Coefficient Of Genetic Differentiation Research Articles

Microsatellite marker-based analysis of the genetic diversity and population structure of three Arnebiae Radix in western China

Arnebiae Radix is an important medicinal and perennial herb found in Western China, particularly in the Xinjiang region. However, the assessment, utilization and conservation of Arnebiae Radix resources are still unexplored. In this study, we evaluated the genetic diversity of three Arnebiae Radix populations across 47 regions (Ae = 16, Ag = 16, Ad = 15) in Xinjiang, China, using inter-simple sequence repeat (ISSR) molecular markers. In total, 48 alleles were amplified by six pairs of primers screened with ISSR markers. The average number of effective alleles (Ne) was 1.5770. The percentage of interspecific genetic polymorphisms in A. guttata (Ag = 89.58 %) was greater than that in A. euchroma. and A. decumbens (Ae = Ad = 87.50 %). Intraspecific genetic polymorphisms, Bo Le (BL) population of A. euchroma exhibited the highest percentage of polymorphic bands (PPB% =58.33 %, Na = 1.313, Ne = 1.467, I = 0.0.366, H = 0.255), which indicated high genetic diversity. In contrast, the Tuo Li (TL) population of A. guttata had the lowest values for these parameters (PPB% =0.00 %, Na = 0.313, Ne = 1,000, I = 0.000, H = 0.000). The Arnebiae Radix germplasms were classified into two major groups (I and II) based on UPGMA cluster analysis (Fig. 8a) and principal coordinate analysis (PCOA). In addition, A. decumbens is placed in a separate category due to its high differentiation coefficient. The AMOVA and genetic differentiation coefficient results indicated that the genetic variation in Arnebiae Radix was predominantly due to intrapopulation differences (78 %). Additionally, the gene flow index (Nm) between populations was 2.4128, which further indicated that the genetic diversity of Arnebiae Radix was greater at the intrapopulation level. The destruction of the ecological environment leads to the continuous reduction and degradation of the genetic diversity of Arnebiae Radix germplasm resources. In this study, we used ISSR molecular markers to analyze the genetic diversity and relatedness of Arnebiae Radix, which revealed the genetic relationship of Arnebiae Radix germplasm resources at the molecular level and provided a scientific basis for future research on selecting and breeding good varieties, evaluating the quality of Arnebiae Radix, and conserving and utilizing its resources.

The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China

Disentangling how climate oscillations and geographical events significantly influence plants’ genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations’ genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle–late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.

Genetic diversity of the common carp black strain population based on mtDNA (D-loop and cytb)

The common strain black carp (Cyprinus carpio var. baisenensis) is a culturally important carp strain that is raised and cultured in Guangxi Province, China. Its color reflects the interactions between the Burau people and their surrounding environment. The population of the common carp black strain was isolated and cultured in a rice-fish integration system. To explore the genetic diversity and protection of germplasm resources, we analyzed mitochondrial DNA (mtDNA) sequences, specifically the displacement loop (D-loop) and cytochrome b (Cytb), using single-nucleotide polymorphisms (SNP). We compared these sequences with those from four other local common carp populations. The study included a total of 136 adult common carps from five strain populations: the common black carp strain (HJ = 31), Jian (F = 30), Heilongjiang (H = 10), Songpu (S = 31), and Saijiang (SJ = 34). The results of the Cytb and D-loop analyses showed that the Heilongjiang carp (H) and Saijiang (SJ) populations had the highest levels of haplotype diversity (0.867 ± 0.034785) and nucleotide diversity (π = 0.0063 ± 0.000137 and 0.0093 ± 0.000411), respectively. On the other hand, the Common carp black strain population (HJ) exhibited the lowest haplotype diversity in both Cytb and D-loop, with haplotype 2 being the most commonly observed among the populations. Private haplotypes dominated the five common carp populations, which were significantly different at P<0.001. Furthermore, analyzing the coefficient of genetic differentiation (Fst), the highest genetic difference was observed between Saijiang (SJ) and Heilongjiang (H) (Fst = 0.963), whereas the lowest was observed between Songpu (S) and the Common carp black strain population (HJ) (Fst = 0.019) for the Cytb gene sequences. For the D-loop, the Common carp black strain population (HJ) and Songpu (S) (Fst = 0.7) had the highest values, and Heilongjiang (H) and Common black carp strain (HJ) had an Fst of 0.125. Additionally, the AMOVA analysis revealed a higher level of variance for the Cytb and D-loop genes, indicating lower genetic diversity within the local carp community. On the other hand, the phylogenetic tree analysis showed that the five carp populations were closely related and formed a distinct cluster. The distinct cluster of populations suggests a common ancestor or recent gene flow, possibly due to geographic proximity or migration history, and unique genetic characteristics, possibly due to adaptations or selective pressures. The results of this study provide valuable insights into the genetic diversity of the common strain black carp, which can have implications for conservation, breeding programs, evolutionary studies, and fisheries management.

Population Variation and Phylogeography of Cherry Blossom (Prunus conradinae) in China.

Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of P. conradinae variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of P. conradinae to ensure adequate germplasm resources in the future. We also found support for a new variant, P. conradinae var. rubrum. We observed high genetic diversity within P. conradinae (haplotype diversity [Hd] = 0.830; ribotype diversity [Rd] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. P. conradinae expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12-5.17 Mya) in the Pliocene. The population of P. conradinae spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47-4.54 Mya), suggesting that the population of P. conradinae differentiated first in Central and East China. The population of P. conradinae experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11-2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for P. conradinae. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of P. conradinae.

Evidence for the Use of Karst Tiankengs as Shelters: The Effect of Karst Tiankengs on Genetic Diversity and Population Differentiation in Manglietia aromatica

Karst tiankengs in China are globally significant locations for studying ecological environments and plant diversity. However, there are few reports on how the unique geographical environment of tiankengs affects plant genetic diversity and genetic structure. This study used Hyper-seq gene sequencing technology to develop large-scale genomic SNPs of Manglietia aromatica, both within and outside the tiankengs. Its aim was to investigate the impact of tiankengs on the genetic diversity and genetic structure of the M. aromatica population. The analysis results indicate that the genetic diversity of the populations within the tiankeng (π = 0.2044) is higher than that of the populations outside of it (π = 0.1671), indicating that the tiankengs have a positive impact on species diversity. The genetic differentiation coefficient (FST) between the populations inside and outside the tiankeng was 0.0534 and the FST values of populations within the tiankeng were 0.077, 0.082, and 0.141, meaning that the genetic variation in the tiankengs is very high. The genetic similarity outside the tiankengs is also very high, indicating that the tiankengs are effectively preserving the genetic diversity of M. aromatica. Furthermore, the gene introgression analysis results gave no proof of gene flow between the three tiankeng populations. This suggests that the tiankengs not only protect species diversity, but also hinder gene flow between populations to some extent. However, this hindrance may gradually subside with the evolution of the tiankengs. The genetic structure analysis revealed that the M. aromatica population in Guangxi, China, can be classified into three subpopulations. The first is the tiankeng subpopulation, including all the populations in tiankengs. The second subpopulation consists of populations surrounding the tiankengs. These two subpopulations are distributed in Leye County in northwestern Guangxi, China, and are very close to each other. The third is the Huanjiang subpopulation, which is located far away from the tiankengs. Considering the direction of gene flow and genetic structure, it is speculated that the populations in the tiankengs evolved from the populations near the pit mouth. This study confirms that the tiankengs are shelters and provide a suitable habitat for the endangered plant M. aromatica, because its genetic diversity is well conserved and the species is well adapted to the habitat within the tiankengs.

SSR Marker–Based Genetic Diversity and Relationship Analyses of Stephania tetrandra S. Moore

AbstractStephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations.

Genetic diversity, population structure and origin of the native goats in Central Laos.

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

GENETIC DIFFERENTIATION OF CULTIVATED CITRUS FRUITS (Citrus spp.) IN COLOMBIA USING SSR MOLECULAR MARKERS

Citrus is the second most important fruit crop in Colombia after bananas, with production taking place in 26 of the country’s 32 departments. Oranges, sour limes, and mandarins are the most economically important crops in terms of area planted and production. Microsatellites were used to assess the genetic differentiation of oranges, mandarins, tangelos, grapefruits, and acid limes from the Colombian Agricultural Research Corporation AGROSAVIA germplasm bank and collection of micro-grafted plants at Palmira Research Center in Colombia. A total of 121 samples from eight citrus groups were analyzed with 30 fluoromarked simple sequence repeats (SSR) microsatellites. The mean expected heterozygosity and mean observed heterozygosity were 0.58 and 0.57, respectively, and the coefficient of genetic differentiation was 0.558, confirming very high genetic differentiation among the citrus groups evaluated. Microsatellites mCrCIR01B02, AMB5, Ci01C09, mCrCIR08B08, and Ci01C07 were the most informative, presenting a high number of alleles and polymorphic loci percentages of more than 45 %; in addition, they allowed the identification of unique alleles, which can be used to establish the genetic fingerprint of citrus. Genetic differentiation was achieved for seven out of the eight groups evaluated. The SSRs used failed to differentiate the orange groups, possibly due to genetic origin; for this group, other molecular markers are recommended.

Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato.

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulationsarefixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.

Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers

BackgroundRhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources.ResultsIn the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity.ConclusionsThis is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.

Genetic Diversity and Virulence Variation of Metarhizium rileyi from Infected Spodoptera frugiperda in Corn Fields.

Metarhizium rileyi is an entomopathogenic fungus that naturally infects the larvae of Spodoptera frugiperda, and has biocontrol potential. To explore more natural entomopathogenic fungi resources, a total of 31 strains were isolated from 13 prefectures in Yunnan Province. All the strains were identified using morphology and molecular biology. The genetic diversity of the 31 isolates of M. rileyi was analyzed using inter-simple sequence repeat (ISSR) techniques. Seven primers with good polymorphism were selected, and fifty-four distinct amplification sites were obtained by polymerase chain reaction amplification. Among them, 50 were polymorphic sites, and the percentage of polymorphic sites was 94.44%. The thirty-one strains were divided into eight subpopulations according to the regions. The Nei's gene diversity was 0.2945, and the Shannon information index was 0.4574, indicating that M. rileyi had rich genetic diversity. The average total genetic diversity of the subpopulations in the different regions was 0.2962, the gene diversity within the populations was 0.1931, the genetic differentiation coefficient was 0.3482 (>0.25), and the gene flow was 0.9360 (<1). The individual cluster analysis showed that there was no obvious correlation between the genetic diversity of the strains and their geographical origin, which also indicated that the virulence of the strains was not related to their phylogeny. Thus, the genetic distance of the different populations of M. rileyi in Yunnan Province was not related to the geographical distance. The virulence of those 32 strains against the 3rd-instar larvae of S. frugiperda were varied with the differences in geographical locations. On the 10th day of inoculation, seventeen strains had an insect mortality rate of 70.0%, and seven strains had an insect mortality rate of 100%. The half-lethal times of the M. rileyi SZCY201010, XSBN200920, and MDXZ200803 strains against the S. frugiperda larvae were less than 4 d. Thus, they have the potential to be developed into fungal insecticidal agents.

Population genetic structure of tropical bed bug (Hemiptera: Cimicidae) populations and their breeding pattern in Iraq.

A study was conducted to investigate the population genetic structure and breeding pattern of 140 tropical bed bugs, Cimex hemipterus (F.) (Hemiptera: Cimicidae), collected from 14 infested sites in major cities in Iraq. The samples were genotyped using a set of 7 polymorphic microsatellite markers. High genetic variety was seen among populations, with an average of 2-9 alleles per locus. The number of alleles across 7 microsatellite loci was between 6 and 18. There was a notable disparity in the alleles per loci when comparing the overall population to those within it. The overall population exhibited an average observed heterozygosity of 0.175 and an average expected heterozygosity of 0.730. Among the population, the average observed heterozygosity was 0.173, while the average expected heterozygosity was 0.673. Analysis of molecular variance (AMOVA) revealed that 93% of the genetic variability was within the populations, and 7% was among them. The genetic differentiation coefficient (FST = 0.045), indicates a low degree of genetic differentiation and a high degree of inbreeding (FIS = 0.761), as indicated by notably significant positive inbreeding coefficients. Admixed individuals were revealed using STRUCTURE and neighbor-joining phylogenetic trees, demonstrating moderate gene flow between populations and a lack of genetic structure in the regional groups. Thus, both active dispersion and human-mediated dispersion possess the potential to influence the low population genetic structure of tropical bed bug C. hemipterus populations in Iraq, which can have implications toward tropical bed bug and management strategies.

Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement.

Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima's D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties.

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

AbstractThe Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (FST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining FST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between FHOM and FGRM, and the lowest between FROH &gt;1.5Mb and FROH &lt;500kb. A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.

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.

SSR molecular marker developments and genetic diversity analysis of Zanthoxylum nitidum (Roxb.) DC

Zanthoxylum nitidum (Roxb.) is a commonly used traditional Chinese medicine. However, the collection and protection of wild germplasm resources of Z. nitidum are still insufficient, and there is limited research on its genetic diversity and fingerprint. In the present study, 15 simple sequence repeat (SSR) markers were developed by genotyping based on multiplexed shotgun sequencing. The genetic diversity of 51 populations (142 individuals) of Z. nitidum was evaluated using these 15 SSRs. A total of 245 alleles (Na) were detected, with an average value of 16.333, and the average polymorphism information content was 0.756. The genetic distance among 51 populations was 0.164~1.000, with an average of 0.659. Analysis of molecular variance showed low genetic differentiation (40%) and high genetic differentiation (60%) between populations and individuals, respectively. The genetic differentiation coefficient (Fst) of the population was 0.338, indicating that 66.2% of the genetic variation occurred within the population, and the gene flow (Nm) was 0.636, demonstrating that the gene exchange between populations was low. Clustering analysis revealed that the genetic similarity coefficient was 0.30, dividing the 51 populations into 4 groups of 2, 17, 3, and 29 populations. There was no specific relationship between geographical location differences and genetic distance. The genetic diversity level of Z. nitidum is relatively high, and our results provide a theoretical basis for the rapid identification of Z. nitidum germplasm resources and variety selection.

Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers.

As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.

Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers.

Polygonatum cyrtonema Hua is a perennial herbaceous plant of the Polygonatum genus, belonging to the Liliaceae family, with significant medicinal and nutritional value. In China, this species is a traditional medicinal and edible herb with a long history of application and is widely appreciated by the people. However, as the demand for medicinal herbs continues to grow, excessive harvesting has led to the depletion of wild resources and the risk of genetic erosion. In addition, the chaotic cultivation of varieties and the lack of high quality germplasm resources have led to inconsistent quality of medical materials. Therefore, it is urgent to conduct genetic diversity evaluation of this species and establish a sound conservation plan. This study assessed the genetic diversity and population structure of 96 samples collected from seven regions in China using the simple sequence repeat (SSR) molecular marker technology. In this study, a total of 60 alleles (Na) were detected across the 10 polymorphic SSR markers used, with an average of 6.0 alleles generated per locus. The values of polymorphic information content (PIC) values ranged from 0.3396 to 0.8794, with an average value of 0.6430. The average value of the effective number of alleles (Ne) was 2.761, and the average value of the Shannon's information index (I) was 1.196. The population structure analysis indicates that the Polygonatum cyrtonema Hua germplasm can be classified into three subpopulations (JZ, QY, JD) at the molecular level, which corresponds to the previous subgroups identified based on individual plant phenotypic traits. Analysis of Molecular Variance (AMOVA) showed that 74% of the genetic variation was between individuals within populations in different regions. The phylogenetic analysis of the 96 germplasm samples divided them into three main populations. The QY and JD subpopulations are largely clustered together, which could be attributed to their mountainous distribution and the local climate environment. The genetic differentiation coefficient (Fst) value was low at 0.065, indicating relatively low population differentiation. The ratio of the genetic differentiation coefficient (Fst) between the JZ population and the other two populations (QY and JD) is much higher than the ratio between the QY and JD populations. Based on the clustering results and the ratio of the genetic differentiation coefficient (Fst), it can be inferred that the genetic relationship between the QY and JD subpopulations is closer, with a certain degree of genetic differentiation from the JZ subpopulation. This study supports the conservation of germplasm resources of Polygonatum cyrtonema Hua in China and provides new parental material for germplasm genetic improvement and breeding programs.

Six Express Sequence Tag-Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species.

Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag-simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.

Comparative Analysis of Genetic Structure and Diversity in Five Populations of Yellowtail Kingfish (Seriola aureovittata)

To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (Seriola aureovittata), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (n = 33) collections in China, a wild collection in Japan (n = 20), and farmed (n = 31) and wild (n = 29) collections in Australia. Using 2b-RAD simplified genome sequencing, we obtained an average of 287,594 unique tags per population, with an average sequencing depth of 27.13×. Our final genotype dataset included 48,710 SNPs (Single Nucleotide Polymorphisms). The five collections were all in Hardy–Weinberg equilibrium, and the interpopulation differentiation varied among the sample collections. The genetic differentiation coefficients (Fst) between the Chinese and Japanese yellowtail kingfish collections were low and the gene flow (Nm) values were high. These results suggest continuous gene flow occurs frequently between the collections, indicating that they belong to the same population. In contrast, genetic differentiation was high between the Australian collections and the Chinese and Japanese populations, suggesting different evolutionary origins and belonging to different populations. The farmed and wild Australian collections fell into distinct clades in a neighbor-joining phylogeny tree, suggesting farmed fish have begun to differentiate from the wild collection. A similar level of genetic diversity between the wild collections in China and Japan suggests that they originated from the same spawning ground. This, therefore, reminds us that in future aquaculture processes attention is needed regarding implementing targeted breeding strategies. In addition, our data will contribute to Chinese yellowtail kingfish genetic breeding and the sustainable use of Chinese yellowtail kingfish germplasms.