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ABC transporter mis-splicing associated with resistance to Bt toxin Cry2Ab in laboratory- and field-selected pink bollworm

Evolution of pest resistance threatens the benefits of genetically engineered crops that produce Bacillus thuringiensis (Bt) insecticidal proteins. Strategies intended to delay pest resistance are most effective when implemented proactively. Accordingly, researchers have selected for and analyzed resistance to Bt toxins in many laboratory strains of pests before resistance evolves in the field, but the utility of this approach depends on the largely untested assumption that laboratory- and field-selected resistance to Bt toxins are similar. Here we compared the genetic basis of resistance to Bt toxin Cry2Ab, which is widely deployed in transgenic crops, between laboratory- and field-selected populations of the pink bollworm (Pectinophora gossypiella), a global pest of cotton. We discovered that resistance to Cry2Ab is associated with mutations disrupting the same ATP-binding cassette transporter gene (PgABCA2) in a laboratory-selected strain from Arizona, USA, and in field-selected populations from India. The most common mutation, loss of exon 6 caused by alternative splicing, occurred in resistant larvae from both locations. Together with previous data, the results imply that mutations in the same gene confer Bt resistance in laboratory- and field-selected strains and suggest that focusing on ABCA2 genes may help to accelerate progress in monitoring and managing resistance to Cry2Ab.

The insecticidal proteins produced by Bacillus thuringiensis (Bt) kill some devastating insect pests, but cause little or no harm to humans and most other non-target organisms 1,2 . Farmers have used Bt toxins in insecticidal sprays for more than 70 years and in transgenic crops since 1996 [3][4][5] . In 2017, genetically engineered corn, cotton and soy producing Bt toxins were planted by millions of farmers on more than 100 million hectares worldwide 5 . The benefits of these Bt crops include pest suppression, reduced insecticide use, enhanced biological control, and increased farmer profits 2,6-11 . However, increasingly rapid evolution of pest resistance to Bt toxins has reduced these benefits 12 .
Strategies designed to delay pest resistance to Bt crops are most likely to succeed if they are implemented proactively, before resistance is widespread 13,14 . To provide the information needed to bolster the proactive development of such strategies, researchers have selected for and analyzed resistance to Bt toxins in many laboratory strains of pests 4,15 . The utility of this approach depends on the largely untested assumption that laboratory-and field-selected resistance are similar 16 .

ABCA2 in Susceptible and Lab-Selected Resistant Pink Bollworm from Arizona. The full-length
consensus PgABCA2 cDNA (GenBank accession no. MG637361) from two Arizona Cry2Ab-susceptible strains, APHIS-S and AZP-R, was identical and had 5,187 bp encoding a predicted protein of 1,729 aa ( Supplementary  Fig. S1). Similar to other ABC transporters in subfamily A, the proposed structure of PgABCA2 includes two transmembrane domains (TMD1 and TMD2) and two nucleotide-binding domains (NBD1 and NBD2) ( Fig. 1a and Supplementary Fig. S1). Each transmembrane domain has six transmembrane helices and both nucleotide-binding domains have a catalytic core domain consisting of Walker A and B motifs and a structurally diverse α-helical domain containing the ABC transporter signature motif (also called Walker C motif) in the cytoplasm.
To test for differences between the susceptible APHIS-S strain and the resistant Bt4-R2 strain in genomic DNA (gDNA) near exon 20 of PgABCA2, we PCR amplified, cloned, and sequenced fragments from exon 18 to exon 21. Compared with APHIS-S, the gDNA from Bt4-R2 contained an indel mutation expected to disrupt the 3′ splice junction of exon 20 ( Fig. 2a and Supplementary Fig. S2). This splice-site mutation includes a 7-bp insertion (GCGCGCC), followed by a 44-bp deletion that spans the exon-intron junction. We name this mutation "r A1 " and refer to the allele containing this mutation as the r A1 allele. Because the r A1 mutation spans the exon-intron splice junction, the Bt4-R2a-d cDNA variants probably result from mis-splicing of intron 20. Further examination of nearby gDNA revealed that, relative to APHIS-S, Bt4-R2 also has a 1,129-bp insertion in intron 18 ( Supplementary Fig. S2).
To distinguish readily between the r A1 resistance allele from Bt4-R2 and the susceptible "s A1 " allele from APHIS-S, we developed allele-specific PCR using primers that flank the r A1 mutation ( Fig. 2 and Supplementary Table S1). These primers yielded a 343-bp fragment from APHIS-S individuals (s A1 s A1 ), a 305-bp fragment from Bt4-R2 (r A1 r A1 ), and both fragments in the Bt4-R2 X APHIS-S (r A1 s A1 ) F 1 offspring from biphasic linkage crosses detailed below (Fig. 2b).
Genetic Linkage between PgABCA2 and Resistance to Cry2Ab. We tested for genetic linkage between PgABCA2 and resistance to Cry2Ab using backcross progeny obtained from single-pair crosses between Bt4-R2 (r A1 r A1 ) and F 1 (r A1 s A1 , from Bt4-R2 X APHIS-S) ( Fig. 3 and Supplementary Table S2). From an initial set of 42 backcross families, we tested larval survival in bioassays with 1 microgram Cry2Ab per ml diet for 20 backcross families that each produced at least 10 progeny (mean = 28 neonates tested per family) ( Supplementary  Fig. S4). We used the allele-specific PCR described above to determine the PgABCA2 genotype of larvae.
In the 10 backcross families where the father was from Bt4-R2, the survivors on Cry2Ab-treated diet consisted of 125 r A1 r A1 and 9 r A1 s A1 , which differs significantly from the ratio of 1:1 expected if resistance is not linked with PgABCA2 (Fisher's exact test, P < 10 −14 ) (Supplementary Table S2). Because crossing over in Lepidoptera occurs only in males, these results from backcross families with r A1 r A1 fathers indicate linkage between resistance and the chromosome carrying PgABCA2. In the other 10 backcross families, where the father was an F 1 , the survivors on Cry2Ab-treated diet consisted of 113 r A1 r A1 and 7 r A1 s A1 , which also differs significantly from the expected 1:1 ratio if resistance is not linked with PgABCA2 (Fisher's exact test, P < 10 −14 ) (Supplementary Table S2). Because crossing over occurs in males, the results from these 10 backcross families with r A1 s A1 fathers indicate tight linkage between resistance and PgABCA2. Furthermore, in the backcross progeny that survived exposure to Cry2Ab, the proportion of individuals with genotype r A1 r A1 was not higher for families with r A1 r A1 fathers (0.93) where crossing over was not a factor, than for families with r A1 s A1 fathers (0.94) where crossing over could occur, which implies tight linkage between resistance and PgABCA2. By contrast with the results described above, larvae from backcross families reared on untreated diet as controls consisted of 15 r A1 r A1 and 12 r A1 s A1 , which does not differ significantly from the expected 1:1 ratio (Fisher's exact test, P = 0.79). Bt4-R2b Bt4-R2c Bt4-R2d Bt4-R2e Bt4-R2f Bt4-R2g Bt4-R2h Arizona Bt4-R2i  ICL1 ICL2  ICL3  ICL4 ICL5   3 M T  4 M T  5 M T  6 M T  7 M T  9 M T  0 1 M T 1 1 M T  2 1 M T   TMD1  TMD2   2 M T  8 M T   1220   1275   1147   1112   373   1291  1025   282   303   524   1046   742   829  706   565  For survivors on diet treated with Cry2Ab in the linkage analysis, mean larval weight (mg) was significantly lower for r A1 s A1 (19, SE = 2.6) than r A1 r A1 (27, SE = 0.5) (t-test, t = 3.8, df = 250, P = 0.0002) ( Supplementary Fig. S4). However, larval weight on untreated diet was similar for r A1 s A1 (26, SE = 1.9) and r A1 r A1 (26, SE = 0.5, SE = 2.8) (t-test, t = 0.14, df = 41, P = 0.89). In addition, larval weight was lower on treated diet versus untreated diet for r A1 s A1 (t-test, t = 2.2, df = 36, P = 0.03), but not for r A1 r A1 . Thus, in terms of larval weight, resistance to Cry2Ab was incomplete in the relatively rare r A1 s A1 survivors, compared with complete resistance in the more abundant r A1 r A1 survivors. The low level of resistance in r A1 s A1 could reflect inheritance of resistance linked with PgABCA2 that was not completely recessive, a contribution to resistance from one or more mutations other than r A1 , or both.
Single-molecule Long-read Sequencing of PgABCA2 cDNA. To check the accuracy of the genotypes assigned by PCR and to determine if Bt4-R2 has mutations in PgABCA2 other than the r A1 splice-site mutation, we used single-molecule, real-time sequencing to analyze barcoded PgABCA2 cDNA from 22 larvae: seven from APHIS-S as controls, and 15 backcross survivors from the linkage analysis ( Fig. 3) that had been genotyped with allele-specific PCR (eight r A1 r A1 and seven r A1 s A1 ). We obtained a total of 369,672 reads, which yielded consensus sequences for 18 of the 22 larvae (Supplementary Table S3). For the other four larvae (two APHIS-S and two r A1 r A1 ), the coverage was not deep enough to give reliable consensus sequences. For 16 of the 18 larvae with consensus sequences, the cDNA sequences confirmed the results from PCR in terms of the presence or absence of the r A1 mutation. As expected, the five APHIS-S larvae had only intact cDNA (s A1 s A1 ), all of the transcripts from the six larvae genotyped by PCR as r A1 r A1 had mutations affecting exon 20, and four of the six larvae genotyped by PCR as r A1 s A1 each had at least one transcript with the r A1 mutation and one without it (Table 1 and  Supplementary Table S3). For the other two larvae genotyped by PCR as r A1 s A1 (r A1 s A1 -6 and r A1 s A1 -7), targeted sequencing yielded consensus reads with the intact sequence (s A1 ) in the region of the r A1 mutation, but not the expected r A1 mutation (Supplementary Table S3). However, subsequent cDNA cloning and Sanger sequencing confirmed the presence of the r A1 mutation. Thus, both of these larvae had transcripts with and without the r A1 mutation, confirming the PCR genotyping.
The long-read sequencing also revealed five previously unidentified transcript variants (Bt4-R2e to i), bringing the total of different cDNA variants in Bt4-R2 that disrupt PgABCA2 to nine, each having either one or two of the eight different cDNA mutations affecting exon 6 or one or more exons from 19 to 24 ( Fig. 1 and Supplementary  Fig. S2; Table 1 and Supplementary Table S3). Four of the 12 larval survivors from the backcross analyzed by targeting sequence shared a cDNA mutation (c.1090_1234del) that completely skips exon 6 (1,090-1,234 bp), yielding a frameshift and a premature stop codon at amino acid 373 ( Fig. 1 and Supplementary Fig. S2; Table 1 and  Supplementary Table S3). For one of these four larvae (r A1 s A1 -7), the transcript without the r A1 mutation lacked exon 6 and thus was not an intact, wild-type transcript. Therefore, when considering the entire PgABCA2 cDNA sequence (rather than just the region harboring the r A1 mutation), this individual had only disrupted transcripts, which may explain its ability to survive when exposed to Cry2Ab.
Including the results from the initial sequencing of 10 pooled resistant larvae and next generation sequencing of 15 individual survivors from the linkage analysis (Table 1 and Supplementary Table S3), mis-splicing is implicated in each of the eight different cDNA mutations in Bt4-R2. Comparison of the Bt4-R2 genomic DNA sequence and the transcript variants at exon 20 revealed that the indel mutation at the splice junction disrupted the 5′ GT intron signature sequence and introduced several cryptic splice sites in the pre-mRNA (Table 1 and Supplementary Fig. S6). The indel mutation thus caused mis-splicing of the Bt4-R2 pre-mRNA and produced nine transcript variants with disruptions in exons 19-24 (Table 1 and Supplementary Fig. S6).

Mutations in PgABCA2 Associated with Field-Selected Resistance to Bt Cotton in India.
To determine if mutations in PgABCA2 are associated with field-selected resistance to Cry2Ab, we compared cDNA from field-collected pink bollworm larvae from India that were either susceptible or resistant to Cry2Ab. We collected the three susceptible larvae from a non-Bt cotton field in Akola, Maharashtra (AMH-1, AMH-2, and AMH-3) in 2010 30 , five years before resistance to Cry2Ab was detected in India (Fig. 4). During December 2015 and January 2016, after pink bollworm resistance to Cry2Ab was widespread in India 20,25 , we collected 11 larvae as fourth instars from fields of dual-toxin Bt cotton at seven sites in India (Fig. 4). We identified these larvae as resistant because immunoassays confirmed that the bolls from which they were collected produced both Cry2Ab and Cry1Ac (Supplementary Table S4). We obtained sufficient material for full-length cDNA sequencing for extracellular loops ECL1-ECL6 (green). The domain structure connected to the exons that encode the respective domains is shown by dotted gray lines. Each predicted domain is numbered, with ECLs on top and ICLs numbered on bottom of protein schematic. Putative exons 1-31 are numbered, with grey exons indicating regions determined by direct PCR sequencing. Exons colored in light blue were further verified by sequencing cDNA clones (either by Sanger or PacBio ® sequencing). Red bars indicate disruption sites within the full-length coding sequence and the The consensus cDNA sequences of PgABCA2 were identical for the three susceptible larvae from India and the susceptible APHIS-S strain from Arizona ( Supplementary Fig. S7). Conversely, the eight resistant larvae from five sites in India yielded 19 distinct PgABCA2 transcript variants, each severely disrupted by one to three mutations ( Fig. 1 and Table 2). Collectively, the eight resistant larvae from India harbored 17 different cDNA mutations, and a total of 40 mutations including several that occurred in more than one larva ( Table 2). The disruptive effects of these 40 PgABCA2 cDNA mutations are expected throughout the encoded protein ( Fig. 1).
The most common cDNA mutation in the resistant larvae from India was loss of exon 6, exactly the same mutation as in the four larvae from Bt4-R2 described above (Table 1 and Fig. 1). This mutation occurred in 75% (6 of 8) of the resistant larvae from India representing all four states studied here (Table 2). In 18 clones from four resistant larvae from India with this cDNA mutation, we found no changes in the corresponding gDNA at or near the exon/intron boundaries of exon 6 (Supplementary Figs S8-S11 and Table 3), which implicates alternative splicing. Thus, in a lab-selected strain from Arizona and field-selected populations from India, pink bollworm resistance to Cry2Ab is associated with mis-splicing that omits exon 6 of PgABCA2.
By contrast, we did not detect the r A1 splice-site mutation from Arizona in any of the 11 resistant larvae from India. We did not find any mutations in exon 20 in full-length PgABCA2 cDNA sequences from the eight resistant larvae from India noted above. In addition, the r A1 mutation was not detected with allele-specific PCR in four of the resistant larvae mentioned above (AM-8, CK-1, KT-1, and RK-1) or in three additional resistant larvae from India that were not fully sequenced (GAP-2, JM-9, and YK-1).
Including 4 of the 19 distinct PgABCA2 cDNA sequences that occurred in larvae from two to three sites each, we found a total of 24 mutant transcripts ( Table 2). The four transcript variants detected at more than one site are: CK-1a, KT-1a, and RK-1b with stop codons at amino acids 282 and 373; CK-1d and KT-1c with stop codons at amino acids 303 and 373; GAP-3a and RK-11c with a stop codon at amino acid 524; and CK-1c and KT-1c with in-frame deletions causing the loss of amino acids 280-315 ( Fig. 1 and Table 2).
Sequencing of gDNA fragments from five resistant larvae from India revealed that five out of the six different cDNA mutations examined involved mis-splicing of pre-mRNA (Table 3). Four entail introduction of 5′ and/or 3′ alternative splice sites and the fifth is skipping of exon 6 described above (Table 3, Supplementary Figs S8-11). In each of these cDNA mutations, except for skipping of exon 6, the corresponding gDNA had splice-site mutations that either disrupted the native splice site or introduced alternative splice sites (Table 3). For example, in one larva (GAP-3), the native 5′ GT dinucleotide splice site of intron 8 was changed to AT, causing the splicing machinery   to use a cryptic GT splice site within exon 8 ( Supplementary Fig. S9 and Table 3). In two larvae (CK-1 and RK-1), a large DNA insertion within exon 4 introduced several alternative splice sites (Table 3, Supplementary  Figs S8 and S11). Only one of the six different cDNA mutations examined did not involve mis-splicing of pre-mRNA (Table 3). This mutation has the same 5-bp deletion in exon 17 in both gDNA and cDNA (Table 3 and Supplementary Fig. S12).

Discussion
The results reported here enable the first direct comparison of the genetic basis of laboratory-and field-selected resistance to Cry2Ab, which is deployed widely in Bt cotton and Bt corn. We discovered that mutations disrupting the ABC transporter gene PgABCA2 are associated with resistance to Cry2Ab in both laboratory-and field-selected pink bollworm, a global pest of cotton. Genetic linkage analysis revealed that >10,000-fold resistance to Cry2Ab in a laboratory-selected strain from Arizona (Bt4-R2) is tightly linked with a disruptive indel mutation (r A1 ) in PgABCA2. In field-selected Cry2Ab-resistant pink bollworm from India, we did not find this mutation, but all of the 24 transcript variants from eight larvae collected from five field sites showed severe disruption of PgABCA2, including 19 distinct variants with one to three mutations each. Moreover, the most common cDNA mutation in field-selected populations from India, which entails mis-splicing that omits exon 6 and introduces a stop codon at amino acid 373, also occurred in Bt4-R2. This was the only mutation shared between Arizona and India. The other mutations were mostly from splice-site mutations that lead to mis-splicing of PgABCA2 and were more diverse in India. The differences in PgABCA2 resistance mutations between India and Arizona could reflect the difference in geographic origin, laboratory versus field selection, or both. Mis-splicing of PgABCA2 pre-mRNA was prevalent in Cry2Ab-resistant larvae from both field-and laboratory-selected pink bollworm. Each of the eight different mutations in resistant larvae from Arizona involves mis-splicing of PgABCA2 (Table 1). For India, we found 17 different cDNA mutations in eight resistant larvae ( Table 2). Evaluation of the corresponding gDNA sequences for 6 of these 17 cDNA mutations revealed that all but one are caused by mis-splicing (Table 3). Previous work showed that mis-splicing of cadherin pre-mRNA is associated with pink bollworm resistance to Bt toxin Cry1Ac in laboratory-and field-selected pink bollworm 30,31 . Also, in laboratory-selected H. armigera, mis-splicing of cadherin and ABCC2 is associated with resistance to Cry1Ac 32-34 . Together with the previous data, our new results suggest that mis-splicing may be a common underlying cause of both field-and laboratory-selected resistance to Bt toxins.
Similar to the results here revealing resistance to Cry2Ab is associated with mutations in PgABCA2 in both laboratory-and field-selected pink bollworm, previous work shows laboratory-selected resistance to Cry2Ab is associated with the homologous genes in H. armigera and H. punctigera from Australia 28 . In Australia, where field populations remain susceptible to Cry2Ab 35 , the three resistance alleles detected in H. armigera result in premature truncation of ABCA2, while the sole reported H. punctigera resistance allele has a 14-bp deletion that causes missense mutations 28 . Like the prevalent role of mis-splicing in pink bollworm resistance to Cry2Ab, our analysis of the previously reported sequences 28 indicates mis-splicing is also implicated in two of the three mutations in H. armigera. Ha2Ab-R01 has an 8-bp insertion at the 5′-end of exon 16 and complete skipping of this exon while Ha2Ab-R02 has a 5-bp deletion at the 5′-end of exon 18 and involves an alternative 5′ splice site. Using CRISPR/ Cas9 to edit HaABCA2 in H. armigera, each of the two introduced frameshift mutations caused >100-fold resistance to Cry2Ab 36 . This gene editing also eliminated binding of Cry2Ab to brush border membrane vesicles of H. armigera, demonstrating that ABCA2 is required for such binding 36 .
In addition to the association between resistance to Cry2Ab and mutations in ABCA2 in three species of Lepidoptera noted above, resistance to Bt toxins in two other families is linked with mutations in two other ABC transporter proteins. Resistance to Cry1 toxins is associated with mutations disrupting ABCC2 in eight lepidopteran pests [37][38][39][40][41] and resistance to Cry3Aa is genetically linked with a 4-bp deletion in ABCB1 in the coleopteran Chrysomela tremula 42 . The association between resistance to Cry toxins and mutations affecting ABC transporters in at least 11 species of insects indicates a key role for these proteins in the Cry toxin mode of action, which may include directly binding toxin or promoting toxin oligomerization and pore formation 37,41,[43][44][45][46][47] .
Results from previous work related to this study show that in both laboratory-selected strains from Arizona and field-selected pink bollworm populations from India, resistance to Cry1Ac is associated with mutations  disrupting a gene encoding a cadherin protein (PgCad1) that binds this toxin in the midgut of susceptible larvae 30,[48][49][50] . Similar to the results with Cry2Ab reported here, the mutations affecting PgCad1 were more diverse in the field-selected populations from India than in several lab-selected strains from Arizona. Whereas only four mutant cadherin alleles were found in pink bollworm from five laboratory-selected strains from Arizona, eight cadherin resistance alleles and 19 transcript isoforms were identified from just eight individuals collected from two field-selected populations in India 30 . Thus, both analyses support the conclusion that laboratory selection may be useful for identifying the genes conferring resistance to Bt toxins, but the resistance alleles are likely to be more diverse in field populations. Unlike the results here with Cry2Ab, none of the Cry1Ac resistance mutations in pink bollworm were shared between Arizona and India. The diverse mutations in PgABCA2 and PgCad1 associated with resistance to Cry2Ab and Cry1Ac, respectively, in field-selected populations of pink bollworm imply that it would not be efficient to screen for specific resistance alleles, as has been done previously 51,52 . Moreover, monitoring by screening DNA would miss the critical mis-splicing variants associated with resistance to Bt toxins in this study and in previous work.
Conversely, monitoring methods such as the F 1 screen, which can readily identify field-collected individuals with diverse and previously unknown resistance mutations, could be especially useful. In the F 1 screen, each field-collected adult is allowed to mate in a single pair with an adult from a strain that is homozygous for a recessive resistance mutation 16,53 . This approach can detect any recessive resistance alleles in the field-collected adults that occur at the same locus as the recessive mutations in the laboratory-selected strain, as well as non-recessive mutations at any locus 15,16 . In addition to the F 1 screen, the use of next generation sequencing is promising for monitoring variants associated with resistance in the field. This approach allowed us to multiplex cDNA samples from 22 individuals and obtain sequencing information from essentially single molecules of full-length PgABCA2 cDNA without post-sequencing assembly. Furthermore, long read sequencing identified five PgABCA2 transcript variants (Bt4-R2e-i) not previously found by cloning and Sanger sequencing. Even though we identified several PgABCA2 mutations in gDNA from resistant larvae from India using traditional PCR, cloning, and Sanger sequencing, this method is laborious and not practical for monitoring the diverse mutations in the field. Given that PgABCA2-mediated resistance to Cry2Ab occurred in pink bollworm populations from Arizona and India, long read sequencing focusing on this gene could provide a valuable alternative to the F 1 screen for monitoring resistance to Cry2Ab in this cosmopolitan pest.
Whereas refuges of non-Bt host plants have helped to delay pest resistance to Bt crops generally, and particularly for the pink bollworm in the United States and China 12,54 , the scarcity of such refuges probably contributed to the rapid evolution of pink bollworm resistance to both Cry1Ac and Cry2Ab in India 21,55,56 . Currently, in some regions of India, no Bt toxins in commercialized transgenic cotton are effective against pink bollworm 20,21 . However, the genetically modified toxins Cry1AbMod and Cry1AcMod are effective against laboratory-selected strains of pink bollworm from Arizona resistant to Cry1Ac and Cry2Ab 57,58 . Because the loci harboring mutations conferring resistance to these toxins are the same in laboratory-and field-selected pink bollworm, we hypothesize that these modified toxins would also kill field-selected resistant larvae from India. Nonetheless, Bt cotton producing these modified toxins is not available and no transgenic cotton effective against resistant pink bollworm in India is likely to be available in the next several years. This difficult situation underscores the value of proactively implementing resistance management to sustain the efficacy of Bt crops.

Materials and Methods
Insect Strains and Rearing. We used three strains of pink bollworm from Arizona: APHIS-S, AZP-R and Bt4-R2. APHIS-S is a susceptible strain that has been reared in the laboratory for more than 30 years without exposure to Bt toxins or other insecticides 59,60 . AZP-R, derived from 10 populations collected from Arizona cotton fields in 1997, has 1,500-3,100-fold resistance to Cry1Ac conferred primarily by the r2 cadherin allele, but only two-fold resistance to Cry2Ab 61,62 . Relative to APHIS-S, Bt4-R2 had 28-fold resistance to Cry1Ac conferred by the mutant cadherin allele r4, and >10,000-fold resistance to Cry2Ab 27,63 . Bt4-R2 was derived from the Bt4R strain and selected in the laboratory for resistance to Cry2Ab 27 . In Bt4-R2, inheritance of resistance to Cry1Ac (10 micrograms Cry1Ac per ml diet) and Cry2Ab (0.1, 0.3, 1 and 10 microgram Cry2Ab per ml diet) was recessive based on results of 21-day diet bioassays 27,50 . All larvae were reared on wheat germ diet 64 at 26 °C with 14 h light:10 h dark.
Genetic Linkage Analysis and Diet Bioassays. We tested the genetic linkage between the PgABCA2 r A1 allele and resistance to Cry2Ab by exploiting the biphasic nature of the genetic linkage in Lepidoptera 65 . We first set up 40 F 0 single-pair crosses between APHIS-S (s A1 s A1 ) and Bt4-R2 (r A1 r A1 ) for both ♀ Bt4-R2 x ♂ APHIS-S and ♀ APHIS-S x ♂ Bt4-R2 reciprocal crosses. From each cross, F 1 eggs were collected and neonates were reared individually on untreated artificial diet until pupation. To generate backcross families, surviving F 1 pupae (n = 22 from ♀ Bt4-R2 x ♂ APHIS-S and n = 20 from ♀ APHIS-S x ♂ Bt4-R2) were sexed and paired with a Bt4-R2 pupa of the opposite sex. A total of 5 informative F 1 backcross families were chosen for each reciprocal cross (A, B, C, D and E from ♀ Bt4-R2 x ♂ APHIS-S and F, G, H, I and J from ♀ APHIS-S x ♂ Bt4-R2). We used diet incorporation bioassays to evaluate the susceptibility of neonates from backcross families on either untreated diet or on 1 microgram Cry2Ab per mL diet 27,62 Table S1) to amplify two internal PgABCA2 cDNA fragments from APHIS-S. PCR was performed with 2.5 U Takara ExTaq Premix (Takara Bio USA Inc., Mountain View, CA), 2 μM of each sense and antisense primer, and 0.3 µg cDNA using a Biometra TProfessional gradient Thermocycler (Biometra, Germany) at: 95 °C for 3 min (1 cycle); 40 cycles of 95 °C for 45 s, 50 °C for 1 min and 72 °C for 2 min; then 72 °C for 5 min. Nested PCR amplification was carried using one microliter of primary PCR product using the primer combinations 2pgABCA2-5 + 6pgABCA2-3 and 15pgABCA2-5 + 23pgABCA2-3, respectively (Supplementary Table S1).

Rapid Amplification of cDNA Ends (RACE).
The partial cDNA sequences obtained from degenerate PCR allowed for design of PgABCA2-specific sense and antisense primers (Supplementary Table S1) and were used for 5′-and 3′-RACE according to Invitrogen's GeneRacer ™ kit protocol. For 5′-RACE, cDNA was reverse transcribed using supplied random hexamer primer from 1 µg of total RNA from APHIS-S and used as templates for PCR. Semi-nested PCR amplification was used, including a first round with the GeneRacer ™ 5′ Primer and 32pgABCA2-3 and the second using GeneRacer ™ 5′ Nested Primer and 32pgABCA2-3. For 3′-RACE, APHIS-S total RNA was reverse transcribed using GeneRacer ™ Oligo-dT Primer and nested PCR was run using 37pgABCA2-5 and the GeneRacer ™ 3′ Primer followed by fully-nested amplification using 38pgABCA2-5 and the GeneRacer ™ 3′ Nested Primer. PCR products were cloned into pCR ® 2.1-TOPO ® and sequenced as indicated above.
Sanger Sequencing of the Full-Length PgABCA2 Coding Region. Oligonucleotide primers, 55pgABCA2-5 and 60pgABCA2-3 (Supplementary Table S1), corresponding to the 5′-and 3′-ends of PgABCA2 were used to amplify the full-length coding sequence from APHIS-S cDNA described earlier. PCR  PCR amplicons and to minimize "leaky" expression of genes. Unfortunately, no PgABCA2-positive E. coli clones were obtained, suggesting that the insert may be cytotoxic to bacteria.
Because of difficulties with cloning the full-length PgABCA2 coding region, we verified the 55pgABCA2-5 + 60pgABCA2-3 PCR products by direct sequencing. PCR products were treated with ExoSAP-IT ™ PCR Product Cleanup Reagent (Affymetrix, Inc. Santa Clara, CA) according to manufacturer's protocol and sequenced directly with oligonucleotide primers, 63pgABCA2-3 through 78pgABCA2-5 (Supplementary Table S1). Similarly, we amplified the full-length coding sequence from cDNA prepared from Bt4-R2 and PCR products were directly sequenced and compared with the APHIS-S PgABCA2 sequence. The full-length coding sequence of PgABCA2 from APHIS-S, AZP-R, and Bt4-R2 are deposited in the GenBank public database (MG637361).
To further validate differences within the PgABCA2 cDNA sequences from APHIS-S and Bt4-R2, three overlapping, partial fragments corresponding to nucleotides 1-1,744, 1,656-3,403, and 3,326-5,187 were PCR amplified and cloned into pCR ® 2.1-TOPO ® . Several clones corresponding to each fragment were Sanger sequenced.
The PgABCA2 cDNA sequences that were unique after sequencing these clones were identified as "variants". We used Mutalyzer 2.0.26 (https://mutalyzer.nl/description-extractor) 68 and Description Extractor 69 to detect all sequence changes (≥2 bp) found within the Bt4-R2 cDNA variants and all mutations were annotated based on nomenclature and recommendations provided by Human Genome Variation Society (http://www.HGVS.org/ varnomen) 70 . Changes resulting from single nucleotide polymorphisms were excluded from our analysis.
Extraction of gDNA, PCR and Cloning. gDNA was extracted from pools of ten APHIS-S and Bt4-R2 using the PUREGENE DNA Isolation Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. We extracted gDNA from the remaining tissues (e.g. larvae minus gut tracts) from the same 10 individuals that were used for RNA extractions. gDNA was similarly extracted from India and Arizona individuals for PCR genotyping and Sanger sequencing.
Allele-Specific PCR. Based on the location of the r A1 mutation in the gDNA, we used allele-specific PCR and primers 83pgABCA2-5 and 84pgABCA2-3 (hereafter referred to as r A1 -F and r A1 -R) (Supplementary Table S1) that flank the r A1 mutation to genotype backcross survivors obtained from biphasic linkage crosses. Reactions contained 0.1 μg gDNA, 2X SaphireAmp ® polymerase premix (Takara Bio USA Inc., Mountain View, CA), and 0.2 μM of both sense and antisense primers. PCR was run using the following conditions: 94 °C for 1 min (1 cycle); 25 cycles of 98 °C for 5 s, 60 °C for 5 s and 72 °C for 5 s. PCR products and 1 kb Plus DNA Ladder (ThermoFisher Scientific) were separated using 3% agarose gel electrophoresis to differentiate size of mutant (r A1 ) and wild-type (s A1 ) DNA bands. To validate allele-specific PCR, amplified products were cloned and sequenced from Bt4-R2 (n = 4) and APHIS-S (n = 4).
Targeted PgABCA2 Sequencing and Bioinformatics Analysis. We used Single Molecule, Real-Time (SMRT ® ) sequencing on a PacBio ® RSII (Pacific Biosciences, Menlo Park, CA) to sequence PgABCA2 cDNA from 22 pink bollworm larvae. Fifteen larvae were survivors obtained from backcross families on 1 microgram Cry2Ab per mL diet, including 7 genotyped by allele-specific PCR as r A1 r A1 and 8 genotyped as r A1 s A1 . APHIS-S larvae were taken directly from our rearing colony on November 17, 2016.
Total RNA was extracted and cDNA was prepared from individual 4 th instar larvae (excluding head) as previously described, except we used a gene-specific primer (150pgABCA2-3; Supplementary Table S1) to enrich the cDNA for PgABCA2. Because of limited available tissue and low abundance of the PgABCA2 transcript, we used nested PCR to generate amplicon templates for library preparation. Initial PCR amplification was performed with primers 158pgABCA2-5 and 150pgABCA2-3 (Supplementary Table S1) using SuperTaq TM DNA polymerase (Applied Biosystems). Nested amplification was carried out with barcode-tailed PCR primers, 163pgABCA2-5 and 166pgABCA2-3 (Supplementary Table S1). The symmetric barcode-tailed PCR primers were designed based on the PacBio ® multiplex PCR primer guidelines (http://www.2einteractive.com/pacbio/ Shared-Protocol-PacBio-Barcodes-for-SMRT-Sequencing.pdf).
Prior to SMRTbell TM library preparation, ~5 kb PCR products were gel purified with QIAquick ® Gel extraction kit (Qiagen, Germantown, MD) and quantified using Qubit TM dsDNA High Sensitivity Assay Kit with the Qubit TM 2.0 Fluorometer (ThermoFisher Scientific). Barcoded samples (n = 22) were pooled in equimolar concentrations and SMRTbell TM libraries were prepared with 0.5 µg of the pooled amplicons following the standard procedures for blunt ligation of hairpin adapters using SMRTbell TM Template Prep Kit 1.0 (Pacific Biosciences).
DNA sequencing was performed on the PacBio ® RSII sequencer using P6-P4 enzyme chemistry at the University of Arizona, Arizona Genomics Institute (Tucson, Arizona). Data were captured using 3-hour movies. Sequence data are deposited in the NCBI TSA under the accession SRP126193, associated with BioProject PRJNA421207.
We initially processed the raw sequences through the PacBio SMRT ® portal (v2.3.0), in which sequences were filtered for a minimum of two passes and a minimum predicted accuracy of 90%. We used Long Amplicon Analysis (LAA v2) protocol to identify and report abundance of differing clusters of sequencing reads within a single library. Custom LAA settings included: minimum subread length = 4,000; maximum number of SCIENtIFIC RepoRTS | (2018) 8:13531 | DOI:10.1038/s41598-018-31840-5 subreads = 1000; barcode score = 30; ignore primer sequence = 30; trim ends = 0; only most supported = 0; cluster per gene family = y; phase alleles = y; split results = y. We also processed the raw sequences by LAA analysis using slightly modified settings to include shorter subreads (minimum subread length = 3000). The latter analysis allowed us to sample more reads and to specifically identify reads containing the exon 6 deletion. Resulting consensus sequences were manually inspected (for length and subread coverage to exclude spurious artifact sequences) and mapped to the PgABCA2 cDNA plus strand using Geneious R10 (Biomatters Inc., Newark, NJ).
Pink Bollworm Field Collections. We analyzed putatively resistant pink bollworm larvae collected from December 11, 2015 to January 3, 2016 at seven sites in four states of India (Fig. 4). Fourth instars were collected by opening mature cotton bolls collected arbitrarily from cotton fields reported to be planted with dual-toxin Bt cotton producing Cry1Ac and Cry2Ab. Fourth instar larvae were saved in RNAlater ® (Ambion-Life Technologies, Carlsbad, CA). We used EnviroLogix QuantiPlate TM ELISA kits (Portland, ME) for Cry1Ab/Cry1Ac and Cry2A to estimate the concentration of Cry1Ac and Cry2Ab in maternal tissue from cotton bolls for which survivors were recovered. ELISAs were conducted according to manufacturer's protocols on boll material stored frozen at −20 °C for 2-4 months prior to analysis. Toxins provided with the kit were used as positive controls, single samples were run, and concentrations were expressed as micrograms Cry toxin per gram wet tissue.
DNA Screening of Populations from India for PgABCA2 r A1 Allele. We extracted gDNA from the head portion of seven pink bollworm survivors on Bollgard II ® that remained following RNA extraction and performed r A1 -specific PCR as described above. PCR products were separated on 3% agarose gels and visually inspected for PgABCA2 product size different from control samples (APHIS-S and Bt4-R2).
Sequencing of PgABCA2 DNA from Field-Collected Resistant and Susceptible Pink Bollworm from India. Genomic DNA, total RNA and cDNA were prepared from pink bollworm recovered from