scholarly journals Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population

2021 ◽  
Author(s):  
R. E. Tarlinton ◽  
J. Fabijan ◽  
F. Hemmatzadeh ◽  
J. Meers ◽  
H. Owen ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genetic Disorders ◽  
South Australia ◽  
Differentially Expressed ◽  
Brain Diseases ◽  
Fixation Index ◽  
Testicular Development ◽  
Genetic Components ◽  
Anion Transporter ◽  
Two Populations

AbstractHistorical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.

Genetic disorders and spermatogenesis

1998 ◽  
Vol 10 (1) ◽  
pp. 97 ◽  
Author(s):  
R. I. McLachlan ◽  
C. Mallidis ◽  
K. Ma ◽  
S. Bhasin ◽  
D. M. de Kretser
Keyword(s):  
Male Fertility ◽  
Genetic Linkage ◽  
Genetic Basis ◽  
Genetic Disorders ◽  
Genetic Regulation ◽  
Testicular Development ◽  
Paracrine Regulation ◽  
Normal Spermatogenesis ◽  
Cell Mitosis ◽  
Spermatogenic Failure

Male infertility affects one man in twenty and a genetic basis seems likely in at least 30% of those men. Genetic regulation of fertility involves the inter-related processes of testicular development, spermatogenesis (involving germ cell mitosis, meiosis and spermatid maturation), and their endocrine and paracrine regulation. In regard to spermatogenesis, particular attention has been given to the Yq11 region, where some spermatogenesis genes (‘azoospermia factors’) appear to be located. Several candidate genes have been identified but have not been shown to have a defined or essential role in spermatogenesis. Microdeletions of Yq11 are found in ~15% of azoospermic or severely oligospermic men. The complexity of the genetic control of male fertility is demonstrated by the evidence for genes involved in spermatogenesis and sexual differentiation on the X chromosome and autosomes. Better understanding of the genetic regulation of normal spermatogenesis will provide new probes for clinical studies; however, at present the majority of spermatogenic failure remains without an identified genetic linkage. The advent of intracytoplasmic sperm injection permits fertility in many previously sterile men and presents the possibility of their transmission of infertility; appropriate counselling is required.

scholarly journals Neurodevelopmental Disorders in Patients With Complex Phenotypes and Potential Complex Genetic Basis Involving Non-Coding Genes, and Double CNVs

2021 ◽  
Vol 12 ◽  
Author(s):  
Martina Servetti ◽  
Livia Pisciotta ◽  
Elisa Tassano ◽  
Maria Cerminara ◽  
Lino Nobili ◽  
...  
Keyword(s):  
Neurodevelopmental Disorders ◽  
Genetic Basis ◽  
De Novo ◽  
Diagnostic Yield ◽  
Genetic Diagnosis ◽  
Brain Diseases ◽  
Comparative Genomic ◽  
Incomplete Penetrance ◽  
Genetic Components ◽  
Complex Phenotypes

Neurodevelopmental disorders (NDDs) are a heterogeneous class of brain diseases, with a complex genetic basis estimated to account for up to 50% of cases. Nevertheless, genetic diagnostic yield is about 20%. Array-comparative genomic hybridization (array-CGH) is an established first-level diagnostic test able to detect pathogenic copy number variants (CNVs), however, most identified variants remain of uncertain significance (VUS). Failure of interpretation of VUSs may depend on various factors, including complexity of clinical phenotypes and inconsistency of genotype-phenotype correlations. Indeed, although most NDD-associated CNVs are de novo, transmission from unaffected parents to affected children of CNVs with high risk for NDDs has been observed. Moreover, variability of genetic components overlapped by CNVs, such as long non-coding genes, genomic regions with long-range effects, and additive effects of multiple CNVs can make CNV interpretation challenging. We report on 12 patients with complex phenotypes possibly explained by complex genetic mechanisms, including involvement of antisense genes and boundaries of topologically associating domains. Eight among the 12 patients carried two CNVs, either de novo or inherited, respectively, by each of their healthy parents, that could additively contribute to the patients’ phenotype. CNVs overlapped either known NDD-associated or novel candidate genes (PTPRD, BUD13, GLRA3, MIR4465, ABHD4, and WSCD2). Bioinformatic enrichment analyses showed that genes overlapped by the co-occurring CNVs have synergistic roles in biological processes fundamental in neurodevelopment. Double CNVs could concur in producing deleterious effects, according to a two-hit model, thus explaining the patients’ phenotypes and the incomplete penetrance, and variable expressivity, associated with the single variants. Overall, our findings could contribute to the knowledge on clinical and genetic diagnosis of complex forms of NDD.

scholarly journals Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

2021 ◽  
Author(s):  
Zhilin Yuan ◽  
Irina S. Druzhinina ◽  
John G. Gibbons ◽  
Zhenhui Zhong ◽  
Yves Van de Peer ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Genomic Island ◽  
Population Genomics ◽  
Growth Yield ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Melanin Biosynthesis ◽  
Two Populations

AbstractUnderstanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

scholarly journals Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 241
Author(s):  
Dongwon Seo ◽  
Sunghyun Cho ◽  
Prabuddha Manjula ◽  
Nuri Choi ◽  
Young-Kuk Kim ◽  
...  
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Fixation Index ◽  
Machine Learning Classification ◽  
Genetic Components ◽  
Marker Combination ◽  
A Genome ◽  
Minimum Number ◽  
Native Chickens

A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.

Reaching Future Scientists, Consumers, & Citizens

2014 ◽  
Vol 76 (6) ◽  
pp. 379-383 ◽  
Author(s):  
Melissa A. Hicks ◽  
Rebecca J. Cline ◽  
Angela M. Trepanier
Keyword(s):  
Personalized Medicine ◽  
Genetic Basis ◽  
Genetic Disorders ◽  
Single Gene ◽  
Personal Health ◽  
Adult Onset ◽  
Biology Textbooks ◽  
Multifactorial Diseases ◽  
Single Gene Disorders

An understanding of how genomics information, including information about risk for common, multifactorial disease, can be used to promote personal health (personalized medicine) is becoming increasingly important for the American public. We undertook a quantitative content analysis of commonly used high school textbooks to assess how frequently the genetic basis of common multifactorial diseases was discussed compared with the “classic” chromosomal–single gene disorders historically used to teach the concepts of genetics and heredity. We also analyzed the types of conditions or traits that were discussed. We identified 3957 sentences across 11 textbooks that addressed multifactorial and “classic” genetic disorders. “Classic” gene disorders were discussed relatively more frequently than multifactorial diseases, as was their genetic basis, even after we enriched the sample to include five adult-onset conditions common in the general population. Discussions of the genetic or hereditary components of multifactorial diseases were limited, as were discussions of the environmental components of these conditions. Adult-onset multifactorial diseases are far more common in the population than chromosomal or single-gene disorders; many are potentially preventable or modifiable. As such, they are targets for personalized medical approaches. The limited discussion in biology textbooks of the genetic basis of multifactorial conditions and the role of environment in modifying genetic risk may limit the public’s understanding and use of personalized medicine.

scholarly journals Transcriptome analysis reveals the genetic basis underlying the development of skin appendages and immunity in hedgehog(Atelerix albiventris)

2020 ◽  
Author(s):  
Hui-Ming Li ◽  
Bi-Ze Yang ◽  
Xiu-Juan Zhang ◽  
Hai-Ying Jiang ◽  
Lin-Miao Li ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mammal Species ◽  
Appendage Development ◽  
Skin Appendage ◽  
Hair Type ◽  
Spine Development ◽  
Skin Appendages ◽  
Development And Differentiation

Abstract Background: The expression of hair features is an evolutionary adaptation resulting from interactions between many organisms and their environment. Elucidation of the mechanisms that underlie the expression of such traits is a topic in evolutionary biology research; however, the genetic basis of skin appendage development and differentiation remains poorly understood. Therefore, we assessed the de novo transcriptome of the hedgehog ( Atelerix albiventris ) at three developmental stages and compared gene expression profiles between abdomen hair and dorsal spine tissues. Results: We identified 328,576 unigenes in our transcriptome, among which 3,598 were differentially expressed between hair- and spine-type tissues. We identified 3 keratin genes related to hair and spine development through comparative analysis of tissues before and after growth of skin appendages. Dorsal and abdomen skin tissues 5 days after birth were compared and the resulting differentially expressed genes (DEGs) were mainly enriched in keratin filament, intermediate filament, epithelium cell differentiation, and epidermis development based on GO enrichment analysis, and tight junction, p53, and cell cycle signaling pathways based on KEGG enrichment analysis. Expression variations of MBP8, SFN, Wnt10, KRT1 , and KRT2 may be the main factors regulating hair and spine differentiation for the hedgehog. Strikingly, DEGs in hair-type tissues were also significantly enriched in immune-related terms and pathways with hair-type tissues exhibiting more upregulated immune genes than spine-type tissues. Thus, we propose that spine development was an adaptation that provided protection against injuries or stress and reduced hedgehog vulnerability to infection. Conclusion: Our study provided a list of potential genes involved in the regulation of skin appendage development and differentiation in A. albiventris . This is the first transcriptome survey of hair traits for a non-model mammal species, and the candidate genes provided here may provide valuable information for further studies of skin appendages and skin disorder treatments.

scholarly journals Analysis of Genetic Diversity in three Kazakh Sheep using 12 Microsatellites

2018 ◽  
Vol 7 (4.38) ◽  
pp. 122
Author(s):  
Kairat Dossybayev ◽  
Aizhan Mussayeva ◽  
Bakytzhan Bekmanov ◽  
Beibit Kulataev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mean Value ◽  
Fixation Index ◽  
Merino Sheep ◽  
Str Markers ◽  
Sheep Breeds ◽  
Str Loci ◽  
High Level ◽  
Two Populations

The genetic structure of three Kazakh sheep breeds was examined by using 12 microsatellite loci. A total of 144 alleles were detected from the 12 STR loci, with a mean value of 12.0. The highest allele diversity was found at the locus CSRD247 (16 alleles). PIC value showed that all studied STR markers are more informative and appropriate for genetic analysis of three Kazakh sheep populations. Beside of INRA006, all markers had high level of genetic variability. As Fixation index shows, the excess of the heterozygosity was observed only in loci MAF065. Obtained number of private alleles in Edilbai, Kazakh Arkhar Merino and Kazakh Fine-wool sheep were 25, 17 and 15 respectively. Genetic diversity was higher in Edilbai population than in other two populations. The genetic variability was lower in Kazakh Arkhar Merino sheep than in the Edilbai and Kazakh Fine-wool sheep breeds. The genetic distance was the largest between Edilbai and Kazakh Arkhar Merinos. Also, the moderate differentiation was observed between Edilbai and Kazakh Arkhar Merinos.   

scholarly journals Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

2019 ◽  
Vol 116 (12) ◽  
pp. 5653-5658 ◽  
Author(s):  
Lin Shao ◽  
Feng Xing ◽  
Conghao Xu ◽  
Qinghua Zhang ◽  
Jian Che ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Sequencing Data ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Parental Allele ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
Allele Specific

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

Analysis of the miRNA transcriptome during testicular development and spermatogenesis of the Mongolian horse

2020 ◽  
Vol 32 (6) ◽  
pp. 582
Author(s):  
Bei Li ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Dandan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Mammalian Species ◽  
Mature Mirnas ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
P Value ◽  
Testicular Development ◽  
Interaction Sites ◽  
Mongolian Horse

Numerous studies have shown that microRNAs (miRNAs) are essential for testicular development and spermatogenesis. In order to further characterise these physiological processes, three immature and three mature testes of the Mongolian horse were collected and six libraries were established. Using small RNA sequencing technology, 531 mature miRNAs were identified, including 46 novel miRNAs without previously ascribed functions. Among the 531 miRNAs, 421 were expressed in both immature and mature libraries, 65 miRNAs were found solely in immature testis libraries and 45 miRNAs were found solely in mature testis libraries. Furthermore, among the miRNAs that were identified in both immature and mature libraries, 107 were significantly differentially expressed (corrected P value (padj)<0.05). Among the miRNAs that were only expressed in immature testes, two miRNAs were differentially expressed, whereas among the miRNAs that were only expressed in mature testes, nine miRNAs were differentially expressed. Comprehensive analysis of miRNA and mRNA expression profiles predicted 107 miRNA–mRNA interaction sites. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted target genes suggested roles of the differentially expressed miRNAs in testicular development and spermatogenesis. These findings identify miRNAs as key factors in the development of the testes and spermatogenesis in the Mongolian horse, which may also help us to understand the mechanisms of fertility in related mammalian species.

scholarly journals Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]

2019 ◽  
Vol 133 (1) ◽  
pp. 23-36 ◽  
Author(s):  
Dorcus C. Gemenet ◽  
Guilherme da Silva Pereira ◽  
Bert De Boeck ◽  
Joshua C. Wood ◽  
Marcelo Mollinari ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Sucrose Synthase ◽  
Genetic Basis ◽  
Starch Content ◽  
Starch Biosynthesis ◽  
Negative Association ◽  
Differentially Expressed ◽  
Phytoene Synthase ◽  
Β Carotene

Abstract Key message β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. Abstract In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.

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