Kinship Analysis Research Articles

From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?

AbstractPremiseLeveraging DNA markers, particularly single‐nucleotide polymorphisms (SNPs), in parentage analysis, sib‐ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. However, the limited availability of genomic information, confined to the most commonly used species, hinders the broader application of SNPs in species of lower economic interest (e.g., most tree species). We explored the possibility of using universal target capture probes, namely Angiosperms353, to identify SNPs and assess their effectiveness in genomic relatedness analysis.MethodsWe tested the approach in 11 tree species, six of which had a half‐sib family structure. Variants were called within species, and genomic relatedness analysis was conducted in species with two or more families. Scalability via amplicon sequencing was tested by designing primers and testing them in silico.ResultsAdequate SNPs for relatedness analysis were identified in all species. Relatedness values from Angiosperms353‐based SNPs highly correlated with those from thousands of genome‐wide DArTseq SNPs in Cordia africana, one of the species with a family structure. The in silico performance of designed primers demonstrated the potential for scaling up via amplicon sequencing.DiscussionUtilizing universal target capture probes for SNP identification can help overcome the limitations of genomic information availability, thereby enhancing the application of genomic markers in breeding plant species with lower economic interest.

Developmental and validation of a novel small and high-efficient panel of microhaplotypes for forensic genetics by the next generation sequencing

BackgroundIn the domain of forensic science, the application of kinship identification and mixture deconvolution techniques are of critical importance, providing robust scientific evidence for the resolution of complex cases. Microhaplotypes, as the emerging class of genetic markers, have been widely studied in forensics due to their high polymorphisms and excellent stability.Results and discussionIn this research, a novel and high-efficient panel integrating 33 microhaplotype loci along with a sex-determining locus was developed by the next generation sequencing technology. In addition, we also assessed its forensic utility and delved into its capacity for kinship analysis and mixture deconvolution. The average effective number of alleles (Ae) of the 33 microhaplotype loci in the Guizhou Han population was 6.06, and the Ae values of 30 loci were greater than 5. The cumulative power of discrimination and cumulative power of exclusion values of the novel panel in the Guizhou Han population were 1-5.6 × 10− 43 and 1-1.6 × 10− 15, respectively. In the simulated kinship analysis, the panel could effectively distinguish between parent-child, full-sibling, half-sibling, grandfather-grandson, aunt-nephew and unrelated individuals, but uncertainty rates clearly increased when distinguishing between first cousins and unrelated individuals. For the mixtures, the novel panel had demonstrated excellent performance in estimating the number of contributors of mixtures with 1 to 5 contributors in combination with the machine learning methods.ConclusionsIn summary, we have developed a small and high-efficient panel for forensic genetics, which could provide novel insights into forensic complex kinships testing and mixture deconvolution.

Differentiation of wild accessions within the Panax bipinnatifidus complex using newly developed polymorphic microsatellite markers

Abstract Panax L., renowned as ginseng genus, is a famous medicinal group of family Araliaceae. Within this genus, the taxa of Panax bipinnatifidus complex are mainly distributed in Himalayas and Hengduan Mountain areas. Due to the complex evolutionary history and short-term rapid radiation, the relationships among species within the complex have not been clearly resolved, and the taxa identification is difficult due to the intermediate morphological traits. This study aimed to use the available restriction-site associated DNA sequence data from 29 individuals of P. bipinnatifidus complex to mine high-polymorphic simple sequence repeat (SSR) markers, with the goal of evaluating their utility in taxa identification. Eleven polymorphic SSR loci were ultimately selected and validated through polymerase chain reactions amplifying across 63 individuals of P. bipinnatifidus complex and 13 individuals of three outgroup species. The subsequent genetic diversity analysis uncovered 76 alleles in total, ranging from 5 to 15 per locus. Observed heterozygosity spanned 0.241–0.512, while expected heterozygosity ranged between 0.345 and 0.644. The genetic kinship analysis revealed a sister relationship between Panax zingiberensis and Panax vietnamensis. The analysis result also supported the classification of samples from Hunan and Hubei provinces into a single genetic unit within the P. bipinnatifidus complex. These newly developed SSR markers will facilitate the identification of wild ginseng plants.

Familial hypodontia in bronze age Northwest China (1046–771BC)

ObjectiveThis research aimed to report hypodontia cases in a Middle Bronze Age high-tier cemetery in China and test the possible hereditary behind hypodontia by performing kinship tests on those individuals. DesignIn this study, dental anomalies were observed on a human skeletal sample (n = 45) uncovered from Yaoheyuan, China. Ancient DNA analysis was subsequently employed on a subsample of the Yaoheyuan individuals (n = 15), including individuals observed hypodontia and individuals randomly sampled from the cemetery for preliminary investigation on the cemetery demography. Kinship estimation tests (READ, TKGWV2, KIN, and F3 test) were subsequently employed. ResultsThe Yaoheyuan elite population had a prevalence (n = 7, 15 %) of tooth agenesis in either the maxilla or mandible, with one to two teeth missing. All missing teeth were incisors, except for one individual missing maxillary second molar. Preliminary ancient DNA results indicate that several kinship groups existed among interred individuals, including those with hypodontia, indicating the hereditary origin of these cases. ConclusionsThe prevalence of hypodontia observed on site is high compared to that in both modern East Asian populations and archaeological samples in the Chinese population. The preliminary kinship analysis suggests a case of familial hypodontia. Ancient DNA analysis should be thoroughly conducted in future studies to understand the genetic markers contributing to those hypodontia cases among the Yaoheyuan individuals.

Development and validation of a 5K low-density SNP chip for Hainan cattle

BackgroundThis study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included.ResultsA total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65–99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways.ConclusionThe development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources.

Does the distribution of Wormian bone frequencies across different world regions reflect genetic affinity between populations?

BackgroundWormian, or sutural bones, are additional, irregularly shaped bone fragments that can occur within cranial sutures. These bones may arise due to various factors, including mechanical pressure on skull bones during early ontogenetic stages, such as during artificial cranial deformations, or due to genetic and environmental influences. This study investigates the potential genetic basis of sutural bones by comparing their frequencies across diverse global regions. It analyzed 33 craniological series, encompassing 2059 crania, to assess the frequency of sutural bones in the coronal, squamous, lambdoid, and occipitomastoid sutures among skeletal populations from regions including Aboriginal Australia, Melanesia, Southeast Asia, Siberia, Europe, and Native America. Biological distances between populations were calculated using Smith’s mean measure of divergence (MMD), with results visualized through multidimensional scaling.ResultsThe analysis identified distinct clusters of Caucasian and Siberian populations. Siberian aboriginal populations are compactly grouped, consistent with mtDNA data indicating genetic roots dating back to the Neolithic inhabitants of the Lake Baikal region. Further, differentiation within these populations is linked to the founder effect and gene flow. Notably, genetically related groups like the Inuit and Chukchi of Chukotka differ from other Siberian groups. In contrast, southern Siberian populations, such as the Buryats and Mongols, are closely positioned, aligning with genetic data. The differentiation between Southeast Asian and African regions was subtler, with their clusters largely overlapping. Yet, genetic links between populations were observed in some cases. Thus, Australians, Melanesians, and Papua New Guineans were located close to each other on the multidimensional scaling map, as were two African populations.ConclusionsThe findings tentatively suggest a potential genetic component in the expression of Wormian bones, although this hypothesis requires further empirical support, particularly through genetic studies. While genetic factors may influence the expression of Wormian bones, environmental conditions and pathological processes also play significant roles. It can be suggested that Wormian bones could potentially serve as an additional tool in kinship analysis within burials; however, their utility significantly depends on the extent of their genetic influence. If future genetic studies confirm a substantial genetic component and its dominance over environmental factors, the use of these bones in anthropological and forensic analyses would receive additional validation.

Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.

Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China

BackgroundWheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.ResultsTo understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.ConclusionsA core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

A Case of Two Full Sisters Share Identical Genotypes on the X Chromosome

Abstract X-chromosomal genetic markers are frequently employed in forensic parentage determination owing to their distinctive inheritance patterns. The kinship analysis revealed that two sisters who were not identical twins had identical genotypes on the X chromosome, encompassing 36 X-chromosomal short tandem repeats (X-STRs) and 29 X-chromosomal single-nucleotide polymorphisms (X-SNPs) that spanned the whole X chromosome from the p-telomere to the q-telomere. The identical X-STRs and X-SNPs in the daughters could be the result of linkage or a rare chance of occurrence. This highlights the need for careful analysis and interpretation when dealing with X chromosome markers and that in individual cases, even if two women share an allele at each locus, this does not necessarily mean that they are paternal sisters. The likelihood of random concordance due to maternal alleles must be taken into account.

Karakter Kuantitatif dan Hubungan Kekerabatan Genotipe Padi (Oryza sativa L.) Beras Merah dan Beras Hitam yang Ditanam secara Gogo

This study aims to determine the appearance of quantitative characters and kinship relationships of the genotype of red rice and black rice grown in gogo. The research was conducted in February – May 2024 on a medium plain land with an altitude of 370 meters above sea level, in Tampak Siring Village, Central Lombok, NTB. The materials used were 21 rice genotypes consisting of 11 red rice strains, 4 black rice strains, 2 red rice elders, 2 black rice elders and 2 comparison varieties (Inpago Unram I and IR64). The analysis used is the Analysis of Variance (ANOVA) of the Group Random Design (GRD) model with a real level of 5%, if there are real different characters, then the Duncan Multiple Range Test (DMRT) will be continued at a real level of 5%. Cluster analysis was carried out based on the average value of quantitative characters using the euclidean distance method using the R-Studio program. The results of the study showed that between strains all characters had different appearances except for the number of non-productive saplings. G-2 strain; G-6; and G-18 had the same results as Inpago Unram I. Kinship analysis conducted based on the average value of quantitative characters obtained four clusters, namely cluster I G-21, G-9, G-20, G-11, G-17; cluster II G-19, G-2, G-18, G-6, G-7; cluster III G-1, G-5, G-8, G10, G-3, G-4, G-16; and cluster IV G-12, G-15, G-13, G-14.

Application of a newly constructed NGS panel with 45 X-linked microhaplotypes demonstrates the unique value of X-MH for kinship testing and mixture analysis

X-linked microhaplotypes (X-MHs) have the potential to be a valuable supplementary tool in complex kinship identification or the resolution of DNA mixtures, because they bring together the distinctive genetic pattern of X chromosomal markers and the benefits of microhaplotypes (MHs). In this study, we used the 1000 Genome database to screen and select 63 X-MHs; 18 MHs were filtered out though a batch sequencing assessment of the DNA samples collected from 112 unrelated Chinese Han individuals. The resulting 45-plex panel performed well in comprehensive assessments including repeatability, sensitivity, species specificity, resistance to PCR inhibitors or degradation, mutation rate, and accuracy in detecting DNA mixture samples. The minimum amount of DNA template that can be tested with this panel is 0.5 ng. Additionally, the alleles of the minor contributor can be accurately detected when the mixture rate is larger than 1:9 in female-male mixture or 1:19 in male-male mixture. Then, we calculated population parameters on each MH based on the allele frequency data obtained from the sequence results of the aforementioned 112 unrelated samples. Combining these parameters on each MH, it can be calculated that TDPm, TDPf, CPET, CPEDFM, CPEDFF and CNCEP3 of the 45-plex system were 1–8.99×10−13, 1–1.62×10−19, 0.9999999995, 0.9999981, 0.9955, 0.9999971 and 0.99940, respectively, indicating that the panel is capable in personal identification and parentage testing. To reveal the unique advantage of X-MHs in the analyses of complex kinship and male DNA mixture, further assessments were made. For complex kinship identification, 22 types of individual pairs with different second-degree kinship were simulated and different types of likelihood ratios (LR) were calculated for each. The results revealed that the panel can achieve accuracy of approximately 70 %∼80 % when dividing each of the three types of second-degree kinships into three or four groups. Theoretically, such sub-division cannot be done by using independent autosomal markers. For male DNA mixture analysis without suspects, the maximum likelihood ratio strategy was derived and employed in the estimation of the number of male contributors (NOMC). Simulations were conducted to verify the efficacy of the 45-plex panel in the field and to compare it with autosomal markers by assuming the 45 MHs as autosomal ones. The results showed that X-MHs can achieve higher accuracy in the estimation of NOMC than autosomal ones when the mixed males were unrelated. The results highlighted the unique value of X-linked MHs in complex kinship and male mixture analyses.

Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders

The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.

Uncovering the Past: DNA Analysis of Skeletal Remains from the Medieval Bosnian City of Bobovac

Numerous archaeological sites in Bosnia and Herzegovina represent a historical heritage and testify to the rich cultural, social, and political life of medieval Bosnia. Bobovac, the capital of the Bosnian Kingdom after King Tvrtko I's coronation in 1377, featured a royal complex with a palace, church, and fortification. Recent molecular-genetic research on skeletal remains from Bobovac aims to uncover medieval ancestors' customs and genetic origins. Fifteen well-preserved teeth samples from Bobovac were processed. STR amplification employed PowerPlex® Fusion and Investigator® 24plex QS Kits, with Y-STR profiles generated using the PowerPlex® Y23 System. Fourteen partial autosomal STR profiles were obtained, enabling sex determination and kinship analysis. STR amplification success varied due to ancient DNA degradation, with larger loci showing lower amplification rates. Kinship analysis confirmed appropriate marker selection, demonstrating high reliability for determining close relationships. Integrating aDNA analysis with archaeological research enhances our understanding of historical populations, connecting archaeology and forensic genetics to contribute to the broader narrative of human history.

MHBase: A comprehensive database of short microhaplotypes for advancing forensic genetic analysis

Microhaplotypes (MHs) were first recommended by Prof. Kidd for use in forensics because they can improve human identification, kinship analysis, mixture deconvolution, and ancestry prediction. Since their introduction, extensive research has demonstrated the advantages of MHs in forensic applications and provided useful data for different populations. Currently, two databases, ALFRED (ALlele FREquency Database) and MicroHapDB (MicroHaplotype DataBase), house the published MH information and population data. We previously constructed a single nucleotide polymorphism SNP-SNP MH database (D-SNPsDB) of MHs within 50 bp on the whole human genome for 26 populations integrating basic data such as physical genome positions, mapping of variant identifiers (rsIDs), allele frequencies, and basic variant information. Building upon the previous research, we further selected MHs containing at least two variants (SNPs and/or insertions/deletions [InDels]) within a short DNA fragment (≤ 50 bp) in 26 populations based on the 1000 Genomes Project dataset (Phase 3) to construct a more comprehensive database. Subsequently, we established a user-friendly website that allows users to search the MH database (MHBase) based on their research objectives and study population to find suitable loci and provides other functions such as querying reported loci, performing online calculations using the PHASE software, and calculating ancestral-related parameters. The loci in the database are classified as SNP-based MHs, which include only SNPs, and InDel-including MHs, which contain at least one InDel. Here, we provide a detailed overview of the MHBase and an analysis of shared loci at the global and continental levels, ancestral markers, the genetic distance within loci, and mapping with the genome annotation file. The website is an accessible and useful tool for researchers engaged in marker discovery, population studies, assay development, and panel design.

METHODS OF KINSHIP ANALYSIS IN FOSSIL POPULATIONS

Introduction. Identifying kinship relationships from skeletal remains is among the various objectives of bioarchaeological studies. This article focuses on reviewing the methods used to analyze biological kinship in human fossil populations through non-metric traits. Methods. Since direct molecular-genetic analysis of kinship is often highly challenging due to the poor preservation of ancient DNA, special attention in such studies is given to nonmetric phenotypic traits. Results. Research with osteological samples that have been documented provides compelling evidence that the level of morphological similarity between individuals is directly related to their degree of biological kinship. In cases where the pedigrees of osteological materials are fully or partially known, phenotypic data can be effectively used in lieu of genetic information. Discussion. The methodology developed for kinship analysis depends on the internal spatial structure of the cemetery being studied. When analyzing small burial sites, the aim is to determine if the people buried there are close relatives. Various methods are used in these analyses, including different techniques for determining the likelihood of kinship, cluster analysis, and correlation coefficients. Identifying kinship is most promising in burial sites where archaeological or historical indicators of biological relationships are present. Kinship analysis in spatially structured cemeteries is aimed at identifying families or social groups. The analysis of uniformly distributed cemeteries focuses on identifying closely related individuals in large burials without clearly defined subgroups. This involves spatial correlation analysis, which tests for significant correlation between the matrix of spatial distances and the matrix of phenotypic distances; various counting methods to test for non-random clustering of traits; the nearest neighbor method; and a non-spatial block search procedure that simultaneously identifies presumed relatives and the traits that indicate the degree of their kinship. Conclusion. Many problems in establishing kinship can be overcome with the availability of skeletal material accompanied by verified genealogical data. Unfortunately, skeletal remains with preserved documentation are quite rare, limiting the opportunities to study the inheritance of non-metric traits and the morphological similarity of biologically related individuals.

Genome identification and diversity analysis of banana (Musa spp.) from Jember based on morphological characters

Introduction: Banana plants are easy to find and grow in Indonesia, including in Jember. Banana production in Jember in 2020 increased by 50% and has the potential to be inventoried and developed. Information regarding the characteristics of various banana cultivars is needed for future banana breeding. This research was conducted to identify and classify the genome of bananas growing in Jember and determine the level of banana diversity. Methods: The banana exploration using a purposive sampling method. The observation of 15 morphological characters followed the method of Simmonds and Shepherd. Determination of the genome followed the method of Silayoi & Chamchalow and Singh & Uma. The kinship analysis uses cluster analysis using the average linkage method and Gower distance, by R Studio software. Results: There were 23 banana cultivars obtained in this research, consisting of 35% dessert bananas and 65% plantain types. Genome identification results in four genome groups, namely AA/AAA, AAB, ABB, and BB. Cluster analysis produces three main groups, where its branch is generally consistent with the genome grouping. The closest relationship is between Rayap and Seribu bananas (0.96), while the furthest is between Gaje and Agung bananas (0.38). The dissimilarity value for 23 banana cultivars is 0.36, or the similarity is 0.64. Conclusion: The 23 banana cultivars are closely related or have low diversity based on the 15 morphological characters observed. Further identification can be carried out with a greater number of morphological characters, accompanied by molecular identification.

X-chromosomal STRs in aDNA kinship analysis.

The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.

Forensic parameters of 10 Y-STR markers in the Nigerian Hausa, Igbo, and Yoruba populations

Y chromosome short tandem repeats, or Y-STRs, are interesting genetic markers suitable for identifying male offenders in forensic investigations because of the haploid nature of the human male determining chromosome. Furthermore, due to the non-recombining nature of the Y chromosome, Y-STRs are choice markers in paternity or kinship analysis, human evolutionary investigations, and population studies. The lack of reference Y-haplotype data for the populace currently hampers the use of these markers in forensic applications in Nigeria. In this study, the 10 Y-STR loci in the UniQTyperTM Y-10 system including DYS385ab, DYS447, DYS449, DYS481, DYS504, DYS518, DYS612, DYS626, DYS644 and DYS710 were studied in 461 males comprising 139 Hausa, 96 Igbo and 226 Yoruba ethnic populations. Sixty alleles were recorded for the pooled dataset across the 10 loci, with allele frequencies ranging from 0.0022 to 0.6052. There were 430 haplotypes detected, 403 unique (singletons), and 27 were shared. The discrimination capacity and haplotype diversity were 0.9330 and 0.9770, respectively. Allelic richness was highest in the locus DYS626 and lowest in DYS504. Private alleles were found in each group, with the Hausa population having the highest number. Duplications and microvariant alleles were also reported. These findings may be helpful for paternal lineage investigations, population genetics, and forensic applications among the Nigerian populations.

In silico EST-SSR Identification and Development through EST Sequences from Metroxylon sagu Rottb. for Genetic Diversity Analysis.

Sago plant (Metroxylon sagu Rottb.) is one of the most carbohydrate-producing plants in the world. Microsatellites or simple sequence repeats (SSRs) play an important role in the genome and are used extensively compared to other molecular markers. For the first time, we are exploiting data expressed sequence tags (EST) of sago plants to identify and characterise markers in this species. EST data about sago plants are obtained through the EST database on the National Center for Biotechnology Information (NCBI) website. We obtained data of 458 Kb (412 contig) with a maximum and minimum length of 1,138 and 124 nucleotides, respectively. We successfully identified 820 perfectly patterned SSR using Phobos 3.3.12 software. The type characterisation of EST-SSR was dominated by tri-nucleotides 36% (294), followed by hexa-nucleotides 24% (202), tetra-nucleotides 15% (120), penta-nucleotides 13% (108) and di-nucleotides 12% (96). The most frequency of SSR motifs in each type is AG, AAG and AAAG. Analysis of synteny on the EST sequence with the online application Phytozome found that sequences were distributed on 12 Oryza sativa chromosomes with a likeness percentage between 63% to 100% and e-value between 0 to 0.094. We developed the primer and generated 19 primers. Furthermore, we validated 7 primers that all generated polymorphic alleles. To our knowledge, this report is the first identification and characterisation of EST-SSR for sago species and these markers can be used for genetic diversity analysis, marker assisted selection (MAS), cultivar identification, kinship analysis and genetic mapping analysis.

Genomic structure analysis and construction of DNA fingerprint for four sheep populations

The Yongdeng Qishan sheep (QS) is a sheep population found locally in China. To gain in-depth knowledge of its population characteristics, three control groups were chosen, comprising the Lanzhou fat-tailed sheep (LFT), TAN sheep (TAN), and Minxian black fur sheep (MBF), inhabiting the nearby environments. This study genotyped a total of 120 individuals from four sheep populations: QS, LFT, TAN, and MBF. Using Specific-Locus Amplified Fragment Sequencing, we conducted genetic diversity, population structure, and selective sweep analysis, and constructed the fingerprint of each population. In total, there were 782 535 single nucleotide polymorphism (SNP) variations identified, with most being situated within regions that are intergenic or intronic. The genetic diversity analysis revealed that the QS population exhibited lower genetic diversity compared to the other three populations. Consistent results were obtained from the principal component, phylogenetic tree, and population structure analysis, indicating significant genetic differences between QS and the other three populations. However, a certain degree of differentiation was observed within the QS population. The linkage disequilibrium (LD) patterns among the four populations showed clear distinctions, with the QS group demonstrating the most rapid LD decline. Kinship analysis supported the findings of population structure, dividing the 90 QS individuals into two subgroups consisting of 23 and 67 individuals. Selective sweep analysis identified a range of genes associated with reproduction, immunity, and adaptation to high-altitude hypoxia. These genes hold potential as candidate genes for marker-assisted selection breeding. Additionally, a total of 86 523 runs of homozygosity (ROHs) were detected, showing non-uniform distribution across chromosomes, with chromosome 1 having the highest coverage percentage and chromosome 26 the lowest. In the high-frequency ROH islands, 79 candidate genes were associated with biological processes such as reproduction and fat digestion and absorption. Furthermore, a DNA fingerprint was constructed for the four populations using 349 highly polymorphic SNPs. In summary, our research delves into the genetic diversity and population structure of QS population. The construction of DNA fingerprint profiles for each population can provide valuable references for the identification of sheep breeds both domestically and internationally.