Population Structure Analysis Research Articles

Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing

BackgroundAs an important genetic resource of chickens, gamecock has unique morphological and behavioral characteristics such as large size, muscular development and strong aggression, making it a good model for studying muscle development and behavior patterns, as well as an excellent breeding material. Gamecocks are distributed worldwide, forming different breeds and strains. However, the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens. Therefore, in this study, based on whole genome data of gamecocks, Chinese indigenous chickens, commercial chickens and wild jungle fowls, we performed population structure analysis, selection signal analysis, and genomic introgression analysis of gamecocks.ResultsThe population structure analysis revealed that gamecocks have multiple origins. In addition, we used Fst, π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks. A total number of fifteen shared candidate genes were identified using the three different detection strategies. Among these candidate genes, ETV1, DGKB, AGMO, MEOX2, ISPD and PLCB4 are related to the growth and muscle development, fighting performance and neurodevelopment of gamecocks. Furthermore, we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations, respectively, indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.ConclusionsIn summary, we conducted a genome-wide exploration of gamecocks from multiple regions worldwide. Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks. More importantly, this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks, which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks. Our findings offer new perspectives on the impact of introgression on gamecocks, and provide a basis for further resource conservation and utilization of gamecock, as well as provide excellent material for the genetic improvement of domestic chickens.

Whole genome re-sequencing in 437 tobacco germplasms identifies plant height candidate genes

Tobacco is one of the most important model plants. Plant height is one of the most important agronomic traits in tobacco. To better understand the population genetic structure and the genetic basis of plant height in tobacco, 437 tobacco germplasms were whole genome re-sequencing in this study. A total of 2,263,775 high-quality single nucleotide polymorphisms were identified. The analysis of the population genetic structure showed that tobacco germplasm could be divided into 8 clusters. In addition, gene flow was found between flue-cured tobacco and ustic tobacco, as well as between oriental tobacco and air-cured tobacco. Three genes associated with plant height were identified as candidate genes by genome-wide association study. This study provides valuable genetic resources for population structure analysis and elucidation of the genetic basis of various traits. It helps to improve the efficiency of molecular breeding.

Genomic epidemiology and phenotypic characterization of Staphylococcus aureus isolated from atopic dermatitis patients in South China

Atopic dermatitis (AD) is a multifactorial, chronic relapsing disease. Staphylococcus aureus is the key microbial factor in AD, linked to disease activity. However, there is limited knowledge of genomic prevalence characteristics and phenotypic features of S. aureus in AD patients in China. We investigated 108 S. aureus of AD in China and globally publicly available genome sequences of 579 S. aureus of AD. Sequence type (ST) 7, ST15 and ST188 were the major lineages in China. Genes esaC, esxB, and sea were only detected in ST7, potentially contributing to its prevalence in AD. ST188 exhibited high virulence and adhesion, possibly due to the cna gene. Phylogenetic and population structure analysis revealed that 579 strains of global AD were classified into 15 sequence clusters (SCs), with SC5, SC2, and SC7 dominating. S. aureus of Chinese AD patients was mainly distributed in SC2, SC7, and SC12. Comparative genomic highlighted genes linked to AD, including enterotoxins (seh, selk, selq, entH), adhesion genes (fnbA, fnbB, sdrD, map, fib, narH). From China and global perspectives, we analyzed S. aureus’s genomic epidemic traits, phylogeny, and population structure in AD skin. These findings contribute to understanding S. aureus-host interactions and genomic diversity in AD.

Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm

Orchardgrass (Dactylis glomerata L.), a widely cultivated cool-season perennial, is an important forage crop due to its adaptability, high nutritional value, and substantial biomass. Understanding its genetic diversity and population structure is crucial for developing resilient cultivars that can withstand climate change, diseases, and resource limitations. Despite its global significance in fodder production, the genetic potential of many regional accessions remains unexplored, limiting breeding efforts. This study investigates the genetic diversity (GD) and population structure of 91 accessions of D. glomerata from Turkey and Iran using genotyping-by-sequencing based single nucleotide polymorphism (SNP) markers. A total of 2913 high-quality SNP markers revealed substantial genetic variability across provinces. Notably, accessions from Erzurum exhibited the highest GD (mean GD: 0.26; He: 0.5328), while provinces such as Bursa and Muğla demonstrated lower GD (mean GD: 0.15; He < 0.22), suggesting potential genetic bottlenecks. Population structure analysis using Bayesian clustering, PCoA and UPGMA dendrograms divided the accessions into three distinct clusters, with cluster membership largely reflecting geographical origins, and dry biomass content. Cluster II revealed higher GD, associated with enhanced biomass production (128 g/plant), the most important agronomic trait in forage species, supporting the notion of heterosis in breeding programs. The majority of the genetic variation (85.8%) was observed within clusters, with minimal differentiation among clusters (FST = 0.007). Genome-wide association studies (GWAS) identified significant marker-trait associations for dry biomass weight, a critical agronomic trait, with markers DArT-100715788, DArT-101043591, and DArT-101171265 and DArT-101090822 located on Chromosomes 1, 6, and 7 respectively. These findings highlight the importance of regional diversity for maintaining adaptive potential in future breeding programs.

Genome-based analysis of the genetic pattern of black sheep in Qira sheep

ObjectiveBlack wool can effectively prevent sheep from DNA damage as well as fungal infection, and can improve reproductive performance. In order to explore the candidate genes related to black wool formation in Qira sheep.MethodsWe selected 123 adult healthy ewes with different coat colors in Qira sheep groups (black (B), brown (Y) and grey (G)) and extracted DNA from their venous blood to obtain Illumina Ovine SNP 50K chip data. Subsequently, our PCA, NJ-tree, and Admixture population structure analyses of the 3 wool color Qira sheep populations showed that the 3 middle wool color populations exhibited the same genetic traits. Fst, xp-EHH, iHS, and π were detected for selection signals, and the 5% SNPs loci positively selected from the analyses were annotated based on SheepOar_v4.0. The region of exon 1 of the TYRP1 gene was further screened, amplified and sequenced through the DNA of the Qira sheep and associated with goodness-of-fit using the chi-square test.ResultsThe results showed that 71 SNPs associated with black wool traits, among which TYRP1, PARD3 and CDH2 genes were strongly associated with black wool production. Three mutations were detected in the exon 1 region of the TYRP1 gene that were significantly associated with coat color variation inQira sheep (2:81,183,168, 2:81,183,281 and 2:81,183,284).ConclusionIn this paper, Qira sheep could not differentiate the genetic structure of this population by wool color, and obtained 71 SNPs related to black wool. Detection of mutation sites on the TYRP1 gene affecting hair color change provides a basis for black sheep line selection as well as breed conservation.

Fingerprinting Chinese Sweetgum (Liquidambar formosana Hance) Accessions and Constructing a Core Collection Using Newly Developed SSR Markers

Liquidambar formosana, endemic to China, is a multifunctional tree species valued for its wood production, urban landscaping, and medicinal applications. Here, 111 superior L. formosana accessions were genotyped using 24 novel expressed sequence tag-simple sequence repeat (EST-SSR) markers to assess genetic diversity and structure, establish DNA fingerprints, and construct a core collection. A high degree of genetic diversity was detected in the tested accessions, with mean values for the number of observed alleles (Na), polymorphism information content (PIC), and Shannon’s information index (I) recorded at 8.458, 0.579, and 1.336 per locus, respectively. Cluster analysis, principal coordinate analysis (PCoA), and population structure analysis collectively categorized these accessions into two major groups. Specifically, those from the SangZ provenance formed a distinct group, whereas accessions from other provenances exhibiting extensive gene exchange were assigned to the second group. The combined values of the probability of identity (PI) and the probability of identity among siblings (PIsibs) across 24 SSR loci were 1.475 × 10−19 and 2.561 × 10−8, respectively, indicating a strong ability for fingerprint identification. Unique fingerprints for the 111 accessions were established using four selected core markers. A final core collection consisting of 34 accessions was constructed using the allele maximization (M) strategy, accounting for 30.63% of the analyzed accessions. No significant differences in genetic diversity indicators, allele frequency distributions, and accession dispersion patterns were observed between the core and original collections, suggesting that the core collection could effectively represent the entire collection. This work will promote the identification, management, and conservation of L. formosana germplasm resources while providing valuable materials for the subsequent selection and breeding of this tree species.

Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks.

In order to provide a low-cost, high efficient, and highly accurate tool for molecular breeding of Jiaji ducks, we constructed a cGPS(Genotyping by Pinpoint Sequencing of captured targets) 20 K liquid-phase microarray using resequencing data from this valuable poultry breed for the first time. The microarray contains 20,327 high-quality snp loci, mainly from the 30 Jiaji duck resequencing samples collected in this study, and some loci were supplemented from the 135 duck resequencing data from KUNMING INSTITUTE OF ZOOLOGY.CAS. This microarray showed excellent performance in two production tests. The microarray was used to genotype a population of 236 Jiaji ducks, and the genotyping data were then used for population structure analysis and genome-wide association studies (GWAS) of plumage color phenotypes. According to the population structure analysis, the population of Jiaji ducks could be divided into four subpopulations using genetic distance matrices. Using GWAS analysis, 38 significant SNP loci were identified within a region on chromosome 14 that contained 30 genes. Among them, EDNRB2 and VAMP7 were identified as strong candidate genes for the regulation of plumage color in Jiaji ducks. Two mutations upstream of EDNRB2 were identified as tightly linked to the colorless phenotype. In addition, two KASP markers were designed for the SNP loci associated with EDNRB2 (HIC_SCAFFOLD_14_14984620, HIC_SCAFFOLD_14_15016766). The KASP genotyping results showed strong correlations between different genotypes on the SNP locus HIC_SCAFFOLD_14_15016766 and the plumage phenotype. In conclusion, this independently designed microarray will be useful for large-scale genotyping and can lay the foundation for future screening of mutation loci and functional genes.

Taenia asiatica: Mitochondrial signatures based analysis of an emerging public health threat in India.

Taenia asiatica is a zoonotic tapeworm, commonly known as Asian Taenia. It is an emerging sister species of T. saginata with pigs as intermediate hosts. The present study aimed at genetic characterization and population structure analysis of T. asiatica metacestodes in slaughtered pigs in Haryana, north India. In total, the vital organs of 253 slaughtered pigs were screened for the presence of T. asiatica metacestodes. The molecular identification and phylogenetics were performed targeting the mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome C oxidase subunit 1 (cox1) genes. The median-joining haplotype network and population structure analyses were performed with the sequences generated herein and GenBank-archived T. asiatica sequences for both mitochondrial signatures. Out of 253 pigs screened, the liver of only one animal showed the presence of T. asiatica metacestodes. The sequences generated herein exhibited 99.60% and 98.85% similarity to the GenBank-archived sequences of T. asiatica corresponding to the nad1 and cox1 genes, respectively. Overall, 2 and 6 haplotypes for the overall data set with low nucleotide (0.00399±0.00237 and 0.00095±0.00042) and low haplotype (0.400±0.237 and 0.131±0.054) diversities were recorded for the nad1 and cox1 genes, respectively. The negative values recorded for the neutrality indices exhibited deviations from neutrality and hence, propounded recent population expansion or purifying selection or selective sweep. The findings of the present study are of significant medical importance considering an emerging global public health threat of the neglected tapeworm T. asiatica.

Genomic characteristics and virulence of common but overlooked Yersinia intermedia, Y. frederiksenii, and Y. kristensenii in food.

Yersinia intermedia, Y. frederiksenii, and Y. kristensenii are a group of pathogens that are commonly found in food and are often overlooked in terms of their pathogenic potential. This study conducted a systematic and comprehensive genomic analysis of 114 Y. intermedia genomes, 20 Y. frederiksenii genomes, and 65 Y. kristensenii genomes from public database and our previous study. The results showed that these species were most frequently detected in Europe (56.28%, 112/199), followed by in Asia (20.6%, 41/199). Additionally, 33.17% (66/199) genomes were isolated from food. Y. intermedia were grouped into Bayesian analysis of population structure (Baps) groups 3 and 4, demonstrating significant genomic diversity. This species has a high proportion of accessory genes (79.43%), approximately 50% of which have unknown functions, indicating a high degree of genomic plasticity. The three species carried a large number of mobile genetic elements (MGEs), including plasmids such as ColRNAI_1, ColE10_1, Col440II_1, Col440I_1, and Col (Ye4449) _1; insertion sequences (ISs) like MITEYpe1, MITEEc1, and IS1635; genomic islands (GIs); and prophages. In Y. intermedia, the following antibiotics resistance genes (ARGs) were detected: qnrD1 in 3.51% (4/114), aph(3')-Ia in 2.63% (3/114), blaA in 1.75% (2/114), and catA1, vat(F), and tet(C) each in 0.88% (1/114). In Y. kristensenii, vat(F) was present in 98.46% (64/65), blaTEM-116 in 7.69% (5/65), and aph(3')-Ia in 1.54% (1/65). However, only one Y. frederiksenii genome carried vat(F). There were differences in the virulence gene composition of the three species, with Y. kristensenii having the highest number of virulence genes, particularly its complete cytotoxic genes (yaxA and yaxB) and flagellar motor proteins genes (motA and motB). The pathogenic mechanisms of Y. intermedia and Y. frederiksenii were more similar, especially in the carriage of O-antigen related genes. Y. frederiksenii's unique mechanisms also include the yapC gene, which encodes the autotransporter protein YapC from Y. pestis. After co-cultured with human colonic epithelial cell lines Caco-2 and HT-29, Y. intermedia and Y. kristensenii demonstrated different adhesive and invasive capabilities, particularly the Y. intermedia strain y7, which exhibited stronger adhesion and invasion in both cell lines. In strains y118 and y119 of Y. intermedia, an Arg378del mutation in the UreC protein was identified, resulting in the loss of urease activity. Therefore, this study revealed the pathogenic potential of Y. intermedia, Y. frederiksenii, and Y. kristensenii. Future research should focus on identifying their unknown virulence genes and strengthening public food safety measures to mitigate potential risks.

Genetic Variation in a Crossing Population of Camellia oleifera Based on ddRAD Sequencing and Analysis of Association with Fruit Traits

Tea oil is an important high-quality edible oil derived from woody plants. Camellia oleifera is the largest and most widely planted oil-producing plant in the Camellia genus in China, and its seeds are the most important source for obtaining tea oil. In current research, improving the yield and quality of tea oil is the main goal of oil tea genetic breeding. The aim of this study was to investigate the degree of genetic variation in an early crossing population of C. oleifera and identify single nucleotide polymorphisms (SNPs) and genes significantly associated with fruit traits, which can provide a basis for marker-assisted selection and gene editing for achieving trait improvement in the future. In this study, we selected a crossing population of approximately 40-year-old C. oleifera with a total of 330 samples. Then, ddRAD sequencing was used for SNP calling and population genetic analysis, and association analysis was performed on fruit traits measured repeatedly for two consecutive years. The research results indicate that over 8 million high-quality SNPs have been identified, but the vast majority of SNPs occur in intergenic regions. The nucleotide polymorphism of this population is at a low level, and Tajima’s D values are mostly greater than 0, indicating that the change in this population was not suitable for the model of central evolution. The population structure analysis shows that the population has seven theoretical sources of genetic material and can be divided into seven groups, and the clustering analysis results support the population structure analysis results. Association analysis identified significant SNPs associated with genes related to the seed number of a single fruit and seed kernel oil content. Our findings provide a basis for molecular breeding and future genetic improvement of cultivated oil tea.

Genetic diversity, population structure in a historical panel of Brazilian soybean cultivars.

Soybean [Glycine max (L.) Merrill] is one of the most widely grown legumes in the world, with Brazil being its largest producer and exporter. Breeding programs in Brazil have resulted from multiple cycles of selection and recombination starting from a small number of USA cultivar ancestors in the 1950s and 1960s years. This process has led to the successful adaptation of this crop to tropical conditions, a phenomenon known as tropicalization. Many studies describe a narrow genetic background in Brazilian soybean cultivars. Various factors can affect the genetic diversity in species, especially in cultivated crops, such as the reproduction type, artificial selection, and the number and sources of variability in the breeding programs. In turns, the genetic diversity can affect the linkage disequilibrium blocks (LD) patterns and, consequently, molecular breeding strategies for selection of target loci for agronomic traits. We used high-throughput genotyping with SoySNP50K Illumina SNP markers to assess a collection of 370 Brazilian soybean accessions covering more than 60 years of soybean breeding in Brazil. Our goal was to investigate population structure and genetic diversity in the Brazilian germplasm, detect patterns of LD blocks, and identify regions presenting signals of selective swaps linked with quantitative trait loci (QTLs) of agronomic interest. Population structure analysis revealed two major groups among all genotypes, primarily differentiated by the year of release, separating old and new cultivars (before and after 2000´s years), and by growth habit (stem termination type-SST). The group I comprises about 75% of the panel and includes cultivars release before 2000`s years, including the oldest cultivars released in Brazil, most of which exhibit a determinate growth habit and maturity groups VI and VII. Group II includes only 83 materials, but shows higher levels of diversity than group I, representing most recent introductions in Brazilian germplasm. Further analysis of substructure within Group I, identified seven subgroups with no clear trend for segregation based on maturity group, STT or year of release. Instead, these subgroups were based on the contribution of key donors of disease resistance and adaptability, as soybean cultivation expanded from the South to Central region of Brazil. This finding is consistent with the history of soybean expansion in Brazil. We identified 123 genomic regions under selection among the groups of Brazilian cultivars associated with 440 quantitative trait loci (QTLs), revealing regions fixed across the breeding process associated with yield, disease resistance, water efficiency use, and others.

Global epidemiology of Mycobacterium tuberculosis lineage 4 insights from Ecuadorian genomic data

Tuberculosis is a global public health concern, and understanding Mycobacterium tuberculosis transmission routes and genetic diversity of M. tuberculosis is crucial for outbreak control. This study aimed to explore the genomic epidemiology and genetic diversity of M. tuberculosis in Ecuador by analyzing 88 local isolates and 415 public genomes from 19 countries within the Euro-American lineage (L4). Our results revealed significant genomic diversity among the isolates, particularly in the genes related to protein processing, carbohydrate metabolism, lipid metabolism, and xenobiotic biodegradation and metabolism. The population structure analysis showed that sub-lineages 4.3.2/3 (35.4%), 4.1.2.1 (22.7%), 4.4.1 (12.7%), and 4.1.1. (10.7%) were the most prevalent. Phylogenetic and transmission network analyses suggest that these isolates circulating within Ecuador share genetic ties with isolates from other continents, implying historical and ongoing intercontinental transmission events. Our findings underscore the importance of integrating genomic data into public health strategies for tuberculosis control and suggest that enhanced genomic surveillance is essential for understanding and mitigating the global spread of M. tuberculosis. This study provides a comprehensive genomic framework for future epidemiological investigations and control measures targeting M. tuberculosis L4 in Ecuador.

Genetic diversity and population structure of Turkish European chestnut (Castanea sativa) genotypes assessed using start codon targeted polymorphism (SCoT) markers

Abstract The European chestnut (Castanea sativa) is an important nut crop that grows naturally in the Black Sea and Aegean regions of Türkiye. This study examined the genetic diversity and population structure of chestnut genotypes from prominent regions in Türkiye using Start Codon Targeted Polymorphism (SCoT) markers. A total of 44 Turkish chestnut genotypes from the Aegean, Marmara, and Black Sea regions, along with a control group of French variety, were analyzed. The SCoT primers underwent tests to select the most suitable ones, producing 8 selected amplified fragments, 65.34% of which were found to be polymorphic. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCoA) analyses showed clear discrimination between two populations based on their origins, which was supported by the population structure analysis. The analysis of molecular variance (AMOVA) analysis revealed that 3% of the genetic variation was within populations and 97% was among individuals. The out-group (French variety) showed the furthest genetic similarity, and genetic similarity values decreased with increasing geographic distance. The SCoT primers successfully fingerprinted chestnut genotypes and could be used in future research to analyze the phylogeny of chestnuts using genomic DNA.

Validation of PCR amplicon-based directed amplified minisatellite DNA (DAMD) markers for analysis of population structure and fruit trait association of promising Indian mangoes

Validation of PCR amplicon-based directed amplified minisatellite DNA (DAMD) markers for analysis of population structure and fruit trait association of promising Indian mangoes

Genetic diversity and population structure analyses of tropical maize inbred lines using Single Nucleotide Polymorphism markers.

Analyses of the genetic distance and composition of inbred lines are a prerequisite for parental selection and to exploit heterosis in plant breeding programs. The study aimed to assess genetic diversity and population structure of a maize germplasm panel comprising 182 founder lines and 866 derived inbred lines using Single Nucleotide Polymorphism (SNP) markers to identify genetically unique lines for hybrid breeding. The founder lines were genotyped with 1201 SNPs, and the derived lines with 1484 SNPs. Moderate genetic variation, with genetic diversity ranging from 0.004 to 0.44 with a mean of 0.25, was recorded for the founder lines, while corresponding values of 0.004 to 0.34 with a mean of 0.13 were recorded for the derived lines. Heterozygosity values ranging from 0.00 to 0.24 and a mean of 0.08 were recorded for both lines. Of the SNP markers used, 82% of the 1201 markers and 84% of the 1484 markers exhibited polymorphism information content ranging from 0.25 to 0.50. Analysis of molecular variance revealed significant genetic differences (P ≤ 0.001) among and within populations in the founder and derived lines. Most detected variations, i.e., 97% and 88.38%, were attributed to within populations in the founder and derived lines, respectively. Population structure analysis identified three distinct subpopulations among founder lines and two among derived lines. Cluster analysis supported the population structure The following genetically distant founder and derived inbred lines were selected: G15NL337 and G15NL312 (Cluster 1), 15ARG152 and RGS-PL44 (Cluster 2), RGS-PL44 and 15ARG149 (Cluster 2), and RGS-PL33 and RGS-PL44 (Cluster 2), respectively. The selected lines are genetically distinct and recommended for marker-assisted hybrid maize breeding to exploit the frequency of beneficial alleles. This study provides valuable insights for maize breeding programs, enabling the exploitation of beneficial alleles and contributing to improved crop yields and food security through hybrid breeding.

Genetic Diversity Analysis of Wild Cordyceps chanhua Resources from Major Production Areas in China

This study investigated the genetic diversity and genomic variation in wild Cordyceps chanhua populations from four regions in China—Dazhou, Sichuan (ICD); Lu’an, Anhui (ICL); Taizhou, Zhejiang (ICT); and Yixing, Jiangsu (ICY)—to elucidate genetic differentiation patterns and provide a scientific foundation for resource conservation and sustainable utilization. Whole-genome resequencing was performed, yielding high-quality sequencing data (Q20 > 98%, Q30 > 94%, coverage: 93.62–95.79%) and enabling the detection of 82,428 single-nucleotide polymorphisms (SNPs) and 12,517 insertion–deletion markers (InDels). Genomic variations were unevenly distributed across chromosomes, with chromosome chrU05 exhibiting the highest SNP density (5187.86), suggesting a potential hotspot of genetic diversity. Phylogenetic analysis confirmed that all samples belonged to the C. chanhua lineage but revealed significant genetic differentiation among regions. Population structure analysis, supported by structure analysis and PCA, identified two distinct subgroups (G1 and G2) closely associated with geographic origins, reflecting the influence of both environmental and geographic factors on genetic differentiation. These findings underscore the substantial interregional genetic diversity in C. chanhua populations, highlighting the importance of tailored conservation strategies and region-specific germplasm utilization. The study provides critical genomic insights to support marker-assisted breeding, regional cultivation optimization, and the sustainable development of C. chanhua resources.

Detection of single nucleotide polymorphisms associated with litter size in goats using genotyping-by-sequencing and association analysis.

Improving fertility is a key goal in goat production. This study aimed to detect single nucleotide polymorphisms (SNPs) associated with female goat reproductive performance for use in selection processes. Nine reproductive traits were evaluated, including litter size and age at the first, second, and third parities, as well as intervals between parities, in 31 female goats (2 purebred and 29 crossbred goats in various combinations of seven breeds). DNA was extracted from blood, and SNP data were obtained using the genotyping by sequencing (GBS) method. After filtering for allele depth and missing genotype data, the retained SNPs were subjected to population structure analysis and association analysis with the nine traits. For the association analysis, SNPs with false discovery rates ≤ 0.05 were considered significant. PCR allele competitive extension (PACE) genotyping assay was applied to develop genetic markers. An average of 304,852 SNPs were initially detected in the 31 female goats. After filtering, 21,665 SNPs were retained. The first two principal components obtained from individual genotypes classified the 31 goats into three clusters. In the association analysis, six SNPs on four chromosomes were significantly associated with the litter size at first parity. The most significant SNP was detected on chromosome 4, and three genes-IKAROS family zinc finger 1 (IKZF1), fidgetin-like 1 (FIGNL1), and dopa decarboxylase (DDC)-were found within 100 kb downstream and upstream of the SNP. The PACE genotyping assay confirmed genotypes at this SNP with a 96% concordance rate. SNPs significantly associated with litter size at first parity, candidate genes, and the PACE genotyping methods applied in this study can be used for selecting female goats in future genetic improvement programs. However, further study on the frequency of genetic mutation with a larger sample size and functional studies of the candidate genes are required.

Monitoring genetic diversity of Torminalis glaberrima for resilient forests in the face of population fragmentation.

Torminalis glaberrima (Gand.) Sennikov & Kurtto is a European tree species currently underutilized in forestry, valued for its high-quality wood and contribution to ecosystem stability. Despite a projected range expansion as climate change progresses, current population fragmentation levels may inhibit the species' ability to migrate and stabilize fragile forest ecosystems. To investigate the relationship between structural and functional connectivity, we surveyed the genetic diversity, spatial genetic structure, and gene flow of T. glaberrima across Austria, to understand which populations should be given conservation priority. Our sampling encompasses 21 natural and planted populations and 910 individuals of T. glaberrima covering the species' distribution in Austria. We estimated genetic diversity indices, the extent of gene dispersal, and conducted SPAGeDi, STRUCTURE, and discriminant analyses of principal components analyses using one chloroplast minisatellite and eight nuclear microsatellite markers. Despite a highly fragmented distribution of T. glaberrima in the southern, western and central part of its range in Austria, we found high genetic diversity, low population differentiation and inbreeding, and estimated higher gene dispersal values than previous studies. Population structure analyses identified two main regions of genetic ancestry in the northwestern and southeastern part of the species' range in Austria and evidence for the usage of foreign genetic material in two planted populations. Only two of the established ex situ plantations and seed orchards appear to well represent the fine-scale population structure present in Austria, and existing in situ gene conservation units (GCUs) are insufficient to conserve the current natural genetic diversity. We suggest the establishment of further in situ GCUs to maximize the conservation of extant forest genetic diversity. Additionally, we encourage corridor plantings between isolated populations, bolstering the genetic connectivity and diversity of populations.

Population structure, floral diversity, habitat geography, and conservation status of Himalayan horse chestnut (Aesculus indica) in western Himalayan moist temperate forest ecosystems of Kashmir region

This study provides a comprehensive assessment of the population structure, floral diversity, habitat geography, phytosociology, threats, and conservation status of Aesculus indica in the western Himalayan region of Kashmir. This study was designed to investigate distribution patterns, community structure, floristic diversity, and phytosociological attributes of A. indica forests, as well as evaluate the habitat geography of species by using GIS analysis. Primary vegetation data and geographic features were collected via systematic quadrat-based sampling from 14 sites in the moist temperate ecosystem of Kashmir, ranging in elevation from 1,400 to 2,800 m. Population structure analysis revealed an average density of 435.85 stems/ha for A. indica, with a significant variation ranging from 220 to 1,100 stems/ha. The species exhibited a high basal cover of 356.33 cm, emphasizing its significant role in the canopy structure of Himalayan forests. The study identified A. indica as a keystone species supporting a diverse floral community comprised of 168 plant species from 51 families. Dominant families, including Asteraceae, Lamiaceae, Rosaceae, Poaceae, and Polygonaceae, contributed to more than 50% of the total recorded plant species. Phytosociological investigations revealed A. indica to be the dominant species with the highest importance value index (IVI) of 48.81, indicating its ecological significance in temperate forest ecosystems. The species exhibited a preference for north-facing aspects and an altitudinal range of 1,400–2,800 m, which constitute the most suitable habitats for A. indica. However, the study identified significant anthropogenic disturbances, including deforestation, overgrazing, and forest land encroachment, as major threats to A. indica populations in the study area. The deforestation intensity averaged 135 stumps/ha, with some sites exceeding 300 stumps/ha, indicating unsustainable fuelwood consumption patterns and habitat degradation. Overgrazing and trampling were also found to be major threats to A. indica seedlings, affecting the species’ regeneration potential. Conservation strategies should prioritize the protection and restoration of A. indica habitats, especially the upper temperate forest zones with north-facing slopes, to ensure the long-term sustainability of the species. It is recommended to formulate effective conservation measures such as promoting sustainable forest practices, controlling invasive species, restoring degraded habitats, controlled grazing practices, community-based conservation initiatives, sustainable harvesting policies, educating local communities, and promoting alternative livelihoods that support local communities to ensure the preservation of A. indica populations as well as ecosystem health. The study emphasizes the urgent need for effective conservation measures to safeguard A. indica and its associated floral diversity in the western Himalayan region.

Population genomics of a natural Cannabis sativa L. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

BackgroundFuture breeding and selection of Cannabis sativa L. for both drug production and industrial purposes require a source of germplasm with wide genetic variation, such as that found in wild relatives and progenitors of highly cultivated plants. Limited directional selection and breeding have occurred in this crop, especially informed by molecular markers.ResultsThis study investigated the population genomics of a natural cannabis collection comprising male and female individuals from various climatic zones in Iran. Using Genotyping-By-Sequencing (GBS), we sequenced 228 individuals from 35 populations. The data obtained enabled an association analysis, linking genotypes with key phenotypes such as inflorescence characteristics, flowering time, plant morphology, tetrahydrocannabinol (THC) and cannabidiol (CBD) content, and sex. We detected approximately 23,266 significant high-quality Single Nucleotide Polymorphisms (SNPs), establishing associations between markers and traits. The population structure analysis revealed that Iranian cannabis plants fall into five distinct groups. Additionally, a comparison with global data suggested that the Iranian populations is distinctive and generally closer to marijuana than to hemp, with some populations showing a closer affinity to hemp. The GWAS identified novel genetic loci associated with sex, yield, and chemotype traits in cannabis, which had not been previously reported.ConclusionThe study's findings highlight the distinct genetic structure of Iranian Cannabis populations. The identification of novel genetic loci associated with important traits suggests potential targets for future breeding programs. This research underscores the value of the Iranian cannabis germplasm as a resource for breeding and selection efforts aimed at improving Cannabis for various uses.