Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research

Abstract Single nucleotide polymorphisms (SNPs) and Insertions/Deletions (InDels) are the major genetic variations and distributed extensively across the plant whole genome. Few investigations of these variations, however, have been performed in the long-lived perennial tea plant. Here, we have investigated the genome-wide genetic variation between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, generating 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting informative with an average 4.02 of the number of alleles ( Na ) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the content of catechin/caffeine between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. The identified genome-wide genetic variation and newly-developed InDel markers will provide a valuable resource for tea plant genetics and genomics studies, especially those SNPs/InDels within catechin/caffeine biosynthesis-related genes can be served as pivotal candidates for elucidating the molecular mechanism of catechin/caffeine biosynthesis.

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Identification and Comparative Profiling of miRNAs in an Early Flowering Mutant of Trifoliate Orange and Its Wild Type by Genome-Wide Deep Sequencing

PLoS ONE ◽

10.1371/journal.pone.0043760 ◽

2012 ◽

Vol 7 (8) ◽

pp. e43760 ◽

Cited By ~ 30

Author(s):

Lei-Ming Sun ◽

Xiao-Yan Ai ◽

Wen-Yang Li ◽

Wen-Wu Guo ◽

Xiu-Xin Deng ◽

...

Keyword(s):

Deep Sequencing ◽

Early Flowering ◽

Trifoliate Orange ◽

Wild Type ◽

Genome Wide

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Systematic pathway-analysis of kinesin protein family (KIF) using genome-wide SNP data in patients with myocardial infarction: Genetic variation in KIFC3 gene associates with myocardial infarction

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0029-1191643 ◽

2009 ◽

Vol 56 (S 01) ◽

Author(s):

S Eifert ◽

A Goetz ◽

P Linsel-Nitschke ◽

A Medack ◽

C Hengstenberg ◽

...

Keyword(s):

Myocardial Infarction ◽

Genetic Variation ◽

Pathway Analysis ◽

Protein Family ◽

Snp Data ◽

Genome Wide

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UNEQUAL CROSSING OVER AT THE rRNA TANDON AS A SOURCE OF QUANTITATIVE GENETIC VARIATION IN DROSOPHILA

Genetics ◽

10.1093/genetics/95.3.727 ◽

1980 ◽

Vol 95 (3) ◽

pp. 727-742 ◽

Cited By ~ 1

Author(s):

R Frankham ◽

D A Briscoe ◽

R K Nurthen

Keyword(s):

Genetic Variation ◽

Selection Response ◽

Crossing Over ◽

Wild Type ◽

X Chromosomes ◽

Unequal Crossing Over ◽

Quantitative Genetic ◽

Y Chromosomes ◽

Homozygous Line ◽

Minimum Estimate

ABSTRACT Abdominal bristle selection lines (three high and three low) and controls were founded from a marked homozygous line to measure the contribution of sex-linked "mutations" to selection response. Two of the low lines exhibited a period of rapid response to selection in females, but not in males. There were corresponding changes in female variance, in heritabilities in females, in the sex ratio (a deficiency of females) and in fitness, as well as the appearance of a mutant phenotype in females of one line. All of these changes were due to bb alleles (partial deficiencies for the rRNA tandon) in the X chromosomes of these lines, while the Y chromosomes remained wild-type bb+. We argue that the bb alleles arose by unequal crossing over in the rRNA tandon.—A prediction of this hypothesis is that further changes can occur in the rRNA tandon as selection is continued. This has now been shown to occur.—Our minimum estimate of the rate of occurrence of changes at the rRNA tandon is 3 × 10-4. As this is substantially higher than conventional mutation rates, the questions of the mechanisms and rates of origin of new quantitative genetic variation require careful re-examination.

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Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽

10.3390/pathogens10030363 ◽

2021 ◽

Vol 10 (3) ◽

pp. 363

Author(s):

Sulochana K. Wasala ◽

Dana K. Howe ◽

Louise-Marie Dandurand ◽

Inga A. Zasada ◽

Dee R. Denver

Keyword(s):

Genetic Variation ◽

Potato Production ◽

Globodera Pallida ◽

Fixation Index ◽

Parasitic Nematodes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Field Samples ◽

Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

BMC Ecology and Evolution ◽

10.1186/s12862-020-01739-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kelly B. Klingler ◽

Joshua P. Jahner ◽

Thomas L. Parchman ◽

Chris Ray ◽

Mary M. Peacock

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Sierra Nevada ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Thermal Sensitivity ◽

Genomic Variation ◽

Genome Wide ◽

A Genome ◽

American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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Epidemiologic Patterns of Wild-Type Hepatitis A Virus Determined by Genetic Variation

The Journal of Infectious Diseases ◽

10.1093/infdis/163.2.286 ◽

1991 ◽

Vol 163 (2) ◽

pp. 286-292 ◽

Cited By ~ 98

Author(s):

B. H. Robertson ◽

B. Khanna ◽

O. V. Nainan ◽

H. S. Margolis

Keyword(s):

Genetic Variation ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Wild Type

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Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽

10.1093/genetics/157.1.283 ◽

2001 ◽

Vol 157 (1) ◽

pp. 283-294 ◽

Cited By ~ 2

Author(s):

Kristie Ashton ◽

Ana Patricia Wagoner ◽

Roland Carrillo ◽

Greg Gibson

Keyword(s):

Heart Rate ◽

Genetic Variation ◽

Recombinant Inbred Lines ◽

Model Organism ◽

Interval Mapping ◽

Activity Levels ◽

Environmental Variance ◽

Genome Wide ◽

A Genome ◽

Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

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