This study investigates the genetic diversity and evolutionary relationships of different Artemisia argyi germplasm resources to provide a basis for germplasm identification, variety selection, and resource protection. A total of 192 germplasm resources of A. argyi were studied, and EST-based simple sequence repeat(EST-SSR) primers were designed based on transcriptomic data of A. argyi. Polymerase chain reaction(PCR) amplification was performed on these resources, followed by fluorescence capillary electrophoresis to detect genetic diversity and construct DNA fingerprints. From 197 pairs of primers designed, 28 pairs with polymorphic and clear bands were selected. A total of 278 alleles were detected, with an average of 9.900 0 alleles per primer pair and an average effective number of alleles of 1.407 2. The Shannon's diversity index(I) for the A. argyi germplasm resources ranged from 0.148 1 to 0.418 0, with an average of 0.255 7. The polymorphism information content(PIC) ranged from 0.454 5 to 0.878 0, with an average of 0.766 9, showing high polymorphism. Cluster analysis divided the A. argyi germplasm resources into three major groups: Group Ⅰ contained 136 germplasm samples, Group Ⅱ contained 45, and Group Ⅲ contained 11. Principal component analysis also divided the resources into three groups, which was generally consistent with the clustering results. Mantel test results showed that the genetic variation in A. argyi populations was to some extent influenced by geographic distance, but the effect was minimal. Structure analysis showed that 190 germplasm materials had Q≥ 0.6, indicating that these germplasm materials had a relatively homogeneous genetic origin. Furthermore, 8 core primer pairs were selected from the 28 designed primers, which could distinguish various germplasm types. Using these 8 core primers, DNA fingerprints for the 192 A. argyi germplasm resources were successfully constructed. EST-SSR molecular markers can be used to study the genetic diversity and phylogenetic relationships of A. argyi, providing theoretical support for the identification and molecular-assisted breeding of A. argyi germplasm resources.
Artemisia/classification* ; Microsatellite Repeats ; Genetic Variation ; Expressed Sequence Tags ; DNA Fingerprinting ; Phylogeny ; Polymorphism, Genetic ; DNA, Plant/genetics* ; Genetic Markers

Forsythia suspensa is a traditional Chinese medicine and a commonly used landscaping plant. Its dried fruit is used in medicine for its functions of clearing heat, removing toxins, reducing swelling, dissipating masses, and dispersing wind and heat. It possesses extremely high medicinal and economic value. However, the genetic differentiation and diversity of its wild populations remain unclear. In this study, chloroplast genome sequences were obtained from 15 wild individuals of F. suspensa using high-throughput sequencing technology. The sequence characteristics and intraspecific variations were analyzed. The results were as follows:(1) The full length of the F. suspensa chloroplast genome ranged from 156 184 to 156 479 bp, comprising a large single-copy region, a small single-copy region, and two inverted repeat regions. The chloroplast genome encoded a total of 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes.(2) A total of 166-174 SSR loci, 792 SNV loci, and 63 InDel loci were identified in the F. suspensa chloroplast genome, indicating considerable genetic variation among individuals.(3) Population structure analysis revealed that F. suspensa could be divided into five or six groups. Both the population structure analysis and phylogenetic reconstruction results indicated significant genetic variation within the wild populations of F. suspensa, with no obvious correlation between intraspecific genetic differentiation and geographical distribution. This study provides new insights into the genetic diversity and differentiation within F. suspensa species and offers additional references for the conservation of species diversity and the utilization of germplasm resources in wild F. suspensa.
Genome, Chloroplast ; Forsythia/classification* ; Phylogeny ; Genetic Variation ; Chloroplasts/genetics* ; Microsatellite Repeats

OBJECTIVE: To analyze the distribution of thalassemia (referred to as "thalassemia") gene variant types in the population of the Wuhan area, aiming to provide a genetic basis for the precise prevention and control as well as clinical diagnosis of thalassemia in the Wuhan region. METHODS: In this study, 2 133 suspected thalassemia patients and individuals undergoing prenatal screening who visited the Department of Hematology, Obstetrics and Gynecology, Reproductive Medicine, Pediatrics, and Neurology at Wuhan First Hospital from October 2022 to October 2024 were selected as the research subjects. Peripheral blood samples were collected from the patients. The common 27 thalassemia genotypes of α- and β-thalassemia were initially screened using fluorescence PCR melting curve analysis technology. For samples where the fluorescence PCR melting curve results indicated unknown variants or where the clinical phenotype was inconsistent with the common genotypes, Sanger sequencing technology was used for review and verification. RESULTS: Among the 2 133 specimens analyzed, common thalassemia gene variants were detected in 210 cases (9.85%, 210/2 133). A total of 156 cases (8.05%, 156/1 938) of thalassemia gene variants were detected in females and 54 cases (27.69%, 54/195) in males. A total of 94 cases (4.41%, 94/2 133) of α-thalassemia were detected, including 46 cases (2.16%, 46/2 133) of silent α-thalassemia, 47 cases (2.20%, 47/2 133) of mild α-thalassemia, and 1 case (0.05%, 1/2 133) of intermediate α-thalassemia. Additionally, 111 cases of β-thalassemia were identified (5.20%, 111/2 133), including 51 cases of β/β⁺ thalassemia (2.39%, 51/2 133), 59 cases of β/β⁰ thalassemia (2.77%, 59/2 133), and 1 case of β⁺/HbE thalassemia (0.05%, 1/2 133). αβ-composite thalassemia gene variants were detected in 5 cases (0.23%, 5/2 133), including 1 complex variant with a genotype of --^SEA/αα combined with CD41-42 (-TTCT) and 29(A>G), representing a heterozygous variant of three genotypes. Rare globin gene variants were detected in 3 cases, including HBB:c.60C>T, HBB:c.-146G>T, and HBA2:c.*12G>A. CONCLUSION The Wuhan region exhibits a relatively high prevalence of thalassemia genes with notable gender disparities. While maintaining focus on thalassemia screening for females, enhanced males screening efforts and genetic counseling should be implemented in future prevention programs.
Humans ; Female ; Male ; Genotype ; beta-Thalassemia/genetics* ; China ; Thalassemia/genetics* ; alpha-Thalassemia/genetics* ; Genetic Variation

We studied the genetic diversity and established the DNA molecular identify for Prunus mume with both ornamental and edible values, aiming to collect, identify, evaluate, and breed new varities of this plant and promote the upgrading of the P. mume industry chain in northern China. We employed 13 pairs of primers with good polymorphism, clear bands, and good repeatability to analyze the genetic diversity and establish the molecular identify of 68 germplasm accessions of P. mume with both ornamental and edible values from Xingtai, Hebei Province. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance. After that, we analyzed the genetic structure of the 68 germplasm accessions based on a Bayesian model. The 13 pairs of SSR primers amplified a total of 124 alleles from 68 P. mume germplasm accessions, with the mean number of alleles (Na) of 9.538 5, the minor allele frequency (MAF) of 0.369 3, the mean number of effective alleles (Ne) of 4.483 5, and the mean Shannon genetic diversity index (I) of 1.712 4. The mean Nei's gene diversity index (H) of 0.763 7, the mean observed heterozygosity (Ho) of 0.719 5, the mean expected heterozygosity (He) of 0.769 3, the mean polymorphism information content (PIC) of 0.733 6, and the mean genetic similarity (GS) of 0.772 9 suggested that there were significant genetic differences and rich genetic diversity among the studied P. mume germplasm accessions. The cluster analysis revealed that the 68 accessions were classified into three groups, with the mean genetic distance of 0.622 6. The population structure analysis classified the germplasm accessions into two populations. According to the PIC of primers, we selected primers for combination and constructed the combination with the fewest primers required for germplasm differentiation of P. mume with both ornamental and edible values. This study provides a theoretical basis for the innovation and industrial upgrading of P. mume with both ornamental and edible values in gardening and the improvement of breeding efficiency.
Prunus/classification* ; Microsatellite Repeats/genetics* ; Genetic Variation ; China ; Phylogeny ; Polymorphism, Genetic ; DNA, Plant/genetics* ; Alleles

To promote the conservation and utilization of the germplasm resources and provide a basis for the breeding of new varieties of Murraya paniculata, this study analyzed the genetic diversity of the germplasm resources and developed the molecular identity(ID) card of M. paniculata. Multiple fluorescence PCR-capillary electrophoresis was performed for 65 germplasm accessions of M. paniculata based on 9 SSR markers identified from the M. paniculata genome, and the molecular weights and alleles of the amplified bands were analyzed. According to the banding patterns of the 9 SSR primers, this study analyzed the genetic diversity of each germplasm accession of M. paniculata and developed molecular ID cards for the test samples. The results showed that 9 pairs of SSR primers detected 78 alleles, with an average of 8.67 alleles. The observed and expected heterozygosity was 0.338-0.831(average of 0.601) and 0.413-0.853(average of 0.721), respectively. The Shannon's information index varied within the range of 0.880-1.994, with an average of 1.41. The polymorphic information content was within the range of 0.391-0.835, with an average of 0.696, which indicated rich genetic diversity. When the genetic identity was 0.347, the 65 germplasm accessions were classified into 5 groups. Based on the results, this study employed the 5 SSR primers with higher polymorphisms to develop the molecular ID cards for the germplasm resources of M. paniculata and created QR code ID cards for the 49 core germplasm accessions preserved in the Yunfu germplasm nursery, laying a foundation for the new variety breeding, production, utilization, and traceability of M. paniculata.
Microsatellite Repeats ; DNA, Plant/genetics* ; Murraya/classification* ; Genetic Variation ; Alleles ; Polymerase Chain Reaction ; Polymorphism, Genetic

Black-bone silky fowls(Gallus gallus domesticus) have a long history of medicinal use, with the origin in Taihe county, Jiangxi province. The unclear family composition, inbreeding rate, and effective population size were inconducive to the resource conservation or breed improvement of black-bone silky fowls. A genome-wide analysis was performed to evaluate the genetic diversity of 80 black-bone silky fowls from random mating in three farms in 2021 in terms of minor allele frequency(MAF), expected heterozygosity(H_e), observed heterozygosity(H_o), effective population size(N_e), and runs of homozygosity(ROH). The results showed that a total of 9 641 411 SNPs were passed quality control from 80 black-bone silky fowls. The polymorphic marker ratio, expected heterozygosity, and observed heterozygosity in this population were 0.81, 0.34, and 0.33, respectively, and the average IBS genetic distance of black-bone silky fowls was 0.38±0.008 2. A total of 15 969 ROHs were identified, with the average length of 0.73 Mb, and most of the ROHs were 0～2 Mb. According to inbreeding ROHs, the average inbreeding coefficient was 0.150 9. The high-frequency ROH regions harbored 424 genes, including two genes, SLC13A4 and DDX6, associated with pigmentation. The results showed that the genetic relationship between individuals of black-bone silky fowls was far. The population had experienced a strong decline in size in recent decades, and the inbreeding degree was high. According to the results, an appropriate family construction scheme was proposed for resource conservation and breeding work of black-bone silky fowls.
Animals ; Chickens/genetics* ; Genetic Variation ; Polymorphism, Single Nucleotide ; Breeding ; Gene Frequency ; Male ; Female

To clarify the genetic diversity and structure of the nucleus population of F1-generation Litopenaeus vannamei, this study utilized 15 pairs of highly polymorphic microsatellite primers to analyze the simple sequence repeat (SSR) markers and genetic diversity in 15 full-sib families of L. vannamei. A total of 112 alleles (N_a) and 60.453 effective alleles (N_e) were identified among the selected 15 SSR loci, with the average polymorphic information content (PIC) of 0.648. The average N_e, observed heterozygosity (H_o), and expected heterozygosity (H_e) in the 15 F1 families varied from 1.925 to 2.626, 0.425 to 0.783, and 0.403 to 0.572, respectively. The 15 full-sib families were primarily clustered into three categories in the phylogenetic analysis, with the genetic distance between families ranging from 0.252 to 0.574. Additionally, the genetic differentiation coefficient (F_st) among the families varied from 0.112 to 0.278, indicating substantial genetic differentiation. Overall, this study suggested that the genetic diversity of the 15 full-sib families was moderate, providing valuable genetic insights for the subsequent breeding initiatives aimed at enhancing the tolerance of L. vannamei to high levels of soybean meal.
Penaeidae/classification* ; Microsatellite Repeats/genetics* ; Animals ; Genetic Variation ; Polymorphism, Genetic ; Phylogeny ; Alleles ; Genetic Markers

Objective: This study aims to investigate the associations between genetic variations of pyroptosis pathway related key genes and adverse events (AEs) of postoperative chemoradiotherapy (CRT) in patients with rectal cancer. Methods: DNA was extracted from the peripheral blood which was collected from 347 patients before CRT. Sequenom MassARRAY was used to detect the genotypes of 43 haplotype-tagging single nucleotide polymorphisms (htSNPs) in eight pyroptosis genes, including absent in melanoma 2 (AIM2), caspase-1 (CASP1), caspase-4(CASP4), caspase-5 (CASP5), caspase-11 (CASP11), gasdermin D (GSDMD), gasdermin E (GSDME) and NLR family pyrin domain containing 3 (NLRP3). The associations between 43 htSNPs and AEs were evaluated by the odd ratios (ORs) and 95% confidence intervals (CIs) by unconditional logistic regression models, adjusted for sex, age, clinical stage, tumor grade, Karnofsky performance status (KPS), surgical procedure, and tumor location. Results: Among the 347 patients with rectal cancer underwent concurrent CRT with capecitabine after surgery, a total of 101(29.1%) occurred grade ≥ 2 leukopenia. rs11226565 (OR=0.41, 95% CI: 0.21-0.79, P=0.008), rs579408(OR=1.54, 95% CI: 1.03-2.29, P=0.034) and rs543923 (OR=0.63, 95% CI: 0.41-0.98, P=0.040) were significantly associated with the occurrence of grade ≥ 2 leukopenia. One hundred and fifty-six (45.0%) had grade ≥ 2 diarrhea, two SNPs were significantly associated with the occurrence of grade ≥ diarrhea, including CASP11 rs10880868 (OR=0.55, 95% CI: 0.33-0.91, P=0.020) and GSDME rs2954558 (OR=1.52, 95% CI: 1.01-2.31, P=0.050). In addition, sixty-six cases (19.0%) developed grade ≥2 dermatitis, three SNPs that significantly associated with the risk of grade ≥2 dermatitis included GSDME rs2237314 (OR=0.36, 95% CI: 0.16-0.83, P=0.017), GSDME rs12540919 (OR=0.52, 95% CI: 0.27-0.99, P=0.045) and NLRP3 rs3806268 (OR=1.51, 95% CI: 1.03-2.22, P=0.037). There was no significant difference in the association between other genetic variations and AEs of rectal cancer patients (all P>0.05). Surgical procedure and tumor location had great impacts on the occurrence of grade ≥2 diarrhea and dermatitis (all P<0.01). Conclusion: The genetic variants of CASP4, CASP11, GSDME and NLRP3 are associated with the occurrence of AEs in patients with rectal cancer who received postoperative CRT, suggesting they may be potential genetic markers in predicting the grade of AEs to achieve individualized treatment of rectal cancer.
Humans ; Pyroptosis ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism* ; Gasdermins ; Chemoradiotherapy/adverse effects* ; Rectal Neoplasms/surgery* ; Caspases/metabolism* ; Diarrhea/chemically induced* ; Leukopenia/genetics* ; Genetic Variation ; Dermatitis

Eleutherococcus senticosus is one of the Dao-di herbs in northeast China. In this study, the chloroplast genomes of three E. senticosus samples from different genuine producing areas were sequenced and then used for the screening of specific DNA barcodes. The germplasm resources and genetic diversity of E. senticosus were analyzed basing on the specific DNA barcodes. The chloroplast genomes of E. senticosus from different genuine producing areas showed the total length of 156 779-156 781 bp and a typical tetrad structure. Each of the chloroplast genomes carried 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes were relatively conserved. Sequence analysis of the three chloroplast genomes indicated that atpI, ndhA, ycf1, atpB-rbcL, ndhF-rpl32, petA-psbJ, psbM-psbD, and rps16-psbK can be used as specific DNA barcodes of E. senticosus. In this study, we selected atpI and atpB-rbcL which were 700-800 bp and easy to be amplified for the identification of 184 E. senticosus samples from 13 genuine producing areas. The results demonstrated that 9 and 10 genotypes were identified based on atpI and atpB-rbcL sequences, respectively. Furthermore, the two barcodes identified 23 genotypes which were named H1-H23. The haplotype with the highest proportion and widest distribution was H10, followed by H2. The haplotype diversity and nucleotide diversity were 0.94 and 1.82×10~(-3), respectively, suggesting the high genetic diversity of E. senticosus. The results of the median-joining network analysis showed that the 23 genotypes could be classified into 4 categories. H2 was the oldest haplotype, and it served as the center of the network characterized by starlike radiation, which suggested that population expansion of E. senticosus occurred in the genuine producing areas. This study lays a foundation for the research on the genetic quality and chloroplast genetic engineering of E. senticosus and further research on the genetic mechanism of its population, providing new ideas for studying the genetic evolution of E. senticosus.
DNA Barcoding, Taxonomic ; Eleutherococcus/genetics* ; Base Sequence ; Chloroplasts/genetics* ; Genetic Variation ; Phylogeny

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.
Humans ; Genetic Variation ; Asarum ; Transcriptome/genetics* ; Microsatellite Repeats/genetics* ; Phylogeny