = 0.260, P < 0.001). Bayesian analysis revealed a pattern of genetic structure consisting of two clusters among the populations. The Mantel regression of genetic and epigenetic variation against geographic distance did not reveal any correlations, but showed a correlative relationship with environmental variables (r = −0.47, P < 0.05). Specially, genetic diversity of T. bispinosa showed a positive correlation with slope aspect. These results indicated that habitat slope may shape the pattern of genetic variation in T. bispinosa, which further illustrated that even in a fine geographical scale, genetic diversity was unevenly distributed, restoration measurements for this aquatic crop should carefully take the habitat slope into account. Data accessibilityAll codes and polymorphism raw data are openly available from the Github repository: https://github.com/yixian185/Data-for-Trapa.

The Clinical Significance of Genetic Variation in Ovarian Cancer.

Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.

Morphological and molecular description of Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) from the Manchurian wapiti Cervus elaphus xanthopygus.

Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) was isolated from the lungs of the Manchurian wapiti in Primorsky kray, Russia. The newly described species exhibits morphological characteristics of Dictyocaulus but is distinct from congeneric species based on morphological (lengths of body and esophagus, distances from the anterior end to nerve ring and to excretory pore, the thickness of the buccal capsule, etc.) and molecular features. High levels of genetic divergence as well as Bayesian phylogenetic analyses based on 18S rRNA nuclear and cox1 mitochondrial genes supported the independence of Dictyocaulus xanthopygus sp. nov. Secondary structures of helix 39 of 18S rRNA were identical, while ES9 adjacent to the helix has a unique conformation for newly described worms. Energy-efficient conformational rearrangements of rRNA secondary structures can be applicable in studies on the pathogenesis, epidemiology, taxonomy and evolutionary biology of parasites. Additionally, bracketed dichotomous keys to six valid species of Dictyocaulus were prepared.

Post-hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*-genome diploid species.

Understanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A-, B- and D-lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S-genome species (Aegilops speltoides) of the B-lineage and four S*-genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D-lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A-, B- and D-lineage species. Our estimates identified frequent genetic introgressions from A- and B-lineages to the D-lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A- and B-lineages along all the seven chromosomes to the extant D-lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B-lineage) and the other four S*-genome diploid species (D-lineage), while natural selection is a potential contributor to divergence among the four S*-genome species at telomeric regions. Our study provides a genome-wide view on how genetic introgression and natural selection acted together yet chromosome-regionally divided to promote genomic divergence among the five S- and S*-genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.

Development of microsatellite markers and genetic diversity of the velvetbean caterpillar Anticarsia gemmatalis (Lepidoptera: Erebidae)

AbstractThe velvetbean caterpillar Anticarsia gemmatalis (VBC) is widely distributed in the Americas and causes severe damage to soybean foliage. This insect presents high ecological plasticity, a feature that is of great importance to understand its genetic diversity and potential gene flow to assist in resistance management strategies. With this objective, we developed microsatellite markers for VBC and applied them to five populations from Brazil. Nine primers were polymorphic, with high values of polymorphic information content (PIC &gt; 0.5), and 134 alleles were identified in 155 individuals. These primers indicated deviation from the Hardy–Weinberg equilibrium for all populations (observed heterozygosity, Ho = 0.48, expected heterozygosity, He = 0.76), with moderate to high levels of genetic diversity and a moderate fixation index (FST = 0.14) among the populations. Analysis of population structure indicated the formation of two principal clusters. The northern one can be divided into the two populations that formed the cluster, with high genetic differentiation between them. The other cluster is formed by three populations, and we found evidence of low gene flow between them in the south–north direction, indicating that these populations may be migratory in certain conditions. These findings indicate that the designed primers were effective in describing the genetic diversity of VBC, with major implications for integrated pest management. Given the little gene flow and the high genetic diversity of populations, they present great potential to become resistant to control practices, which can lead to increased management costs.

Historical land use patterns provide insight into contemporary insect diversity loss.

Healthy insect populations are vital for maintaining natural ecosystems and essential to global food security. The ongoing dramatic loss of insect species and biomass is thus a global cause for concern, with much focus on this topic in the media. Yet, determining the mechanism behind these declines remains difficult, particularly when attempting to differentiate between anthropogenic drivers of biodiversity loss and long-term natural fluctuations. In a From the Cover manuscript in this issue of Molecular Ecology, Crossley et al. (2022) examined the long-term impact of land use change on freshwater insects by estimating levels of genetic diversity with publicly available data for the cytochrome c oxidase subunit 1 (CO1) mitochondrial locus from >700 aquatic insect species across the United States. Contemporary genetic diversity measures reflect both current and past demography and therefore are related to both past and present habitat change. Crossley et al. found that environments with greater cropland extent over the last 200 years were associated with lower genetic diversity in contemporary aquatic insect populations. This indicates that historical land use is an important factor in contemporary population dynamics. Most critically, in regions of historical cropland cover that have been converted towards other uses (such as urban environments) more recently, aquatic insect populations exhibited higher levels of genetic diversity, indicating a possible rebound in insect populations after cessation of agricultural activity. This study highlights the power of using publicly available data to answer crucial questions regarding the current biospheric emergency.

Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken.

Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.

Микросателлитные локусы в генетической оценке плюсовых деревьев Pinus sylvestris L.

In this study, a comparative analysis was performed to estimate the genetic diversity levels of Pinus sylvestris L. in 49 seed orchards of I generation and progeny test plantings using 4-nucleus microsatellite loci. The seed orchards are located in the Petrozavodsk and Zaonezhye regions of the Republic of Karelia. The progeny trials were created by half-sibling seed progenies of the clones in the Petrozavodsk seed orchard. Micro-Checker software was used to identify null alleles and exclude genotyping errors. Coefficients of genetic originality were determined by examining the genetic structure of breeding objects in relation to the proportion between the rare and the dominant alleles for each selected tree. A major part of the rarest alleles (27.3–37.0 %) and a small fraction of the most common alleles (3.3–14.8 %) were detected for the distinct range of the pine trees in both seed orchards and test cultures. The largest number (40) of all identified alleles (51) was found in the Petrozavodsk seed orchard. The Hardy-Weinberg test comparing allele rates to expectational values showed a lack of heterozygotes in each category of the empirical substances. The selected material also had high levels of allelic and genetic diversity. The average number of alleles per locus ranged from 7.75 to 10.50. The average effective number was from 5.00 to 6.54. The observed heterozygosity varied from 0.60 to 0.70. The expected heterozygosity was 0.63–0.71. The numerical deviations were statistically insignificant. The AMOVA molecular dispersion result was 5 %, indicating the absence of significant genetic differentiation between the breeding objects. The heterozygote deficiency was caused not only by the presence of null alleles, but also by the selection. Namely, the set of alleles in the experimental material, randomly selected from a limited number of genotypes (clones), may differ from the natural population. The high level of the rarest alleles in the given range of the pine trees can also be explained as a selection effect. The results obtained in this study are important for creating breeding objects with higher genetic value. For citation: Ilinov A.A., Raevsky B.V. Genetic Evaluation by Microsatellite Loci of Pinus sylvestris L. Plus Trees. Lesnoy Zhurnal = Russian Forestry Journal, 2023, no. 3, pp. 48–68. (In Russ.). https://doi.org/10.37482/0536-1036-2023-3-48-68

Variability of cell wall recalcitrance and composition in genotypes of Miscanthus from different genetic groups and geographical origin.

Miscanthus is a promising crop for bioenergy and biorefining in Europe. The improvement of Miscanthus as a crop relies on the creation of new varieties through the hybridization of germplasm collected in the wild with genetic variation and suitable characteristics in terms of resilience, yield and quality of the biomass. Local adaptation has likely shaped genetic variation for these characteristics and is therefore important to quantify. A key biomass quality parameter for biorefining is the ease of conversion of cell wall polysaccharides to monomeric sugars. Thus far, the variability of cell wall related traits in Miscanthus has mostly been explored in accessions from limited genetic backgrounds. Here we analysed the soil and climatic conditions of the original collection sites of 592 Miscanthus genotypes, which form eight distinct genetic groups based on discriminant analysis of principal components of 25,014 single-nucleotide polymorphisms. Our results show that species of the genus Miscanthus grow naturally across a range of soil and climate conditions. Based on a detailed analysis of 49 representative genotypes, we report generally minor differences in cell wall characteristics between different genetic groups and high levels of genetic variation within groups, with less investigated species like M. floridulus showing lower recalcitrance compared to the other genetic groups. The results emphasize that both inter- and intra- specific variation in cell wall characteristics and biomass recalcitrance can be used effectively in Miscanthus breeding programmes, while also reinforcing the importance of considering biomass yield when quantifying overall conversion efficiency. Thus, in addition to reflecting the complexity of the interactions between compositional and structural cell wall features and cell wall recalcitrance to sugar release, our results point to traits that could potentially require attention in breeding programmes targeted at improving the Miscanthus biomass crop.

Assessment of genetic diversity and population structure of Neocaridina denticulata sinensis in the Baiyangdian drainage area, China, using microsatellite markers and mitochondrial cox1 gene sequences

Neocaridina denticulata sinensis is a crustacean of major economic significance in the Baiyangdian drainage area. In this study, the first assessment of N. denticulata sinensis genetic diversity and population structure was performed based on sequence analysis of nine polymorphic microsatellite loci and the mitochondrial cytochrome oxidase subunit I (cox1) gene. Samples (n = 192) were collected from four different regions in the Baiyangdian drainage area i.e., Baiyangdian Lake, Jumahe River, Xidayang Reservoir, and Fuhe River. Microsatellite loci analysis identified high levels of genetic diversity represented by observed heterozygosity (Ho) of 0.6865 ∼ 0.9583, expected heterozygosity (He) of 0.7151 ∼ 0.8723, and polymorphism information content (PIC) of 0.6676 ∼ 0.8585. Based on the analysis of cox1 sequences, haplotype diversity (Hd) ranged from 0.568 to 0.853 while nucleotide diversity (π) ranged from 0.0029 to 0.2236. Furthermore, there was no evidence of expansion events in the N. denticulata sinensis populations. Pairwise FST revealed pronounced genetic differentiation, and clustering analyses showed defined genetic structures within the N. denticulata sinensis population. Three groups were identified from four sampled stocks, with Xidayang Reservoir, and Fuhe River populations clustered in the same group. This work identified novel molecular markers and provided an important reference to guide management strategies to assist conservation of N. denticulata sinensis resources.

Growth-related phenotypic and genetic diversity analysis of successive mass selected generations of Kumamoto oyster (Crassostrea sikamea)

The Kumamoto oyster, Crassostrea sikamea, is widely found in China, from Jiangsu to Guangxi, and has high aquaculture potential due to its beautiful shape and unique flavor. The individual size of C. sikamea in China is significantly smaller than that in the United States of America, the main reason should be the lack of artificial breeding. In 2012, a mass selective breeding program for C. sikamea was initiated to improve growth performance of our successive mass-selected C. sikamea generations, with the ultimate aim of improving the growth rate of C. sikamea. At harvest, each selective breeding generation showed superior growth performance compared to the corresponding control line. In the four generations of mass selection, the response to selection (SR), realized heritability (hR2) and genetic gain (GG) for shell height were 0.63–0.82, 0.38–0.51 and 5.54–9.50%, respectively. Meanwhile, the average SR, hR2 and GG of the total weight of C. sikamea after mass selection for four successive generations were 0.61–0.90, 0.36–0.56 and 12.25–15.34%, respectively. The positive selection response for the fast growth of C. sikamea suggested that they have high levels of genetic variation, that can be used in future breeding programs to further improve their aquaculture traits. In addition, we also studied the genetic variability of successive mass-selected generations using microsatellite markers, and the results indicated that the selected line F4 exhibited significant lower genetic variation compared to F0 population. In future, we will use the F4 population to cross with other fast-growing breeding populations from other wild populations to retain the fast-growing traits while restoring its population genetic diversity.

Population genetic assessment of Viburnum japonicum in China using ddRAD-seq.

Viburnum japonicum is a rare plant species and endemic to the coastal region of Eastern Asia with extremely small populations. Within mainland China, this species can be only found in narrow habitats of the northeast coastal islands of Zhejiang Province. However, there are scarce conservation genetic studies on V. japonicum, which has limited the effective conservation and management of this rare species. Here, 51 individuals in four natural populations covering the Chinese geographic range of the species were sampled to assess the genetic diversity and population structure. A total of 445,060 high-quality single nucleotide polymorphisms (SNPs) were identified using double digest restriction-site associated sequencing (ddRAD-seq). The overall average values of observed heterozygosity (Ho), expected heterozygosity (He), and average nucleotide diversity (π), were 0.2207, 0.2595, and 0.2741, respectively. The DFS-2 population exhibited the highest level of genetic diversity among all the populations. Genetic differentiation between populations was moderate (F ST = 0.1425), and there was selfing between populations (F IS = 0.1390, S = 24.52%). Of the total genetic variation, 52.9% was found among populations through AMOVA analysis. The Mantel test (r = 0.982, p = 0.030) combined with analyses of the Maximum Likelihood (ML) phylogenetic tree, ADMIXTURE, and principal component analysis (PCA), revealed that populations of V. japonicum were genetically segregated and significantly correlated with their geographical distribution. Our study demonstrated that V. japonicum maintained a medium level of genetic diversity and differentiation with a strong population structure, and the results were mainly affected by its island distribution pattern and self-crossing characteristics. These results provide insights into the genetic diversity and population history of V. japonicum, critical information for conserving and sustainably developing its genetic resources.