CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus in Tomato

G C A T T A C G G C A T genes

Article CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus in Tomato

Ilan Ben Shlush †, Aviva Samach †, Cathy Melamed-Bessudo, Daniela Ben-Tov, Tal Dahan-Meir , Shdema Filler-Hayut and Avraham A. Levy *

Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel; [email protected] (I.B.S.); [email protected] (A.S.); [email protected] (C.M.-B.); [email protected] (D.B.-T.); [email protected] (T.D.-M.); shdema.ﬁ[email protected] (S.F.-H.) * Correspondence: [email protected]; Tel.: +972-8-934-2734; Fax: +972-8-934-4181 † These authors contributed equally to this work.

Abstract: Homologous recombination (HR) in somatic cells is not as well understood as meiotic recombination and is thought to be rare. In a previous study, we showed that Inter-Homologous Somatic Recombination (IHSR) can be achieved by targeted induction of DNA double-strand breaks (DSBs). Here, we designed a novel IHSR assay to investigate this phenomenon in greater depth. We

utilized F1 hybrids from divergent parental lines, each with a different mutation at the Carotenoid isomerase (CRTISO) locus. IHSR events, namely crossover or gene conversion (GC), between the two CRTISO mutant alleles (tangerine color) can restore gene activity and be visualized as gain-of- function, wildtype (red) phenotypes. Our results show that out of four intron DSB targets tested, three showed DSB formation, as seen from non-homologous end-joining (NHEJ) footprints, but only

one target generated putative IHSR events as seen by red sectors on tangerine fruits. F2 seeds were grown to test for germinal transmission of HR events. Two out of ﬁve F1 plants showing red sectors had their IHSR events germinally transmitted to F2, mainly as gene conversion. Six independent recombinant alleles were characterized: three had truncated conversion tracts with an average length Citation: Ben Shlush, I.; Samach, A.; of ~1 kb. Two alleles were formed by a crossover as determined by genotyping and characterized Melamed-Bessudo, C.; Ben-Tov, D.; by whole genome sequencing. We discuss how IHSR can be used for future research and for the Dahan-Meir, T.; Filler-Hayut, S.; Levy, development of novel gene editing and precise breeding tools. A.A. CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus Keywords: DNA double-strand break repair; homologous recombination; CRISPR/Cas9; inter Genes 12 in Tomato. 2021, , 59. homologous somatic recombination; targeted gene conversion; targeted crossover; tomato https://doi.org/10.3390/genes12010059

Received: 3 December 2020 Accepted: 29 December 2020 1. Introduction Published: 31 December 2020 Homologous recombination (HR) is the most common way to generate genetic varia- Publisher’s Note: MDPI stays neu- tion in sexually reproductive organisms. It is achieved through the exchange of parental tral with regard to jurisdictional clai- chromosomal segments between two homologous chromosomes followed by segregation ms in published maps and institutio- of the new recombinant alleles into separate germinal cells [1]. This process is initiated nal afﬁliations. by Spo11-mediated DNA double-strand breaks (DSBs) happening during meiosis at various locations along the chromosomes [1–5]. The outcomes of HR are crossovers (COs) in case of a reciprocal exchange of homologous segments, or non-crossovers (NCOs) in case of non-reciprocal transfer of a small DNA segment from one parent to the other, Copyright: © 2020 by the authors. Li- which is also known as gene conversion (GC) [6]. The ability to obtain plants with a censee MDPI, Basel, Switzerland. combination of desired traits during a breeding program is limited by several features This article is an open access article distributed under the terms and con- of meiotic recombination such as genetic interference, the difﬁculty to segregate linked ditions of the Creative Commons At- favorable and unfavorable traits, non-random Spo-11-induced DSBs along the chromo- tribution (CC BY) license (https:// some [3] and crossover suppression in heterochromatic regions [6]. Moreover, generating creativecommons.org/licenses/by/ genetic variation of new desirable traits in vegetatively propagated crops cannot rely on 4.0/). meiotic recombination.

Genes 2021, 12, 59. https://doi.org/10.3390/genes12010059 https://www.mdpi.com/journal/genes Genes 2021, 12, 59 2 of 12

In plants, germ line cells giving rise to pollen or egg cells are formed late in development, when somatic meristematic cells differentiate into floral meristems [7]. Hence, inducing HR in somatic cells in a precise manner could lead to targeted recombination that can be transmitted to the germinal cells, paving the way to overcome meiotic recombination limitations. This could also generate genetic diversity in vegetatively propagated crops. HR in somatic cells is not as well understood as meiotic recombination and it is thought to be extremely rare, but a few studies showed that it is possible to induce HR by gamma irradiation in Vicia faba [8] and by transposon in tobacco (Nicotiana tabacum) as shown in the Hyrec mutant [9]. In addition, in recent work we showed that Inter-Homologous Somatic Recombination (IHSR) repair is possible in tomato plants (Solanum lycopersicum) and can be achieved by targeted induction of DNA double-strand breaks (DSBs) using the CRISPR-Cas9 system [10]. Only a few events were analyzed, showing the occurrence of targeted gene conversion, and one putative CO event was identified. Conversion tracts were interrupted, possibly as a result of mismatch repair. These findings raised a number of questions that require further investigation to better understand the somatic HR repair mechanisms. In this study, we designed a new assay for tomatoes to induce DSBs in somatic cells using the CRISPR-Cas9 system, targeting introns in the Carotenoid isomerase (CRTISO) locus, originally referred to as tangerine [11], in a way that enables us to promote, screen, and characterize HR repair events based on a gain-of-function color assay in a hybrid between two parents with a sequenced genome. We describe the assay design, and the analysis of DSB repair products, mainly non-homologous end-joining (NHEJ) or repair via HR between homologues resulting in GC or CO.

2. Materials and Methods 2.1. Plant Material Micro-Tom (Solanum lycopersicum) tangerine tomato mutant plants #18-3 described by [12], and M82 tangerine e3406 [13], were grown in one-liter pots and five-liter pots respectively in a greenhouse for crossing. The controlled climate conditions were of 26 ± 1 ◦C and under 12 h light period. The intron targeting cassettes were transformed into F1 hybrids. The Cas9-only cassette was transformed into the M82 parental genotype, or into F1 hybrids. Following transformation, regeneration, and selections, the plantlets were transferred from rooting media in a tissue culture growing room to five-liter pots. F2 and F3 progeny plants were sown in five-liter pots.

2.2. Plasmids Construction Single guide RNAs (sgRNAs) targeting four different introns within the CRTISO gene between the two tangerine mutations were designed and checked for off-targets using Ensembl Plants [14] and cloned into a construct containing Streptococcus pyogenes Cas9 (SpCas9) gene. Cloning was performed by utilizing the Golden Braid (GB) system [15]. The constructs were composed of SpCas9 that was expressed under constitutive Ubiquitin4-2 promoter from Petroselinum crispum (PcUbi4-2) and Pea3A terminator [16]. The sgRNA was expressed under the control of Arabidopsis thaliana U6-26 RNA Pol III promoter and the Kanamycin resistance gene (Kana) was expressed under the Nopaline Synthase (Nos) promoter and Nos terminator (referred to as Nos:NptII:Nos).

2.3. Plant Transformation and Genotyping Plasmids were transformed into Agrobacterium tumefaciens of the strain GV3101 by electroporation. The colonies were grown on LB plates with 200 µg/mL spectinomycin and 50 µg/mL gentamycin antibiotics. F1 cotyledons were transformed with the plasmid- carrying Agrobacterium. Swollen green cotyledons were transferred through several selection phases. Transformation and selection protocols were previously described [12]. Regenerated plantlets (containing T-DNA with Kanamycin resistance gene) were transferred to rooting media with Kanamycin and IBA (rooting hormone). Two to three small Genes 2021, 12, 59 3 of 12

tomato leaflets were collected from different branches into 1.5 mL tubes and were put inside liquid nitrogen. The frozen leaflets were crushed by electric drill with designated frozen plastic sticks and DNA extraction was performed as previously described [12]. Verification of transgenic F1 plants was done by PCR amplification of SpCas9 sequence from genomic DNA. Amplification was done by 35 cycles PCR using RedTaq® ReadyMix™ (Sigma-Aldrich, St Louis, MO, USA). Primers used for the amplification are specified in Supplementary Table S1. F2 and F3 plants were tested as well in a similar fashion. Genomic DNA samples were used for PCR amplification of the CRTISO gene and its flanking regions. PCR fragments were amplified by 35 cycles using KAPA HiFi HotStart ReadyMix (KAPA Biosystems-50 µL reactions according to the manufacturer’s protocol), and sequenced by Sanger sequencing. The list of primers is given in Supplementary Table S2.

2.4. NHEJ Analysis Using Illumina HTS

Genomic DNA from F1 and M82 transgenic plants for all four SpCas9 + gRNA constructs were amplified by 18 cycles of PCR, using 50 µL reaction of KAPA HiFiTM ReadyMix (KAPA-BIOSYSTEMS) to produce amplicons in order to build libraries for high-throughput Illumina® sequencing. Three sets of primers, targeting amplicons of ~300 bp, were designed to amplify two CRISPR target sites at each amplicon. Targets 7–8 and 8–9 were amplified from both sides of the target due to an overlap of two amplicons (Supplementary Tables S3 and S4). Primers were 20–60 bp from each DSB site and were attached at the 50 end with specific barcodes that had varied length between 4–7 bp with a unique sequence to indicate the plant origin. Deep sequencing was done using Illumina NextSeq 550 system at the Life Sciences Core facilities unit at the Weizmann Institute of Science. The sample sequences were analyzed using NGS Cas-analyzer as described by [17].

2.5. HR Events Analysis in the CRTISO Region The SL4.0 chromosome 10 region between 61,795,407 and 61,787,754 (7653 bp), spanning the tangerine mutations of both Micro-Tom and M82 was sequenced for each IHSR candidate plant. We used Sanger sequencing of PCR products in CRTISO regions of het- erozygous F2 plants or homozygous F3 plants. For F2 plants that did not have seeds, and therefore could not give homozygous F3 plants, PCR products were cloned into pGEM T-easy and single colonies were sent for sequencing. Primers used for the ampliﬁcation are speciﬁed in Supplementary Table S5.

2.6. CO Events Analysis Using Illumina Whole Genome Sequencing (WGS)

DNA was puriﬁed from leaves of F2, and F3 plants using a DNA puriﬁcation kit (MACHEREY-NAGEL®) and then 300 ng sheared by sonication (Bioruptor ®, Diagenode) to 200–500 bp. A total of 10 ng of fragmented DNA per plant was used for libraries preparation as described by [18]. High-throughput sequencing was performed at the Life Sciences Core facilities unit at the Weizmann Institute of Science with the Illumina NovaSeq 6000, 150 bp paired-end reads. The whole genome sequencing of tomato plants was aligned to the Heinz tomato genome, version SL4.0 (Sol Genomic Network), using BWA [19] and Samtools [20]. Poten- tial PCR duplicates were removed using Samtools rmdup and by the Picard tool FilterSam- reads [21]. The reads were viewed and documented using the IGV browser [22]).

3. Results 3.1. Gain-of-Function Phenotypic Assay Design for HR Events Identiﬁcation A recessive mutation in the Carotenoid isomerase (CRTISO) gene from the carotenoid biosynthesis pathway in tomatoes gives rise to a tangerine phenotype [11], which causes pale yellow petals, orange fruits, and a less robust yet still visible phenotype with yellowish young leaves (Figure1). We took advantage of the availability of several CRTISO mutants to design an assay whereby intergenic HR between mutant alleles can restore the WT yellow petals and red fruit phenotype. DSB induction was targeted to introns so that Genes 2021, 12, 59 4 of 12

the recombination product can tolerate NHEJ mutations without affecting WT activity (Figure1). Two CRTISO mutants in the background of divergent parental lines were used: one in Micro-Tom (MT), tangerine 18-3, and one in the cultivar M82 background, tangerine e3406; the distance between the two mutations is ~2 Kb. Both mutations result in a homozygote recessive tangerine phenotype (see red stars in Figure2). MT CRTISO has a “-A” frameshift mutation in exon 4 that was generated by CRISPR-Cas9 creating a premature stop codon [12], and M82 CRTISO has a G to A missense mutation in exon 11, generated by Ethyl Methanesulfonate (EMS) mutagenesis [13]. Crossing these lines resulted in tangerine F1 hybrid plants that had one mutant allele from each parent, whose origin could be differentiated by unique insertions or deletions (indels), and single nucleotide polymorphisms (SNPs) (Figure2B, Supplementary Table S6). Plant and fruit size of the F 1 hybrid are similar to M82, however, fruit shape is rounded and resembles MT. Four different CRISPR-Cas9 gRNA targets were designed to induce DSBs in introns in between the mutations in F1 plants to allow HR to take place in somatic cells following transformation (Figure2B, Supplementary Tables S3 and S6). In case one mutant allele would be repaired via somatic HR using the homologue as a repair template, a WT allele would be formed, leading to chimeric CRTISO plants with whole WT branches of red fruits for early HR events, or red sectors in orange fruits for later somatic events. Target locations were 180 to 279 bp from each other and were chosen based on several criteria: 1. Targeting introns to prevent gene activity disruption by NHEJ footprints, which could be formed after HR. In exons, recurring cuts would affect gene activity and our ability to select IHSR events based on the phenotype. 2. Putative off-targets were checked to avoid collateral genome damage as much as possible. 3. Splicing sites were verified to be distant from the targets to avoid intron splicing interruption (Supplementary Table S3). For the target between exon 6 and 7 (6–7 gRNA), we took advantage of the T to G SNP that results in an NGG protospacer adjacent motif (PAM), hence targeting a DSB only in the MT allele (Figure2). The distance between the tangerine mutations is ~2 kb, making it very unlikely for meiotic recombination to occur in the progeny of F1 plants. SpCas9 presence was verified by PCR, using SpCas9 primers (Supplementary Table S1). SpCas9 positive plants Genes 2021, 12, 59 5 of 12 were continuously monitored for WT phenotypes, focusing mainly on the flowers and fruits. Total transformation success rates were 76.40% and 65.12% for F1 and M82 respectively.

Figure 1. Phenotypic Inter-Homologous Somatic Recombination (IHSR) assay in the Carotenoid isomerase (CRTISO) gene Figure 1. Phenotypic Inter-Homologous Somatic Recombination (IHSR) assay in the Carotenoid isomerase (CRTISO) gene utilizing visible gain-of-function events in F1 plants. (A) CRTISO recessive mutant tangerine phenotypes seen as pale yellow petals,utilizing orange visible fruits, gain-of-function and yellowish events young in F leaves.1 plants. IHSR (A) CRTISO can lead recessive to the correction mutant oftangerine one mutant phenotypes allele to seen the dominantas pale yellow WT petals, orange fruits, and yellowish young leaves. IHSR can lead to the correction of one mutant allele to the dominant allele and hence the plant will show WT phenotypes of yellow petals, red fruit, and green young leaves. (B)F1 hybrid has WT allele and hence the plant will show WT phenotypes of yellow petals, red fruit, and green young leaves. (B) F1 hybrid two recessive CRTISO alleles (schematic not-to-scale representation). Each allele mutation is represented by a red asterisk. has two recessive CRTISO alleles (schematic not-to-scale representation). Each allele mutation is represented by a red Exonsasterisk. are Exons shown are as wideshown boxes. as wide The boxes. Micro-Tom The Micro-Tom background background is blue and theis blue M82 and background the M82 yellow. background The lightning yellow. boltThe correspondslightning bolt to corresponds a DSB site; theto a NHEJDSB site; footprint the NHEJ is in footprint pink; and is thein pink; X structure and the shows X structure the site shows of IHSR the site repair of IHSR induced repair by double-strandinduced by double-strand break (DSB). break IHSR (DSB). can generate IHSR can recombinant generate reco WTmbinant or mutant WT alleles. or mutant NHEJ alleles. footprints NHEJ that footprints would that occur would after IHSRoccur repairafter IHSR are not repair expected are not to changeexpected the to WT change phenotype the WT since phenotype the DSB since sites arethe inDSB introns sites inare non-splicing in introns in sites. non-splicing sites.

Figure 2. CRTISO gene map of targeted DSB IHSR assay. (A) Tomato Chromosome#10 scheme. The centromere is shown in black. The CRTISO gene is located at the sub-telomeric region of chromosome 10, on the reverse strand. Its approximate location is in orange. (B) The scheme of CRTISO gene region with exon 1 close to the telomere and exon 13 to the centromere. Exons are marked by blue arrows. Micro-Tom tangerine allele and its-A mutation at exon 4, and M82 allele G to A mutation at exon 11 are marked by red asterisks. The distance between the mutations is ~2 kb. Indels are marked by purple triangles. Single nucleotide polymorphisms (SNPs) are marked by green triangles. Four gRNAs for DSBs (lightning bolts) in between the two mutations were designed to target introns, and named according to their location; for example, the target in intron between exon 8 and exon 9 was called target 8–9. Three targets can break both alleles. Target 6–7 is allele specific, targeting only the Micro-Tom allele due to a SNP resulting in an NGG forming a protospacer adjacent motif (PAM).

3.2. Three out of Four CRTISO Targets Induce Efficient NHEJ DSB Repair

NHEJ DSB repair was evaluated for the four CRTISO targets in six F1 lines per target. We analyzed Cas9 and gRNA NHEJ footprints using Illumina sequencing of PCR products flanking each gRNA target (Figure 3 and Supplementary Figure S1). F1 lines with Cas9 only were tested as controls (Supplementary Table S7). Indels frequency, a traceable outcome of NHEJ DSB repair, was measured per F1 line. Three out of the four targets showed significant NHEJ repair activity. Target 6–7, as predicted and designed, showed indels only in the MT allele. Four out of six target 6–7 lines were positive, with average indel frequency of 21.7% in positive plants (Supplementary Figure S1A). Target 7–8 had four out of six positive lines, with average indel frequency of 92.5% in positive plants (Supplementary Figure S1B). All six target 8–9 F1 lines were positive, with average indel

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Figure 1. Phenotypic Inter-Homologous Somatic Recombination (IHSR) assay in the Carotenoid isomerase (CRTISO) gene utilizing visible gain-of-function events in F1 plants. (A) CRTISO recessive mutant tangerine phenotypes seen as pale yellow petals, orange fruits, and yellowish young leaves. IHSR can lead to the correction of one mutant allele to the dominant WT allele and hence the plant will show WT phenotypes of yellow petals, red fruit, and green young leaves. (B) F1 hybrid has two recessive CRTISO alleles (schematic not-to-scale representation). Each allele mutation is represented by a red asterisk. Exons are shown as wide boxes. The Micro-Tom background is blue and the M82 background yellow. The lightning bolt corresponds to a DSB site; the NHEJ footprint is in pink; and the X structure shows the site of IHSR repair induced by double-strand break (DSB). IHSR can generate recombinant WT or mutant alleles. NHEJ footprints that would Genes 2021, 12, 59 5 of 12 occur after IHSR repair are not expected to change the WT phenotype since the DSB sites are in introns in non-splicing sites.

Figure 2. CRTISO genegene mapmap ofof targetedtargeted DSBDSB IHSRIHSR assay. assay. ( A(A)) Tomato Tomato Chromosome#10 Chromosome#10 scheme. scheme. The The centromere centromere is shownis shown in black.in black. The TheCRTISO CRTISOgene gene is is located located at at the the sub-telomeric sub-telomeric region region of of chromosome chromosome 10, 10, on on the the reversereverse strand.strand. Its approximate location is in orange. (B) The scheme of CRTISO gene region with exon 1 close to the telomere and exon 13 to the location is in orange. (B) The scheme of CRTISO gene region with exon 1 close to the telomere and exon 13 to the centromere. centromere. Exons are marked by blue arrows. Micro-Tom tangerine allele and its-A mutation at exon 4, and M82 allele G Exons are marked by blue arrows. Micro-Tom tangerine allele and its-A mutation at exon 4, and M82 allele G to A mutation to A mutation at exon 11 are marked by red asterisks. The distance between the mutations is ~2 kb. Indels are marked by atpurple exon triangles. 11 are marked Single by nucleotide red asterisks. polymorphisms The distance (SNPs) between are the marked mutations by green is ~2 triangles. kb. Indels Four are markedgRNAs for by purpleDSBs (lightning triangles. Singlebolts) in nucleotide between polymorphismsthe two mutations (SNPs) were are designed marked to by target green introns, triangles. and Four named gRNAs according for DSBs to (lightningtheir location; bolts) for in example, between the twotarget mutations in intron were between designed exon to 8 targetand exon introns, 9 was and called named target according 8–9. Three to their target location;s can break for example, both alleles. the target Target in intron6–7 is betweenallele specific, exon 8targeting and exon only 9 was the called Micro-Tom target allele 8–9. Three due to targets a SNP can resulting break bothin an alleles. NGG forming Target 6–7 a protospacer is allele speciﬁc, adjacent targeting motif only(PAM). the Micro-Tom allele due to a SNP resulting in an NGG forming a protospacer adjacent motif (PAM).

3.2. Three out of Four CRTISO Targets Induce Efficient NHEJ DSB Repair 3.2. Three out of Four CRTISO Targets Induce Efﬁcient NHEJ DSB Repair NHEJ DSB repair was evaluated for the four CRTISO targets in six F1 lines per target. We analyzedNHEJ DSB Cas9 repair and was gRNA evaluated NHEJ for footpr the fourintsCRTISO using targetsIllumina in sixsequencing F1 lines per of target. PCR We analyzed Cas9 and gRNA NHEJ footprints using Illumina sequencing of PCR products products flanking each gRNA target (Figure 3 and Supplementary Figure S1). F1 lines with Cas9flanking only each were gRNA tested target as controls (Figure (Supplementa3 and Supplementaryry Table Figure S7). Indels S1). F frequency,1 lines with a Cas9traceable only were tested as controls (Supplementary Table S7). Indels frequency, a traceable outcome of outcome of NHEJ DSB repair, was measured per F1 line. Three out of the four targets NHEJ DSB repair, was measured per F line. Three out of the four targets showed significant showed significant NHEJ repair activity.1 Target 6–7, as predicted and designed, showed NHEJ repair activity. Target 6–7, as predicted and designed, showed indels only in the MT indels only in the MT allele. Four out of six target 6–7 lines were positive, with average allele. Four out of six target 6–7 lines were positive, with average indel frequency of 21.7% indel frequency of 21.7% in positive plants (Supplementary Figure S1A). Target 7–8 had in positive plants (Supplementary Figure S1A). Target 7–8 had four out of six positive lines, four out of six positive lines, with average indel frequency of 92.5% in positive plants with average indel frequency of 92.5% in positive plants (Supplementary Figure S1B). All six (Supplementary Figure S1B). All six target 8–9 F1 lines were positive, with average indel target 8–9 F1 lines were positive, with average indel frequency of 56.5% in positive plants (Figure3). Target 9–10 did not show any activity (Supplementary Figure S1D).

3.3. CRTISO Target 8–9 Gives Germinal Transmission of Somatic DSB IHSR Events

Monitoring F1 plants phenotypes did not result in any WT ﬂowers expected for IHSR events. However, at later growth stages as the fruits ripened, we found a few plants with red sectors on orange (tangerine) fruits, a sign of late IHSR events (Figure4). All the plants that had fruits with a red sector were from target 8–9. Five out of eighteen Cas9- independent transgenic plants from this target had fruits with red sectors (Supplementary Table S7). Overall, we obtained ten fruits with red sectors. Two out of the ﬁve transgenic plants had three fruits with red sectors, one plant had two fruits with red sectors, and two plants had just one fruit with red sectors. We noticed that these fruits were located on different branches, which may indicate independent IHSR events. Each fruit seed was separately collected for subsequent monitoring. F1 plants of targets 6–7, 7–8, and 9–10 did not show any WT phenotype sectors (Supplementary Table S7). As expected, all M82 control target plants and Cas9-only cassette plants (of both M82 and F1) displayed the tangerine phenotype with no red sectors. Plant#1 and plant#2 of target 8–9, each containing three fruits with red sectors, were from lines that showed 99.5% and 96.3% indel frequencies respectively (Figure3C). Both plant#1 and plant#2 of target 8–9 had one red sector fruit, with germinally transmitted IHSR (Figure4A,B). Plant#5 of target 8–9, which had one red sector fruit, showed only 14.5% indel frequency (Figure3C). Obtaining detectable somatic recombination events in target 8–9 only raises questions as to the genomic context necessary of targeted IHSR to occur. Genes 2021, 12, 59 6 of 12

Target 8-9 Non-mutated target Positive plants - 6/6 Average indel frequency in positive plants - 56.5% -A 100 -T -AT 90 -ATG -ATT 80 -ATGA -CATT 70 -TGAT -ATGAT 60 -TGATT 50 -ATGATT -TGATTC 40 -CATTCA -ATTCATG 30 -TGATTCC -CATGATTC 20 -TGTTCCCATTCAT -CTTGATGTTCCCATTCATGATTC 10 -CATGATTCCTTG -ATGATTCCTTG 0 +A Plant 1 Plant 2 Plant 3 Plant 4 Plant 5 Plant 6 +AA

Figure 3. NHEJ frequency in F1 plants of CRTISO assay DSB target 8–9. Illumina NextSeq high-throughput sequencing results for F1 plants analyzed using NGS Cas-Analyzer and presented for CRTISO assay DSB target 8–9. Six F1 plants were Genes 2021, 12analyzed., 59 The indels frequency was calculated by the number of indel reads out of the total number of reads (including 7 of 12

non-mutated target footprint) and shown as a percentage. No indels were detected in three control plants with Cas9 only.

Figure 4. CRTISO target 8–9 induces IHSR events. Red sector fruits indicating late IHSR event, were detected in CRTISO Figure 4. CRTISO target 8–9 induces IHSR events. Red sector fruits indicating late IHSR event, were detected in CRTISO DSB target 8–9 only. (A) The red sector of F1 8–9 DSB target plant#1 fruit#1 reached the mesocarp, unlike all other smaller DSB target 8–9 only. (A) The red sector of F1 8–9 DSB target plant#1 fruit#1 reached the mesocarp, unlike all other smaller red sector fruits that remained in the pericarp. Seeds were collected separately from the tangerine and red WT parts of the red sector fruits that remained in the pericarp. Seeds were collected separately from the tangerine and red WT parts of the fruit. Eleven seeds of each tangerine and red WT sector were grown. Four IHSR WT and one IHSR mutant progeny were fruit. Eleven seeds of each tangerine and red WT sector were grown. Four IHSR WT and one IHSR mutant progeny were found from the red WT sector. Two more IHSR WT progeny were found from the tangerine fruit part, leading to a total of found from the red WT sector. Two more IHSR WT progeny were found from the tangerine fruit part, leading to a total seven IHSR progeny out of 22 F2 plants. (B) The red sector of F1 8–9 DSB target plant#2 fruit#1 was present in the pericarp of seven IHSR progeny out of 22 F2 plants. (B) The red sector of F1 8–9 DSB target plant#2 fruit#1 was present in the pericarp only, therefore, seeds were collected as one pool. Twenty-two seeds were grown. Three IHSR WT and one IHSR double only, therefore, seeds were collected as one pool. Twenty-two seeds were grown. Three IHSR WT and one IHSR double mutant progeny were found out of 22 F2 plants. mutant progeny were found out of 22 F2 plants.

3.4.3.4. CRTISO CRTISO Target Target 8–9 8–9 Activity Activity inin SomaticSomatic Tissue Tissu Leadse Leads to Germinalto Germinal Transmission Transmission of GC of and GC and COCO Events Events To test the germinal transmission and to conduct molecular analysis of IHSR events, To test the germinal transmission and to conduct molecular analysis of IHSR events, each red sector fruit from target 8–9 was collected and its seeds were extracted separately. each red sector fruit from target 8–9 was collected and its seeds were extracted separately. Three orange tangerine fruits and their seeds were collected from each F1 plant and from Threeﬁve orange plants of tangerine the other fruits targets and and their controls. seeds Seeds were were collected sown from to compare each F the1 plant progeny and from fivephenotype plants of of the the other orange targets fruits and to the controls progeny. Seeds of the were fruits sown with theto redcompare sector. the In theprogeny phenotype of the orange fruits to the progeny of the fruits with the red sector. In the tangerine fruits progeny, neither red sector fruits nor WT fruits were detected, indicating no meiotic activity of SpCas resulting in visible IHSR events. We hypothesized that seeds extracted from fruits with red sectors might give rise to either WT or tangerine F2 plants, depending on whether the somatic cells that underwent IHSR (red sector) differentiate into germline cells producing gametes. Fruit#1 from F1 plant#1 had a large red sector (Figure 4A) compared to the other fruits which had a rather small red sector (Figure 4B). The large red sector reached the mesocarp (Figure 4A), unlike the small sectors which were limited to the pericarp. The large red sector (Figure 4A) was carefully cut out and the seeds were collected separately from the seeds of the orange part of the fruit. To test whether only the red sector seeds would give rise to WT F2 plants, 11 seeds from the red sector of plant#1 and 11 seeds from the orange part of the fruit were sown for comparison. Four IHSR WT, and one IHSR mutant progeny were found from the 11 red WT sector progeny. Two more IHSR WT progeny were found from the 11 tangerine fruit part progeny. In total, 7 IHSR progeny out of 22 F2 plants were obtained from red sector fruit#1 of plant#1. In F1 8–9 DSB target plant#2 fruit#1, the red sector was present in the pericarp only, therefore, seeds were collected from the fruit regardless of the sector position. Twenty-two seeds were grown. Three IHSR WT and one IHSR mutant progeny were found out of 22 F2 progeny. We next characterized IHSR events in target 8–9 plant#1 fruit#1 (Figure 5), and plant#2 fruit#1 (Figure 6), F2 and F3 progeny by Sanger sequencing around the DSB site. The sequence data for this analysis (detailed in Supplementary Figures S2 and S3 and shown schematically in Figures 5 and 6) provided insight into conversion tract length and continuity and suggested which repair pathway occurred, namely GC or CO. F3 plants homozygous in the CRTISO region were selected to facilitate sequence analysis and further confirm germinal transmission of the IHSR events. Target 8–9 from F1 plant#1 fruit#1 gave seven F2 progeny with IHSR events out of 22 progeny: five F2 IHSR progeny were derived from the red sector (Figure 5, Supplementary Figure S2): Plants F2-7, F2-3,

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tangerine fruits progeny, neither red sector fruits nor WT fruits were detected, indicating no meiotic activity of SpCas resulting in visible IHSR events. We hypothesized that seeds extracted from fruits with red sectors might give rise to either WT or tangerine F2 plants, depending on whether the somatic cells that underwent IHSR (red sector) differentiate into germline cells producing gametes. Fruit#1 from F1 plant#1 had a large red sector (Figure4A) compared to the other fruits which had a rather small red sector (Figure4B). The large red sector reached the mesocarp (Figure4A), unlike the small sectors which were limited to the pericarp. The large red sector (Figure4A) was carefully cut out and the seeds were collected separately from the seeds of the orange part of the fruit. To test whether only the red sector seeds would give rise to WT F2 plants, 11 seeds from the red sector of plant#1 and 11 seeds from the orange part of the fruit were sown for comparison. Four IHSR WT, and one IHSR mutant progeny were found from the 11 red WT sector progeny. Two more IHSR WT progeny were found from the 11 tangerine fruit part progeny. In total, 7 IHSR progeny out of 22 F2 plants were obtained from red sector fruit#1 of plant#1. In F1 8–9 DSB target plant#2 fruit#1, the red sector was present in the pericarp only, therefore, seeds were collected from the fruit regardless of the sector position. Twenty-two seeds were grown. Three IHSR WT and one IHSR mutant progeny were found out of 22 F2 progeny. We next characterized IHSR events in target 8–9 plant#1 fruit#1 (Figure5), and plant#2 fruit#1 (Figure6), F 2 and F3 progeny by Sanger sequencing around the DSB site. The sequence data for this analysis (detailed in Supplementary Figures S2 and S3 and shown schematically in Figures5 and6) provided insight into conversion tract length and continuity and suggested which repair pathway occurred, namely GC or CO. F3 plants homozygous in the CRTISO region were selected to facilitate sequence analysis and further confirm germinal transmission of the IHSR events. Target 8–9 from F1 plant#1 fruit#1 gave seven F2 progeny with IHSR events out of 22 progeny: five F2 IHSR progeny were derived from the red sector (Figure5, Supplementary Figure S2): Plants F 2-7, F2-3, F2-5, F2-9 which bear red fruits (WT), and plant F2-12 bearing tangerine fruits. Two F2 IHSR progeny derived from the tangerine sector of F1 plant#1, F2-16 and F2-18 bear red fruits (WT). All F2 and F3 plants contained SpCas9. Among this group, two independent types of gene conversion events, GC1 and GC2, were found. In GC1, the DSB was repaired by HR that led to copying a segment of ~50 bp length from the MT homologue to the targeted M82 allele, which generated a tangerine CRTISO allele (Figure5, Supplementary Figure S2, Plant F2-12, and F3-6 (F2-3)). In GC2, the DSB was repaired by HR that led to copying a segment of ~983 bp from the MT homologue to the targeted M82 allele, resulting in the repair of the M82 mutation and generation of a WT CRTISO allele. The GC2 conversion tract is continuous and the DSB site is located in the middle of it between coordinates −456 and +526 (Figure5, plants F 2-7, F2-5, F2-9, F2-3, F2-16, F2-18; F3-12(F2-3), F3-N). Of the 22 F2 progeny from F1-plant# 2, fruit#1 showing IHSR events, 4 were identified from target 8–9 (Figure6, Supplementary Figure S3). Plant F 2-2 bore tangerine fruits, and plants F2-3, F2-1, and F2-8 bore red fruits. All F2 and F3 plants contained SpCas9 except for plant F2-8 (F1-2) and its progeny. Among this group, two independent types of IHSR events were found, GC3 and GC4, and two independent putative CO events. GC3 and GC4 IHSR repair events both appear to result from a DSB in F1 parent plant (red sector in the fruit, Figure4B). GC3 tract from F 1 plant#2 is similar in length and coordinates/location to GC2 in F1 plant#1. However, it is clear that these are two independent events because each occurred in a different plant and because we see that they have a different NHEJ footprint. In GC4, the DSB was repaired by HR leading to copying a segment of ~983 bp from the M82 homologue to the targeted MT allele, resulting in both MT and M82 mutations in cis, and generation of double mutant tangerine CRTISO allele. The GC4 conversion tract is interrupted with the DSB site located in the center. CO1 and CO2 are putative crossover events as determined by Sanger sequencing around the DSB region (Figure6, Supplementary Figure S3). They were further analyzed by whole genome sequencing (WGS) to confirm the presence of COs rather than long conversion tracts. WGS of plant F2-1 confirmed that an induced crossover event, CO1, had occurred, taking place Genes 2021, 12, 59 8 of 12 Genes 2021, 12, 59 8 of 12

F2-5, F2-9 which bear red fruits (WT), and plant F2-12 bearing tangerine fruits. Two F2 IHSR precisely at the DSB-induced site and consisting of a very large segment (Figure7A). CO1 progeny derived from the tangerine sector of F1 plant#1, F2-16 and F2-18 bear red fruits has an interrupted conversion tract and a NHEJ footprint (Figure7A). Note that plant F 2-1 (WT). All F2 and F3 plants contained SpCas9. Among this group, two independent types had no seeds. WGS of CO2 also conﬁrmed that it corresponds to an induced CO event. of gene conversion events, GC1 and GC2, were found. In GC1, the DSB was repaired by For CO2, we sequenced the F progeny (Plant F -3 (F -8)) that was homozygous around HR that led to copying a segment3 of ~50 bp length3 from2 the MT homologue to the targeted the CO site. CO2 showed a clean transition (from the centromere direction to the telom- M82 allele, which generated a tangerine CRTISO allele (Figure 5, Supplementary Figure ere) from MT SNPs to M82 SNPs and has no NHEJ footprint at the target 8–9 break site S2, Plant F2-12, and F3-6 (F2-3)). In GC2, the DSB was repaired by HR that led to copying a (Figure7B). Both CO1 and CO2 events gave rise to a WT CRTISO allele. Additionally, they segment of ~983 bp from the MT homologue to the targeted M82 allele, resulting in the both have a CO junction that occurred between 47 bp and 418 bp from the DSB site towards repair of the M82 mutation and generation of a WT CRTISO allele. The GC2 conversion the telomere direction. The transition between the genotypes in both events continues in tract is continuous and the DSB site is located in the middle of it between coordinates −456 each direction at least 1 Mb from the 8–9 DSB. Further CO events are also detected and are and +526 (Figure 5, plants F2-7, F2-5, F2-9, F2-3, F2-16, F2-18; F3-12(F2-3), F3-N). likely products of meiotic CO events unrelated to the DSB in target 8–9.

Figure 5. Schematic representation of IHSR events in the CRTISO 8–9 region around the targeted DSB in plant #1. The Figure 5. Schematic representation of IHSR events in the CRTISO 8–9 region around the targeted DSB in plant #1. The lightning bolt represents the CRISPR/Cas9 DSB site in the intron between exons 8 and 9 of the CRTISO locus. The DSB was lightning bolt represents the CRISPR/Cas9 DSB site in the intron between exons 8 and 9 of the CRTISO locus. The DSB wasinduced induced between between the twothe mutationstwo mutations in the intangerine the tangerinealleles alleles in the in backgrounds the backgrounds of M82 of M82 (red star,(red 1500star, bp1500 upstream bp upstream from fromthe DSB) the DSB) and Micro-Tomand Micro-Tom (white (white star, 526star, bp 526 downstream bp downstream of the of break).the break). The The F1 has F1 has also also a tangerine a tangerine phenotype, phenotype, unless unless an anIHSR IHSR event event occurs. occurs. In progenyIn progeny of plant of plant #1 where#1 where a red a red fruit frui sectort sector was was observed, observed, two typestwo types of gene of gene conversion conversion events events were wereobserved. observed. GC1 0GC1s conversion′s conversion tract tract did notdid spannot span any ofany the of twothe two mutations mutations and and had had a tangerine a tangerine phenotype. phenotype. For For GC2, GC2, the theconversion conversion tract tract enabled enabled to correct to correct the close-by the close-by M82 mutation M82 mu intation a M82 in chromosomea M82 chromosome background, background, giving rise giving to a dominant rise to a dominantred fruit phenotype. red fruit phenotype. SNPs that enabledSNPs that the enabled monitoring the ofmonitori the originng of the parentalorigin of genotype the parental are showngenotype in yellow are shown for M82 in yellow for M82 homozygotes, blue for Micro-Tom homozygotes, and orange for the heterozygote. Self-pollinated F3 plants homozygotes, blue for Micro-Tom homozygotes, and orange for the heterozygote. Self-pollinated F3 plants were grown to were grown to obtain a homozygous conversion tract and to confirm the sequence of these tracts and the plant phenotype. obtain a homozygous conversion tract and to conﬁrm the sequence of these tracts and the plant phenotype. F3-N refers F3-N refers to several F3 progeny that had the same genotype. The black star represents NHEJ DSB repair footprints that to several F progeny that had the same genotype. The black star represents NHEJ DSB repair footprints that occurred in occurred in 3the intron, probably following recombination. The fruit color phenotype is indicated on the right side. A full detailthe intron, of the probably various alleles’ following sequences recombination. in all progeny The fruit is shown color phenotype in Supplementary is indicated Figure on S2. the right side. A full detail of the various alleles’ sequences in all progeny is shown in Supplementary Figure S2.

Of the 22 F2 progeny from F1-plant# 2, fruit#1 showing IHSR events, 4 were identified from target 8–9 (Figure 6, Supplementary Figure S3). Plant F2-2 bore tangerine fruits, and plants F2-3, F2-1, and F2-8 bore red fruits. All F2 and F3 plants contained SpCas9 except for plant F2-8 (F1-2) and its progeny. Among this group, two independent types of IHSR events were found, GC3 and GC4, and two independent putative CO events. GC3 and GC4 IHSR repair events both appear to result from a DSB in F1 parent plant (red sector in the fruit, Figure 4B). GC3 tract from F1 plant#2 is similar in length and coordinates/location to GC2 in F1 plant#1. However, it is clear that these are two independent events because

Genes 2021, 12, 59 9 of 12

each occurred in a different plant and because we see that they have a different NHEJ footprint. In GC4, the DSB was repaired by HR leading to copying a segment of ~983 bp from the M82 homologue to the targeted MT allele, resulting in both MT and M82 mutations in cis, and generation of double mutant tangerine CRTISO allele. The GC4 conversion tract is interrupted with the DSB site located in the center. CO1 and CO2 are putative crossover events as determined by Sanger sequencing around the DSB region (Figure 6, Supplementary Figure S3). They were further analyzed by whole genome sequencing (WGS) to confirm the presence of COs rather than long conversion tracts. WGS of plant F2-1 confirmed that an induced crossover event, CO1, had occurred, taking place precisely at the DSB-induced site and consisting of a very large segment (Figure 7A). CO1 has an interrupted conversion tract and a NHEJ footprint (Figure 7A). Note that plant F2- 1 had no seeds. WGS of CO2 also confirmed that it corresponds to an induced CO event. For CO2, we sequenced the F3 progeny (Plant F3-3 (F2-8)) that was homozygous around the CO site. CO2 showed a clean transition (from the centromere direction to the telomere) from MT SNPs to M82 SNPs and has no NHEJ footprint at the target 8–9 break site (Figure 7B). Both CO1 and CO2 events gave rise to a WT CRTISO allele. Additionally, they both have a CO junction that occurred between 47 bp and 418 bp from the DSB site towards Genes 2021, 12, 59 9 of 12 the telomere direction. The transition between the genotypes in both events continues in each direction at least 1 Mb from the 8–9 DSB. Further CO events are also detected and are likely products of meiotic CO events unrelated to the DSB in target 8–9.

Figure 6. Schematic representation of IHSR events in the CRTISO 8–9 region around the targeted DSB in plant #2. The Figure 6. Schematiclightning representation bolt represents the of CRISPR/Cas9 IHSR events DSB si inte thein theCRTISO intron between8–9 regionexons 8 and around 9 of the the CRTISO targeted locus. The DSB DSB in plant #2. The lightning bolt representswas induced the between CRISPR/Cas9 the two mutations DSB in site the intangerine the intron alleles in between the backgrounds exons of 8 andM82 (red 9 of star, the 1500CRTISO bp upstreamlocus. The DSB was induced betweenfrom the the twoDSB) and mutations Micro-Tom in (white the star,tangerine 526 bp downstreamalleles in of the the backgroundsbreak). The F1 has ofalso M82 a tangerine (red phenotype, star, 1500 unless bpupstream from an IHSR event occurs. In progeny of plant #2 where a red fruit sector was observed, two types of gene conversion events the DSB) and Micro-Tomwere observed (white as well as star, two putative 526 bp crossover downstream events. The of theGC3 break).conversion The tract Fwas1 has similar also in sequence a tangerine to GC2 phenotype, in plant unless an IHSR event occurs.#1 and In gave progeny rise to a of red plant fruit. GC4 #2 where did not arestore red fruitgene ac sectortivity, even was though observed, it corrected two typesthe M82 of mutation gene conversionbut it was events were homozygous for the Micro-Tom mutation. The two putative crossover events both gave rise to red fruits; CO1 had a observed as wellconversion as two putativetract and CO2 crossover did not show events. evidence The forGC3 a conversion conversion tract. The tract fruit wascolor similarphenotype in is sequenceindicated onto the GC2 right in plant #1 and gave rise to a redside. fruit. All plants GC4 showed did not NHEJ restore DSB repair gene footprints activity, that even occurred though in the it intron, corrected probably the following M82 mutation recombination but (black it was homozygous star). A full detail of the various alleles’ sequences in all progeny is shown in Supplementary Figure S3. for the Micro-Tom mutation. The two putative crossover events both gave rise to red fruits; CO1 had a conversion tract and CO2 did not show evidence for a conversion tract. The fruit color phenotype is indicated on the right side. All plants showed NHEJ DSB repair footprints that occurred in the intron, probably following recombination (black star). A full detail of the various alleles’ sequences in all progeny is shown in Supplementary Figure S3.

- -

SL4.0: Chr 10

61795407 61795391 61795017 61794975 61794822 61794727 61794689 61794582 61794270 61794037 61793909 61792886 61792682 61792320 61791276 61791238 61790867 61790820 61790357 61790294 61788761 61788182 61788068 61787754

61795387 61795021 Distance from -4587 -4567 -4201 -4155 -4002 -3907 -3869 -3762 -3450 -3217 -3089 -2066 -1862 -1500 -456 -418 -47 +463 +526 +2059 +2638 +2752 +3066 DSB

8-9 Tom Tom

- gRNA HR Variant indel indel indel SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP 82 SNP SNP SNP SNP

cutting M type

mutation mutation Phenotype Micro site F2-1 A/+16bp CACG/- AATA/- C/T C/T G/A C/T C/A T/A A/-A G C/T C/T A/-A T/G T/C C -4 bp/+A C G G A A A WT CO1

64,783,875  64,399,301 64,399,301  61,791,238 61,790,867  1 Chromosome 10 64.7Mb

- -

SL4.0: Chr 10

61795387 61795021 Distance from -4587 -4567 -4201 -4155 -4002 -3907 -3869 -3762 -3450 -3217 -3089 -2066 -1862 -1500 -456 -418 -47 +463 +526 +2059 +2638 +2752 +3066 DSB

8-9 Tom Tom

- gRNA HR Variant indel indel indel SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP SNP 82 SNP SNP SNP SNP

cutting M type

mutation

mutation Phenotype Micro site F3-3 (F2-8) - CACG AATA C C G C C T A T C C A T T C - C G G A A A WT CO2

 60,795,944  60,447,761 64,783,875  63,657,639 63,198,664  61,791,238 60,341,687  1,914,064 950,045  1 61,790,867 60,795,894 Chromosome 10 64.7Mb

Figure 7. Whole genome sequencing of the two CO events from Plant#2 DSB-induced in CRTISO 8–9. Each plant was sent

for whole genome sequencing. (A)F2-1: F2 plant 1 and (B)F3-3 (F2-8) F3 plant 3, progeny of F2 plant 8 homozygote in the CRTISO region. Transition from one parental type, M82 (yellow) and Micro-Tom (blue), to a heterozygote state (orange), or to the other parental type correspond to IHSR events. Indels at the DSB site represent NHEJ events in one or both alleles. DSB site footprint was determined to be homozygote (single character), heterozygote (two characters divided by “/”), “-” in case no footprint is found. Lightning bolts represent the CRISPR/Cas9 DSB region. Grey boxes represents a rough estimate of the centromere region (SL4.0 Chr10: 22482995) based on [23]. Genes 2021, 12, 59 10 of 12

4. Discussion In a previous study, we showed that somatic homologous recombination between homologs can be targeted via DSB induction at the tomato Phytoene Synthase1 locus [10]. We extended this work by (i) testing a new locus (CRTISO), (ii) developing a new gain-of- function phenotypic IHSR assay targeting introns (the previous assay was loss of function), (iii) expanding the number of events analyzed, (iv) demonstrating the occurrence of two targeted COs through whole genome sequencing (the single earlier case was a putative CO event). We confirm earlier findings that IHSR events can be germinally transmitted and that gene conversion tracts could be continuous or interrupted. The red sector fruit phenotypic marker was a reliable marker to detect germinally transmitted IHSR events, but the presence of red sectors was not a guarantee of germinal transmission, in particular with small-size sectors where there is only partial correspondence between the maternal fruit tissue and the gametes. Nevertheless, the correlation between the presence of red sectors in fruit somatic tissues of F1 plants and the finding of recombination between the two very close (2 Kb apart) mutations in CRTISO in the progenies supports the somatic origin of these recombination events. Moreover, a meiotic origin for such events is very unlikely because of the proximity of the two mutations, because of the presence of red sectors in F1 plants and because of the lack of red sectors in all F2 negative control plants. Out of eighteen transgenic F1 plants, we had two plants that together gave six germinally transmitted somatic recombinant alleles. Of these six alleles, five were different. Three alleles were GC events, and two were CO events. Three GC alleles and one CO event were successfully transmitted to further F3 fertile plants. By analyzing the conversion tract, we found that two independent fruits of two independent plants had the same NCO recombinant allele, with a continuous conversion tract of ~983 bp length (Figures5 and6, GC2). This could be due to a preferential IHSR repair or to our limited ability to determine size precisely due to low polymorphism between the two parental alleles. One out of three independent GC tracts as well as one out of two CO conversion tracts were interrupted. This phenomenon was observed in yeast [24] and in tomatoes [10]. In F2 plant#1, we observed two types of GC events, with ~50 bp (GC1) and ~1000 bp (GC2) conversion tract lengths, both of which were due to invasion of the M82 allele into the MT allele. These could hint to a Synthesis Dependent Strand Annealing (SDSA) mechanism leading to GC [25]. In F2 plant#2, we detected two types of GC events, with ~1000 bp tract lengths (GC3, GC4) spanning the same SNPs. GC3 is due to invasion of the M82 allele into the MT allele, generating a WT allele. GC4 is due to invasion of the MT allele into the M82, resulting in formation of an allele with both mutations. Intriguingly, having a strong DSB induction was not sufficient to induce IHSR. Indeed, only one out of three gRNAs tested showed high DSB-inducing activity that yielded red sectors indicative of IHSR. The factors determining the ability of a given sequence to be repaired by IHSR remains unclear. Is it due to the “loop-out” of some sequences, the kinetics of repair at this locus, chromatin features, or somatic association? Our sample remains too small to determine the underlying mechanism. The novel assay that we designed and described in this work could be used for future research such as the characterization of candidate genes involved in DNA DSB repair and their effect in IHSR, and the rates of crossover versus non-crossover. In addition, a better understanding of the IHSR phenomenon might be useful to develop precise genome editing breeding tools, for both vegetatively propagated crops and sexually propagated crops, by inducing homologous recombination in somatic cells and thus bypassing the need for meiotic recombination and its limitations.

Supplementary Materials: The following are available online at https://www.mdpi.com/2073-4 425/12/1/59/s1, Supplementary Table S1. Primers used for T-DNA positive plants screening and selection, Supplementary Table S2. Primers used for sequencing of the CRTISO parental mutant lines Micro-Tom 18-3, M82 e3406, and their F1 hybrid plants, Supplementary Table S3. SpCas9 DSB Genes 2021, 12, 59 11 of 12

targets design and considerations, Supplementary Table S4. Primers for Illumina high throughput sequencing of DSB targets NHEJ footprints, Supplementary Table S5. Primers used for sequencing of CRTISO region in F2 and F3 plants, Supplementary Table S6. CRTISO gene coordinates of targeted DSB IHSR assay, Supplementary Table S7. CRTISO targeted DSB IHSR phenotypic assay targets comparison, Supplementary Figure S1. NHEJ frequency in F1 plants of CRTISO assay DSB targets, Supplementary Figure S2. Sequencing of IHSR events in the CRTISO 8–9 region around the targeted DSB in plant#1, Supplementary Figure S3. Sequencing of IHSR events in the CRTISO 8–9 region around the targeted DSB in plant#2. Author Contributions: I.B.S. performed most of the experimental work as part of his Master thesis. A.S. performed part of the experimental work and wrote most of the manuscript. C.M.-B. performed part of the experimental work. D.B.-T., T.D.-M. and S.F.-H. advised the experimental design and analysis. A.A.L. was involved in the planning and supervising of the work and writing of the manuscript. All authors have read and agreed to the published version of the manuscript. Funding: This research and the APC were funded by Israel Science Foundation, grant number 1027/14, and by Minerva Foundation, grant number 2016. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: The data presented in this study are available on request from the corresponding author. Acknowledgments: The authors would like to thank Tal Dahan-Meir for the CRTISO 18-3 Micro-Tom mutant; Joseph Hirschberg and Dani Zamir for the CRTISO M82 e3406 mutant plant materials; Ziva Amsellem for guidance in tissue culture; and the Weizmann Institute greenhouse staff for the plants’ maintenance. The authors would like to thank all the Levy lab members for fruitful discussions and assistance during the course of this study. This work was funded by Israel Science Foundation and Minerva grants to A.A.L. Conﬂicts of Interest: The authors declare no conﬂict of interest.

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