Analysis Of Genetic Structure Research Articles

Analysis of maternal genetic structure of mitochondrial DNA control region from Tai-Kadai-speaking Buyei population in southwestern China

BackgroundEven though the Buyei are a recognised ethnic group in southwestern China, there hasn’t been much work done on forensic population genetics, notably using mitochondrial DNA. The sequences and haplogroups of mitochondrial DNA control regions of the Buyei peoples were studied to provide support for the establishment of a reference database for forensic DNA analysis in East Asia.Methods and resultsThe mitochondrial DNA control region sequences of 200 Buyei individuals in Guizhou were investigated. The haplotype frequencies and haplogroup distribution of the Buyei nationality in Guizhou were calculated. At the same time, the paired Fst values of the study population and other populations around the world were computed, to explore their genetic polymorphism and population relationship. A total of 179 haplotypes were detected in the Buyei population, with frequencies of 0.005–0.015. All haplotypes were assigned to 89 different haplogroups. The haplotype diversity and random matching probability were 0.999283 and 0.0063, respectively. The paired Fst genetic distances and correlation p-values among the 54 populations revealed that the Guizhou Buyei was most closely related to the Henan Han and the Guizhou Miao, and closer to the Hazara population in Pakistan and the Chiang Mai population.ConclusionsThe study of mitochondrial DNA based on the maternal genetic structure of the Buyei nationality in Guizhou will benefit the establishment of an East Asian forensic DNA reference database and provide a reference for anthropological research in the future.

Astyanax caucanus: microsatellite loci development and population genetics in the Cauca River, Colombia

Astyanax caucanus is an endemic fish species to the Magdalena-Cauca basin in Colombia. It is considered a Least Concern species by the International Union for Conservation of Nature, and currently, it is not a fishery resource. Its fertilized eggs may drift up to 4–5 days before hatching and can be carried up to 340 km given the water velocity of the river. Although A. caucanus is listed as short -migratory species (< 50 km), this study hypothesized that it exhibits gene flow along the middle and lower section of the Cauca River due to the great potential for larval dispersal. To test this hypothesis, we developed a set of species-specific microsatellite primers suitable for population genetic studies. Genetic structure analyses with 193 samples evidenced two genetic stocks that coexist, comigrate, and exhibit gene flow along the study area. Both stocks show high genetic diversity indices (Na and HE) and effective population sizes (Ne > 1000), but also show evidence of bottlenecked populations and high values of the inbreeding coefficient (FIS). Finally, these results are useful to understand the effects of other anthropic activities, besides fishing pressure on population bottlenecks found for other fish species cohabiting the area.

Genetic Variability of Mass-Selected and Wild Populations of Yellow Drum (Nibea albiflora) Revealed Using Microsatellites

In this study, twelve polymorphic microsatellite loci were screened to evaluate the genetic diversity of five yellow drum (Nibea albiflora) populations in the Zhoushan Sea region of the East China Sea, including one wild population (WP), one artificially propagated population (common population, CP), and three breeding populations (parent population, F4; all-female population, AF; and neo-male population, NeoG). The results of genetic diversity analyses showed that all five yellow drum populations had relatively high genetic diversity, with the highest in WP and the lowest in NeoG. Genetic structure analyses showed that the level of genetic differentiation among populations was low, with that between CP and F4 being the largest, whereas that between CP and WP was the smallest. Mutation–drift equilibrium analysis showed that the five populations likely did not experience a recent bottleneck. Our results suggest the CP population was the most suitable for large-scale release for stock enhancement, and precautionary measures shall be taken for the AF population before it is used for cage culture to avoid potential genetic concerns of the wild population. Nevertheless, further genetic diversity monitoring is needed to evaluate genetic effects and avoid the negative impact of excessive genetic differentiation between breeding and wild populations.

Genetic diversity analysis of different geographic populations of black carp (Mylopharyngodon piceus) based on whole genome SNP markers

Black carp, Mylopharyngodon piceus, is one of the major farmed fish in China, generating a considerable amount of economic value annually. To investigate the genetic variation of black carp germplasm resources in China, this study was the first to use the whole genome SNPs of black carp for analysis. A total of 139 samples of nine black carp populations in the Yangtze River and Pearl River Systems of China were collected, and 53,322 high-quality SNP loci were obtained after GBS sequencing and filtering. Genetic diversity parameters were calculated for nine populations of black carp based on these genetic data. All 7 populations from the Yangtze River system and 2 populations from the Pearl River system showed high level of genetic diversity. For each population, the nucleotide diversity (π) varied from 0.283 to 0.308, the observed heterozygosity (Ho) from 0.271 to 0.317, the expected heterozygosity (He) from 0.273 to 0.292，the number of effective alleles (Ne) from 1.440 to 1.475, and the polymorphism information content (PIC) from 0.224 to 0.239. The fixation index (Fst) between populations ranged from 0.036 to 0.133, remaining at low and medium differentiation. Phylogenetic tree analysis, principal component analysis (PCA) and population genetic structure analysis revealed that the nine populations could be divided into three ancestral populations. The seven populations of the Yangtze River system comprised two primary ancestral groups, with a small amount of gene flow between populations. The internal genetic structure of populations within the Pearl River system was homogeneous, with one common ancestral source as the dominant component. In conclusion, the data and results generated from this study will provide a useful addition to the genetic resources of black carp and will provide reference information for further germplasm conservation and genetic improvement of black carp.

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in southwestern China.

The Sichuan-Yunnan region is the main production area of yaks in southwestern China, with rich genetic resources of Yaks. Nevertheless, there have been limited study on the genetic characteristics of the entire yak populations in Tibet and southwestern China. In this study, we performed whole-genome resequencing to identify genetic variation information in a total of 198 individuals from six yak breeds (populations) in Sichuan (Muli yak, Jinchuan yak, Changtai yak, Maiwa yak), Yunnan (Zhongdian yak), and Tibet (Tibetan yak). The aim was to investigate the whole-genome genetic diversity, population genetic structure, and genome selection signatures. We observed that all six populations exhibit abundant genetic diversity. Except for Tibetan yaks, which showed low nucleotide diversity (0.00104), the remaining yak populations generally displayed high nucleotide diversity (0.00129-0.00153). Population genetic structure analysis revealed that, among the six yak populations, Muli yak exhibited greater differentiation from other yak populations and formed a distinct cluster independently. The Maiwa yak population displayed a complex genetic structure and exhibited gene exchange with Jinchuan and Changtai yaks. Positive selection signals were detected in candidate genes associated with growth (GNB4, HMGA2, TRPS1, and LTBP1), reproduction (PI4KB, DYNC1I1, and GRIP1), immunity (CD200 and IL1RAP), lactation (SNX13 and CPM), hypoxia adaptation (NDUFB6, PRKN, and MRPS9), hair (KRT24, KRT25, and KRT26), meat quality (SUCLG2), digestion and absorption (CLDN1), and pigment deposition (OCA2) using the integrated Pi and F ST methods. This study provides significant insights into understanding the whole-genome genetic characteristics of yak populations in Tibet and southwestern China.

Impact of feralization on evolutionary trajectories in the genomes of feral cat island populations.

Feralization is the process of domesticated animals returning to the wild and it is considered the counterpart of domestication. Molecular genetic changes are well documented in domesticated organisms but understudied in feral populations. In this study, the genetic differentiation between domestic and feral cats was inferred by analysing whole-genome sequencing data of two geographically distant feral cat island populations, Dirk Hartog Island (Australia) and Kaho'olawe (Hawaii) as well as domestic cats and European wildcats. The study investigated population structure, genetic differentiation, genetic diversity, highly differentiated genes, and recombination rates. Genetic structure analyses linked both feral cat populations to North American domestic and European cat populations. Recombination rates in feral cats were lower than in domestic cats but higher than in wildcats. For Australian and Hawaiian feral cats, 105 and 94 highly differentiated genes compared to domestic cats respectively, were identified. Annotated genes had similar functions, with almost 30% of the divergent genes related to nervous system development in both feral groups. Twenty mutually highly differentiated genes were found in both feral populations. Evolution of highly differentiated genes was likely driven by specific demographic histories, the relaxation of the selective pressures associated with domestication, and adaptation to novel environments to a minor extent. Random drift was the prevailing force driving highly divergent regions, with relaxed selection in feral populations also playing a significant role in differentiation from domestic cats. The study demonstrates that feralization is an independent process that brings feral cats on a unique evolutionary trajectory.

Whole-genome sequencing identified candidate genes associated with high and low litter size in Chuanzhong black goats.

The reproductive performance of goats significantly influences breeding efficiency and economic returns, with litter size serving as a comprehensive indicator. Despite this, research on the genetic control of litter size remains limited. Therefore, we aimed to explore the candidate genes affecting fecundity and compared the whole-genome sequences (WGS) of 15 high-litter (HL) and 15 low-litter (LL) size in Chuanzhong black goats. Then genetic diversity and genomic variation patterns were analyzed by phylogenetic, principal component and population genetic structure analysis, it was found that HL and LL subpopulations diverged. Population evolutionary selection elimination analysis was performed by Fst and θπ resulted in 506 genes were annotated in HL and 528 genes in LL. These genes were mainly related to Hippo signaling pathway, G protein-coupled signaling pathway, G protein-coupled receptor activity, cell surface receptor signaling pathway, gonadal and reproductive structure development. According to the significantly selected genomic regions and important pathways, we found that the g.89172108T > G variant locus in the exon of the AMH gene was significantly associated with litter size (P < 0.05), which could be used as an auxiliary selection gene for the high fertility of Chuanzhong black Goat.

Population genetics of the Ixodes affinis (Ixodida: Ixodidae) complex in America: new findings and a host-parasite review.

Ticks are hematophagous ectoparasites associated with a wide range of vertebrate hosts. Within this group, the Ixodidae family stands out, in which the Ixodes genus contains at least 245 species worldwide, from which 55 species are present in the Neotropical region. Ixodes affinis, a tick described in 1899, has a wide distribution from the Southern Cone of America to the United States. However, since its description, morphological variability has been reported among its populations. Furthermore, attempts have been made to clarify its status as a species complex using mitochondrial markers, but mainly in restricted populations of South and Central America. Thus, information related to populations of the transition region between the Neotropical and Nearctic zones is lacking. For these reasons, the objectives of the study were to evaluate the genetic diversity and structure of I. affinis across the Americas and to compile all the published records of I. affinis in America, to elucidate the host-parasite relationships and to identify their geographical distribution. For this, a phylogeny, and AMOVA analyses were performed to assess the genetic structure of samples obtained by field work in South Carolina, USA and Yucatán, Mexico. A total of 86 sequences were retrieved from a fragment of the 16S region. Phylogeny and genetic structure analysis showed four groups that were geographically and genetically related with high branch support and Fst values, all of them statistically significant. The results obtained support the hypothesis that I. affinis it corresponds to a complex of four species, which must be validated through future morphological comparisons.

Unfolding genomic regions and identification of novel marker-trait associations for therapeutic traits flavonoid and anthocyanin content in rice (Oryza sativa L.)

The genetic diversity, structure analysis, and marker-trait association for total flavonoid content (TFC) and anthocyanin content (AC) were studied in rice using 79 germplasm lines with 210 polymorphic microsatellite markers. Among the landraces studied, RG83 (RPHP 93) had the highest level of TFC (227.78 QE/100g) and RG126 (Kallimadayan) contained the highest level of AC (0.416 CE/100g). The STRUCTURE analysis grouped the studied landraces into three genetic structure groups which nearly matched the geographical distance. The results of the marker-trait associations study using MLM with PCA and kinship indicated that the SSR markers RM287 and RM19358 were closely associated with AC while another two markers RM452 and RM 2197 were closely linked with TFC and these two markers were found to be in the genomic regions related to the candidate genes for TFC and AC biosynthesis. In addition, the markers RM10961, RM5963, and RM559 were also found to have significant marker-trait associations with both AC and TFC.

Genetic structure of southern populations of Hydrochoerus hydrochaeris (Rodentia: Caviidae)

Abstract The capybara (Hydrochoerus hydrochaeris) is a large semi-aquatic rodent with a broad distribution across South America. Although it is a relatively common and well-known species, there are few studies on its evolutionary history. Consequently, we decided to investigate the genetic diversity, population structure, and demographic history of capybaras, including new populations from its southern distribution range, by using a 226 bp fragment of the mitochondrial D-loop region. We found 16 haplotypes and populations, with moderate levels of haplotype and nucleotide diversity. In addition, the genetic structure analyses suggested high genetic divergence among populations, mainly among Pampean and Chacoan populations. We also found a consistent phylogeographical pattern with the distribution of main rivers. In agreement with palaeontological data, we propose two colonization pathways towards the south driven by main basins: Paraná–Paraguay and Uruguay–Atlantic.

Genomic prediction and allele mining of agronomic and morphological traits in pea (Pisum sativum) germplasm collections.

Well-performing genomic prediction (GP) models for polygenic traits and molecular marker sets for oligogenic traits could be useful for identifying promising genetic resources in germplasm collections, setting core collections, and establishing molecular variety distinction. This study aimed at (i) defining GP models and key marker sets for predicting 15 agronomic or morphological traits in germplasm collections, (ii) verifying the GP model usefulness also for selection in breeding programs, (iii) investigating the consistency between molecular and phenotypic diversity patterns, and (iv) identifying genomic regions associated with to the target traits. The study was based on phenotyping data and over 41,000 genotyping-by-sequencing-generated SNP markers of 220 landraces or old cultivars belonging to a world germplasm collection and 11 modern cultivars. Non-metric multi-dimensional scaling (NMDS) and an analysis of population genetic structure indicated a high level of genetic differentiation of material from Western Asia, a major West-East diversity gradient, and quite limited genetic diversity of the improved germplasm. Mantel's test revealed a low correlation (r = 0.12) between phenotypic and molecular diversity, which increased (r = 0.45) when considering only the molecular diversity relative to significant SNPs from genome-wide association analyses. These analyses identified, inter alia, several areas of chromosome 6 involved in a largely pleiotropic control of vegetative or reproductive organ pigmentation. We found various significant SNPs for grain and straw yield under severe drought and onset of flowering, and one SNP on chromosome 5 for grain protein content. GP models displayed moderately high predictive ability (0.43 to 0.61) for protein content, grain and straw yield, and onset of flowering, and high predictive ability (0.76) for individual seed weight, based on intra-population, intra-environment cross-validations. The inter-population, inter-environment assessment of the models trained on the germplasm collection for breeding material of three recombinant inbred line (RIL) populations, which was challenged by much narrower diversity of the material, over eight-fold less available markers and quite different test environments, led to an overall loss of predictive ability of about 40% for seed weight, 50% for protein content and straw yield, and 60% for onset of flowering, and no prediction for grain yield. Within-RIL population predictive ability differed among populations.

Genetic underpinning of historical afforestation with allochthonous Pinus cembra in the northwestern Swiss Alps

AbstractThroughout the last centuries, the structure and genetic composition of forests have been strongly affected by forest management. Over 30% of European forests are artificially regenerated, very often using translocated forest reproductive material, among these species the Swiss stone pine (Pinus cembra L.). In the late nineteenth and early twentieth centuries, the species was largely used for artificial afforestation in the northern Alps. However, only a few planted trees have survived. Therefore, we aimed to evaluate if the historical afforestation of P. cembra in the northwestern Swiss Alps relied on allochthonous material. We sampled 12 sites, genotyping 11 nuclear microsatellites, to infer the spatial genetic structure of regional populations, to test for genetic differences between natural and planted stands, and to infer potential source regions of planted stands using reference samples covering the entire Alps. Population genetic structure analysis allowed us to distinguish planted from natural stands and to determine that forest reproductive material used for plantations was not of regional origin. We found similar levels of genetic diversity between natural and planted stands. Assignment tests revealed that reproductive material for planting was translocated to the study area from two source regions, i.e., near the border of Switzerland and Austria, and further to the East, between Austria and Italy. Our study shows how genetic tools may inform about historical transfer of forest reproductive material, which still may affect the population genetic make-up of regional occurrences, e.g., because of reduced natural regeneration.

Population genetics analysis of the black rockfish Sebastes schlegelii in Northern China based on 2b-RAD simplified genome sequencing

The black rockfish Sebastes schlegelii is an important fishery species in Japan, South Korea, and China. Overfishing has severely depleted the natural resources of S. schlegelii in recent years, leading to the initiation of programs aimed at enhancing fish stock. However, the genetic structure of northern populations remains elusive, posing challenges in collecting and preserving germplasm resources. In this study, a total of 191 S. schlegelii individuals from seven populations, including one cultured population (Changdao: CDYZ) and six wild populations (Lianyungang: LYG; Qingdao: QD; Weihai: WH; Changdao: CDYS; Beidaihe: BDH) sequenced by 2b-RAD method and their population genetics was analyzed using 27,064 SNPs obtained. The results indicated low genetic diversity in both wild and cultured populations (PIC &lt; 0.25, Ho: 0.174-0.273, He: 0.173-0.234), with the cultured population exhibiting higher diversity than the wild ones. Moderate genetic differentiation existed between the cultured population and six wild populations (0.05 &lt; Fst &lt; 0.25). However, the genetic differentiation was lower among the other wild populations (Fst &lt; 0.05). The analyses of population genetic structure indicated that the wild populations clustered together first and finally with the cultured population CDYZ, which clustered separately except for one individual. Therefore, scientific breeding programs and germplasm conservation can be important in stabilizing genetic structure. In addition, gene flow among the seven populations was high (Nm &gt; 1). This study provides a theoretical basis for conserving and rationalizing germplasm resources for S. schlegelii.

Genomic data inform taxonomy and conservation of Critically Endangered shrubs: a case study of Zieria (Rutaceae) species from eastern Australia

Abstract Zieria buxijugum, Z. formosa, and Z. parrisiae are three closely related, Critically Endangered species of questionable taxonomic validity that occur within six kilometres of each other on the south coast of New South Wales, Australia. We investigated genetic relationships and diversity of these species, along with two related but taxonomically distinct congeners, Z. granulata and Z. tuberculata, and a possible undescribed taxon, Z. aff. tuberculata. Double-digest restriction-site associated sequencing (ddRADseq) was used to generate anonymous genomic loci that were used for phylogenetic, network, and genetic structure analyses, and for estimating genetic diversity of the threatened species. Our results support the current taxonomic status of Z. buxijugum, Z. formosa, and Z. parrisiae, and suggest that Z. aff. tuberculata warrants recognition as a distinct species. We detected no evidence of inbreeding in the three Critically Endangered species, and found their genetic diversity to be similar to that of the more widespread species Z. granulata and Z. tuberculata. Comparison of plant material held in ex situ collections at the Australian National Botanic Gardens with wild plants highlighted several genotypes of the Critically Endangered species that are not represented in the ex situ collection, and we provide suggestions for the future inclusion of those unrepresented genotypes.

Weak Population Genetic Structure of the Eurasian Crane &lt;i&gt;Grus grus&lt;/i&gt; L.

The article presents an extended (as compared with our previous studies) analysis of the population genetic structure of a migratory wide-range bird species with a high abundance, the Eurasian Crane Grus grus L. Using seven highly polymorphic microsatellite loci, high and very similar values of genetic diversity parameters were obtained in the samples of both the western (G. g. grus) and eastern (G. g. lilfordi) subspecies. Coefficients of genetic differentiation between these subspecies (FST = 0.008, GST = 0.002) were also found to be low. According to AMOVA, 99% of genetic variation of G. grus is attributed to individual levels. Using the Bayesian clustering algorithm implemented in STRUCTURE software, no clear population-genetic structuring of the species was revealed. However, visualization of spatial patterns of genetic variability in Geneland showed the presence of a cluster of “pure” subspecies G. g. grus and G. g. lilfordi surrounding a cluster of individuals from the zone of intergradation of these subspecies. This result, along with the observed very low FST values, may indicate subtle genetic differences between cranes from the studied area, possibly having a mutational nature. The lower allelic richness and lack of private alleles in the eastern subspecies suggest that G. g. lilfordi is relatively evolutionary young and suggest its recent origin from some eastern marginal populations of the nominative western subspecies.

Genetic diversity and population structure analysis of grapevine germplasm of theAegean region (Türkiye) by SSR markers

Genetic diversity and population structure analysis of grapevine germplasm of theAegean region (Türkiye) by SSR markers

Discovery of a new population of the endangered giant water bug Kirkaldyia deyrolli (Heteroptera: Belostomatidae) in Kyushu and evaluation of their genetic structure

AbstractThe giant water bug Kirkaldyia deyrolli is one of the most well‐known endangered aquatic insects in Japan. The population of this species in Kyushu, one of the four major islands of the Japanese Archipelago, is extremely limited. In the present study, we identified a new population of K. deyrolli and undertook population genetic structure analyses based on genome‐wide nuclear DNA single nucleotide polymorphisms (SNPs). We collected samples using a nonlethal sampling method and obtained 59,279 SNPs. The results of our study confirm that sufficient SNP data for population genetic structure analysis can be obtained through nonlethal sampling. We determined that the newly identified population is genetically differentiated from a previously identified population on Kyushu. Therefore, this population is considered highly important for the conservation of K. deyrolli in Kyushu.

Genetic diversity and population structure analysis in early generations maize inbreds derived from local germplasm of Eastern Himalayan regions using microsatellite markers

Abstract The North-Eastern region (NER) of India falls under the Eastern Himalayan region and it is a bio-diversity hub. Diverse maize landraces with wide adaptability to extreme climatic and soil scenario like heavy rainfall, drought and acidic soil conditions have been grown in NER since time immemorial. However, maize diversity in NER region has drastically reduced due to introduction of high yielding varieties and hybrids. Modern maize breeding programmes are focused on high yield but other unique traits like stay green trait, prolificacy (more than one fertile ear per plant), self-fertilizing ability are also important and the local germplasm of the NER region can contribute with these unique traits. Prior to the selection of any lines in several breeding programmes, assessment of genetic diversity and population structure are basic requirements. Hence, in the present study assessment of genetic diversity and population structure study in 30 maize inbreds developed from different germplasm of NER was undertaken using SSR markers, selected for their broad distribution throughout the genome, in order to assess the extent of allelic diversity among the lines and whether any population structure could be established. In addition to assessing molecular diversity, the study aims to evaluate the potential for yield and other beneficial and unique alleles that have high potential to contribute in the genetic enhancement programme of maize.

Genetic diversity and population structure analysis of bread wheat (Triticum aestivum L.) germplasms as revealed by inter simple sequence repeat (ISSR) markers

Genetic diversity and population structure analysis of bread wheat (Triticum aestivum L.) germplasms as revealed by inter simple sequence repeat (ISSR) markers

Characterization of agronomic traits and genomic diversity in a newly assembled radish core collection

AbstractCrop breeding programs are reliant on the genetic diversity of varieties and germplasm collections. Raphanus sativus L. is a root crop species of the Brassicaceae family that accounts for ∼2% of global vegetable production. We recently reported the assembly of a new radish core collection consisting of 125 accessions obtained from worldwide germplasm banks. To develop a comprehensive plant resource for radish research and breeding, we characterized the agronomic traits of 83 accessions and analyzed their genome‐wide DNA variations along with 17 previously analyzed accessions. A total of 14 agronomically important root, leaf, and flower phenotypic traits were examined according to the guidelines of the International Union for the Protection of New Plant Varieties. Chemical diversity in radish roots was investigated by measuring their sugar, glucosinolate, and anthocyanin contents. Through high‐depth whole‐genome resequencing of 100 accessions and multi‐sample genotyping analysis using the Rs2.0 genome assembly as a reference, we identified a total of 796,294 homozygous high‐quality single‐nucleotide polymorphisms. Genetic structural analysis using a neighbor‐joining algorithm and multi‐dimensional scaling analysis of the variations were applied to classify the accessions into three major groups, including 37 and 55 accessions of European and Asian cultivated radishes, respectively, and eight wild radish accessions. For each accession, the mitochondria‐encoded Ogura cytoplasmic male‐sterility determinant orf138 and nuclear fertility restorer PPR‐B genes were reconstructed by reference‐guided assembly. It is anticipated that these genetic diversity and agronomic properties of the radish core collection will facilitate breeding programs to develop new radish cultivars with desirable profiles.