scholarly journals Portrait of a genus: the genetic diversity of Zea

2021 ◽  
Author(s):  
Lu Chen ◽  
Jingyun Luo ◽  
Minliang Jin ◽  
Ning Yang ◽  
Xiangguo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Flowering Time ◽  
Genetic Model ◽  
Genomic Variation ◽  
Model Organisms ◽  
Nucleotide Polymorphisms ◽  
Indel Polymorphisms ◽  
In The Wild ◽  
Modern Breeding ◽  
Direct Use

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

scholarly journals Genetic potential for disease resistance in a critically endangered frog decimated by chytridiomycosis

2018 ◽  
Author(s):  
Tiffany A. Kosch ◽  
Catarina N. S. Silva ◽  
Laura A. Brannelly ◽  
Alexandra A. Roberts ◽  
Quintin Lau ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Disease Resistance ◽  
Batrachochytrium Dendrobatidis ◽  
Population Level ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Southeastern Australia ◽  
Challenge Study ◽  
In The Wild ◽  
Functional Extinction

AbstractSouthern corroboree frogs (Pseudophryne corroboree) have been driven to functional extinction in the wild after the emergence of the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd) in southeastern Australia in the 1980s. This species is currently maintained in a captive assurance colony and is managed to preserve the genetic diversity of the founding populations. However, it is unlikely that self-sustaining wild populations can be re-established unless Bd resistance increases. We performed a Bd-challenge study to investigate the association between genetic variants of the major histocompatibility complex class IA (MHC) and genome-wide single nucleotide polymorphisms (SNPs). We also investigated differences in Bd susceptibility among individuals and populations, and the genetic diversity and population genetic structure of four natural P. corroboree populations. We found several MHC alleles and SNPs associated with Bd infection load and survival, provide evidence of significant structure among populations, and identified population-level differences in the frequency of influential variants. We also detected evidence of positive selection acting on the MHC and a subset of SNPs as well as evidence of high genetic diversity in P. corroboree populations. We suggest that low interbreeding rates may have contributed to the demise of this species by limiting the spread of Bd resistance genes. However, our findings demonstrate that despite dramatic declines there is potential to restore high levels of genetic diversity in P. corroboree. Additionally, we show that there are immunogenetic differences among captive southern corroboree frogs, which could be manipulated to increase disease resistance and mitigate the key threatening process, chytridiomycosis.

New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

2020 ◽  
Vol 36 (6) ◽  
pp. 49-54
Author(s):  
A.A. Nalbandyan ◽  
T.P. Fedulova ◽  
I.V. Cherepukhina ◽  
T.I. Kryukova ◽  
N.R. Mikheeva ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Flowering Time ◽  
Molecular Genetic ◽  
Bioinformatic Analysis ◽  
Early Flowering ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Time Control ◽  
Flowering Time Control ◽  
Exon 10

The flowering time control gene of various sugar beet plants has been studied. The BTC1 gene is a regulator for the suppressor (flowering time 1) and inducer (flowering time 2) genes of this physiological process. The F9/R9 primer pair was used for polymerase chain reaction; these primers are specific to the BTC1 gene region containing exon 9, as well as intron and exon 10. For the first time, nucleotide substitutions in exon 10 of BTC1 gene were identified in bolting sensitive samples (HF1 and BF1), which led to a change in the amino acid composition of the coded polypeptide chain. Based on the results of bioinformatic analysis, it can be assumed that certain nucleotide polymorphisms in the BTC1 gene may determine with a high probability the predisposition of sugar beet genotypes to early flowering. The use of the Geneious Prime tool for the analysis of the BTC1 gene sequences may allow the culling of genotypes prone to early flowering at early stages of selection. sugar beet, flowering gene, BTC1, genetic polymorphism, PCR, molecular genetic markers, selection

Analysis of Inter-Chromosomal Distribution of Disease-Related Genes in Human Genome

2020 ◽  
Vol 21 (11) ◽  
pp. 1068-1077
Author(s):  
Xiaochao Sun ◽  
Bin Yang ◽  
Qunye Zhang
Keyword(s):  
Spatial Distribution ◽  
Model Organisms ◽  
Nucleotide Polymorphisms ◽  
Chromosomal Distribution ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Single Chromosome ◽  
Deletion Mutations ◽  
Protein Coding Genes ◽  
Disease Related Genes

: Many studies have shown that the spatial distribution of genes within a single chromosome exhibits distinct patterns. However, little is known about the characteristics of inter-chromosomal distribution of genes (including protein-coding genes, processed transcripts and pseudogenes) in different genomes. In this study, we explored these issues using the available genomic data of both human and model organisms. Moreover, we also analyzed the distribution pattern of protein-coding genes that have been associated with 14 common diseases and the insert/deletion mutations and single nucleotide polymorphisms detected by whole genome sequencing in an acute promyelocyte leukemia patient. We obtained the following novel findings. Firstly, inter-chromosomal distribution of genes displays a nonstochastic pattern and the gene densities in different chromosomes are heterogeneous. This kind of heterogeneity is observed in genomes of both lower and higher species. Secondly, protein-coding genes involved in certain biological processes tend to be enriched in one or a few chromosomes. Our findings have added new insights into our understanding of the spatial distribution of genome and disease- related genes across chromosomes. These results could be useful in improving the efficiency of disease-associated gene screening studies by targeting specific chromosomes.

scholarly journals A Genome Scan for Quantitative Trait Loci in a Wild Population of Red Deer (Cervus elaphus)

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1863-1873 ◽  
Author(s):  
J Slate ◽  
P M Visscher ◽  
S MacGregor ◽  
D Stevens ◽  
M L Tate ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Cervus Elaphus ◽  
Quantitative Trait ◽  
Red Deer ◽  
Wild Population ◽  
Additive Genetic Variance ◽  
Model Organisms ◽  
A Genome ◽  
Trait Loci ◽  
In The Wild

Abstract Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

scholarly journals Phylogeographic Genetic Diversity in the White Sucker Hepatitis B Virus across the Great Lakes Region and Alberta, Canada

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 285
Author(s):  
Cynthia R. Adams ◽  
Vicki S. Blazer ◽  
Jim Sherry ◽  
Robert Scott Cornman ◽  
Luke R. Iwanowicz
Keyword(s):  
Genetic Diversity ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Lake Michigan ◽  
Illumina Miseq ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
White Sucker ◽  
Fish Health ◽  
B Virus

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.

scholarly journals Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

scholarly journals Microsatellite analysis reveals low genetic diversity in managed populations of the critically endangered gharial (Gavialis gangeticus) in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Surya Prasad Sharma ◽  
Mirza Ghazanfarullah Ghazi ◽  
Suyash Katdare ◽  
Niladri Dasgupta ◽  
Samrat Mondol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indian Subcontinent ◽  
Population Decline ◽  
Mitochondrial Control Region ◽  
Critically Endangered ◽  
Term Survival ◽  
Low Level ◽  
Genetic Status ◽  
In The Wild ◽  
Gavialis Gangeticus

AbstractThe gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G’ST = 0.058, P < 0.05 Jost’s D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.

scholarly journals Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cooper J. Park ◽  
Nicole A. Caimi ◽  
Debbie C. Buecher ◽  
Ernest W. Valdez ◽  
Diana E. Northup ◽  
...  
Keyword(s):  
New Mexico ◽  
Genetic Manipulation ◽  
Distinct Species ◽  
Biosynthetic Gene Cluster ◽  
Genomic Variation ◽  
Species Variation ◽  
Nucleotide Polymorphisms ◽  
Peptide Synthetases ◽  
Genome Wide ◽  
Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

scholarly journals Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

Abstract 2924: Association of NOS1AP Genetic Variants with QT Interval Duration in Families from the Diabetes Heart Study

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Allison B Lehtinen ◽  
Christopher Newton-Cheh ◽  
Julie T Ziegler ◽  
Carl D Langefeld ◽  
Barry I Freedman ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Qt Interval ◽  
Genetic Model ◽  
Additive Model ◽  
Adaptor Protein ◽  
European Ancestry ◽  
Nucleotide Polymorphisms ◽  
Interval Duration ◽  
Common Genetic Variants ◽  
Qt Interval Duration

Background: Prolongation of the electrocardiographic QT interval is a risk factor for sudden cardiac death (SCD) in unselected samples as well as in post-myocardial infarction patients or those with diabetes. Common genetic variants in the nitric oxide synthase 1 adaptor protein (NOS1AP) gene have been reported to be associated with QT interval duration in individuals of European ancestry. We sought to replicate the association of NOS1AP variants with QT interval duration in pedigrees enriched for type 2 diabetes mellitus (T2DM). Methods and Results: Two single nucleotide polymorphisms (SNPs) in the NOS1AP gene, rs10494366 and rs10918594, were genotyped in a collection of 937 European Americans (EAs) and 177 African Americans (AAs) in 450 pedigrees containing at least two siblings with T2DM. An additive genetic model was tested for each SNP in ancestry-specific analyses using SOLAR in the total sample and in the diabetic subset (EA n=778, AA n=159), with and without exclusion of QT-altering medications. In the EA individuals, rs10494366 minor allele homozygotes had an 8.9 msec longer mean QT interval compared to major homozygotes (additive model p=4.4x10 -3 ); rs10918594 minor homozygotes had a 12.9 msec longer mean QT interval compared to major homozygotes (p=9.9x10 -5 ). Excluding users of QT-altering medications in the diabetic-only EA sample (n=514) strengthened the association despite the reduction in sample size (20.6 msec difference, p=2.0x10 -5 ; 23.4 msec difference, p=8.9x10 -7 , respectively). No association between the NOS1AP SNPs and QT interval duration was observed in the limited number of AA individuals examined. Conclusions: Two NOS1AP SNPs are strongly associated with QT interval duration in a predominately diabetic EA sample. Stronger effects of NOS1AP variants in diabetic individuals compared to previously reported unselected samples suggest that this patient subset may be particularly susceptible to genetic variants that influence myocardial depolarization and repolarization as manifest in the QT interval.

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