CoChat
Sign Up
PreprintCited by 35Insect Resistance and GeneticsGenetically Modified Organisms ResearchInsect-Plant Interactions and Control

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

Open access
Benowitz, Kyle M., Allan, Carson W., Degain, Benjamin A., Li, Xianchun, Fabrick, Jeffrey A., Tabashnik, Bruce E., Carrière, Yves, Matzkin, Luciano M.·2021·Genetics
DOI 10.1101/2021.11.09.467966PMC PMC9071530

Preprint — published as 10.1093/genetics/iyac037 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Crops genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bt toxins can improve resistance monitoring, resistance management, and design of new insecticides. Here, we investigated the genetic basis of resistance to Bt toxin Cry1Ac in the lepidopteran Helicoverpa zea , one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species, which has 31 chromosomes containing 375 Mb and 15,482 predicted proteins. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250-kb quantitative trait locus (QTL) on chromosome 13 that was strongly associated with resistance in a strain of H. zea that had been selected for resistance in the field and lab. The mutation in this QTL contributed to but was not sufficient for resistance, which implies alleles in more than one gene contributed to resistance. This QTL contains no genes with a previously reported role in resistance or susceptibility to Bt toxins. However, in resistant insects, this QTL has a premature stop codon in a kinesin gene which is a primary candidate as a mutation contributing to resistance. We found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2021.11.09.467966

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 122

  1. 10.1603/0022-0493(2006)099[0164:SOHZAH]2.0.CO;2 · DOI
  2. 10.1080/19336918.2020.1810939 · DOI
  3. 10.1128/AEM.01612-07 · DOI
  4. 10.1038/s41587-019-0036-z · DOI
  5. 10.1038/75556 · DOI · Paper page
  6. 10.1371/journal.pgen.1002812 · DOI
  7. Baxter SW , Badenes-Pérez FR , Morrison A , Vogel H , Crickmore N , et al. Parallel evolution of Bacillus thuringiensis toxin resistance in Lepidoptera. Genetics. 189:675–679. · DOI
  8. 10.1093/bioinformatics/16.2.135 · DOI
  9. 10.1534/g3.119.400036 · DOI
  10. 10.1093/bioinformatics/btu170 · DOI · Paper page
  11. 2011, Bacillus thuringiensis: a story of a successful bioinsecticide, Ins Biochem Mol Biol, 41, 423, 10.1016/j.ibmb.2011.02.006 · DOI
  12. 10.1073/pnas.1216719110 · DOI
  13. 10.1038/srep09807 · DOI
  14. 10.1128/AEM.00523-12 · DOI
  15. 2019, Field-evolved resistance of northern and western corn rootworm (Coleoptera: Chrysomelidae) populations to corn hybrids expressing single and pyramided Cry3Bb1 and Cry34/35Ab1 Bt proteins in North Dakota, J Econ Entomol, 112, 1875, 10.1093/jee/toz111 · DOI
  16. 10.1603/0022-0493-94.4.935 · DOI
  17. 10.1038/nbt.3099 · DOI · Paper page
  18. 10.1002/ps.4746 · DOI
  19. 10.1093/jee/toz236 · DOI
  20. 10.1073/pnas.2003604117 · DOI · Paper page
  21. 2020, Gene flow between Bt and non-Bt plants in a seed mixture increases dominance of resistance to pyramided Bt corn in Helicoverpa zea (Lepidoptera: Noctuidae), J Econ Entomol, 113, 2041, 10.1093/jee/toaa138 · DOI
  22. 2021, Effects of gene flow between Bt and non-Bt plants in a seed mixture of Cry1A.105 + Cry2Ab corn on performance of corn earworm in Arizona, Pest Manag Sci, 77, 2106, 10.1002/ps.6239 · DOI
  23. 10.1093/nar/gkw654 · DOI
  24. 2019, Effect of midgut specific binding protein ABCC1 on Cry1Ac toxicity against Helicoverpa armigera, Sci Ag Sin, 52, 3337
  25. 2019, A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni, Mole Ecol Res, 19, 485, 10.1111/1755-0998.12966 · DOI
  26. 10.1038/nmeth.2474 · DOI · Paper page
  27. 10.1093/bioinformatics/btv195 · DOI
  28. 2017, Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools, Genome, 60, 310, 10.1139/gen-2016-0067 · DOI
  29. 10.1073/pnas.1720692115 · DOI · Paper page
  30. 2021, CRISPR-mediated mutations in the ABC transporter gene ABCA2 confer pink bollworm resistance to Bt toxin Cry2Ab, Sci Rep, 11, 10377, 10.1038/s41598-021-89771-7 · DOI
  31. 10.1534/g3.120.401344 · DOI
  32. 10.1073/pnas.1921046117 · DOI · Paper page
  33. 10.1534/g3.120.401053 · DOI
  34. 10.1126/science.1060949 · DOI
  35. 1993, Type I repressors of P element mobility, Genetics, 135, 81, 10.1093/genetics/135.1.81 · DOI
  36. 10.2307/2411080 · DOI
  37. 2015, MAPK signaling pathway alters expression of midgut ALP and ABCC genes and causes resistance to Bacillus thuringiensis Cry1Ac toxin in diamondback moth, PLoS Genetics, 11, e1005124, 10.1371/journal.pgen.1005124 · DOI
  38. 2020, MAPK-dependent hormonal signaling plasticity contributes to overcoming Bacillus thuringiensis toxin action in an insect host, Nat Commun, 11, 3003, 10.1038/s41467-020-16608-8 · DOI
  39. 2021, The regulation landscape of MAPK signaling cascade for thwarting Bacillus thuringiensis infection in an insect host, PLoS Path, 17, e1009917, 10.1371/journal.ppat.1009917 · DOI
  40. 2013, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat Prot, 8, 1494, 10.1038/nprot.2013.084 · DOI · Paper page
  41. 2019, Hybrid genome assembly of a neotropical mutualistic ant, Genom Biol Evol, 11, 2306, 10.1093/gbe/evz159 · DOI
  42. 2007, The diversity of Bt resistance genes in species of Lepidoptera, J Inv Biol, 95, 192
  43. 2020, Chromosome-level hybrid de novo genome assemblies as an attainable option for nonmodel insects, Mol Ecol Res, 20, 1277, 10.1111/1755-0998.13176 · DOI
  44. 10.1111/eva.12099 · DOI
  45. 10.1073/pnas.1812138115 · DOI
  46. 10.1093/bioinformatics/btu031 · DOI
  47. 10.1371/journal.pone.0017606 · DOI
  48. 10.1146/annurev-ento-052620-073348 · DOI
  49. 10.1101/gr.170720.113 · DOI · Paper page
  50. 10.1093/nar/gkr1006 · DOI
  51. 2011, Inheritance of resistance to Bacillus thuringiensis Cry1Ac toxin in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) from India, Pest Man Sci, 67, 1294, 10.1002/ps.2185 · DOI
  52. 10.1016/j.jip.2019.02.007 · DOI
  53. 10.1093/molbev/msu302 · DOI
  54. 10.1038/s41587-019-0201-4 · DOI · Paper page
  55. 10.1371/journal.pone.0015925 · DOI
  56. 10.1101/gr.215087.116 · DOI
  57. 10.1093/bioinformatics/btz595 · DOI
  58. 10.1038/nmeth.1923 · DOI · Paper page
  59. 10.3390/ijms21186528 · DOI
  60. 2022, Characterization of long non-coding RNAs in the bollworm, Helicoverpa zea, and their possible role in Cry1Ac-resistance, Insects, 13, 12
  61. 10.1093/bioinformatics/btr509 · DOI
  62. 10.1093/bioinformatics/btp324 · DOI · Paper page
  63. 2019, Kinesins in MAPK cascade: how kinesin motors are involved in the MAPK pathway?, Gene, 684, 1, 10.1016/j.gene.2018.10.042 · DOI
  64. 1997, Inheritance of resistance to the Bacillus thuringiensis toxin Cry1C in the diamondback moth, Appl Env Microbiol, 63, 2218, 10.1128/aem.63.6.2218-2223.1997 · DOI
  65. 10.1038/srep07219 · DOI
  66. 10.1093/jee/92.1.21 · DOI
  67. 2020, A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis, Mol Ecol Res, 20, 268, 10.1111/1755-0998.13078 · DOI
  68. 2022, Bt Cry1Ac resistance in Trichoplusia ni is conferred by multi-gene mutations, Insect Biochem Mol Biol, 140, 103678, 10.1016/j.ibmb.2021.103678 · DOI
  69. 2011, The statistics of bulk segregant analysis using next generation sequencing, PLoS Comp Biol, 7, e1002255, 10.1371/journal.pcbi.1002255 · DOI
  70. 2018, QTLseqr: an R package for bulk segregant analysis with next-generation sequencing, Plant Genom, 11, 180006, 10.3835/plantgenome2018.01.0006 · DOI
  71. 2018, MUMmer4: a fast and versatile genome alignment system, PLoS Comp Biol, 14, e1005944, 10.1371/journal.pcbi.1005944 · DOI · Paper page
  72. 10.1534/g3.119.400954 · DOI
  73. 2019, 2018 Soybean insect losses in the United States, Midsouth Entomol, 12, 1
  74. National Academies of Sciences, Engineering, and Medicine. 2016. Genetically Engineered Crops: Experiences and Prospects. Washington DC, National Academies Press.
  75. 10.1111/eea.12308 · DOI
  76. 10.1093/jee/tov226 · DOI
  77. 2017, Salmon provides fast and bias-aware quantification of transcript expression, Nat Meth, 14, 417, 10.1038/nmeth.4197 · DOI · Paper page
  78. 2017, Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species, BMC Biol, 15, 63, 10.1186/s12915-017-0402-6 · DOI
  79. 2021, Genetic knockouts indicate that the ABCC2 protein in the bollworm Helicoverpa zea is not a major receptor for the Cry1Ac insecticidal protein, Genes, 12, 1522, 10.3390/genes12101522 · DOI
  80. 10.1038/nbt.3122 · DOI
  81. 10.1093/jee/tow310 · DOI
  82. 2021, MAPK-activated transcription factor PxJun suppresses PcABCB1 expression and confers resistance to Bacillus thuringiensis Cry1Ac toxin in Plutella xylostella (L.), Appl Env Microbiol, 87, 13
  83. 10.1042/BJ20081152 · DOI
  84. 2020, Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files, BMC Genom, 21, 230, 10.1186/s12864-020-6635-8 · DOI · Paper page
  85. 10.1093/jee/toy106 · DOI
  86. Reisig DD , DiFonzo C , Dively G , Fargan Y , Gore F , et al. 2021. Best management practices to delay the evolution of Bt resistance in Lepidopteran pests without high susceptibility to Bt toxins in North America. J Econ Entomol. https://doi.org/10.1093/jee/toab247. · DOI
  87. 10.1038/ng.3036 · DOI
  88. 2018, Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies, BMC Bioinf, 19, 460, 10.1186/s12859-018-2485-7 · DOI
  89. 10.1093/bioinformatics/btp616 · DOI · Paper page
  90. 10.1158/0008-5472.CAN-17-0337 · DOI
  91. 10.1534/g3.119.400710 · DOI
  92. 2019, Gene Prediction. Methods in Molecular Biology, 1962, 227
  93. 10.1371/journal.pone.0163962 · DOI · Paper page
  94. 10.1002/PRO.3290 · DOI · Paper page
  95. 2021, orfipy: a fasta and flexible tool for extracting ORFs, Bioinformatics, 37, 3019, 10.1093/bioinformatics/btab090 · DOI
  96. 2019, Practical resistance of Ostrinia nubilalis (Lepidoptera: Crambidae) to Cry1F Bacillus thuringiensis maize discovered in Nova Scotia, Canada, Sci Rep, 9, 18247, 10.1038/s41598-019-54263-2 · DOI
  97. 10.1126/science.1146453 · DOI
  98. 2016, Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences, F100Research, 4, 1521, 10.12688/f1000research.7563.2 · DOI · Paper page
  99. 10.1093/jee/toz173 · DOI
  100. 10.1098/rstb.1998.0327 · DOI
  101. 10.1038/nbt1382 · DOI
  102. 2021, Genetically engineered cotton synergizes eradication of the pink bollworm a century after its invasion of the United States, Proc Natl Acad Sci USA, 118, e2019115118, 10.1073/pnas.2019115118 · DOI
  103. 10.1073/pnas.2020853118 · DOI
  104. 2020, Adaptive introgression across semipermeable species boundaries between local Helicoverpa zea and invasive Helicoverpa armigera moths, Mol Biol Evol, 37, 2568, 10.1093/molbev/msaa108 · DOI
  105. 10.1371/journal.pone.0112963 · DOI
  106. 2019, A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance, Nat Commun, 10, 4237, 10.1038/s41467-019-12175-9 · DOI
  107. 2020, Polycalin is involved in the toxicity and resistance to Cry1Ac toxin in Helicoverpa zea, Arch Ins Biochem Physiol, 104, e21661, 10.1002/arch.21661 · DOI
  108. 2021, A haploid diamondback moth (Plutella xylostella L.) genome assembly resolves 31 chromosomes and identifies a diamide resistance mutation, Ins Biochem Mol Biol, 138, 103622, 10.1016/j.ibmb.2021.103622 · DOI
  109. 10.1016/S0960-9822(01)00476-6 · DOI
  110. 10.1016/j.jip.2015.10.003 · DOI
  111. 10.1093/nar/gkt1229 · DOI · Paper page
  112. 2021, Chromosome-level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera), Mol Ecol Res, 21, 561, 10.1111/1755-0998.13274 · DOI
  113. 2021, A chromosome-level genome assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae), Genom Biol Evol, 13, evab114, 10.1093/gbe/evab114 · DOI
  114. 10.7717/peerj.2016 · DOI
  115. 10.1038/srep31900 · DOI · Paper page
  116. 2021, The challenge and promise of estimating the de novo mutation rate from whole-genome comparisons among closely related individuals, Mol Ecol, 30, 6087, 10.1111/mec.16007 · DOI
  117. 2021, Extended investigation of field-evolved resistance of the corn earworm Helicoverpa zea (Lepidoptera: Noctuidae) to Bacillus thuringiensis Cry1A.105 and Cry2Ab2 proteins in the southeastern United States, J Inv Pathol, 183, 107560, 10.1016/j.jip.2021.107560 · DOI
  118. 2009, Mutation of an aminopeptidase N gene is associated with Helicoverpa armigera resistance to Bacillus thuringiensis Cry1Ac toxin, Ins Biochem Mol Biol, 39, 421, 10.1016/j.ibmb.2009.04.003 · DOI
  119. 10.1002/ps.5224 · DOI
  120. 10.3389/fphys.2019.00029 · DOI
  121. 2020, Chromosome-level genome assembly of an important pine defoliator, Dendrolimus punctatus (Lepidoptera; Lasiocampidae), Mol Ecol Res, 20, 1023, 10.1111/1755-0998.13169 · DOI
  122. 2021, Independent and synergistic effects of knocking out two ABC transporter genes on resistance to Bacillus thuringiensis toxins Cry1Ac and Cry1Fa in diamondback moth, Toxins, 13, 9

Metadata

Authors
Benowitz, K. M., Allan, C. W., Degain, B. A., Li, X., Fabrick, J. A., Tabashnik, B. E., Carrière, Y., & Matzkin, L. M.
Affiliations
  • University of Arizona (US)
  • Agricultural Research Service (US)
Corresponding author
Benowitz, Kyle M.
ORCID
Venue
Genetics
Publisher
openRxiv
Published
2021-11-09
Volume
221
Issue
1
ISSN
0016-6731 (ISSN-L)
DOI
10.1101/2021.11.09.467966
PMC
PMC9071530
OpenAlex
W4214913712
Cited by
35
References
2
Citations by year
2026: 4 · 2025: 10 · 2024: 11 · 2023: 3 · 2022: 7
FWCI
2.53
Type
journal article
Language
en
Open access
Locations
  • Genetics (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • U.S. Department of Agriculture (2020-67013-31924)
  • Corteva Agriscience
  • National Institute of Food and Agriculture (2020-33522-32268, 2020-67013-31924)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Insect Resistance and Genetics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
  • Life Sciences › Agricultural and Biological Sciences › Insect Science › Insect-Plant Interactions and Control
Keywords
corn earworm, Cry1Ac resistance, Bacillus thuringiensis toxin, Bt resistance, genetic basis of resistance, quantitative trait loci, polygenic resistance, chromosome-level genome assembly, genome-wide association study, resistance management, insecticide resistance
MeSH terms
Bacillus thuringiensis Toxins, Animals, Bacillus thuringiensis, Bacterial Proteins, Zea mays, Endotoxins, Hemolysin Proteins, Insecticide Resistance, Insecticides, Larva, Moths, Plants, Genetically Modified, Genome-Wide Association Study

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review