Skip to main content
NCBI home page
Plant Physiology logoLink to Plant Physiology
. 2013 Jul 29;163(1):21–29. doi: 10.1104/pp.113.221903

Insertional Mutagenesis Using Tnt1 Retrotransposon in Potato1,[OPEN]

Saowapa Duangpan 1,2, Wenli Zhang 1,2, Yufang Wu 1,2, Shelley H Jansky 1,2, Jiming Jiang 1,2,*
PMCID: PMC3762642  PMID: 23898040

A transposon-based insertional mutagenesis system potentially enables mutation of every potato gene.

Abstract

Insertional mutagenesis using transfer DNA or transposable elements, which is an important tool in functional genomics and is well established in several crops, has not been developed in potato (Solanum tuberosum). Here, we report the application of the tobacco (Nicotiana tabacum) Tnt1 retrotransposon as an insertional mutagen in potato. The Tnt1 retrotransposon was introduced into a highly homozygous and self-compatible clone, 523-3, of the diploid wild potato species Solanum chacoense. Transposition of the Tnt1 elements introduced into 523-3 can be efficiently induced by tissue culture. Tnt1 preferentially inserted into genic regions in the potato genome and the insertions were stable during sexual reproduction, making Tnt1 an ideal mutagen in potato. Several distinct phenotypes associated with plant stature and leaf morphology were discovered in mutation screening from a total of 38 families derived from Tnt1-containing lines. We demonstrate that the insertional mutagenesis system based on Tnt1 and the 523-3 clone can be expanded to the genome-wide level to potentially tag every gene in the potato genome.

Insertional mutagenesis is one of the most important tools in plant functional genomics. Application of T-DNA, the transfer DNA of the Ti plasmid of Agrobacterium tumefaciens, was the first and the most successful methodology of genome-wide insertional mutagenesis in plants. Many T-DNA lines were developed in two of the most important model plant species, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa; Krysan et al., 1999; Jeon et al., 2000; Alonso et al., 2003; Sallaud et al., 2004). These T-DNA stocks have served as the foundation for the identification and characterization of numerous genes in these two species. A major limitation of the T-DNA-based technique is the requirement for a highly efficient transformation system to generate a large number of transgenic lines. Unfortunately, in many plant species, A. tumefaciens-based transformation is either not yet developed or is not efficient enough to produce a sufficient number of T-DNA lines that would allow a genome-wide gene tagging.

Several transposable elements (TEs) have been used for insertional mutagenesis in plants, including the Activator and Mutator transposons in maize (Zea mays; Walbot, 1992), the Tam3 transposon in Antirrhinum majus (Luo et al., 1991), the Tos17 retrotransposon in rice (Hirochika, 2010), and the LORE1 retrotransposon in Lotus japonicus (Fukai et al., 2012). Most remarkably, the Tnt1 retrotransposon, originally identified in tobacco (Nicotiana tabacum; Grandbastien et al., 1989), has been successfully used in insertional mutagenesis in several heterologous species, including Arabidopsis (Courtial et al., 2001), Medicago truncatula (d’Erfurth et al., 2003), lettuce (Lactuca sativa; Mazier et al., 2007), and soybean (Glycine max; Cui et al., 2013). Tnt1 was used to generate approximately 12,000 independent lines that represent over 300,000 insertions in M. truncatula (Tadege et al., 2008; Cheng et al., 2011). Many M. truncatula genes have been identified through forward and reverse genetics approaches using the Tnt1 retrotransposon insertion population (Pang et al., 2009; Zhao et al., 2010; Laurie et al., 2011; Tadege et al., 2011; Zhou et al., 2011; Cheng et al., 2012; Bourcy et al., 2013).

Potato (Solanum tuberosum) is one of the most important food crops in the world. Cultivated potato is an autotetraploid (2n = 4x = 48) with a highly heterozygous genome. These characteristics make potato a poor model for both forward and reverse genetics research. Very few potato genes have been cloned using the traditional map-based cloning strategy. The lack of fertile homozygous clones makes insertional mutagenesis infeasible in potato. However, the recent sequencing of the potato genome (Xu et al., 2011) has significantly changed the status of potato genetics and genomics research. Highly efficient genotyping systems based on DNA microarrays or DNA sequencing will make genetic mapping and association mapping much more efficient in potato (Hamilton et al., 2011; Felcher et al., 2012). We expect an acceleration of forward genetics-based gene identification in potato. A genome-wide mutagenesis system is urgently needed for the potato research community. Here, we report the development of an insertional mutagenesis system in potato using the Tnt1 retrotransposon. This system is built on a highly homozygous and self-compatible clone (523-3) of the diploid potato species Solanum chacoense (2n = 2x = 24), one of the most widespread wild Solanum species (Miller and Spooner, 1996). S. chacoense is sexually compatible with diploid cultivated potato (Leue and Peloquin, 1980; Hermundstad and Peloquin, 1985). It has been an important germplasm source for the improvement of potato cultivars, especially those for use in the processing market (Love et al., 1998). We demonstrate that this system can be used to potentially tag every potato gene and serve as an important foundation for potato functional genomics research.

RESULTS

Transposition of Tnt1 Occurred during in Vitro Transformation of Potato

A self-compatible clone of S. chacoense was first reported by Hosaka and Hanneman (1998a, 1998b). An S7 clone from the Hanneman program, 523-3, was derived from seven generations of selfing from the original S. chacoense clone. The high level of homozygosity of 523-3 was confirmed by a genome-wide single-nucleotide polymorphism-based genotyping (S.H. Jansky, unpublished data) and the uniform phenotype of the progeny derived from selfing 523-3. The 523-3 clone readily self-pollinates and can generate an average of 100 seeds per fruit. More importantly, this clone can produce tubers in both greenhouse and field conditions.

We developed several transgenic 523-3 lines by transforming internode explants using A. tumefaciens strain GV3101 containing an autonomous copy of Tnt1 in plasmid Tnk23 (d’Erfurth et al., 2003; Fig. 1A). A total of 17 transgenic plants (T0) were generated and confirmed by PCR for the presence of both the nptII gene and Tnt1-specific sequences. Genomic DNA was isolated from the T0 plants, double digested with HindIII (three sites in the construct; Fig. 1A) and EcoRI (no site in the construct), and hybridized sequentially by an nptII gene probe (Fig. 1B) and a Tnt1-specific probe (Fig. 1C), respectively.

Figure 1.

Figure 1.

Open in a new tab

Transpositions of Tnt1 elements in transgenic potato lines. A, Structure of the Tnk23 T-DNA plasmid. The two small horizontal arrows point to the Tnt1-specific probe designed from the long terminal repeat (LTR) region. Vertical black arrows point to the three HindIII sites within the Tnt1 element. Each Tnt1 element will result in an 879-bp fragment after HindIII digestion. LB, Left border; RB, right border. B, Southern-blot hybridization of five T0 lines using an nptII-specific probe. Genomic DNAs were double digested with EcoRI and HindIII. Each hybridization band represents a single transgenic Tnt1 site. C, Southern-blot hybridization of the same blot as in B using the Tnt1-specific probe. The expected 879-bp fragment, as indicated by the black arrow, was observed in every line. Each of the remaining bands represents an independent Tnt1 element.

All T0 lines contained at least one copy of the transgenic Tnt1 element, based on the number of bands hybridized to the nptII gene. The numbers of transgenic Tnt1 elements among the T0 lines ranged from one to six, based on the number of nptII gene-specific bands on the Southern blots (Fig. 1B). The Tnt1-specific probe hybridized to two DNA fragments derived from each Tnt1 element, a common 879-bp fragment and another fragment that represents an individual Tnt1 element (Fig. 1C). The 879-bp fragment was detected in every T0 line. The numbers of total Tnt1 elements among the T0 lines ranged from one to more than 20, based on Tnt1-specific hybridization bands (Fig. 1C). The total numbers of Tnt1 elements in all T0 lines, except line CT1, were more than the numbers of the original transgenic Tnt1 elements. These results suggest that some of the transgenic Tnt1 elements transposed immediately after integrating into the 523-3 genome, resulting in additional Tnt1 elements that are not associated with the nptII gene.

Tnt1 Transposition Can Be Induced by in Vitro Regeneration

Tissue culture-induced retrotransposition of Tnt1 was previously reported in several plant species (Courtial et al., 2001; d’Erfurth et al., 2003; Mazier et al., 2007; Cui et al., 2013). We wanted to confirm whether tissue culture can also induce Tnt1 transposition in the potato genome. The T0 line CT1, which contains a single copy of Tnt1 (Fig. 1), was selected for in vitro regeneration experiments. Internode explants were cut from in vitro CT1 plants and were transferred to regeneration medium. The explants were kept in an incubator and were transferred to new medium every 2 weeks. Regenerated shoots were then transferred to root-inducing medium. We developed a total of 13 regenerated T1 plants (CT1:1–CT1:13). Southern-blot hybridization of the regenerated plants revealed that each of the 13 T1 plants contains at least one additional copy of Tnt1 compared with CT1 (Fig. 2). The numbers of additional Tnt1 elements ranged from one to more than 20 among the 13 plants. These results showed that tissue culture can effectively induce Tnt1 transpositions in potato.

Figure 2.

Figure 2.

Open in a new tab

Tissue culture-induced transposition of Tnt1 in potato. DNAs from the original transgenic line CT1 and four regenerated lines from CT1 were digested with both EcoRI and HindIII and hybridized with the Tnt1-specific probe. Arrows point to the two bands derived from the original Tnt1 element from CT1. Other bands represent new Tnt1 elements retrotransposed from the original copy.

Tnt1 Insertions Are Stable during Sexual Reproduction

Reverse genetics using TE as a mutagen involves self-pollination to develop homozygous insertional mutants. Therefore, the stability of inserted TEs during sexual reproduction is essential for maintaining the mutation. To investigate the stability of the Tnt1 elements in the potato genome, we conducted Southern-blot hybridization analysis of 80 selfed progeny derived from each of four T1 lines (CT1:3, CT1:4, CT1:5, and CT1:7). For each T1 line, DNA samples isolated from 20 selfed progenies were pooled, digested with HindIII and EcoRI, and hybridized with the Tnt1-specific probe. We did not observe any additional hybridization bands in these progenies compared with the parental T1 lines (Fig. 3A), suggesting that the Tnt1 elements in these four T1 lines were stable during sexual reproduction.

Figure 3.

Figure 3.

Open in a new tab

Stability of Tnt1 insertions during sexual reproduction. A, Genomic DNAs were pooled from 20 selfed progenies from one of the four lines (CT1:3, CT1:4, CT1:5, and CT1:7), digested with EcoRI and HindIII, and hybridized to a Tnt1-specific probe. An 879-bp fragment can be observed in each lane. The hybridization patterns associated with the selfed progenies are identical to the patterns of the parental lines. B, Southern-blot hybridization analysis of two DNA samples. Lane 1, DNA isolated from CT1:3; lane 2, pooled DNA from 19 progenies of CT1:3 and genomic DNA from CT1:4. Arrows point to the two bands associated with CT1:4.

To confirm that the potentially retransposed Tnt1 element(s) is detectable in this pooled hybridization approach, we developed a blot by mixing an equal amount of DNA from each of 19 progenies from CT1:3 with DNA from CT1:4. The Tnt1 elements associated with CT1:4 can be unambiguously detected in the mixed DNA sample (Fig. 3B).

Retrotransposition Efficiency Does Not Depend on the Number of Tnt1 Elements

We were interested to know if the average number of transpositions during tissue culture can be controlled by using lines with different copy numbers of the Tnt1 element. We conducted regeneration experiments using four lines (CT1, CT1:4, CT1:3, and CT6), which contain one, three, eight, and nine Tnt1 copies, respectively. The Tnt1 copy numbers of 10 regenerated progeny from each of these four lines were determined by Southern-blot hybridization. Interestingly, we did not observe a correlation between initial Tnt1 copy number and the average Tnt1 copy number in the regenerated progenies (Table I). For example, CT1 contains a single Tnt1 element, while the 10 regenerated progenies from CT1 contained an average of 10.4 Tnt1 elements, resulting in an average of 9.4 new insertions. In comparison, CT6 contains nine copies of Tnt1, and the 10 progenies from CT6 contained an average of 13.5 Tnt1 elements, resulting in only an average of 4.5 new insertions.

Table I. Tnt1 copy numbers in progeny derived from four start lines.

Progeny from CT1 Total Tnt1 Copies Progeny from CT6 Total Tnt1 Copies Progeny from CT1:3 Total Tnt1 Copies Progeny from CT1:4 Total Tnt1 Copies
CT1:1 >20a CT6:5 11 CT1:3:1 8 CT1:4:2 15
CT1:3 9 CT6:7 16 CT1:3:7 >20 CT1:4:3 >20
CT1:4 3 CT6:9 9 CT1:3:5 14 CT1:4:4 8
CT1:5 2 CT6:11 16 CT1:3:13 12 CT1:4:5 7
CT1:6 2 CT6:15 13 CT1:3:12 10 CT1:4:8 8
CT1:7 10 CT6:17 9 CT1:3:11 8 CT1:4:12 >20
CT1:10 >20 CT6:22 15 CT1:3:10 8 CT1:4:13 12
CT1:12 16 CT6:23 9 CT1:3:6 >20 CT1:4:15 16
CT1:14 >20 CT6:24 18 CT1:3:4 11 CT1:4:16 8
CT1:16 2 CT6:29 19 CT1:3:2 >20 CT1:4:42 9
Averageb 10.4 13.5 13.1 12.3
Parental Tnt1 copies 1 9 8 3
New Tnt1 copies 9.4 4.5 5.1 9.3
Open in a new tab
a

If a plant contains more than 20 Tnt1 elements, the number cannot be accurately counted based on Southern-blot hybridization.  bFor average, 20 was used in the calculation if a plant contained more than 20 copies.

All progenies from CT1 (one Tnt1 copy) and CT1:4 (three Tnt1 copies) contained more Tnt1 copies than the parental lines, suggesting that retrotransposition occurred in every plant. In contrast, three plants from CT1:3 (eight Tnt1 copies) and three plants from CT6 (nine Tnt1 copies) contained the same numbers of Tnt1 as the parental lines. These results suggest that most of the Tnt1 elements in CT1:3 and CT6 were not activated by tissue culture. Thus, the retrotransposition efficiency of a line is likely dependent on how easily the Tnt1 element(s) can be activated rather than on the number of original Tnt1 elements.

Tnt1 Preferentially Inserts into Genic Regions in the Potato Genome

We developed a Tnt1-seq method to map the genomic positions of a large number of Tnt1 insertions (Fig. 4). Genomic DNA was isolated from 70 T0 and T1 lines. Tnt1-flanking DNA sequences were isolated by two rounds of DNA walking using PCR. The PCR products were then pooled and used for the preparation of a paired-end Tnt1-seq library (Fig. 4). To check the quality of the library, we cloned and sequenced 20 randomly selected DNA fragments from this library. All clones contained the expected left- and right-border adapters. A total of nine independent inserts were identified (some inserts were identical). This library was sequenced using the Illumina MiSeq platform, resulting in a total of 5,931,429 paired-end sequence reads (150 bp). The sequences from the adapter immediately adjacent to the partial Tnt1 sequence were found to contain sequence errors. Thus, only the sequences adjacent to the left adapter were used in mapping. We mapped 474,424 sequences to the DM1-3 reference genome (PGSC_DM_v3_2.1.11; Xu et al., 2011), corresponding to 1,667 insertion sites, including all nine inserts identified by manual cloning and sequencing. Thus, the 70 different T0 and T1 lines contain an average of 24 Tnt1 insertions. Mapping of the 1,667 insertion sites revealed a near-random distribution on all 12 potato chromosomes (Fig. 5).

Figure 4.

Figure 4.

Open in a new tab

Development of the Tnt1-seq library. DNA walking was performed on pooled genomic DNA from 70 T0 and T1 lines. Each of the Annealing Controlled Primer (ACP) primers (DW-ACP1, DW-ACP2, DW-ACP3, and DW-ACP4) and the TSP1 primer (for Tnt1-specific primer 1) were used to amplify the target region from pooled genomic DNAs in the first PCRs. The second PCR using the DW-ACP-N primer and the TSP2 primer was performed using the first PCR product as a template. The PCR products were then combined and subjected to DNA end blunting, adding adenine (A) to the 3′ end, and paired-end adaptor ligation. The third PCR was conducted to enrich the Tnt1-flanking sequences. Each DNA fragment in the Tnt1-seq library contains an adaptor-specific primer (black), DW-ACP-N primer (red), Tnt1-flanking region (white), Tnt1 sequence from amplification (green), synthesized Tnt1 sequence, which is part of the Tnt1 enrichment-specific primer (purple), and part of the Tnt1 enrichment-specific primer, which was used for Illumina sequencing (sky blue).

Figure 5.

Figure 5.

Open in a new tab

Distribution of Tnt1 insertion sites in the DM1-3 genome (PGSC_DM_v3_2.1.11). Vertical lines above and below the line represent the positions of Tnt1 insertions in the forward and reverse strands of the DM1-3 reference genome. Thick horizontal bars associated with chromosomes 1, 2, 5, and 12 indicate large physical gaps in the pseudomolecules.

A total of 533 insertions (33%) were associated with genic regions in the DM1-3 reference genome, including 15% in exons, 13% in introns, 3% in the 3′ untranslated region, and 2% in the 5′ untranslated region. The genic sequences account for approximately 14% of the potato genome; thus, Tnt1 elements preferentially insert in genic regions. In comparison, 78.6% of the Tnt1-flanking sequences matched coding sequence in M. truncatula (Tadege et al., 2008). The difference in the frequencies of Tnt1 insertions into genic regions in the two species may be caused by the differences in the accuracy of annotations of the two genomes and the lengths of the Tnt1-flanking sequences generated for analysis. The DM1-3 genome was based on the cultivated diploid species S. tuberosum group phureja (Xu et al., 2011). The level of sequence divergence between S. tuberosum group phureja and S. chacoense is unknown. The sequence divergence between the two species may prevent accurate mapping of the relatively short Illumina sequence reads derived from S. chacoense to the DM1-3 genome.

Preliminary Screening of Mutations Caused by Tnt1 Insertions

To investigate the potential of Tnt1 as an insertional mutagen, we developed 38 families by selfing independent T0 and T1 lines. We sowed 30 seeds from each family and then grew 15 randomly selected plants in a greenhouse, along with progenies from wild type 523-3. The germination rate and all visible phenotypes were recorded.

Plants from five families showed seven phenotypes that were unambiguously distinguishable from wild-type 523-3 (Table II; Fig. 6). The germination rate of wild-type 523-3 seeds was 90%. In contrast, seeds from the CT4:33 family showed a much lower germination rate of 60%. A Tnt1 element in CT4:33 possibly landed in a gene that is essential to embryo/seed development; thus, progeny homozygous for this insertion may not be viable. Extreme dwarf plants were observed in the CT4:20 family. These plants showed a severely stunted growth and died approximately 1 month after being transplanted into individual pots.

Table II. Putative mutation phenotypes associated with families selfed from T0 and T1 lines.

Phenotype Family Number of Plants Showing the Phenotypea
Low germination rate CT4:33 60% germination rate
Extreme dwarf and stunted growth CT4:20 5
Bushy, short internode CT4:50, CT4:33 4, 4
Small leaf CT1:13 3
Small and curling-up leaf CT41 3
Round and curling-up leaf CT4:20 3
Open in a new tab
a

Number of plants from a total of 15 in each family.

Figure 6.

Figure 6.

Open in a new tab

Visible phenotypes observed in selfed progeny from some T0 and T1 families compared with wild-type 523-3 plants. A, Short internodes of a plant from the CT4:50 family (left) and internodes from a wild-type 523-3 plant (right). B, Bushy phenotype of a plant from the CT4:33 family (left) and a wild-type 523-3 plant (right). C, A plant with small, inward-curling leaves from the CT41 family (left) and a wild-type 523-3 plant (right). D, Rounded, inward-curling leaves of plants from the CT4:20 family (left) and wild-type leaves (right).

Plants in several families showed distinctive leaf shapes. Plants in the CT4:20 family had large, round leaves that curled inward (Fig. 6D). Some plants from CT4:50 and CT4:33 had short internodes and, as a consequence, were bushy (Fig. 6, A and B). Small and inward-curling leaves were observed in plants from the CT41 family (Fig. 6C).

DISCUSSION

A mutation caused by a T-DNA or TE insertion into a gene will interrupt only one of the two homologs in diploid species. Selfing of the heterozygous mutation line is required to identify the homozygous recessive mutant. Therefore, insertional mutagenesis is most appropriately applied only in homozygous and self-compatible inbred lines. Most asexually propagated species, such as potato, contain highly heterozygous genomes and are often self-incompatible; thus, they cannot benefit from insertional mutagenesis technology. Ishizaki and Kato (2005) introduced the Tto1 retrotransposon from tobacco into a sterile diploid potato clone. However, transposition of Tto1 was not induced by tissue culture in potato (Ishizaki and Kato, 2005), although Tto1 can be activated by tissue culture in rice and Arabidopsis (Hirochika et al., 1996; Okamoto and Hirochika, 2000).

An alternative approach in plant species with a heterozygous genome is to develop activation-tagging lines by transforming a construct containing a strong promoter (Weigel et al., 2000). Insertion of a strong promoter may result in an overexpression of an adjacent gene or a gain-of-function phenotype for the gene. Such a dominant phenotype can be observed in T0 transgenic lines, avoiding the selfing process. The Canadian Potato Genome Project generated 10,000 activation-tagged potato lines (Regan et al., 2006). However, the phenotype-inducing efficiency of the activation-tagging approach is not known in potato. In addition, each tagging line has to be individually transformed. Thus, the value of activation-tagging technology remains to be seen in potato.

We have demonstrated that the Tnt1-based insertional mutagenesis system using S. chacoense clone 523-3 can be used to tag individual potato genes. This is because of the following reasons. (1) The 523-3 clone can be easily transformed and regenerated. Thus, many regenerated lines from a selected starter line can be readily developed, and it will be feasible to develop a large number of Tnt1 lines to saturate the entire potato genome (see below). (2) A sufficient amount of seeds from each regenerated line can be readily produced by self-pollination. Each plant can produce dozens of berries, each of which typically contains about 100 seeds. Potato seeds are small and can be stored in small-sized tubes or envelopes in a −20°C freezer for decades. (3) The 523-3 plants are much smaller than typical tetraploid potato cultivars and can be grown in small-sized pots for large-scale screening in greenhouses. (4) The 523-3 clone tuberizes well in both greenhouses and the field, even under long-photoperiod conditions (Kittipadukal et al., 2012). Thus, tuber-related traits can be screened.

Tnt1-based genome-wide mutagenesis has already been well demonstrated in M. truncatula (Tadege et al., 2008; Cheng et al., 2011). The Tnt1 element in potato showed similar activity and behavior to that documented in other plant species, including activation by tissue culture, stability during sexual reproduction, and preferential transposition into genic regions (Courtial et al., 2001; d’Erfurth et al., 2003; Mazier et al., 2007; Cui et al., 2013). We examined several factors that may affect the Tnt1 retrotransposition. We observed that the Tnt1 copy numbers in the new regenerants do not correlate with the length of time that the callus was grown on the regeneration medium (data not shown). This is consistent with a similar study in M. truncatula (Tadege et al., 2008). The new Tnt1 copy numbers in regenerants were not correlated with the original Tnt1 copy numbers in the parental lines (Table I). It was demonstrated in Arabidopsis that the transcription of Tnt1 was often silenced in plants containing numerous copies. The silencing of Tnt1 was associated with 24-nucleotide short-interfering RNAs targeting the promoter localized in the long terminal repeat region and with the non-CG site methylation of these sequences (Pérez-Hormaeche et al., 2008). Our data are in agreement with those in Arabidopsis. Potato lines with more copies of Tnt1 generated fewer new Tnt1 copies during regeneration than CT1, a T0 line containing a single copy of Tnt1 (Table I). Thus, most Tnt1 copies in lines with numerous insertions are likely silenced and cannot be activated by tissue culture.

Our preliminary mutation screening revealed the potential of the Tnt1-based system to generate potato mutants. Seven distinct phenotypic changes were observed in five of the 38 T0/T1 families. Each phenotype was observed in three to five plants in a particular family (Table II), indicating that each change was likely caused by a recessive mutation of a single gene. More subtle changes were observed in several additional families. In the screening of the M. truncatula mutant population, approximately 30% of the lines showed new recognizable phenotypes (Tadege et al., 2008). However, the screening involved inoculation with arbuscular mycorrhizal fungi and Sinorhizobium meliloti and was performed under low-nitrogen and low-phosphorus conditions. In this study, only a few families were screened, under regular greenhouse growing conditions, but the Tnt1-based system appears to have a similar phenotype-changing efficiency to that in M. truncatula.

Our ultimate goal is to develop a 523-3 population that is large enough to tag every potato gene with a Tnt1 element. The average number of Tnt1 insertions will directly affect the number of Tnt1-tagged 523-3 lines needed for mutation saturation. The transposed Tnt1 copy numbers of the regenerants derived from CT1 ranged from one to more than 20, which is similar to the numbers observed in other plant species. The transposition events ranged from four to more than 30 in M. truncatula (d’Erfurth et al., 2003), zero to 26 in Arabidopsis (Courtial et al., 2001), and four to 19 in soybean (Cui et al., 2013). A total of 1,667 insertions was recovered from 70 Tnt1-harboring lines, averaging 24 insertions per line. The possibility of finding an insertion in a given gene can be estimated by P = 1 − (1 − [X/G])n, where P = the possibility of finding an insertion in a given gene, X = the length of the gene in kilobases, G = the genome size in kilobases, and n = the number of insertions in the population (Krysan et al., 1999). Considering that the size of the potato genome is 845 Mb and the average gene size is 2.5 kb, we estimate that approximately 1 million insertions are needed to achieve 95% genome saturation. If each Tnt1 tagging line contains 24 insertions, then 42,000 lines will be required. However, this equation assumes the random insertion of Tnt1. Therefore, the number of mutants needed to saturate the potato gene complement would be significantly reduced due to the preferential insertions of Tnt1 in genic regions. In a comparison, the genome size of M. truncatula is approximately 500 Mb, and approximately 90% of the M. truncatula genes were covered by a population of approximately 12,000 Tnt1 insertion lines (Cheng et al., 2011).

MATERIALS AND METHODS

Plant Material

Solanum chacoense clone 523-3, developed by Robert Hanneman in Madison, Wisconsin (Hosaka and Hanneman, 1998a, 1998b), was used for transformation. For germination, seeds were soaked in 1,500 ppm GA3 for 24 h to break dormancy. The seeds were then sown in square pots (10 cm × 10 cm) using soilless potting mix. After 4 weeks, the seedlings were transplanted to individual pots and maintained in a greenhouse. Growth conditions were a 16-h photoperiod and 18°C and 15°C day and night temperatures, respectively.

Potato Transformation and Regeneration

Agrobacterium tumefaciens strain LBA4404 was transformed with the Tnk23 vector (Lucas et al., 1995). Internode explants from in vitro 523-3 plantlets were then transformed using the LBA4404 strain following standard A. tumefaciens-mediated potato (Solanum tuberosum) transformation (Bhaskar et al., 2008). The transformed shoots were transferred to rooting medium without antibiotics. In vitro regeneration was performed by cutting the internodes of each Tnt1-containing plant into explants approximately 5 mm long. The explants were then placed on medium used for transformation but without any antibiotics and transferred to new medium every 2 weeks. Regenerated shoots were transferred to rooting medium.

Identification of Plants Containing Tnt1 Elements

Genomic DNA was extracted from leaf tissue of transgenic plants grown in greenhouses using the Qiagen DNeasy Plant Mini Kit. The oligonucleotides KAN1 (5′-CCAACGCTATGTCCTGATAG-3′) and KAN2 (5′-TTTGTCAAGACCGACCTGTC-3′) were used to verify the presence of the nptII gene, and the oligonucleotides LTR1 (5′-ATGTCCATCTCATTGAAGAAGTA-3′) and LTR2 (5′-GGGAATAAACCCCTTACCAAAA-3′) were used to verify the presence of the Tnt1 element. PCR conditions for both primer pairs were 30 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 1 min.

For Southern-blot hybridization, approximately 20 μg of genomic DNA was digested with HindIII and EcoRI and then blotted on a membrane. The blots were probed with a 528-bp fragment complementary to nucleotides 141 to 669 of the nptII gene or with a 194-bp fragment complementary to nucleotides 1 to 194 of Tnt1. The blots were hybridized overnight at 65°C using standard protocols (Sambrook et al., 2001).

Identification of the Tnt1-Flanking Region

DNA walking on pooled genomic DNA from T0 and T1 lines was performed using the DNA walking SpeedUP Kit II (Seegene). Tnt1-specific primers used in the first and second PCR were TSP1 (5′-CCCGAGAGGAGCAACTGATA-3′) and TSP2 (5′-AAGAAATGAGAGTTGAAGCTCTCC-3′), respectively. The PCR products from the second round of DNA walking were used for the preparation of a paired-end Tnt1-seq library following the standard protocol provided by Illumina. Briefly, the protocol includes end blunting, adding an “A” tail, ligation of paired-end adaptors, and enrichment of the flanking region of Tnt1 insertions. The flanking sequences immediately adjacent to Tnt1 were amplified using the Tnt1 enrichment-specific primer 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCACATGCCTAATACTTCTTCAATGAG-3′ and the adapter-specific primer 5′-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3′. The amplification program was as follows: 30 s at 98°C; 18 cycles of 10 s at 98°C, 30 s at 65°C, and 30 s at 72°C; and then 5 min at 72°C. DNA fragments between 300 and 550 bp were cut from a 2% agarose gel and purified using MinElute PCR purification columns (Qiagen). The quality of purified DNA (Tnt1-seq library) was checked by cloning into pCR4-TOPO TA vector (Invitrogen). Twenty clones were randomly selected and sequenced by Sanger sequencing. The Tnt1-seq library was then quantified using the Agilent Bioanalyzer 2100 and sequenced on the Illumina MiSeq platform. The sequence reads were mapped to the DM1-3 reference genome using BLAT (Kent, 2002).

Acknowledgments

We thank Marie-Angele Grandbastien and Pascal Ratet for sharing the Tnk23 vector and Kiran Mysore for sharing his experience on Tnt1-mediated mutagenesis in Medicago species. We are grateful to Scott Jackson and Christian Hans for helping on the Illumina MiSeq sequencing.

Glossary

T-DNA

transfer DNA

TE

transposable element

References

  1. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen HM, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653–657 [DOI] [PubMed] [Google Scholar]
  2. Bhaskar PB, Raasch JA, Kramer LC, Neumann P, Wielgus SM, Austin-Phillips S, Jiang JM. (2008) Sgt1, but not Rar1, is essential for the RB-mediated broad-spectrum resistance to potato late blight. BMC Plant Biol 8: 8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bourcy M, Brocard L, Pislariu CI, Cosson V, Mergaert P, Tadege M, Mysore KS, Udvardi MK, Gourion B, Ratet P. (2013) Medicago truncatula DNF2 is a PI-PLC-XD-containing protein required for bacteroid persistence and prevention of nodule early senescence and defense-like reactions. New Phytol 197: 1250–1261 [DOI] [PubMed] [Google Scholar]
  4. Cheng XF, Peng JL, Ma JY, Tang YH, Chen RJ, Mysore KS, Wen JQ. (2012) NO APICAL MERISTEM (MtNAM) regulates floral organ identity and lateral organ separation in Medicago truncatula. New Phytol 195: 71–84 [DOI] [PubMed] [Google Scholar]
  5. Cheng XF, Wen JQ, Tadege M, Ratet P, Mysore KS. (2011) Reverse genetics in Medicago truncatula using Tnt1 insertion mutants. Methods Mol Biol 678: 179–190 [DOI] [PubMed] [Google Scholar]
  6. Courtial B, Feuerbach F, Eberhard S, Rohmer L, Chiapello H, Camilleri C, Lucas H. (2001) Tnt1 transposition events are induced by in vitro transformation of Arabidopsis thaliana, and transposed copies integrate into genes. Mol Genet Genomics 265: 32–42 [DOI] [PubMed] [Google Scholar]
  7. Cui Y, Barampuram S, Stacey MG, Hancock CN, Findley S, Mathieu M, Zhang ZY, Parrott WA, Stacey G. (2013) Tnt1 retrotransposon mutagenesis: a tool for soybean functional genomics. Plant Physiol 161: 36–47 [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. d’Erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A, Ratet P. (2003) Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 34: 95–106 [DOI] [PubMed] [Google Scholar]
  9. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS. (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7: e36347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fukai E, Soyano T, Umehara Y, Nakayama S, Hirakawa H, Tabata S, Sato S, Hayashi M. (2012) Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1. Plant J 69: 720–730 [DOI] [PubMed] [Google Scholar]
  11. Grandbastien MA, Spielmann A, Caboche M. (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376–380 [DOI] [PubMed] [Google Scholar]
  12. Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR. (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12: 302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hermundstad SA, Peloquin SJ. (1985) Germplasm enhancement with potato haploids. J Hered 76: 463–467 [Google Scholar]
  14. Hirochika H. (2010) Insertional mutagenesis with Tos17 for functional analysis of rice genes. Breed Sci 60: 486–492 [Google Scholar]
  15. Hirochika H, Otsuki H, Yoshikawa M, Otsuki Y, Sugimoto K, Takeda S. (1996) Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell 8: 725–734 [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hosaka K, Hanneman RE. (1998a) Genetics of self-compatibility in a self-incompatible wild diploid potato species Solanum chacoense. 1. Detection of an S locus inhibitor (Sli) gene. Euphytica 99: 191–197 [Google Scholar]
  17. Hosaka K, Hanneman RE. (1998b) Genetics of self-compatibility in a self-incompatible wild diploid potato species Solanum chacoense. 2. Localization of an S locus inhibitor (Sli) gene on the potato genome using DNA markers. Euphytica 103: 265–271 [Google Scholar]
  18. Ishizaki T, Kato A. (2005) Introduction of the tobacco retrotransposon Tto1 into diploid potato. Plant Cell Rep 24: 52–58 [DOI] [PubMed] [Google Scholar]
  19. Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, Kim C, Jang S, Yang K, Nam J, et al. (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22: 561–570 [DOI] [PubMed] [Google Scholar]
  20. Kent WJ. (2002) BLAT: the BLAST-like alignment tool. Genome Res 12: 656–664 [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kittipadukal P, Bethke PC, Jansky SH. (2012) The effect of photoperiod on tuberisation in cultivated × wild potato species hybrids. Potato Res 55: 27–40 [Google Scholar]
  22. Krysan PJ, Young JC, Sussman MR. (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11: 2283–2290 [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Laurie RE, Diwadkar P, Jaudal M, Zhang LL, Hecht V, Wen JQ, Tadege M, Mysore KS, Putterill J, Weller JL, et al. (2011) The Medicago FLOWERING LOCUS T homolog, MtFTa1, is a key regulator of flowering time. Plant Physiol 156: 2207–2224 [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Leue EF, Peloquin SJ. (1980) Selection for 2n gametes and tuberization in Solanum chacoense. Am Potato J 57: 189–195 [Google Scholar]
  25. Love SL, Pavek JJ, Thompson-Johns A, Bohl W. (1998) Breeding progress for potato chip quality in North American cultivars. Am J Potato Res 75: 27–36 [Google Scholar]
  26. Lucas H, Feuerbach F, Kunert K, Grandbastien MA, Caboche M. (1995) RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. EMBO J 14: 2364–2373 [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Luo D, Coen ES, Doyle S, Carpenter R. (1991) Pigmentation mutants produced by transposon mutagenesis in Antirrhinum majus. Plant J 1: 59–69 [PubMed] [Google Scholar]
  28. Mazier M, Botton E, Flamain F, Bouchet JP, Courtial B, Chupeau M-C, Chupeau Y, Maisonneuve B, Lucas H. (2007) Successful gene tagging in lettuce using the Tnt1 retrotransposon from tobacco. Plant Physiol 144: 18–31 [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Miller JT, Spooner DM. (1996) Introgression of Solanum chacoense (Solanum sect Petota): upland populations reexamined. Syst Bot 21: 461–475 [Google Scholar]
  30. Okamoto H, Hirochika H. (2000) Efficient insertion mutagenesis of Arabidopsis by tissue culture-induced activation of the tobacco retrotransposon Tto1. Plant J 23: 291–304 [DOI] [PubMed] [Google Scholar]
  31. Pang YZ, Wenger JP, Saathoff K, Peel GJ, Wen JQ, Huhman D, Allen SN, Tang YH, Cheng XF, Tadege M, et al. (2009) A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis but not for trichome development. Plant Physiol 151: 1114–1129 [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Pérez-Hormaeche J, Potet F, Beauclair L, Le Masson I, Courtial B, Bouché N, Lucas H. (2008) Invasion of the Arabidopsis genome by the tobacco retrotransposon Tnt1 is controlled by reversible transcriptional gene silencing. Plant Physiol 147: 1264–1278 [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Regan S, Gustafson V, Mallubhotla S, Chakravarty B, Bagchi M, Siahbazi M, Rothwell C, Sardana R, Goyer C, Audy P, et al. (2006) Finding the perfect potato: using functional genomics to improve disease resistance and tuber quality traits. Can J Plant Pathol 28: S247–S255 [Google Scholar]
  34. Sallaud C, Gay C, Larmande P, Bès M, Piffanelli P, Piégu B, Droc G, Regad F, Bourgeois E, Meynard D, et al. (2004) High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J 39: 450–464 [DOI] [PubMed] [Google Scholar]
  35. Sambrook J, Fritsch EJ, Maniatis T (2001) Molecular Cloning: A Laboratory Manual, Ed 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY [Google Scholar]
  36. Tadege M, Lin H, Bedair M, Berbel A, Wen JQ, Rojas CM, Niu LF, Tang YH, Sumner L, Ratet P, et al. (2011) STENOFOLIA regulates blade outgrowth and leaf vascular patterning in Medicago truncatula and Nicotiana sylvestris. Plant Cell 23: 2125–2142 [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tadege M, Wen JQ, He J, Tu HD, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M, et al. (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54: 335–347 [DOI] [PubMed] [Google Scholar]
  38. Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, et al. (2011) Genome sequence and analysis of the tuber crop potato. Nature 475: 189–195 [DOI] [PubMed] [Google Scholar]
  39. Walbot V. (1992) Strategies for mutagenesis and gene cloning using transposon tagging and T-DNA insertional mutagenesis. Annu Rev Plant Physiol Plant Mol Biol 43: 49–82 [Google Scholar]
  40. Weigel D, Ahn JH, Blázquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrándiz C, Kardailsky I, Malancharuvil EJ, Neff MM, et al. (2000) Activation tagging in Arabidopsis. Plant Physiol 122: 1003–1013 [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Zhao Q, Gallego-Giraldo L, Wang H, Zeng Y, Ding S-Y, Chen F, Dixon RA. (2010) An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula. Plant J 63: 100–114 [DOI] [PubMed] [Google Scholar]
  42. Zhou C, Han L, Pislariu C, Nakashima J, Fu C, Jiang Q, Quan L, Blancaflor EB, Tang Y, Bouton JH, et al. (2011) From model to crop: functional analysis of a STAY-GREEN gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement. Plant Physiol 157: 1483–1496 [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Plant Physiology are provided here courtesy of Oxford University Press

RESOURCES