Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome
© Ríos et al; licensee BioMed Central Ltd. 2008
Received: 04 February 2008
Accepted: 09 August 2008
Published: 09 August 2008
Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background.
Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues.
In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement.
The rapid increase of world population, the field degradation by soil salinization and erosion, and the likely fluctuations in climate caused by global warming will pose new and known challenges to agriculture during this century . Crop improvements required to cope with these challenges could be attained through agronomic advances, leading to a better use of fertilizers, protection agents or soil rescue, and exploitation of recent technologies for plant breeding. Despite the outstanding importance of genetics-based breeding applied to spontaneous mutations and conventional hybrids, molecular and genomic tools are expected to develop their great potential for crop improvement through functional genetics analysis, involving gene and function discovery and genome modification.
Citrus, some of the most important fruit crops worldwide, are perennial trees requiring a juvenility period of several years and frequently are parthenocarpic and sexually self-incompatible [2, 3], which considerably impairs traditional breeding. Genomic technology, including methods to rapidly identify and manipulate genes of agricultural interest, holds promise of improvements that may be difficult through traditional approaches. In recent years, Citrus has been the target of several genomic developments including large EST collections [4–7], cDNA and oligonucleotide-based microarrays [4, 8, 9], BAC libraries and BAC end sequencing (BES) (to be published). However, functional studies, i.e. genetic transformation and the capability to perform reverse genetic analyses, are also considerably impaired. In citrus, high throughput transgenic programs such as the generation of RNA interference knockouts, activation tagging through enhancer elements, gene-trap T-DNA insertions, or transposon tagging systems have not been developed yet. Since no efficient tagging or insertional procedures are available in these species, other gene disruption methods including strategies based on genome-wide mutagenesis such as TILLING and fast neutron mutagenesis have been initiated. These approaches are non-transgenic and may have particular interest for the industry where the debate on genetically modified organisms has restricted application of these technologies to crop improvement. Both approaches, however, are of limited usefulness as strategies for reverse genetics because of the lack of knowledge on Citrus genomic sequence and the large amount of space required for the establishment of mutant populations. ECOTILLING on natural citrus variants and microarray-based detection of deletions in fast neutron citrus mutants are apparently very straightforward approaches. In this work we explore the potential of this last idea using two fast neutron Citrus clementina hemizygous mutants from the IVIA collection and a 20K cDNA citrus microarray.
Physical mutagenesis through fast neutron irradiation has been reported to cause variable genomic deletions ranging in size from few base pairs to 12 kb in Arabidopsis thaliana [10, 11]. Several approaches have been used to characterize plant genomic deletions at the molecular level. These mostly include positional cloning , a method applicable to any kind of genetic lesion that, however, needs highly saturated genetic maps; PCR-based reverse genetics techniques [11, 13], requiring a previous considerable knowledge of genomic sequence; and genomic subtraction procedures [14–16], which do not need sequence information but are strongly dependent on the gene dosage. Since very little is known about Citrus genome sequence and the Citrus induced deletions are in hemizygous gene dosage, an array-based procedure as the one employed for identifying homozygous gene deletions in Arabidopsis  seems more suitable for our purpose than those methods. Although the main application of microarrays is transcriptome profiling analysis, microarrays can also be used to study DNA variation. Oligonucleotide arrays are particularly suited for the detection of single nucleotide mismatches during hybridization, and hence for the discovery of novel DNA variants or the determination of known variants. The origin of this technique relies on a cytogenetic method described 25 years ago named "Comparative Genomic Hybridization" (CGH) that used differential DNA hybridization on chromosome spreads for visualization of deleted or amplified genomic regions in tumour tissues . Subsequently, different laboratories mostly working on cancer research independently applied microarray technology to genomic DNA hybridization procedure, a technique consequently named array-CGH [19–23]. Array-CGH was successfully utilized to detect gene duplications in Arabidopsis and rice , and to validate aneuploidy analysis performed by quantitative fluorescent PCR in Arabidopsis . Therefore, this method has proven to be suitable to study chromosomal imbalances in plants.
For the characterization of the deleted regions we also leaned on comparative genomics with other dicots since available physical citrus maps are not yet integrated with known genetic maps. Comparative genomics takes advantage of available information on gene content and order in genomic DNA from different species to infer phylogenetic relationships and formulate hypotheses on DNA evolutionary dynamics. Whole genomes are preferentially compared when available, but more often relatively short stretches of DNA or polymorphic markers are used.
The main objective of this work was to identify deleted genes on a heterozygous genetic Citrus background, provided by fast neutron generated mutants, through array-Comparative Genomic Hybridization. In addition, we also explored the possibility of using comparative genomics with annotated dicot genomes assisted by BAC end sequencing for the generation of partial physical maps of the deleted Citrus regions.
Results and discussion
Procedure for the characterization of hemizygous deletions in Citrus
Identification of deleted alleles in 39B3 and 39E7 fast neutron mutants of Citrus clementina
For this study, two mutants obtained by fast neutron mutagenesis of wild type Citrus clementina were selected from the IVIA mutant collection. These mutants, named 39B3 and 39E7, were expected to carry DNA deletion lesions in hemizygous dosage and showed a delay in natural colour break in fruit peel. The 39B3 mutant exhibited a delay in colour change from green to orange while 39E7 was better characterized by an abnormal final yellowish colour instead of the natural orange coloration. Putative deleted genes in the mutants were first identified through an approach based on genomic hybridization (array-CGH) that exploited a recently developed Citrus microarray containing 21240 cDNAs [4, 5]. To this end, total genomic DNA from four independent samples of mutants 39B3 and 39E7 were Cy3 or Cy5-labelled and cohybridized with wild type DNA labelled with the complementary Cy5 or Cy3 probe on four independent microarray slides. Fluorescence intensity data were normalized and single ESTs showing a mutant/wild type signal ratio lower than 0.7 fold, with a P-value lower than 0.2 (39B3) or 0.1 (39E7), were selected as putative candidates.
Gene dosage measurement of deleted genes in 39B3 and 39E7 Citrus mutants.
EST accession number (GenBank)
Real-time PCR gene dosage
0.56 ± 0.02
0.99 ± 0.09
0.60 ± 0.08
0.96 ± 0.04
0.60 ± 0.03
0.98 ± 0.03
0.50 ± 0.02
0.98 ± 0.11
0.56 ± 0.06
0.96 ± 0.11
0.59 ± 0.04
1.15 ± 0.07
1.05 ± 0.13
0.59 ± 0.11
1.04 ± 0.12
0.59 ± 0.12
1.14 ± 0.19
0.58 ± 0.08
1.12 ± 0.10
0.64 ± 0.04
1.24 ± 0.22
0.61 ± 0.05
1.04 ± 0.07
0.63 ± 0.11
Clustering of homologues of Citrus deleted genes in the poplar genome
Overall, these observations suggest that the Populus genomic regions homologous to the Citrus deletions were less fragmented than their counterparts in Arabidopsis and Vitis, and consequently microsynteny on the considered segments was higher with the Populus genome. These results are striking since Citrus and Arabidopsis belong to Sapindales and Brassicales orders (inside the same clade eurosids II) while Populus is included in the eurosids I clade, and Vitis is part of Vitaceae, a family outside of rosids .
Gene arrangement and partial physical map of the 39B3 deletion
Gene components of the Citrus 39B3 deletion.
EST accession number (GenBank)
Ubiquitin conjugating enzyme
Sterile alpha motif (SAM) domain-containing protein
ATP-dependent Clp protease, clpC homolog
Putative pol polyprotein
Tudor domain-containing protein
Respiratory burst oxidase homolog
FHA domain-containing protein
Putative pentatricopeptide (PPR) repeat protein
ERD1 protein, chloroplast precursor
Poly(A)-binding protein II-like
Tubulin-specific chaperone C-related
Listing of BACs included in the Citrus 39B3 deletion.
BES ID (GenBank)
BLASTX against plant proteins
gi| 91805627| hypothetical protein
gi| 7576215| hypothetical protein
gi| 7576215| hypothetical protein
gi| 25411577| probable retroelement pol polyprotein
gi| 6469119| mitochondrial phosphate transporter
gi| 92895029| Polynucleotidyl transferase (retrotransposon protein)
gi| 30027167| auxin response factor-like protein
gi| 87240692| Helix-loop-helix DNA-binding
gi| 79331867| AML1; RNA binding/nucleic acid binding
gi| 33113977| putative copia-type pol polyprotein
gi| 51968598| peroxisomal Ca-dependent solute carrier-like protein
gi| 51968598| peroxisomal Ca-dependent solute carrier-like protein
gi| 25402907| protein F5M15.26 (retrotransposon protein)
gi| 14334878| putative ATP-dependent Clp protease ClpD
gi| 14334878| putative ATP-dependent Clp protease ClpD
gi| 6729532| putative protein
gi| 6729532| putative protein
This mapping contained three gaps, one at the 5' deletion junction and two internal ones (Figure 5B) delimiting three main BAC clusters, composed of B1 to B4, B5 to B8, and B9 to B13. BACs B11 and B12 were connected by unigene aCL4690Contig1 coding for a putative subunit ClpD of an ATP-dependent Clp protease, whose sequence was shared by both BACs. Similarly B12 and B13 interaction is mediated by unigene aCL1915Contig2 (Table 2, 3). Real-time PCR quantification of gene dosage for some of the BAC ends (Figure 5A) confirmed the presence of these sequences at half dosage in the mutant genotype, indicating that the 39B3 mutation is a hemizygous deletion. Indeed, all analyzed BACs covered an internal segment of the deletion except B13 that exhibited haploid gene dosage on the left end and diploid dosage on the right one, suggesting that B13 contained the 3' border of the 39B3 deletion.
The above results indicated that the microsynteny between Citrus and Populus genomes was high enough to predict gene arrangement and to build a partial physical map of a Citrus genomic segment of about 700 kb, as inferred from the length of poplar homologous regions. Nevertheless, the observation that a 700 kb Citrus fragment only contains 21 genes may result striking considering an average distance of 10 Kb between adjacent genes, as deduced from the estimations of Citrus genome size (367 Mb) and gene number (35,000–40,000). It should be noted, however, that the microarray used in these analyses contains between approximately 2/3 and 1/2 of the estimated gene content of the Citrus genome, which may account for a major part of the hypothetical "loss" of deleted candidates. While this is a weakness of the currently available Citrus arrays, non-attributable to the array-CGH procedure, more complete results are expected after the development of a more representative cDNA microarray. Other limitations of the method may be related to the differential hybridization potential of different cDNAs, including for instance cross-hybridizations. In this regard, oligonucleotide arrays are particularly suited for the detection of dissimilar DNA variants. Alternatively, synteny might be limited to several genes located on a bulk of non-conserved sequences inside this 700 Kb region, a possibility that may only be corroborated after genome sequencing.
Overall, the data indicated that the Populus genome is a useful model for comparative genomics which may be used to characterize hemizygous deletions in Citrus.
The Citrus 39B3 deletion shows higher local gene colinearity with Populus than with Arabidopsis
These results confirm high local gene colinearity with poplar in the genomic region covered by 39B3 deletion. Taking together gene content and order conservation (Figures 2, 3 and 6), it is inferred that in the studied DNA deleted segment there was higher gene colinearity with Populus, which diverged about 109 million years ago (Mya), than with Arabidopsis, splitting from the Citrus lineage about 87 Mya , despite gene colinearity generally being correlated with phylogenetic relatedness. A similar conclusion has been reached in our group, after comparing the whole collection of Citrus BES with the poplar and Arabidopsis genomes (to be published), and also in previous works in papaya and melon. In papaya, BES alignment to the annotated genomes rendered higher gene colinearity with Populus than with Arabidopsis, although both Arabidopsis and papaya belong to the order Brassicales . In melon, microsynteny studies based on the sequence of two BACs also concluded that melon was closer to Populus than to Arabidopsis or Medicago truncatula . These observations may be explained by a differential genome evolutionary dynamics in poplar and Arabidopsis lineages . The more recent appraisals estimated that last whole genome duplications occurred not later than 60–65 Mya in Populus and around 24–40 Mya in Arabidopsis lineages [28, 34–36]. Despite the older poplar event, genome rearrangements involving gene loss and translocation following these duplications were much more frequent in Arabidopsis ancestors . Such a highly active genome dynamics probably caused the dispersion of genes and the subsequent reduction in synteny and gene colinearity with even related species. The different behaviour of Populus and Arabidopsis ancestral genomes still deserves further explanation. It has been suggested that woody long-lived species like poplar trees may undergo a slower genome dynamics due to their juvenile period that delays sexual fecundation for several years and to the recurrent contribution of gametes from aged individuals of previous generations . In addition, species like Arabidopsis thaliana may have very active mechanisms for unequal or illegitimate recombination causing frequent chromosomal rearrangements such as translocations, insertions and deletions. In this context, it is notable that nearly all Citrus species and many related genera have 2n = 18, probably indicating slow chromosomal evolution in this group.
Chlorophyll a/b ratio is modified in 39B3 mutant
Total chlorophyll content in green tissues from 39B3 mutant and "wild type" cultivar of Citrus clementina.
0.76 ± 0.25
2.23 ± 0.19
0.15 ± 0.05
0.71 ± 0.24
2.49 ± 0.17
0.48 ± 0.01
0.29 ± 0.01
In this study, we propose a procedure for the genetic characterization of genomic hemizygous deletions in citrus mutants. The procedure that might be applied to other non-sequenced species of similar genome size and ploidy level is illustrated with the study of the 39B3 Citrus clementina deletion, generated by fast neutron bombardment. The proposed strategy utilizes several genomic resources such as array-Comparative Genomic Hybridization (array-CGH) technology, EST and BAC end sequencing databases and poplar genome annotation.
The array-CGH results led to the conclusion that the 39B3 deletion removed at least 21 genes while a partial physical map of about 700 kb of the deleted region was inferred by comparison of two homologous genomic regions from poplar with a Citrus BES database.
Structural data including gene content and order in the deletion was utilized for microsynteny and local gene colinearity studies concluding that in the studied region Citrus is more similar to Populus than to Arabidopsis, a phylogenetically closer species. This observation supports previous works on other species and suggests that the Arabidopsis lineage underwent a quicker genome evolutionary dynamics than the Populus one.
Among the deleted alleles, the function of ClpC-like, coding for a putative subunit of a protease involved in chlorophyll b synthesis was directly related to the mutant phenotype since green mutant tissues had a lower chlorophyll a/b ratio.
Approximately 6 years-old clementine trees (Citrus clementina Hort. Ex Tan. cv. clemenules) grown under standard agricultural practices at the Instituto Valenciano de Investigaciones Agrarias (IVIA) were used in this study. Commercial highly heterozygous clementine cultivars are considered "wild type" material, while the 39B3 and 39E7 genotypes that belong to the IVIA mutant collection were obtained through bud irradiation with fast neutrons (5–6 Gy) at the Instituto Tecnologico e Nuclear (Sacavem, Portugal) in the frame of a much wider breeding program. Both mutants are expected to carry DNA deletion lesions in hemizygous dosage and showed altered patterns of colour change of fruit peel.
The protocol was adapted from several published array-Comparative Genomic Hybridization (array-CGH) methods pursuing mainly the measurement of copy-number changes in human genomic DNA [48–50], and the study of large-scale genetic variation of the symbiotic bacteria Sinorhizobium meliloti . Genomic DNA was isolated from leaves of wild type and mutant plants, using DNeasy plant mini kit (Qiagen). Four Cy3 or Cy5-labelled independent biological samples from each mutant plant were co-profiled on four 20K Citrus cDNA microarrays containing 21240 EST, using Cy5 or Cy3-labelled control genomic DNA, respectively. Label probes were prepared as follow: Cy3- or Cy5-dCTP fluorescent nucleotides (Amersham Biosciences) were incorporated directly in control and mutant genomic DNA (2 μg) using BioPrime Array CGH Genomic Labelling System (Invitrogene). Purified Cy5 and Cy3 labelled probes (about 50 μl each) were combined and mixed with 30 μg Cot-1 DNA (Invitrogene), 100 μg yeast tRNA (Invitrogene), and 346 μl TE buffer pH 7.4. Cot-1 DNA and yeast tRNA were used to block non-specific hybridization. Samples were laid on a microcon YM-30 filter (Millipore), and subsequently centrifuged until sample volume was reduced to approximately 48 μl. Finally, 10.2 μl 20× SSC and 1.8 μl 10% SDS were added to the probe mixture to reach a final volume of 60 μl containing 3.4× SSC and 0.3% SDS. For microarray hybridization, the probe mixture was denatured by heating at 97°C for 5 minutes, and immediately incubated at 37°C during 30 minutes to block repetitive DNA sequences. Hybridization mixture was applied to a 37°C pre-warmed hybrid-slip (Sigma), and a pre-warmed array slide was lowered onto the mix. Microarrays were hybridized in darkness at 65°C overnight (16–20 hours) using a glass array cassette following manufacturer's instructions (Ambion, cat. n° AM10040). To prevent evaporation of hybridization solution during incubation, 5 μl of 3× SCC were poured into the reservoir inside the cassette chamber. Following hybridization, microarray slides were placed in a rack and the cover slip removed by 10 minutes immersion in a washing chamber containing 2× SSC and 0.03% SDS at room temperature (RT). Microarray slides were passed through a series of washes on a shaking platform. Wash series were as follow: 2× SSC, 0.03% SDS for 5 min at 65°C, followed by 1× SSC for 5 min at RT, and 3 × 15 min washes in 0.2× SSC at RT. After first wash slides were transferred to new racks to minimize transference of SDS to the next washing solution. Microarray slides were dried by centrifugation for 5 min at 300 rpm by using an Eppendorf 5804-R tabletop centrifuge. Arrays were immediately scanned at 5 μm. Cy3 and Cy5 fluorescence intensity was collected by using a ScanArray Gx (Perkin Elmer). The resulting images were overlaid and spots identified by the ScanArray Express program (Perkin Elmer). Spot quality was first measured by the signal-to-background method with parameters lower limit (200) and multiplier (2), and subsequently confirmed by visual test. Data analysis was performed using the Limma package from the R statistical computing software [52–54]. A mutant/wild type signal lower than 0.7, with a P-value not higher than 0.1 (39E7) or 0.2 (39B3) were the cut-off values for positive EST identification. The experimental design of microarray experiments has been loaded into the ArrayExpress database  under accessions E-MEXP-1432 and E-MEXP-1433.
Gene dosage measurements
Quantitative real-time PCR was performed on a LightCycler 2.0 instrument (Roche), using the LightCycler FastStart DNA MasterPLUS SYBR Green I kit (Roche). Reaction composition and conditions followed manufacturer's instructions. Each individual PCR reaction contained 2 ng of genomic DNA from wild type or mutant, obtained with the DNeasy plant mini kit (Qiagen). Cycling protocol consisted of 10 min at 95°C for pre-incubation, then 40 cycles of 10 sec at 95°C for denaturation, 10 sec at 60°C for annealing and 10–25 sec at 72°C for extension. Fluorescent intensity data were acquired during the extension time. Specificity of the PCR reaction was assessed by the presence of a single peak in the dissociation curve after the amplification and through size estimation of the amplified product. For gene dosage measurements, we used the relative quantification-monocolor analysis from the LightCycler Software 4.0 package (Roche). This program compares the ratio of a target sequence to a reference DNA sequence in the mutant sample with the ratio of these sequences in a wild type sample. PCR and normalized calculations were repeated in at least three independent samples from each mutant and wild type, rendering an estimation of target gene dosage in the mutant genotype. Primers for the reference sequence were obtained from CX293764.
DNA sequences of Citrus unigenes containing positive array-CGH ESTs were used in online TBLASTX searches against genomic databases from the annotated genomes of Arabidopsis thaliana , Populus trichocarpa  and Vitis vinifera  at an E-value cut-off of 10-5. For each gene, the best hit was placed on a chromosomal map while the second and third hits were only positioned in the map if they were located closer than 250 kb to any other hit. Two 700 kb regions from chromosomes 12 and 15 from the Populus genome including homologous genes to 39B3 array-CGH positive unigenes, were used as queries in a BLASTN local search on a Citrus BAC end sequence database. Only hits corresponding to those BAC ends showing an E-value lower than 10-5 in both chromosome searches were considered for the building of a local physical map of the 39B3 deletion.
BAC isolation and analysis
DNA from Citrus BACs was isolated with the Rapid Plasmid Miniprep System (Marligen Biosciences). Purified BACs were used as templates in PCR reactions in a total volume of 15 μl, including 0.2 mM dNTP, 2 mM MgCl2, 0.5 μM of each primer, 0.38 units of Netzyme DNA polymerase (Molecular Netline Bioproducts) and 0.1 ng of BAC DNA. After an initial denaturing step for 5 min at 95°C, amplification was performed for 35 cycles of 30 sec at 95°C, 30 sec at 60°C and 30 sec at 72°C, followed by 5 min incubation at 72°C. The PCR product was subjected to 1.5% agarose DNA electrophoresis.
At least, three developing and mature leaves and fruit exocarp sectors from standard and 39B3 mutant lines of clementine were randomly collected per sample. Fruit exocarp tissues from a wild type clementine tree showing fruit colour delay due to altered environmental conditions were also sampled for chlorophyll analyses. Chlorophylls a and b were extracted with N,N-dimethylformamide for 72 h in the dark at 4°C and quantified through the absorbance at 647 and 664 nm following a reported procedure . Absorbance was measured using a Varian Cary 50 UV-visible spectrophotometer (Varian).
Gene expression measurements
Total RNA was extracted from fruit exocarp of wild type and 39B3 mutant using the RNeasy Plant Mini Kit (Qiagen). RNA concentration was determined by a fluorometric assay with the RiboGreen dye (Molecular Probes) following the manufacturer's instructions. About 5 μg of total RNA were reverse transcribed with the SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen) in a total volume of 20 μl. Single strand cDNA corresponding to ClpC-like and ClpD-like genes was amplified by quantitative real-time PCR on a LightCycler 2.0 instrument (Roche), using the LightCycler FastStart DNA MasterPLUS SYBR Green I kit (Roche). One μl of a 20 times diluted first-strand cDNA was used for each amplification reaction. Cycling protocol consisted of 10 min at 95°C for pre-incubation, then 40 cycles of 10 sec at 95°C for denaturation, 10 sec at 60°C for annealing and 15 sec at 72°C for extension. Melting curve analysis by applying increasing temperature from 65°C to 95°C (0.1°C/s) and gel electrophoresis of final product confirmed single amplicons. For expression measurements, we used the absolute quantification analysis from the LightCycler Software 4.0 package (Roche), and calculated expression levels relative to wild type values. Three independent biological samples were analyzed for wild type and mutant genotypes. Primers sequences are provided in Additional file 2.
ClpC-like genomic sequence
ClpC-like genomic sequence from very few base pairs after the ATG until few base pairs before the stop codon was divided in four PCR fragments: Amplicon 3/4 (1820 bp) was amplified and sequenced with primers CLPC3 and CLPC4, amplicon 5/8 (2168 bp) was amplified with primers CLPC5 and CLPC8 and sequenced with primers CLPC5, CLPC8, CLPC10 and CLPC11, amplicon 7/2 (1446 bp) was amplified and sequenced with primers CLPC7 and CLPC2, and amplicon 1/6 (1158 bp) was amplified and sequenced with primers CLPC1 and CLPC6. Each amplicon was obtained by combining the product of 6–8 independent reactions. Primers sequences are provided in Additional file 2.
Work at Centro de Genómica was supported by INIA grant RTA04-013, INCO contract 015453 and Ministerio de Educación y Ciencia grant AGL2007-65437-C04-01/AGR. We also thank Dr. José Marqués at the Instituto Tecnologico e Nuclear (Sacavem, Portugal) for irradiation with fast neutrons. Help and expertise of A. Almenar, E Blázquez, I. López, I. Sanchís and M. Sancho are gratefully acknowledged.
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