The utility of flow sorting to identify chromosomes carrying a single copy transgene in wheat
© Cápal et al. 2016
Received: 20 February 2016
Accepted: 19 April 2016
Published: 25 April 2016
Identification of transgene insertion sites in plant genomes has practical implications for crop breeding and is a stepping stone to analyze transgene function. However, single copy sequences are not always easy to localize in large plant genomes by standard approaches.
We employed flow cytometric chromosome sorting to determine chromosomal location of barley sucrose transporter construct in three transgenic lines of common wheat. Flow-sorted chromosomes were used as template for PCR and fluorescence in situ hybridization to identify chromosomes with transgenes. The chromosomes carrying the transgenes were then confirmed by PCR using DNA amplified from single flow-sorted chromosomes as template.
Insertion sites of the transgene were unambiguously localized to chromosomes 4A, 7A and 5D in three wheat transgenic lines. The procedure presented in this study is applicable for localization of any single-copy sequence not only in wheat, but in any plant species where suspension of intact mitotic chromosomes suitable for flow cytometric sorting can be prepared.
During the past 30 years, many cultivars of agricultural crops beneficial to humankind have been developed by means of genetic engineering, including plants resistant to herbicides, pests or viruses, bearing fruits with prolonged shelf life and products more suited for industrial processing [for review see 1]. Wheat ranks 5th in the commodities produced worldwide and is the second most-produced food crop occupying more than 50 % of the world crop area (http://faostat3.fao.org/). In the light of climate change and world population growth, future challenges for the increase of crop production have constantly been discussed. However, FAO statistics show that the wheat production is reaching a plateau and is severely affected by climate change. This is a consequence of a slowdown in wheat yield increase, accounting for only 0.5 % per year in the last decade .
Breeding improved cultivars with increased tolerance to adverse climatic conditions and with increased yield and quality could be facilitated by genetic engineering and introduction of beneficial genes from other organisms. The insertion site of a transgene is of great importance for the transgene function [3, 4] which is also influenced by its position on the chromosome, including the flanking DNA sequences . However, transgene localization is not easy by routine approaches, like fluorescence in situ hybridization (FISH), or Southern blotting. A prevalent method for detection of transgenes in animals and plants is FISH, which has its pros and cons . In barley and common wheat, FISH enables cytological localization of cDNAs, as short as 1.5 kb, on a chromosome or chromosomes that had already been known to carry the cDNAs [7, 8]. Although some authors succeeded in localizing transgenes on plant chromosomes using FISH [9–11], this approach has not become a routine application.
Weichert et al.  obtained transgenic lines (HOSUT) of hexaploid wheat carrying barley (Hordeum vulgare) sucrose transporter HvSUT1 (SUT) gene that is overexpressed under the control of the endosperm-specific Hordein B1 promoter (HO). The HOSUT lines were found to increase grain yield significantly as compared to control non-transformed plants . However, the genomic location of the transgene in these lines was not known. In the present work we employed a novel approach for unambiguous identification of chromosomes carrying the transgene in three HOSUT lines. The protocol takes the advantage of the availability of a procedure for flow cytometric chromosome sorting in wheat and the fact that flow-sorted chromosomes are suitable as templates for PCR and FISH . Moreover, a protocol has been developed recently for representative DNA amplification from single copies of chromosomes . By combining these approaches we could assign the transgene to particular chromosomes in three HOSUT lines of wheat.
Results and discussion
PCR and FISH analysis of chromosomes sorted from each of the sort gates in three HOSUT lines
Chromosomes identified FISHc
4A (92.65 %)
7A (90.90 %)
4A (4.45 %)
1A (63.75 %)
3D (36.25 %)
5D (94.66 %)
1A (5.33 %)
7A (83.19 %)
4A (12.39 %)
2A (4.42 %)
4A (97.30 %)
FISH analysis showed that more than 90 % of chromosomes flow-sorted from the region defined by the green rectangle consisted of one type of chromosome in each of the HOSUT lines. This fact together with the results of PCR suggested that the transgene was located on chromosome 7A in HOSUT 12/44, on chromosome 5D in HOSUT 20/6 and on chromosome 4A in HOSUT 24/31. In the former two lines, the critical type of chromosome was not found among the chromosomes flow-sorted from the region defined by red rectangles. However, chromosome 4A was found to represent 12.39 % of chromosomes flow-sorted from the red region in HOSUT 24/31. This was probably due to the similarities in size and the amount of GAA-FITC fluorescence of chromosomes 4A and 7A. Due to this similarity, mixture of the two chromosomes 4A and 7A was also observed in the chromosome fraction sorted from the green region in HOSUT 12/44.
To confirm chromosomal locations of the transgene and avoid ambiguous results due to possible contamination of flow-sorted fraction by other chromosomes, PCR was done on DNA amplified from single flow-sorted chromosomes. As each time only one copy of chromosome is sorted, the DNA cannot be contaminated by other chromosomes. Five single chromosomes were sorted from the green sort regions of the HOSUT lines and their DNA was separately amplified using multiple displacement amplification (MDA). Out of the five sorted chromosomes, whole genome amplification was successful with three chromosomes in HOSUT 12/44, two chromosomes in HOSUT 20/6 and four chromosomes in HOSUT 24/31. The successful amplification was defined by the production of measurable amount of DNA after MDA and by the presence of at least one marker for the transgene and one marker for the wheat chromosome. The reason for occasional failure to amplify DNA from single chromosomes, which was observed previously  is not clear. One explanation is that a droplet with sorted chromosome lands on side wall of PCR tube and the chromosome is excluded from the MDA reaction. The amount of chromosomal DNA in successfully amplified samples ranged from 0.3 to 1.7 µg DNA.
Coupling PCR and FISH mapping using flow-sorted mitotic chromosomes as templates narrowed down the list of candidate chromosomes harboring the transgene to one or two chromosomes. PCR on DNA amplified from single flow-sorted chromosomes then unambiguously identified the chromosomes with the integrated transgene. If chromosome-specific PCR-based markers are available, mapping on single copy chromosomes could be an ultimate approach to assign single copy DNA sequences, including transgenes, to particular chromosomes. Moreover, the sequence assembly of amplicons from the chromosome could allow detecting the position of transgene insertion, if enough sequence information on the chromosome is available. However the main purpose of this work was to assign a transgene to particular chromosomes. The approach presented here is currently applicable to more than 25 plant species, which include important cereals and legumes  where liquid suspensions of mitotic chromosomes suitable for flow cytometric sorting can be prepared.
We used German winter wheat cultivar Certo (Triticum aestivum L., 2n = 6x = 42, genome formula AABBDD) and its three transgenic lines, HOSUT 12/44, HOSUT 20/6 and HOSUT 24/31. The transgenic lines contain a single copy of the HvSUT1-cDNA (1894 bp) fused to the barley HorB1 promoter (550 bp) and the barley HorB1 terminator (1663 bp) . We also used euploid and nullisomic–tetrasomic (Nt1A1B, Nt7A7B, Nt5D5B) lines of hexaploid wheat cultivar Chinese Spring (obtained from NBRP-wheat) to confirm the specificity of PCR markers to particular wheat chromosomes.
Flow cytometric chromosome sorting
Cell cycle synchronization and metaphase accumulation of root tip meristem cells was performed as described previously , except for the formaldehyde fixation, which was shortened to 15 min. Isolated chromosomes were labelled by FISHIS (fluorescence in situ hybridization in suspension) using FITC-labeled GAA probe following the protocol of Giorgi et al. . Flow cytometric analysis and sorting was done on BD FACSAria II high speed flow sorter equipped with 390 nm laser for DAPI excitation and 488 nm laser for FITC excitation. Sort gates were initially drawn on monovariate flow karyotypes of DAPI fluorescence (not shown) and subsequently on bivariate flow karyotypes of DAPI fluorescence versus GAA-FITC fluorescence as shown in Fig. 1.
Fluorescence in situ hybridization (FISH)
For microscopic observations, 1000 chromosomes were sorted onto microscope slides from each of the sort regions. The slides were left to air-dry in the dark overnight. Then the preparations were used for FISH following the protocol of Kubaláková et al.  using a Cy5-labeled probe targeting Afa-family repeats, the chromosomes were already labeled by a GAA microsatellite probe during the FISHIS procedure.
List of PCR primers for the HOSUT transgene construct and PCR primers for wheat STS markers on chromosomes 1A, 4A, 7A and 5D
Forward primer sequence
Reverse primer sequence
Amplicon size (bp)
Annealing temperature (°C)
Whole genome amplification of single chromosomes
DNA amplification of single chromosomes was performed by MDA using a GE Healthcare GenomiPhi V2 kit (GE Healthcare Life Sciences, Little Chalfont, UK) according to Cápal et al. . Five individual chromosomes were flow-sorted into five 0.2 ml PCR tubes from green sort gates from each HOSUT line and their DNA amplified. The amplified DNA was evaluated on 1.5 % agarose gel, purified using magnetic beads (AMPure XP system, Beckman Coulter, Inc., Brea, CA, USA) and the concentration was measured by a spectrophotometer (NanoDrop, Thermo Fisher Scientific Inc., Waltham, MA, USA).
The study was conceived and designed by TE, PC and JD, experiments were performed by PC, TE, M Ka, M Ku, JV, IMR and EK, manuscript was written by PC, TE, JD and WW. All authors read and approved the final manuscript.
We thank Zdeňka Dubská for technical assistance with flow cytometric chromosome sorting. This work was supported by the National Program of Sustainability (Award No. LO 2014) and the Czech Science Foundation (Award No. P501-12-G090).
The authors declare that they have no competing interests.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Ahmad P, Ashraf M, Younis M, Hu X, Kumar A, Akram NA, Al-Qurainy F. Role of transgenic plants in agriculture and biopharming. Biotechnol Adv. 2012;30:524–40.View ArticlePubMedGoogle Scholar
- Fischer RA. The importance of grain or kernel number in wheat: a reply to Sinclair and Jamieson. Field Crops Res. 2008;105:15–21.View ArticleGoogle Scholar
- Svitashev S, Anaiev E, Pawlowski WP, Somers DA. Association of transgene integration sites with chromosome rearrangements in hexaploid oat. Theor Appl Genet. 2000;100:872–80.View ArticleGoogle Scholar
- Kumar S, Fladung M. Gene stability in transgenic aspen (Populus). II. Molecular characterization of variable expression of transgene in wild and hybrid aspen. Planta. 2001;213:731–40.View ArticlePubMedGoogle Scholar
- Kooter JM, Matzke A, Meyer P. Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci. 1999;4:340–7.View ArticlePubMedGoogle Scholar
- Svitashev KS, Somers DA. Characterization of transgene loci in plants using FISH: a picture is worth a thousand words. Plant Cell Tiss Org Cult. 2002;69:205–14.View ArticleGoogle Scholar
- Danilova TV, Friebe B, Gill BS. Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae. Theor Appl Genet. 2014;127(3):715–30.View ArticlePubMedPubMed CentralGoogle Scholar
- Karafiátová M, Bartoš J, Kopecký D, Ma L, Sato K, Houben A, Doležel J. Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res. 2013;21:739–51.View ArticlePubMedGoogle Scholar
- Pedersen C, Zimny J, Becker D, Jähne-Gärtner A, Lörz H. Localization of introduced genes on the chromosomes of transgenic barley, wheat and triticale by fluorescence in situ hybridization. Theor Appl Genet. 1997;94:749–57.View ArticleGoogle Scholar
- Dong J, Pushpa K, Cervera M, Hall TC. The use of FISH in chromosomal localization of transgenes in rice. Methods Cell Sci. 2001;23:105–13.View ArticlePubMedGoogle Scholar
- Khrustaleva LI, Kik C. Localization of single-copy T-DNA insertion in transgenic shallots (Allium cepa) by using ultra-sensitive FISH with tyramide signal amplification. Plant J. 2001;25:699–707.View ArticlePubMedGoogle Scholar
- Weichert N, Saalbach I, Weichert H, Kohl S, Erban A, Kopka J, Hause B, Varshney A, Sreenivasulu N, Strickert M, Kumlehn J, Weschke W, Weber H. Increasing sucrose uptake capacity of wheat grains stimulates storage protein synthesis. Plant Physiol. 2010;152:698–710.View ArticlePubMedPubMed CentralGoogle Scholar
- Saalbach I, Mora-Ramírez I, Weichert N, Andersch F, Guild G, Wieser H, Koehler P, Stangoulis J, Kumlehn J, Weschke W, Weber H. Increased grain yield and micronutrient concentration in transgenic winter wheat by ectopic expression of a barley sucrose transporter. J Cereal Sci. 2014;60:75–81.View ArticleGoogle Scholar
- Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv. 2014;32:122–36.View ArticlePubMedGoogle Scholar
- Cápal P, Blavet N, Vrána J, Kubaláková M, Doležel J. Multiple displacement amplification of the DNA from single flow-sorted plant chromosome. Plant J. 2015. doi:10.1111/tpj.13035.PubMedGoogle Scholar
- Vrána J, Kubaláková M, Číhalíková J, Valárik M, Doležel J. Preparation of sub-genomic fractions enriched for particular chromosomes in polyploid wheat. Biol Plant. 2015;59:445–55.View ArticleGoogle Scholar
- Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J. Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics. 2000;156:2033–41.PubMedPubMed CentralGoogle Scholar
- Giorgi D, Farina A, Grosso V, Gennara A, Ceoloni C, Lucretti S. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS One. 2013;8:e57994.View ArticlePubMedPubMed CentralGoogle Scholar
- Kubaláková M, Kovářová P, Suchánková P, Číhalíková J, Bartoš J, Lucretti S, Watanabe N, Kianian SF, Doležel J. Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics. 2005;170:823–9.View ArticlePubMedPubMed CentralGoogle Scholar