scholarly journals High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest

PLoS Genetics ◽  
2021 ◽  
Vol 17 (6) ◽  
pp. e1009422
Author(s):  
Seyedeh Masoumeh Fotoukkiaii ◽  
Nicky Wybouw ◽  
Andre H. Kurlovs ◽  
Dimitra Tsakireli ◽  
Spiros A. Pergantis ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
High Resolution ◽  
Copy Number Variation ◽  
Genetic Mapping ◽  
Copy Number ◽  
Spider Mite ◽  
Bulked Segregant Analysis ◽  
Resistant Population ◽  
Number Variation

Chemical control strategies are driving the evolution of pesticide resistance in pest populations. Understanding the genetic mechanisms of these evolutionary processes is of crucial importance to develop sustainable resistance management strategies. The acaricide pyflubumide is one of the most recently developed mitochondrial complex II inhibitors with a new mode of action that specifically targets spider mite pests. In this study, we characterize the molecular basis of pyflubumide resistance in a highly resistant population of the spider mite Tetranychus urticae. Classical genetic crosses indicated that pyflubumide resistance was incompletely recessive and controlled by more than one gene. To identify resistance loci, we crossed the resistant population to a highly susceptible T. urticae inbred strain and propagated resulting populations with and without pyflubumide exposure for multiple generations in an experimental evolution set-up. High-resolution genetic mapping by a bulked segregant analysis approach led to the identification of three quantitative trait loci (QTL) linked to pyflubumide resistance. Two QTLs were found on the first chromosome and centered on the cytochrome P450 CYP392A16 and a cluster of CYP392E6-8 genes. Comparative transcriptomics revealed a consistent overexpression of CYP392A16 and CYP392E8 in the experimental populations that were selected for pyflubumide resistance. We further corroborated the involvement of CYP392A16 in resistance by in vitro functional expression and metabolism studies. Collectively, these experiments uncovered that CYP392A16 N-demethylates the toxic carboxamide form of pyflubumide to a non-toxic compound. A third QTL coincided with cytochrome P450 reductase (CPR), a vital component of cytochrome P450 metabolism. We show here that the resistant population harbors three gene copies of CPR and that this copy number variation is associated with higher mRNA abundance. Together, we provide evidence for detoxification of pyflubumide by cytochrome P450s that is likely synergized by gene amplification of CPR.

scholarly journals High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest

2021 ◽  
Author(s):  
Seyedeh Masoumeh Fotoukkiaii ◽  
Nicky Wybouw ◽  
Andre H. Kurlovs ◽  
Dimitra Tsakireli ◽  
Spiros A. Pergantis ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
High Resolution ◽  
Genetic Mapping ◽  
Genetic Variants ◽  
Spider Mite ◽  
Cytochrome P450s ◽  
Cytochrome P450 Reductase ◽  
Resistant Population ◽  
Number Variation

AbstractChemical control strategies are driving the evolution of pesticide resistance in pest populations. Understanding the genetic mechanisms of these evolutionary processes is of crucial importance to develop sustainable resistance management strategies. The acaricide pyflubumide is one of the most recently developed mitochondrial complex II inhibitors with a new mode of action that specifically targets spider mite pests. In this study, we characterize the molecular basis of pyflubumide resistance in a highly resistant population of the spider mite Tetranychus urticae. Classical genetic crosses indicated that pyflubumide resistance was incompletely recessive and controlled by more than one gene. To identify resistance loci, we crossed the resistant population to a highly susceptible T. urticae inbred strain and propagated resulting populations with and without pyflubumide exposure for multiple generations in an experimental evolution set-up. High-resolution genetic mapping by a bulked segregant analysis approach led to the identification of three quantitative trait loci (QTL) linked to pyflubumide resistance. Two QTLs were found on the first chromosome and centered on the cytochrome P450 CYP392A16 and a cluster of CYP392E6-8 genes. Comparative transcriptomics revealed a consistent overexpression of CYP392A16 and CYP392E8 in the experimental populations that were selected for pyflubumide resistance. We further corroborated the involvement of CYP392A16 in resistance by in vitro functional expression and metabolism studies. Collectively, these experiments uncovered that CYP392A16 N-demethylates the toxic carboxamide form of pyflubumide to a non-toxic compound. A third QTL coincided with cytochrome P450 reductase (CPR), a vital component of cytochrome P450 metabolism. We show here that the resistant population harbors three gene copies of CPR and that this copy number variation is associated with higher mRNA abundance. Together, we provide evidence for detoxification of pyflubumide by cytochrome P450s that is likely synergized by gene amplification of CPR.Author summaryOur understanding of the causal genetic variants that drive the evolution of quantitative traits, such as polygenic pesticide resistance, remains very limited. Here, we followed a high-resolution genetic mapping approach to localize the genetic variants that cause pyflubumide resistance in the two-spotted spider mite Tetranychus urticae. Three well-supported QTL were uncovered and pointed towards a major role for cytochrome P450-mediated detoxification. Cis-regulatory variation for cytochrome P450s was observed, and in vitro cytochrome P450 experiments showed that pyflubumide was metabolized into a non-toxic derivate. A third QTL centered on cytochrome P450 reductase (CPR), which is required for cytochrome P450 activity, and is amplified in pyflubumide resistant populations. Our results indicate that pyflubumide resistance is mediated by cytochrome P450 detoxification that is enhanced by gene amplification at the CPR locus.Data availabilitySequence data has been deposited at the Sequence Read Archive (PRJNA596790). Phenotypic quantification data is available at Supplementary Data S1.

scholarly journals High-Resolution Survey in Familial Parkinson Disease Genes Reveals Multiple Independent Copy Number Variation Events in PARK2

2013 ◽  
Vol 34 (8) ◽  
pp. 1071-1074 ◽  
Author(s):  
Liyong Wang ◽  
Karen Nuytemans ◽  
Guney Bademci ◽  
Cherylyn Jauregui ◽  
Eden R. Martin ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number Variation ◽  
Parkinson Disease ◽  
Copy Number ◽  
Disease Genes ◽  
Independent Copy ◽  
Number Variation

Identification of Novel Recurrent Copy Number Variations and Regions of Copy-Neutral Loss of Heterozygosity by High Resolution Genomic Array in Pre-Treatment and Relapsed B-CLL.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1098-1098
Author(s):  
Samantha JL Knight ◽  
Elham Sadighi Akha ◽  
Adele Timbs ◽  
Tariq Enver ◽  
Andrew R Pettitt ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number Variation ◽  
B Cell ◽  
Genomic Instability ◽  
Loss Of Heterozygosity ◽  
Copy Number ◽  
Neutral Loss ◽  
Single Gene ◽  
Number Variation ◽  
Pre Treatment

Abstract Abstract 1098 Poster Board I-120 Background B-cell chronic lymphocytic leukaemia (B-CLL) is the most common form of adult leukaemia in the Western World. It is a heterogeneous disease and important biological and clinical differences have been identified. However, the molecular mechanisms underlying emergence and maintenance of B-CLL after treatment remain elusive. Array based comparative genomic hybridization (aCGH) has revolutionized our ability to perform genome wide analyses of copy number variation (CNV) within cancer genomes. Single Nucleotide Polymorphism arrays (aSNP) provide genotyping and copy number variation data and detect regions of copy neutral Loss of Heterozygosity (cnLOH) with the potential to indicate genes involved in leukaemia pathogenesis. Both technologies are evolving rapidly and emerging platforms are thought to allow high resolution (HR) of abnormalities down to a single gene level. Aim The aim of the current study was therefore to test a HR-aCGH and a HR-aSNP platform for their ability to detect large and small CNVs and regions of cnLOH in B-CLL. More specifically, we wanted to: Method We used a high resolution 244K aCGH platform and a 1Mio SNP array in parallel to test and characterize enriched B-CLL peripheral blood samples (>80% CD19+;CD5+) from 44 clinically annotated patients collected at our institution. To distinguish CNVs seen commonly in the general population the results were compared with ‘in house’ control data sets and the Database of Genomic Variants (http://projects.tcag.ca/variation/). Results Our results show that large abnormalities, already noted by FISH, were reliably identified and the boundaries of abnormalities at 11q22.3, 13q14.2 and 17p could be defined more precisely. In addition, novel and recurrent CNVs within the sample set were identified (1p33; 3p24.3; 3p14.2; 4q12; 4q13.3; 6q21; 6q27; 8p22; 10q24; 11p15.4; 11q12; 11q13.4; 11q14.1; 11q22.1; 11q23.3; 13q14.11; 14q21.1; 15q15.1; 15q25.3; 17p13.3; 17q22; 18p11.32; 18p23; 19p13.13; 19p13.12; 19p13.32; 22q11.21; 22q11.22). Interestingly, some of these abnormalities contain single gene alterations involving oncogenes, chemokine receptors, kinases and transcription factors important in B cell development and differentiation. Assessment of smaller CNVs (less then 10 consecutive oligonucleotides) also revealed recurrent CNVs involving single genes that were clustered according to function and pathways. Comparison of paired pre-treatment and relapse samples showed differences in large CNVs in 6 out of the 14 pairs with the majority being losses within the relapse sample. In particular, relapse samples contained new losses within 2q33.1-2q37.1; 4q13.2-4q13.3; 5q31.3-5q34; 7q36.3; 10q23.1-10q25.1 11q12.3 and multiple losses within 13q14.1-13q14.3. Taken together, these data indicates that genomic instability plays a role in clonal evolution and selection after treatment in at least some patients. Analysis of a bigger cohort of matched pre-treatment and relapse samples is on-going. The importance of copy neutral LOH in B-CLL has been a subject of debate. Using the 1Mio HR-aSNP, we were able to detect multiple regions of cnLOH throughout the genome. Examination of the four regions that are known to have prognostic significance when deleted identified cnLOH involving 13q11-13q34(ter) and cnLOH of 13q21.1-q34(ter) outside the FISH region. Deletions of the 17p13.1 locus including the p53 gene confer poor prognosis in B-CLL and direct treatment decisions. Interestingly, we were able to identify cnLOH involving this region in 5% of samples. In addition, we also noticed cnLOH in 17p13.2 containing genes previously implicated in cancer. The exact pathogenetic and prognostic implications of these findings remain to be established. Conclusion Using HR-aCGH and HR-aSNP we have identified novel recurrent CNVs and regions of cnLOH in patients with B-CLL. Sequential analysis of the same patients over time suggests that at least in some patients, clonal complexity and dynamics are driven by genomic instability. Disclosures No relevant conflicts of interest to declare.

175 Testis-Specific Protein Y Encoded Copy Number Variation in In Vitro-Produced Bovine Early Embryos

2018 ◽  
Vol 30 (1) ◽  
pp. 227
Author(s):  
N.Y. Rho ◽  
L. A. Favetta ◽  
T. Mogas ◽  
W. A. King
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Specific Protein ◽  
Development Rate ◽  
Male Reproduction ◽  
Cell Stage ◽  
Early Embryos ◽  
Number Variation ◽  
Developmental Rates

Testis-specific protein Y (TSPY) is one of the genes located in the male-specific region of the Y chromosome involved in male reproduction, particularly in spermatogenesis. It has been shown to have different copy number (CN) in different species, in different individuals within a species and in the same family (i.e. among brothers from the same father). Previous studies from our laboratory in the bovine species showed that different TSPY CN was correlated with fertility, as bulls with higher CN showed higher fertility rate. In this study, we investigated development rate in in vitro-produced (IVP) bovine early embryos produced by sex-sorted semen (X and Y) from 3 bulls (1, 2, and 3) and TSPY copy number variation (CNV) in the male blastocysts. The IVP embryos by the 3 different types of semen (sub-divided: 1X, 1Y, 2X, 2Y, 3X, 3Y) and parthenotes (PART) for the negative control were assessed for developmental rates (shown in Table 1 below) and individually collected at each cell stage from zygote to blastocyst to extract DNA for TSPY CN analysis. The DNA from individual blastocysts was treated with a restriction enzyme for relative quantification of TSPY CN using digital droplet PCR (ddPCR) with SRY, known to have only one copy in bovine, as a reference gene. Developmental data showed that Y-carrying semen had higher rates both in cleavage and blastocyst compared with X-carrying semen from the same bull. Particularly, bull 3 (both 3X and 3Y) had the highest developmental rates compared with the other 2 types of bulls. TSPY was detected in male blastocyst, where both parthenotes and female embryos were negative. Relative CN of TSPY versus SRY from blastocysts produced from bulls 1, 2, and 3 averaged to 87.5, 55, and 20, respectively. Interestingly, the CN among brother blastocysts showed a variation of less than 7.5, where bull-to-bull variation was approximately from 20 to 60 copies. Our results show that TSPY CN in the embryo varies according to the sire and among brother blastocysts. Moreover, TSPY CNV among brother blastocysts allows us to speculate that individually different recombination events occurred in meiosis during spermatogenesis. Table 1.Embryo development rate by semen type This research was funded by the Canada Research Chair’s program, Natural Sciences and Engineering Research Council of Canada and the Ontario Veterinary College.

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