Identity Status Research Articles

Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis

The population structure of the malaria parasite Plasmodium falciparum can reveal underlying adaptive evolutionary processes. Selective pressures to maintain complex genetic backgrounds can encourage inbreeding, producing distinct parasite clusters identifiable by population structure analyses. We analysed population structure in 3783 Pfalciparum genomes from 21countries across Africa, provided by the MalariaGEN Pf7 dataset. We used Principal Coordinate Analysis to cluster parasites, identity by descent (IBD) methods to identify genomic regions shared by cluster members, and linkage analyses to establish their co-inheritance patterns. Structural variants were reconstructed by de novo assembly and verified by long-read sequencing. We identified a strongly differentiated cluster of parasites, named AF1, comprising 47 (1·2%) of 3783samples analysed, distributed over 13countries across Africa, at locations over 7000km apart. Members of this cluster share a complex genetic background, consisting of up to 23loci harbouring many highly differentiated variants, rarely observed outside the cluster. IBD analyses revealed common ancestry at these loci, irrespective of sampling location. Outside the shared loci, however, AF1 members appear to outbreed with sympatric parasites. The AF1 differentiated variants comprise structural variations, including a gene conversion involving the dblmsp and dblmsp2 genes, and numerous single nucleotide polymorphisms. Several of the genes harbouring these mutations are functionally related, often involved in interactions with red blood cells including invasion, egress, and erythrocyte antigen export. We propose that AF1 parasites have adapted to some unidentified evolutionary niche, probably involving interactions with host erythrocytes. This adaptation involves a complex compendium of interacting variants that are rarely observed in Africa, which remains mostly intact despite recombination events. The term cryptotype was used to describe a common background interspersed with genomic regions of local origin. Bill & Melinda Gates Foundation.

Factors Influencing Special Education Career Choices: Interplay of Personality Traits and Identity Statuses

<p style="text-align:justify">Recent research has identified factors influencing the choice of a special education career; however, it has not thoroughly examined their connection with personality traits and identity status. Thus, the present study was designed to explore how different personality traits and identity statuses correlate with the motives and perceptions associated with the choice to teach in special education. The study involved 209 pre-service special education teachers. The NEO-Five Factor Inventory was used to measure the Big 5 personality traits. The Ego Identity Process Questionnaire assessed identity commitment and exploration. The Factors Influencing Teaching Choice Scale was used to evaluate motivations and perceptions about teaching. Regarding the factors that influenced the decision to pursue a career in special education, intrinsic value, shaping children’s future, social equity, making social contributions, working with children, task demands, and job satisfaction were highly rated. Additionally, extraversion, openness to experience, conscientiousness, and identity statuses were identified as positive predictors for certain factors influencing the choice of a teaching career in special education. Finally, the study identified two distinct groups of students: "Identity Achievers" characterized by high positive personality traits, and identity commitment, and "Identity Explorers" characterized by lower positive personality traits and higher identity exploration. Differences were observed between the groups in their motives and perceptions concerning teaching in special education. In conclusion, this study highlights the relationships between personality, identity status, and career decision factors, offering insights into the factors that influence this critical career decision among future special educators. Directions for future research are discussed.</p>

Evaluation of Four Forensic Investigative Genetic Genealogy Analysis Approaches with Decreased Numbers of SNPs and Increased Genotyping Errors

Background: Forensic investigative genetic genealogy (FIGG) has developed rapidly in recent years and is considered a novel tool for crime investigation. However, crime scene samples are often of low quality and quantity and are challenging to analyze. Deciding which approach should be used for kinship inference in forensic practice remains a troubling problem for investigators. Methods: In this study, we selected four popular approaches—KING, IBS, TRUFFLE, and GERMLINE—comprising one method of moment (MoM) estimator and three identical by descent (IBD) segment-based tools and compared their performance at varying numbers of SNPs and levels of genotyping errors using both simulated and real family data. We also explored the possibility of making robust kinship inferences for samples with ultra-high genotyping errors by integrating MoM and the IBD segment-based methods. Results: The results showed that decreasing the number of SNPs had little effect on kinship inference when no fewer than 164 K SNPs were used for all four approaches. However, as the number decreased further, decreased efficiency was observed for the three IBD segment-based methods. Genotyping errors also had a significant effect on kinship inference, especially when they exceeded 1%. In contrast, MoM was much more robust to genotyping errors. Furthermore, the combination of the MoM and the IBD segment-based methods showed a higher overall accuracy, indicating its potential to improve the tolerance to genotyping errors. Conclusions: In conclusion, this study shows that different approaches have unique characteristics and should be selected for different scenarios. More importantly, the integration of the MoM and the IBD segment-based methods can improve the robustness of kinship inference and has great potential for applications in forensic practice.

Modeling recent positive selection using identity-by-descent segments

Recent positive selection can result in an excess of long identity-by-descent (IBD) haplotype segments overlapping a locus. The statistical methods that we propose here address three major objectives in studying selective sweeps: scanning for regions of interest, identifying possible sweeping alleles, and estimating a selection coefficient s. First, we implement a selection scan to locate regions with excess IBD rates. Second, we estimate the allele frequency and location of an unknown sweeping allele by aggregating over variants that are more abundant in an inferred outgroup with excess IBD rate versus the rest of the sample. Third, we propose an estimator for the selection coefficient and quantify uncertainty using the parametric bootstrap. Comparing against state-of-the-art methods in extensive simulations, we show that our methods are more precise at estimating s when s≥0.015. We also show that our 95% confidence intervals contain s in nearly 95% of our simulations. We apply these methods to study positive selection in European ancestry samples from the Trans-Omics for Precision Medicine project. We analyze eight loci where IBD rates are more than four standard deviations above the genome-wide median, including LCT where the maximum IBD rate is 35 standard deviations above the genome-wide median. Overall, we present robust and accurate approaches to study recent adaptive evolution without knowing the identity of the causal allele or using time series data.

The Future of Multiracial Democracy: The Rise of Multicultural Nationalism

ABSTRACT: Some liberals argue that political polarization is caused by "identity politics" that has created a kind of new tribalism. This essay argues that this is a misreading. Instead, the essay addresses polarization between those who are pro-diversity (possibly also pro-immigration) and those who fear that their national identities are being demoted at the expense of other identities. The clash is not between universalism and identitarianism but over the value or recognition to be accorded to different group identities. While multiculturalism has been concerned with the normative status of minority identities, it has been counterposed, sometimes aggressively, by those who bemoan the neglect of majorities and their identity-based anxieties. This essay focuses on how we can tackle and lessen the polarization that is fostering mutual distrust and threatening the national, democratic citizenships upon which any multiculturalist, egalitarian, and unifying project must be built, and which multiculturalists, together with others, must defend. This involves developing a multicultural national identity to which all citizens can have a sense of belonging without giving up other identities that are important to them. Such national and group identities should not be conceived as monistic or static but rather as interactive and dialogical. Such a sense of the national allows one to be sensitive to minority-identity vulnerabilities and majority-identity anxieties within an integrated theoretical and political framework.

The relationship between ego identity status and acculturation strategies (comparative study)

The present study aims to investigate the acculturation strategies employed by Yemeni students in Turkey and China, and their relationship with Ego identity status and perceived cultural distance. The study involved 506 Yemeni students enrolled in Turkish and Chinese universities, with 290 participants studying in Turkey (57.3 %) and 216 studying in China (42.7 %). The age of the participants ranged from 18 to 42 years, with a standard deviation of 5.45 and a mean of 27.34 years. The results indicated that the strategies adopted by Yemeni students were similar in both countries. Ego-identity states were found to be predictors of acculturation strategies. Identity achievement was found to predict integration strategy, while foreclosure identity predicted separation strategy. Additionally, identity moratorium and identity diffusion predicted the marginalization strategy. Knowledge of the host country's language was a predictor of willingness to integrate into the host society. The immigrant's lack of knowledge of the host country's language led them to adopt a separation strategy. Cultural distance was also found to be highly predictive of the assimilation and separation strategy. Furthermore, the presence of family members with the immigrants led to the adoption of tendencies to preserve the native culture, while immigrants living without their families in the host country tended to adopt the assimilation strategy.

Contrasting genomic epidemiology between sympatric Plasmodium falciparum and Plasmodium vivax populations.

The malaria parasites Plasmodium falciparum and Plasmodium vivax differ in key biological processes and associated clinical effects, but consequences on population-level transmission dynamics are difficult to predict. This co-endemic malaria study from Guyana details important epidemiological contrasts between the species by coupling population genomics (1396 spatiotemporally matched parasite genomes, primarily from 2020-21) with sociodemographic analysis (nationwide patient census from 2019). We describe how P. falciparum forms large, interrelated subpopulations that sporadically expand but generally exhibit restrained dispersal, whereby spatial distance and patient travel statistics predict parasite identity-by-descent (IBD). Case bias towards working-age adults is also strongly pronounced. P. vivax exhibits 46% higher average nucleotidediversity (π) and 6.5x lower average IBD. It occupies a wider geographic range, without evidence for outbreak-like expansions, only microgeographic patterns of isolation-by-distance, and weaker case bias towards adults. Possible latency-relapse effects also manifest in various analyses. For example, 11.0% of patients diagnosed with P. vivax in Greater Georgetown report no recent travel to endemic zones, and P. vivax clones recur in 11of46 patients incidentally sampled twice during the study. Polyclonality rate is also 2.1x higher than in P. falciparum, does not trend positively with estimated incidence, and correlates uniquely to selected demographics. We discuss possible underlying mechanisms and implications for malaria control.

Clinical Expression of Familial Hypercholesterolemia in Patients from France and French Canada Carrying Identical-by-Descent Pathogenic LDLR Gene Variants: A Proof-of-Concept Study.

Background: Studying patients carrying identical-by-descent (IBD) pathogenic gene variants allows us to control for the disease-causing genetic background and to more accurately document the impact of modifiers. Familial hypercholesterolemia (FH) is characterized by elevated low-density lipoprotein cholesterol (LDL-c) levels and premature atherosclerosis and is often caused by defects in the LDLR gene. There is a high prevalence of FH in French Canada as a result of a founder effect from France in the 17th century. Several FH patients currently living in French Canada (founder population) and in France (colonizing population) carry IBD FH-causing variants. The expression of FH is affected by environmental and genetic modifiers, and patients with IBD variants may present different characteristics. Methods: In this study, we compared FH clinical expression patients carrying IBD LDLR pathogenic variants living in France or Canada. Four IBD variants, namely c.259T>G p.(Trp87Gly), c.2000G>A p.(Cys667Tyr), c.682G>A p.(Glu228Lys), and c.1048C>T p.(Arg350*), were selected. Untreated plasma lipid profiles, the apolipoprotein E (APOE) genotype, cardiovascular risk factors, and the occurrence of symptomatic ASCVD were compared in 105 adult carriers (30 from France and 75 from French Canada). Results: All parameters were similar between the two populations, except for untreated total cholesterol (10.14 ± 1.89 mmol/L vs. 8.65 ± 1.84 mmol/L, p = 0.0006) and LDL-c concentrations (7.94 ± 1.86 mmol/L vs. 6.93 ± 1.78 mmol/L, p = 0.016), which were significantly higher in FH patients living in France, an observation that was revealed across all studied LDLR variants. Conclusions: This study illustrates that FH patients sharing IBD pathogenic LDLR variants that have evolved in different geographic, cultural, and socio-economic environments for hundreds of years differ in terms of cholesterol levels, highlighting the importance of better understanding the interplay between genetic and environmental modulators of FH expression.

Мотивационные корреляты жизнестойкости и виртуальной идентичности молодых геймеров

The research is relevant due to the necessity to explore how gaming motivational mechanisms reduce internal tension and shape gamers’ identity in massively multiplayer online role-playing games (MMORPG). The aim of the research is to investigate the role of gaming motivation shaping virtual identity and hardiness of young gamers. Hypothesis: gaming motivation correlates with reduced internal tension and influences the formation of gamers’ virtual identity in cyber space. Participants: N = 120 aged 18–25 years (n male = 72; n female = 48; M = 20.4; SD = 2.5) living in the central region of the Russian Federation. Methods (tools): The Gaming Motivation Scale (Nick Yee adapted by N. V. Bogacheva, V. E. Epishina, A. V. Milyanskaya) was used to assess game motivation for playing massively multiplayer online role-playing games (MMORPG); an abridged version of the Hardiness Test (S. Maddi adapted by E. N. Osin, E. I. Rasskazova) was used to assess resilience; the Virtual Identity Status Inventory (VISI) (M. V. Klementyeva) was used to assess the status of virtual identities; the Game Experience Questionnaire (W. A. Ijsselsteijn, Y. A. W. de Kort, and K. Poels adapted by M. V. Klementyeva, M. V. Kurguzov) was used to assess players’ competence. Results: the research demonstrated significant differences in the manifestation of gamers’ “hardines”: higher values were recorded during gameplay. We found strong links between gaming motives, hardines, gaming skills and virtual identity. Despite their seamless gaming motivation and perfect gaming competence, gamers experience internal tension, helplessness in real life and strive to escape reality while forming a virtual identity based on the images of their gaming avatars. Main conclusions: in an online game, young gamers are able to cope more effectively with internal stress, compared with the real environment; they are able to maintain identity, and successfully implement gaming motives. Practical application: the research results can be used to develop techniques aimed at strengthening hardines and supporting identity formation in young gamers.

From the Margins to the Center: A Reading of 'Antarah Ibn Shaddad' through Hegel's Master-Slave Dialectic

This study analyzes the Al-Moallaqa, a poem traditionally hung on the walls of the Kaaba, the holiest shrine for Muslims, by the pre-Islamic poet Antara bin Shaddad, through the lens of Hegel’s Master-Slave Dialectic. It explores the status of marginal identity, focusing on the poet’s portrayal of the suffering endured due to slavery, humiliation, and deprivation of honor in a tribal society that devalues the enslaved. It also examines self-awareness and the desire for change, addressing the essential awakening of the 'Self', which drives a rejection of marginalization and a commitment to struggle and risk in pursuit of freedom. A qualitative textual analysis is employed, focusing on the thematic exploration of identity, self-awareness, and the struggle for recognition within the poem. Antara’s poetry illustrates this self-awareness through vivid depictions of bravery, heroism, and chivalry, emphasizing the idea of testing oneself and others in the existential struggle between life and death. The contribution of this manuscript lies in its application of Hegelian philosophy to classical Arabic poetry, offering a new interpretative framework for understanding the dynamics of identity and freedom in pre-Islamic literature.

Employment discrimination against transgender women in England

PurposeThe study aimed to assess whether transgender women, who were students at a university in London, England, faced hiring discrimination when seeking employment.Design/methodology/approachThree comparable university classmates—a cisgender woman, a cisgender man and a transgender woman—studying Engineering applied to the same job openings. Similarly, another set of three university classmates—a cisgender woman, a cisgender man and a transgender woman—studying Social Work applied to the same job openings. The degree of discrimination was quantified by calculating the difference in the number of interview invitations received by each group.FindingsWhen three comparable university classmates apply for the same job openings, the rate of interview invitations differs based on gender identity. For cisgender women, the invitation rate is 31.3%, while for cisgender men, it stands at 35.1%. However, for transgender women, the rate drops significantly to 10.4%. Additionally, transgender women face further challenges in male-dominated sectors (STEM), where their chance of being invited for a job interview is even lower compared to those in female-dominated sectors, with a reduction of 8.7 percentage points. The study also reveals that firms with written equality policies on gender identity diversity show a 25.7 percentage point increase in invitation rates for transgender women compared to firms without such policies. Furthermore, the research highlights that negative beliefs among job recruiters regarding various aspects of transgender women, including their gender identity status, disclosure, job performance, vocational relationships and turnover, contribute to their exclusion from job interviews. Moreover, for transgender women who do receive interview invitations, these tend to be for lower-paid jobs compared to those received by cisgender women (by 20%) and cisgender men (by 21.3%). This wage sorting into lower-paid vacancies suggests a penalty in terms of lower returns on education, which could drive wage and income differences.Practical implicationsTransgender women received a higher number of job interview invitations when firms had written equality policies on gender identity diversity. This outcome can help policymakers identify actions to reduce the exclusion of transgender people from the labour market.Originality/valueThe study gathers information from job recruiters to quantify the roots of hiring discrimination against transgender women. It also enables an examination of whether workplaces' written equality policies on gender identity diversity are related to transgender women’s invitations to job interviews.

ИССЛЕДОВАНИЕ СТРЕССА В ПРОЦЕССЕ ФОРМИРОВАНИЯ ПРОФЕССИОНАЛЬНОЙ ИДЕНТИЧНОСТИ СТУДЕНТОВ

The article presents the results of the study of stress, coping strategies in the process of forming the professional identity of students of the Ural Federal University and the impact on the studied parameters of their hardiness. Stress levels were measured using various questionnaires. Coping strategies were investigated using the WCQ methodology R. Lazarus and S. Folkman, hardiness and its components — with the help of a questionnaire by S. Muddy, the statuses of professional identity — by the method of A. A. Azbel. The analysis of the results revealed medium and low levels of stress among students, but showed significant use of non-adaptive strategies for coping with stress. The correlation analysis showed a strong correlation between the stress level indicators measured by various methods. The correlation analysis showed a strong relationship between stress levels measured by various methods. The degree of tension of a number of coping strategies showed a significant relationship with stress levels, with the hardiness and the representation of individual statuses of professional identity by A. A. Azbel method. According to the correlation analysis, it was also found that stress accumulated due to problematic situations during the year (the Holmes-Rahe questionnaire) contributes to the status of an uncertain (diffusion) professional identity. Recommendations are given on minimizing the stress load in the process of professional development of students.

Joint identity among loci under mutation and regular inbreeding

This study describes a compact method for determining joint probabilities of identity-by-state (IBS) within and between loci in populations evolving under genetic drift, crossing-over, mutation, and regular inbreeding (partial self-fertilization). Analogues of classical indices of associations among loci arise as functions of these joint identities. This coalescence-based analysis indicates that multi-locus associations reflect simultaneous coalescence events across loci. Measures of association depend on genetic diversity rather than allelic frequencies, as do linkage disequilibrium and its relatives. Scaled indices designed to show monotonic dependence on rates of crossing-over, inbreeding, and mutation may prove useful for interpreting patterns of genome-scale variation.

Vocational Identity Statuses Among Hong Kong Sub-degree Students: Pattern Identification and Relationship to Career Development and Academic Performance

The process model of vocational identity was well applied in various Western countries to study the vocational identity process and statuses of college students. However, such research is limited in Hong Kong. Moreover, the relation between vocational identity development and academic performance was inconclusive in the literature, and it was also not tested among Hong Kong students. In light of these, the current study aimed to empirically identify and validate vocational identity statuses among a sample of 576 sub-degree students in Hong Kong using the vocational identity process model. Relations of vocational identity processes and statuses with perceived academic performance were also tested. Six vocational identity statuses were empirically derived in the Hong Kong Chinese context. Vocational identity statuses also differentiate perceived academic performance. Moreover, we found that career flexibility and self-doubt were significantly related to perceived academic performance. Implications of the results for theory and practice are discussed.

Fluidity of social identities: implications for applying intersectionality

PurposeIntersectionality addresses complex avenues of oppression that emanate at the intersections of one’s identities. However, the intersectional framework assumes static identities, which are increasingly being acknowledged for their fluidity. This research explored the extent of the fluidity of social identities to draw implications for the application of the framework in research.Design/methodology/approach27 participants from a post-graduate elective course on diversity and inclusion identified their significant social identities, and submitted a write-up using hermeneutic phenomenology in which the participants shared their lived experiences of the fluidity of their social identities in different spaces they occupy or find themselves in.FindingsFluidity-triggering stimuli in different environments and their associations with identity-related motives were uncovered using thematic analysis. Stimuli operating at micro-, meso- and macro-levels rationally explained identity fluidity. However, in addition to types, intensity and frequency of stimuli, psychological factors, such as identity status, were decisive in determining the degree of generalization of stimuli across individuals and spaces that significantly influenced identity fluidity.Originality/valueThis research explored the extent of the fluidity of social identities to draw implications for the application of the intersectional framework in research. The findings contribute to future research by identifying limitations of the intersectional framework based on the fluidity of social identities arising from environmental stimuli that operate at micro-, meso- and macro-levels, and the extent of psychological generalization of these stimuli across spaces.

The Vocational Ability, Vocational Motivation and Professional Identity of Xiamen University Teachers

With the rapid development of China's higher education, the quality of teachers is becoming more and more important. On the one hand, the vocational ability of college teachers directly affects the effectiveness of higher education; On the other hand, the vocational motivation of college teachers determines the efficiency of higher education. Therefore, whether from the perspective of higher education development, reform, or university management, it is of great theoretical significance and practical value to discuss the professional ability and motivation of university teachers.A modern higher education system cannot be separated from a stable and high-quality teaching team. In order to maintain the stability of the team and continuously improve the professional quality, it is necessary to cultivate the professional identity of college teachers. Professional identity is the recognition degree of college teachers to higher education. Only teachers with strong professional identity can devote themselves to the cause of higher education. Only by systematically summarizing the current situation of professional ability, professional motivation and professional identity of college teachers can we draw the map of college teachers deeply. At the same time, on the basis of the research data, the relationship between professional ability, professional motivation and professional identity can be deeply explored to explore the path to motivate the enthusiasm of college teachers. According to the components of vocational ability, vocational motivation and professional identity, interviews was utilized to determine the educational background and academic background, teaching skills, diversified teaching ability, project management ability, educational innovation ability, communication ability with students and parents, personal ambition, working environment, salary, social identity and career prospects. Salary satisfaction, welfare security satisfaction, personal value realization, social recognition and other dimensions, to deeply explore the professional characteristics of Xiamen university teachers. Through narrative inquiry , the present status of vocational ability ,vocational motivation and occupational identity was explored, and the generation mechanism of occupational identity is sorted out. Future directions of this study was presented as to exploring on other methodology and increasing the locale and sample size.

Secure discovery of genetic relatives across large-scale and distributed genomic data sets.

Finding relatives within a study cohort is a necessary step in many genomic studies. However, when the cohort is distributed across multiple entities subject to data-sharing restrictions, performing this step often becomes infeasible. Developing a privacy-preserving solution for this task is challenging owing to the burden of estimating kinship between all the pairs of individuals across data sets. We introduce SF-Relate, a practical and secure federated algorithm for identifying genetic relatives across data silos. SF-Relate vastly reduces the number of individual pairs to compare while maintaining accurate detection through a novel locality-sensitive hashing (LSH) approach. We assign individuals who are likely to be related together into buckets and then test relationships only between individuals in matching buckets across parties. To this end, we construct an effective hash function that captures identity-by-descent (IBD) segments in genetic sequences, which, along with a new bucketing strategy, enable accurate and practical private relative detection. To guarantee privacy, we introduce an efficient algorithm based on multiparty homomorphic encryption (MHE) to allow data holders to cooperatively compute the relatedness coefficients between individuals and to further classify their degrees of relatedness, all without sharing any private data. We demonstrate the accuracy and practical runtimes of SF-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.

Origins and Genetic Characteristics of Egyptian Peach.

Peach (Prunus persica), a significant economic fruit tree in the Rosaceae family, is extensively cultivated in temperate and subtropical regions due to its abundant genetic diversity, robust adaptability, and high nutritional value. Originating from China over 4000 years ago, peaches were introduced to Persia through the Silk Road during the Han Dynasty and gradually spread to India, Greece, Rome, Egypt, Europe, and America. Currently grown in more than 80 countries worldwide, the expansion of peach cultivation in Egypt is mainly due to the development and utilization of peach varieties with low chilling requirements. These varieties exhibit unique phenotypic characteristics such as early maturity, reduced need for winter cold temperatures, low water requirements, and high economic value. In this study, a systematic analysis was conducted on the genetic characteristics and kinship relationships of peaches with low chilling requirements in Egypt. We conducted a comprehensive evolutionary and Identity-by-Descent (IBD) analysis on over 300 peach core germplasm resources, including Egyptian cultivars with low chilling requirements, to investigate their origin and genetic characteristics. The evolutionary analysis revealed that 'Bitter almond' is closely related to China's wild relative species Prunus tangutica Batal, while 'Early grand' shares one branch with Chinese ornamental peach cultivars, and 'Nemaguard' clusters with some ancient local varieties from China. The IBD analysis also indicated similar genetic backgrounds, suggesting a plausible origin from China. Similarly, the analysis suggested that 'Swelling' may have originated from the Czech Republic while 'Met ghamr' has connections to South Africa. 'Desert red', 'Early swelling', and 'Florida prince' are likely derived from Brazil. These findings provide valuable insights into the genetic characteristics of Egyptian peach cultivars. They offer a significant foundation for investigating the origin and spread of cultivated peaches worldwide and serve as a valuable genetic resource for breeding low chilling requirement cultivars, which is of considerable significance for the advancement of peach cultivation in Egypt.

Integrative genomics reveals the polygenic basis of seedlessness in grapevine

Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated the haplotype-resolved genomes for two seedless grape cultivars, "Thompson Seedless" (TS, syn. "Sultania") and "Black Monukka" (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genes VvTT16 and VvSUS2 located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, and the identity-by-descent (IBD) results indicated that the origin of the seedlessness trait could be traced back to "Sultania." Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including previously unidentified candidate genes, such as three 11S GLOBULIN SEED STORAGE PROTEIN and two CYTOCHROME P450 genes, and well-known genes like VviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 functional categories related to seed development. Machine learning-based genomic selection achieved a remarkable prediction accuracy of 97% for seedlessness in grapevines. Our findings highlight the polygenic nature of seedlessness and provide candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.

Modeling QTL-by-environment interactions for multi-parent populations.

Multi-parent populations (MPPs) are attractive for genetic and breeding studies because they combine genetic diversity with an easy-to-control population structure. Most methods for mapping QTLs in MPPs focus on the detection of QTLs in single environments. Little attention has been given to mapping QTLs in multienvironment trials (METs) and to detecting and modeling QTL-by-environment interactions (QEIs). We present mixed model approaches for the detection and modeling of consistent versus environment-dependent QTLs, i.e., QTL-by-environment interaction (QEI). QTL effects are assumed to be normally distributed with variances expressing consistency or dependence on environments and families. The entries of the corresponding design matrices are functions of identity-by-descent (IBD) probabilities between parents and offspring and follow from the parental origin of offspring DNA. A polygenic effect is added to the models to account for background genetic variation. We illustrate the wide applicability of our method by analyzing several public MPP datasets with observations from METs. The examples include diallel, nested association mapping (NAM), and multi-parent advanced inter-cross (MAGIC) populations. The results of our approach compare favorably with those of previous studies that used tailored methods.