QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

Mansfeld, Ben N.; Grumet, Rebecca

doi:10.1101/208140

Cited by 42 publications

(52 citation statements)

References 15 publications

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“…We performed the BSA analyses using the R package QTLseqr (Mansfeld and Grumet 2018). We first defined extreme-QTLs by looking for regions with false discovery rate (FDR) < 0.01 using the G’ approach (Magwene et al 2011).…”

Section: Methodsmentioning

confidence: 99%

Genetic mapping of fitness determinants across the malaria parasitePlasmodium falciparumlife cycle

Kumar

McDew-White

et al. 2019

Preprint

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28Malaria is transmitted through female Anopheline mosquitoes where gamete fusion and meiosis 29 occurs, and humans where parasites proliferate asexually. We describe a powerful approach to 30 identify the genetic determinants of parasite fitness across both invertebrate and vertebrate life-31 cycle stages in human malaria parasite Plasmodium falciparum using bulk segregant analysis 32 (BSA). We combined experimental genetic crosses using humanized mice, with selective whole 33 genome amplification and BSA at multiple developmental stages in both mosquito and vertebrate 34 host to examine parasite competition and identify genomic regions under selection. We generated 35 crosses between artemisinin resistant (ART-R, kelch13-C580Y) and ART-sensitive (ART-S, 36 kelch13-WT) parasite clones recently isolated from Southeast Asian patients. We then quantified 37 genome-wide changes in allele frequency in the parasite progeny population from infected midgut 38 and salivary glands of Anopheles stephensi mosquitoes, infected livers, emerging merozoites and 39 aliquots of in vitro cultured progeny parasites at intervals over 30 days. Three striking results 40 emerge: we observed (i) a strong skew (>80%) towards alleles from the ART-R parent in the 41 mosquito stage, that dropped to ~50% in the blood stage as selfed ART-R parasites were selected 42 against; (ii) highly repeatable skews in allele frequencies across the genome in blood stage 43 parasites; (iii) particularly strong selection (selection coefficient (s) ≤ 0.18/asexual cycle) against 44 alleles from the ART-R parent at loci on chromosome 12 containing MRP2 and chromosome 14 45 containing ARPS10. This approach robustly identifies selected loci and has strong potential for 46 identifying parasite genes that interact with the mosquito vector or compensatory loci involved in 47 drug resistance. 48 49 3 50 Parasitic organisms frequently use multiple hosts and have several morphologically and 51 transcriptionally distinctive life cycle stages. Within each host, parasites must circumvent immune 52 defenses and navigate to new tissues. There are frequently extreme bottlenecks in parasite numbers 53 during transmission (Hopp et al. 2015), with rapid proliferative growth within hosts, and intense 54 competition between co-infecting parasite genotypes. For example, the life cycle of malaria 55 parasites involves successive infection of two hosts: female Anopheles mosquitoes, where gamete 56 fusion, meiosis and recombination occurs, and humans in which parasites travel from the skin, 57 develop in the liver and then proliferate asexually in the blood stream. Ideally, we would like to 58 understand how natural selection operates across the complete life cycle and document the genes 59 subject to selection pressures at each life cycle stage: during erythrocytic growth, gametocyte 60 production, oocyst development in the mosquito midgut, migration of sporozoites to the salivary 61 glands, transmission from the salivary glands, sporozoite survival in the skin, and est...

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Section: Methodsmentioning

confidence: 99%

Genetic mapping of fitness determinants across the malaria parasitePlasmodium falciparumlife cycle

Kumar

McDew-White

et al. 2019

Preprint

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“…Background SNPs (also present in the XS134 sequence) were removed. The final 375 VCF file was imported into the QTLseqr R package (Mansfeld & Grumet, 2018) and 376 the "deltaSNP" index was calculated and plotted. 377…”

Section: Mutation Mapping: 359mentioning

confidence: 99%

“…We performed paired-end, short read sequencing on the two contrasting 157 bulks and used the R package QTLseqr (Mansfeld & Grumet, 2018), with an 158 approach similar in concept to MUT-map (Abe et al, 2012). This analysis identified a 159 candidate region on chromosome 8 that contained the likely causative mutation 160 underlying the E104-SR root phenotype ( Fig S2).…”

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confidence: 99%

VST Family Proteins are Regulators of Root System Architecture in Rice andArabidopsis

Shao

Lehner

Zhou

et al. 2020

Preprint

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30 31 One Sentence Summary: 32 VST proteins control root meristem size and root system architecture in rice and 33 Arabidopsis. 34 35 Abstract: 36Root System Architecture (RSA) is a key factor in the efficiency of nutrient capture 37 and water uptake in plants. Understanding the genetic control of RSA will be useful 38 in minimizing fertilizer and water usage in agricultural cropping systems. Using a 39 hydroponic screen and a gel-based imaging system we identified a rice gene, OsVST1, 40 which plays a key role in controlling RSA. This gene encodes a homolog of the 41Arabidopsis VAP-RELATED SUPPRESSORS OF TMM (VSTs), a class of proteins that 42 promote signaling in stomata by mediating plasma membrane-endoplasmic 43 reticulum contacts. OsVST1 mutants have shorter primary roots, decreased root 44 meristem size, and a more compact root system architecture. We show that the 45 Arabidopsis VST triple mutants have similar phenotypes, with reduced primary root 46 growth and smaller root meristems. Expression of OsVST1 largely complements the 47

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“…by permutation, and the G' method was developed for and previously applied for QTL detection with 736 simpler genetic designs (Magwene et al 2011;Mansfeld and Grumet 2018). 737…”

Section: Genomic Regions Associated With Selection By Tomato 614mentioning

confidence: 99%

Long-term population studies uncover the genome structure and genetic basis of xenobiotic and host plant adaptation in the herbivoreTetranychus urticae

Clark

Leeuwen

Wybouw

et al. 2018

Preprint

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Pesticide resistance arises rapidly in arthropod herbivores, as can host plant adaptation, and both are significant problems in agriculture. These traits have been challenging to study as both are often polygenic and many arthropods are genetically intractable. Here, we examined the genetic architecture of pesticide resistance and host plant adaptation in the two-spotted spider mite, Tetranychus urticae, a global agricultural pest. We show that the short generation time and high fecundity of T. urticae can be readily exploited in experimental evolution designs for high-resolution mapping of quantitative traits. As revealed by selection with spirodiclofen, an acetyl-CoA decarboxylase inhibitor, in populations from a cross between a spirodiclofen resistant and a susceptible strain, and which also differed in performance on tomato, we found that a limited number of loci could explain quantitative resistance to this compound. These were resolved to narrow genomic intervals, suggesting specific candidate genes, including acetyl-CoA decarboxylase itself, clustered and copy variable cytochrome P450 genes, and NADPH cytochrome P450 reductase, which encodes a redox partner for cytochrome P450s. For performance on tomato, candidate genomic regions for response to selection were distinct from those responding to the synthetic compound and were consistent with a more polygenic architecture. In accomplishing this work, we exploited the continuous nature of allele frequency changes across experimental populations to resolve the existing fragmented T.urticae draft genome to pseudochromosomes. This improved assembly was indispensable for our analyses, as it will be for future research with this model herbivore that is exceptionally amenable to genetic studies.

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QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

Cited by 42 publications

References 15 publications

Genetic mapping of fitness determinants across the malaria parasitePlasmodium falciparumlife cycle

Genetic mapping of fitness determinants across the malaria parasitePlasmodium falciparumlife cycle

VST Family Proteins are Regulators of Root System Architecture in Rice andArabidopsis

Long-term population studies uncover the genome structure and genetic basis of xenobiotic and host plant adaptation in the herbivoreTetranychus urticae

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