Number Of Alleles Research Articles

Influence of Sires on Population Substructure in Dülmen Wild Horses.

The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185 male foals sired by nine stallions. As females could not be sampled, we could not make inferences on all yearlings and test whether there are differences in the genetic population parameters between both sexes. The mean number of progeny was 19.92 with a range of 2-32, caused by the length of the service period per stallion. The average observed and unbiased expected heterozygosity was 0.688 and 0.631, the mean number of alleles was 4.448, and Wright's FIS was -0.173. Pairwise genetic distances (FST and Nei's unbiased genetic distances) were significant and varied between 0.038 to 0.091 and 0.085 to 0.290, respectively. Neighbor-joining dendrogram plots clustered a large proportion of the paternal progeny groups in different branches. Posterior Bayesian analyses using seven paternal half-sib groups with 10-74 members supported a maximum of six clusters, with two paternal progeny groups not differing, and a median of five clusters, with two groups of two sires each falling into the same clusters. When sires were employed in non-consecutive years, progeny from these different years of the same sires were grouped in the same cluster, whereas the progeny of one sire from two consecutive years were in different clusters. We were able to distinguish male progeny from Dülmen wild horse stallions and to show the effects of stallion use on the genetic substructure in the Dülmen wild horse herd. In conclusion, the analyses showed the genetic potential of the Dülmen wild horse stallions to maintain a high genetic diversity and also the effects in which breeding seasons and for how long stallions are used to sire foals. The selection of stallions may be sensitive for the further development of genetic diversity and preserve this closed population as a valuable resource for further studies on the evolution of the horse.

Assessing the population structure and genetic diversity of wheat germplasm with the iPBS-retrotransposons marker system

Context Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars. Aims This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system. Methods A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis. Key results Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon’s information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations. Conclusions This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat. Implications The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat.

Genetic diversity and origin of Kazakh Tobet Dogs

The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.

Common Variants in the TYR Gene with Unclear Pathogenicity as the Cause of Oculocutaneous Albinism in a Cohort of Russian Patients.

Background: oculocutaneous albinism (OCA) is a hereditary impairment of skin, hair, and eye pigmentation. The most common form of albinism is autosomal recessive albinism, caused by mutations in the TYR gene, accounting for approximately 40-50% of all cases of the disease in European populations. Common hypomorphic variants in the TYR gene could lead to a mild form of albinism in a compound heterozygous state with a pathogenic variant. Methods: we examined by allele specific MLPA a cohort consisting of 118 unrelated patients with albinism and 10 parents of these patients. The control cohort consisted of 200 unexamined Russian residents. Results: the patients with albinism were divided into three groups: without pathogenic variants in the TYR gene-70 patients, with one pathogenic variant in the TYR gene-20 patients, and with two pathogenic variants in the TYR gene-28 patients. Among the 20 patients with a single heterozygous variant in the TYR gene, 15 patients had the c.575C>A p.(Ser192Tyr) variant, and 15 had the c.1205G>A p.(Arg402Gln) variant. Both the c.575C>A p.(Ser192Tyr) and c.1205G>A p.(Arg402Gln) variants were identified in 12 patients. In addition to the aforementioned variants, an intronic variant c.1185-6208A>G (rs147546939) was identified in seven patients. Conclusions: the frequencies and the number of alleles c.575A, c.1205A, and c.1185-6208G in different groups of patients and the control group were compared. In this study, we demonstrate that the complex alleles [c.575C>A p.(Ser192Tyr); c.1205G>A p.(Arg402Gln)] and [c.575C>A p.(Ser192Tyr); c.1185-6208A>G; c.1205G>A p.(Arg402Gln)] are associated with oculocutaneous albinism, which is consistent with findings from other researchers.

Developmental validation of NeoTyper autosomal STR kit

BackgroundShort Tandem Repeats (STRs) are pivotal to efficient human DNA profiling. Including mini-STRs can further improve the assay's efficiency. The FBI's (Federal Bureau of Investigation) expanded Combined DNA Index System (CODIS) list contains twenty STRs for human identification. The NeoTyper Autosomal kit developed by Neom Scientific Solutions Pvt. Ltd. enables the amplification of 28 loci, which include markers from the expanded CODIS list, are National DNA Index System (NDIS) recommended markers, and comply with the NDIS recommended allelic range. In addition, the kit also includes 8 more markers including Penta D and Penta E. The NeoTyper Autosomal kit STR markers includes 14 mini-STR which makes it very effective for the human identification of the degraded samples like unidentified body remains.This is a developmental validation study for NeoTyper, based on the listed Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. MethodologyWe extracted the human genomic DNA from blood and FFPE (Formalin-Fixed Paraffin-Embedded) samples, and performed PCR amplification for the 28 loci using the developed kit, NeoTyper, which features a six-dye chemistry. The amplified products were run on 3500xL Genetic Analyzer. We used GeneMapper ID-X v.1.4 (Applied Biosystems) to analyse peak height and allele calling. Developmental validation parameters, including genetic characterization, analysis of sensitivity, female-male mixture, precision, and accuracy (repeatability and reproducibility), were investigated and analysed. Furthermore, intra- and inter-laboratory comparisons, as well as mini-STR analysis and validation were done. ResultsThe developed NeoTyper Autosomal kit demonstrated 100 % sensitivity up to a DNA concentration of 62.5 pg, as measured by the number of alleles called. The assay also demonstrated good precision (measured in terms of standard deviation, SD ranging between 0.60 and 0.77) and reproducibility, with alleles called at 100 % accuracy. Furthermore, precision was high (measured as SD ranging from 0.50 to 0.66), with a 100 % accuracy. In 90.9 % of the samples (10 out of 11 female-male sample varied ratio), the mixture analysis revealed 100 % of the alleles being called. A comparative analysis of mini-STRs in GlobalFiler and NeoTyper Autosomal kit revealed a 100 % accuracy of the NeoTyper mini-STRs. ConclusionIn conclusion, the NeoTyper Autosomal kit developed by Neom Scientific Solutions Pvt. Ltd. enables the amplification of 28 loci, which includes markers from expanded CODIS list; are NDIS accepted markers and comply with their recommended allelic range. The integration of mini-STRs in the kit demonstrates its efficacy and reliability, particularly when addressing the difficulties posed by degraded samples. This developmental validation study demonstrates consistent performance with high sensitivity, precision and accuracy (repeatability and reproducibility) which is indicative of an advanced and efficient system for human identification.

The Characteristics of Microsatellites and Development of SSR Markers in the Genome of Periplaneta americana

The research was to analyze the number and pattern of microsatellites in Periplaneta americana’s genome, and also developed tetranucleotide SSR markers. We thoroughly scrutinized and dissected the inherent traits that govern the allocation of microsatellite sequences within the profound domain of P. americana’s genome, software MSDBv2 allowed for the utilization of 2.67 Gb. There were precisely 1,498,458 flawless microsatellite sequences, encompassed approximately 1.57%. The cumulative length of microsatellites was 45,076,707 bp, and the abundance of microsatellites was 16889.577 loci/Mb. Out of all the microsatellite repeat variations, the trinucleotide repeats accounted for 44.83% of the total, with a count of 671,830, which were the most abundant type. The tetranucleotide, mononucleotide, pentanucleotide, dinucleotide, and hexanucleotide repeats accounted for 29.01%, 13.62%, 8.37%, 3.70% and 0.47%, respectively. The numbers of different repeat copy categories in each repeat type were also quite different, such as the A in mononucleotide repeat type, the AT in dinucleotides, the AAT in trinucleotides, and AAAT in tetranucleotide were the most of each categories. 143 primers were designed. After undertaking the arduous task of enhancing the initial PCR conditions to perfection, we successfully determined and analyzed a gargantuan number of 38 different polymorphic tetranucleotide microsatellite markers with utmost precision, employed the assistance of two-color fluorescence markers and ingenious genotyping scaned for their comprehensive characterization. The genetic variation in P. americana population involved analyzing the diversity of microsatellite loci, which exhibited varying numbers of alleles per locus ranging from 4 to 21 among the 32 individuals studied. Among them, there were 24 microsatellite loci whose alleles were greater than 10, accounted for 63.16% of the total number of polymorphic microsatellite. The calculated degrees of genetic diversity varied between 0 and 1, the observed heterozygosities was between 0.219 and 1.0, with a mean of 0.6391. The expected heterozygosities was between 0.312 and 0.942, with a mean of 0.7663. The PIC was between 0.296 and 0.923, with a mean of 0.7294, and there were 36 microsatellite loci whose PIC was greater than 0.5, accounted for 94.74%. This study indicated that new development of microsatellite markers for P. americana was feasible. Furthermore, these new development microsatellite markers will provide adequate and reliable molecular genetics data for carrying out the research of molecular ecology and conservation genetics for P. americana.

Development and characterization of 15 polymorphic microsatellite markers for Hepatica insularis (Ranunculaceae) endemic to the Korean Peninsula

Hepatica insularis Nakai, a perennial herb endemic to warm-temperate regions on the Korean Peninsula, has been a subject of taxonomic debate due to its morphological similarities with Hepatica asiatica Nakai. To address the taxonomic ambiguity and provide evolutionary insights into H. insularis, we developed 15 polymorphic microsatellite markers. Of these, eight markers were successfully cross-amplified in H. asiatica, demonstrating their broader applicability. The markers exhibited high levels of polymorphism, with the number of alleles per locus ranging from two to eleven. The expected heterozygosity (H<sub>E</sub>) and observed heterozygosity (H<sub>O</sub>) values ranged from 0.180 to 0.802 and from 0.000 to 0.933, respectively. The developed markers will serve as a valuable tool for future phylogeographic studies aiming to understand the genetic structure and diversity of H. insularis and related taxa.

Distribution of Plasmodium falciparum Chloroquine Resistance Transporter (Pfcrt) and Plasmodium falciparum Multidrug Resistance 1(Pfmdr-1) Genes in Ilorin North-central Nigeria

Malaria remains a major health problem globally, especially in Sub-Saharan Africa. The ease of developing resistance to anti-malaria drugs by Plasmodium falciparum is a serious challenge to malaria control and elimination programs. Consequently, continuous monitoring of drug efficacy is necessary to ascertain effective treatment policies. The study investigated the distribution pattern of these genes in Plasmodium falciparum isolates in Ilorin metropolis. One hundred and three samples were collected randomly from 5 hospitals in Ilorin metropolis. The samples were amplified at codon 76 and 86 for Pfcrt and Pfmdr-1 respectively using PCR/Restricted Fragment Length Polymorphism (RFLP). Drug susceptible alleles were most prevalent in the study area (K76 and N86) with 31% and 40% respectively, followed by drug resistance alleles (86Y) with 13%, and the least prevalent (2%) was the mixed alleles K76T. UITH has the highest number of susceptible alleles followed by CSC 38% and 46% for K76 and N86 respectively. There are significant differences in the distribution of these alleles and the study sites (P55< 0.05). The prevalence of resistance alleles in the area is a welcome development that can be employed for the possible re-introduction of CQ to treat malaria in the study area. It will be an advantage over expensive ACT because it is safe, cheap, and readily affordable.

Genetic characterisation of a recovered Italian chicken breed: the Millefiori Piemontese

The recent rediscovering of the Millefiori Piemontese breed, previously considered as extinct, has led to its genetic characterisation: establishing the basis for its recovery and preservation. This study describes the morpho-biometric traits and compares the genetic variability of the Millefiori Piemontese breed with that of other local chicken breeds using 26 microsatellite markers. A subset of 14 markers was used to compare the genetic variation of the Millefiori Piemontese breed with that of two other Piedmontese chicken breeds (Bionda Piemontese and Bianca di Saluzzo) as well as 17 Italian and 2 commercial hybrids, whose genetic variability has already been investigated. The present study confirmed the sexual dimorphism and assessed the genetic variability of the Millefiori Piemontese in terms of number of alleles/locus (Na = 4), the effective number of alleles (Nea = 3), observed (Ho = 0.56) and expected heterozygosity (He = 0.53), self-coancestry (IB = 0.65), potential extinction risk (ERI = 2), and its contribution to the Italian poultry biodiversity (GDT = −0.60). The results indicate that, despite its small population size (Ne = 56), the Millefiori Piemontese population exhibits significant genetic diversity, making it a valuable resource for breeding programs focused on preserving the breed and safeguarding its biodiversity. This study is the first to investigate the genetic variability of the Millefiori Piemontese breed and compare it with other local poultry breeds. The findings highlight the genetic uniqueness of the Millefiori breed and its significant contribution to the biodiversity of chickens in Piedmont and Italy, emphasising the importance of its conservation.

Sanitary Waters: Is It Worth Looking for Mycobacteria?

The freshwater environment is suitable for nontuberculous mycobacteria (NTMs) growth. Their high adaptability represents a considerable risk for sanitary water systems, which are a potential vector for NTMs transmission. This study investigated the occurrence of NTMs, such as Mycobacterium saskatchewanense, in hospital water systems to support the surveillance and control of potentially pathogenic NTMs. We analyzed 722 ultrapure dialysis fluid samples from Emilia Romagna Dialysis Services. Among these, 35 samples were found to be positive for M. saskatchewanense. The strains were characterized using whole-genome sequencing (WGS) and variability analysis was carried out along the whole M. saskatchewanense genome. This investigation revealed the exclusive presence of M. saskatchewanense in these dialysis machines, with low genetic variability among all strains (with a low number of different alleles: <15). The strong similarity among the strain groups was also confirmed in the WGS-based ML tree, with very few significant nodes, and no clusters were identified. This research highlights the necessity of implementing surveillance protocols and investigating any potential link to human infections, as well as stressing the urgency of enhancing surveillance and infection control measures.

Divergence and serial colonization shape genetic variation and define conservation units in Asian elephants

Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analyzed 34 whole genomes (between 11× and 32×) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern), Central, and three in Southern India. Our data reveal signatures of divergence and serial colonization and a potential dilution of genetic diversity from north to south of India. The northern populations diverged from others more than 70,000 years ago, have higher genetic diversity, and have low inbreeding (pi= 0.0016± 0.0001; FROH>1 MB= 0.09± 0.03). Two of three populations in Southern India have low diversity and are inbred, with very low effective population sizes compared with census sizes (pi= 0.0014± 0.00009 and 0.0015± 0.0001; FROH>1 MB= 0.25± 0.09 and 0.17± 0.02). Analyses of genetic load reveal the purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the southern populations and a decreasing number of deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity, make southernmost populations high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to genomic signatures of serial founding events, even in large, highly mobile, endangered mammals.

Systematic Modeling of Risk-Associated Copy Number Alterations in Cancer.

The determination of the cancer prognosis is paramount for patients and medical personnel so that they can devise treatment strategies. Transcriptional-based signatures and subtypes derived from cancer biopsy material have been used in clinical practice for several cancer types to aid in setting the patient prognosis and forming treatment strategies. Other genomic features in cancer biopsies, such as copy number alterations (CNAs), have been underused in clinical practice, and yet they represent a complementary source of molecular information that can add detail to the prognosis, which is supported by recent work in breast, ovarian, and lung cancers. Here, through a systematic strategy, we explored the prognostic power of CNAs in 37 cancer types. In this analysis, we defined two modes of informative features, deep and soft, depending on the number of alleles gained or lost. These informative modes were grouped by amplifications or deletions to form four single-data prognostic models. Finally, the single-data models were summed or combined to generate four additional multidata prognostic models. First, we show that the modes of features are cancer-type dependent, where deep alterations generate better models. Nevertheless, some cancers require soft alterations to generate a feasible model due to the lack of significant deep alterations. Then, we show that the models generated by summing coefficients from amplifications and deletions appear to be more practical for many but not all cancer types. We show that the CNA-derived risk group is independent of other clinical factors. Furthermore, overall, we show that CNA-derived models can define clinically relevant risk groups in 33 of the 37 (90%) cancer types analyzed. Our study highlights the use of CNAs as biomarkers that are potentially clinically relevant to survival in cancer patients.

Screening a new set of microhaplotypes in exonic regions for sample identity testing and paternity testing during whole exome sequencing analysis.

Whole exome sequencing (WES) is widely used in clinical diagnosis. Before obtaining an accurate diagnosis, it is essential to conduct sample identity testing and paternity testing on trio samples. Currently, there is a lack of optimal genetic markers for these purposes, with limited literature available in this area. Microhaplotypes (MHs) are promising genetic markers due to their high polymorphism, low mutation rate, short amplified fragments, absence of stutter and amplification bias. These characteristics make them suitable for sample tracking and paternity testing during WES analysis. In this study, we screened out a set of polymorphic MHs in exonic regions for the above purposes. The results showed that the power of discrimination (PD) and probability of exclusion (PE) of this set of markers ranged from 0.2682 to 0.8878 and 0.0178 to 0.4583, respectively. Both the cumulative power of discrimination (CPD) and cumulative probability of exclusion (CPE) exceeded 0.999999, indicating the great value of these markers in paternity testing and individual identification in the study population. However, these markers had the effective number of alleles (Ae) values ranging from 1.1784 to 3.8727 (average 2.1805) and informativeness (In) values ranging from 0.0151 to 0.2209 (average 0.0766), showing limited value in DNA mixture analysis and biogeographical ancestry inference.

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip.

This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima's D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima's D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

Development of microsatellite markers and evaluation of the genetic diversity of the edible sea anemone Paracondylactissinensis (Cnidaria, Anthozoa) in China.

Paracondylactissinensis Carlgren, 1934 is a sea anemone with economic value in China. The wild population of P.sinensis has been shrinking due to overfishing and environmental pollution, which have caused price instability. In winter, the price of P.sinensis can reach 25 USD per kilogram. Up to now, there are no genetic markers developed for P.sinensis, preventing a further exploration of their population genetic diversity. In this study, the full-length transcriptome of P.sinensis was sequenced and microsatellite DNA markers (simple sequence repeats [SSRs]) were developed from those transcripts. A total of 52 primer pairs, which can amplify specific polymorphic bands in PCR experiments, were designed for the SSR markers. Genetic diversity and population genetics were analysed for P.sinensis populations collected from the coasts of Taizhou and Rizhao using six microsatellite DNA loci. While inbreeding was detected in both populations (Fis > 0), the overall number of alleles (Na = 11.3) and bottleneck analysis suggested that the genetic diversity of P.sinensis has not been greatly impacted. Clustering analyses using STRUCTURE, principal coordinate analysis and unweighted pair group method with arithmetic mean tree revealed that the Taizhou population diverged from the Rizhao population; however, the genetic differentiation between the populations was moderate. Human-mediated commercial activities may be the principal reasons for the gene flow between the populations. Our study provides the first evaluation of the genetic resources of wild P.sinensis populations in China, which can serve as a useful reference for future comparative studies on population genetics and may guide policy-makers in initiating strategies for germplasm conservation and artificial breeding.

Exploring Sampling Strategies and Genetic Diversity Analysis of Red Beet Germplasm Resources Using SSR Markers

By using 14 SSR primer pairs, we here analyzed and compared the amplification results of 534 DNA samples from six red sugar beet germplasm resources under three treatments. These data were used to explore the sampling strategy for the aforementioned resources. Based on the sampling strategy results, 21 SSR primer pairs were used to evaluate the genetic diversity of 47 red sugar beet germplasm resources. The six population genetic parameters used for exploring the sampling strategy unveiled that individual plants within the population had a relatively large genetic distance. The genetic parameters Ne, I, and Nei’s of the randomly mixed sampling samples increased rapidly between 10 and 30 plants before decreasing. Therefore, when SSR technology was used to analyze the genetic diversity of the red sugar beet germplasm resources, the optimal sampling gradient for each population was the adoption of a random single-plant mixed sampling sample of no less than 10 plants and no more than 30 plants. The 21 SSR primer pairs were used to detect genetic diversity in 30 random mixed samples of 47 resources. The average polymorphic information content (PIC) was 0.5738, the average number of observed alleles (Na) was 4.1905, the average number of effective alleles (Ne) was 2.8962, the average Shannon’s information index (I) was 1.1299, the average expected heterozygosity (Nei’s) was 0.6127, and the average expected heterozygosity (He) was 0.6127. The genetic distance of the 47 germplasm resources ranged from 0.0225 to 0.551 (average: 0.316). According to the population structure analysis, the most suitable K value was six, which indicated the presence of six populations. Based on the clustering analysis results, the 47 germplasm resources were segregated into six groups, with obvious clustering and some germplasm resources noted for having groups with close genetic relationships. We here established a more accurate and scientific sampling strategy for analyzing the genetic diversity of red sugar beet germplasm resources by using SSR molecular markers. The findings provide a reference for collecting and preserving red sugar beet germplasms and protecting their genetic diversity.

Genetic Diversity of Tulipa alberti and T. greigii Populations from Kazakhstan Based on Application of Expressed Sequence Tag Simple Sequence Repeat Markers.

The genus Tulipa L., renowned for its ornamental and ecological significance, encompasses a diversity of species primarily concentrated in the Tian Shan and Pamir-Alay Mountain ranges. With its varied landscapes, Kazakhstan harbors 42 Tulipa species, including the endangered Tulipa alberti Regel and Tulipa greigii Regel, which are critical for biodiversity yet face significant threats from human activities. This study aimed to assess these two species' genetic diversity and population structure using 15 expressed sequence tag simple sequence repeat (EST-SSR) markers. Leaf samples from 423 individuals across 23 natural populations, including 11 populations of T. alberti and 12 populations of T. greigii, were collected and genetically characterized using EST-SSR markers. The results revealed relatively high levels of genetic variation in T. greigii compared to T. alberti. The average number of alleles per locus was 1.9 for T. alberti and 2.8 for T. greigii. AMOVA indicated substantial genetic variation within populations (75% for T. alberti and 77% for T. greigii). The Bayesian analysis of the population structure of the two species indicated an optimal value of K = 3 for both species, splitting all sampled populations into three distinct genetic clusters. Populations with the highest level of genetic diversity were identified in both species. The results underscore the importance of conserving the genetic diversity of Tulipa populations, which can help develop strategies for their preservation in stressed ecological conditions.

Molecular fingerprinting of highly resistant maize lines to turcicum leaf blight

AbstractThe present study generates information related to the molecular divergence between turcicum leaf blight (TLB)-resistant and -susceptible lines. During molecular diversity studies, a total of 212 alleles were detected at 75 marker loci and ranged from two to five with an average of 2.83 alleles per locus. A direct correlation for the number of alleles and polymorphism information content (PIC) values was ascertained. For instance, marker phi123 produced high number of alleles (5) with PIC values of 0.77. Using the DARwin 6.0 programme, the UPGMA dendrogram grouped 40 maize inbreds into two distinct clusters, cluster-I (36 inbreds) and cluster-II (4 inbreds). Cluster-I contained two subclusters; the first subcluster contained 28 inbreds and the second subcluster contained eight inbreds whereas cluster-II contained four inbreds. This major cluster-II was further classified into two subclusters which contained two inbreds each. Most of the inbred lines except V-25 from cluster-II were highly resistant to TLB disease. These inbred lines can be used in crossing programmes to develop TLB-resistant hybrids by using divergent parents. In this study, allelic diversity and PIC values indicated a good efficiency of markers for studying the polymorphism level available in studied inbred lines. High level of diversity among the inbreds detected with simple sequence repeat markers indicated their suitability for the further breeding programme.

Genetic Diversity and Population Genetic Structure of Jatropha curcas L. Accessions from Different Provenances Revealed by Amplified Fragment-Length Polymorphism and Inter-Simple Sequence Repeat Markers

The genetic diversity and structure of 17 populations of J. curcas, including 92 accessions from different provenances (tropical and subtropical), were investigated and effectively evaluated using twelve inter-simple sequence repeats (ISSRs) and seven pairs of florescence-amplified fragment-length polymorphism (AFLP) primers. Genetic diversity, at the overall level among populations of J. curcas based on the ISSR markers, showed that the observed number of alleles (Na) was 1.593, the effective number of alleles (Ne) was 1.330, Nei’s gene diversity (H) was 0.200, Shannon’s information index (I) was 0.303, and the percentage of polymorphic loci was 59.29%, indicating moderate genetic diversity between and within the different populations of J. curcas. Based on the genetic diversity analysis of AFLP markers, there were 1.464 (Na) and 1.216 (Ne) alleles, Nei’s gene diversity (H) was 0.132, Shannon’s information index (I) was 0.204, and the percentage of polymorphic loci was 46.40%. The AMOVA analysis showed that this large variance was due to differences within the populations, with genetic distinctions and limited gene flow among those from varied regions. The 17 populations were clustered into five main groups via UPGMA clustering analysis based on Nei’s genetic distance, and the genetic relationships among the populations exhibited no significant correlations with geographical provenances. The genetic variation among Chinese populations of J. curcas distributed in dry-hot valley areas was remarkable, and the American germplasm presented with distinct genetic differentiation.

CFTR complex alleles and phenotypic variability in cystic fibrosis disease.

Cystic fibrosis (CF) is inherited by CFTR (cystic fibrosis transmembrane conductance regulator) gene mutations. A variety of mutations have been identified in the CFTR gene that may be associated with cystic fibrosis, and these mutations demonstrate extensive molecular genetic heterogeneity in this disease. Little is known about the molecular mechanism by which mutations affect CFTR function, and only a minority of mutations have been characterized by functional studies. There has been an increase in the number of complex alleles. This may partly explain the difficulty in establishing genotype-phenotype correlations and complicate genetic counseling and diagnosis in some cases. Therefore, the identification of complex alleles has several important implications for recessive disorders. This will facilitate diagnosis; improve judgements concerning prognosis, and enable appropriate genetic counselling for affected families. This review describes the complex cystic fibrosis allele to better understand the contribution of this allele in the wide phenotypic variability of cystic fibrosis disease. It occurs in the complex allele that the second cis mutation can modulate the effects of the first mutation or vice versa. The phenotypic variability between CF or CFTR-RD (CFTR related disease) patients may be due to several factors, including different genetic and environmental backgrounds. It is important to determine the allele complex so that optimal treatment can be established.