Possible use of RFLP in Repeated Sequence - assbt
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Possible use of RFLP in Repeated Sequence - assbt
January.June 1994 Possible Use of RFLP in Repeated Sequence Families 43 Possible Use of RFLP in Repeated Sequence Families in Sugar Beet Breeding and For Management of Sugar Beet Genetic Resources Jean Fram;ois Bonavent, Anne Sophie Bournay, Sylvain Santonf and Andre BerviUe2 INRA-Dijon, Station d'Amelioration des Plantes, BV 1540, F- 21034 Dijon Cedex, France. I Present address: INRA, Ferme du Mouton, F-91190 Gifsur Yvette, France. 2Present address: INRA-ENSAM, Station d'Ameiioration des Plantes, 2 Place Pierre Via/a, F-34060 Montpellier Cedex, France. ABSTRACT Because they usually correspond to unique sequences, RFLP markers are used in genomic mapping, variety distinction, variety homogeneity and in reconstruction of phylogenies. Nevertheless, they are not the most suitable markers for all these applications. Their use in taxonomy is not always straightforward, since these sequences may be highly conserved as in the genus Beta L. The analysis of genetic variability allows calculation of genetic distances and enables the construction of phenograms, but not phylogenetic trees. Phylogenetic trees are constructed using other methods based on parsimony analysis and, hence, they do not always fit within taxonomic groups. Therefore, we have turned to other molecular markers which have already been found in sections Beta, Corollinae and Procumbentes, and, therefore, fit well into the main taxonomic divisions. RFLPs with repeated sequences are generally not used, although they offer a wide range of potential applications. Some have already been used and others appear suitable for use as markers. Here we present results with moderately and highly repeated sequences which display RFLP or are genome specific when used as probes. The main advantages and disadvantages of both RFLP types are discussed. Additional Key Words: moderately and highly repeated sequences, satellite DNA, molecular taxonomy, genetic variability, variety identification. 44 Journal of Sugar Beet Research Vol 31 No 1 and 2 The polymorphisms that exist at the DNA level can now be revealed through a wide range of methods for use as genetic markers in plant breeding (Landry et aI., 1987). The specific advantages of each kind of marker have already been analyzed. In the case of RFLP, several classes of DNA are involved. It appears that each class displays differential utility for various applications. Usually the polymor phisms are sought among unique sequences, a class that corresponds to truly unique sequences or sequences present in few copies. Isozymes, RFLP and some RAPD correspond to the same class of unique sequences. The polymorphisms that might exist in the moderately or highly repeated sequences are generally not useful, primarily because of the difficulties in visualizing the markers. Recently, several studies have been carried out on sugar beet involv ing RFLP types from non-repetitive DNA (Pillen et aI., 1992), and in moderately (Santoni and Berville, 1992a) and highly repetitive DNA sequences (Schmidt and Metzlaff, 1991; Santoni and Berville, 1992b) which enabled us to choose the most suitable field of applications for both types of RFLP. Some reviews of the classical RFLP methods are necessary. The DNA fragments coming either from cDNA libraries or from genomic libraries have to be checked for the degree of repetition in the genome. To avoid selection of repetitive fragments, which leads to redundan cy among clones, techniques are recommended which take advan tage of the high degree of methylation in repeated sequences. Genomic clones are obtained using a methylation sensitive restric tion enzyme (usually PstI) in order to enrich the library for unique sequences. However, in the library obtained, it is still necessary to eliminate those clones corresponding to repeated sequences. The col ony dot hybridization method, with genomic DNA as a probe, allows us to differentiate unique fragments, which give no or a faint signal, compared to cloned repeated fragments, which give a strong hybridization signal. The technique has been improved using minipreparations of plasmid DNA probed with genomic DNA. In fine probes corresponding to unique sequences are evaluated during autoradiography. The time of autoradiogram exposure must be two to three days prior to hybridization signal appearance to provide for identification of unique sequences within a genomic size of 1.3 pg. All the sequences that correspond to moderately and highly repetitive genomic DNA are thus eliminated in the RFLP probe screening steps. The genus Beta has recently been divided into 15 species includ ed within 4 sections. The section Beta includes the cultivated beets, sugar beet, table beet, Swiss chard, forage beet and B. maritima. The section Corollinae includes Eastern European species. The section January.June 1994 Possible Use of RFLP in Repeated Sequence Families 4S Nanae, from Anatolia, includes one species. The Procumbentes are from the coast of Morocco and the Canary Islands. Repeated gene families, such as ribosomal DNA and 5S DNA, have been widely used in plant analyses because homologies between species allow the use of heterologous probes to probe similarities. In sugar beet there are about 1,500 rDNA and 50,000 sDNA copies. For example, the phylogenetic study by Santoni and Berville (1992a) was developed for Beta based upon rDNA polymorphisms, which correspond to the chloroplastic DNA studies (Fritzche et aI., 1987) and agrees with the taxonomy proposed by Barocka (1966). RFLP in rDNA were used to examine gene flux between cultivated and wild beets (Santoni and Berville, 1992c). Bolting plants in sugar beet fields displayed both rDNA unit types found in cultivated and wild beet such as B. maritima. It is therefore likely that they have hybridized with the B. maritima that surround hybrid seed production fields. Cloning of highly repeated fragments has been carried out in three ways in Beta. The first way was to pick clones which yield intense hybridization signals when genomic DNA was used as a probe, as described above (Santoni and Berville, 1992b). However, here the library has to be prepared with a restriction enzyme which cuts methylated DNA. The second way was to cut genomic DNA with one of a series of restriction enzymes in order to detect discrete bands of the same size in the smear. These bands are selected , cloned and verified for the degree of repetition (Pillen et aI., 1992; Santoni and Berville, 1992b). The third method involves pulse field gel electrophoresis (PFGE) to detect large size fragments which may correspond to tandemly repeated sequences. In this case the restriction enzyme chosen does not restrict within the repeated sequences (lung et al. 1990; Schmidt and Metzlaff, 1991). For sugar beet and wild beet species all these methods have been used to obtain RFLP probes in unique and highly repeated DNA sequences, also called satellite DNAs. MATERIALS AND METHODS The list of plant materials is given in Table I. The plants were cultivated in a glasshouse at 25 °C for 16h (day) and 15°C (night). Leaves were harvested on at least 3-month-old plants. Three to five preparations were made using 5g fresh weight. Seeds from accessions unable to germinate were used to prepare DNAs. The methods used to obtain total DNA from dry seeds (Santoni et aI., 1991) or leaves, and for DNA preparation, DNA restriction, membrane transfer, hybridization and autoradiography were described by Santoni and Berville (l992a). Total DNA was restricted with ten units Table 1. List, origin and code numbers of wild and cultivated beet accessions. WB refers to the IVT stocks. Other codes are from INRA. Section Procumbentes Species Subspecies or common name B. procumbens B. patel/aris B. webbiana Corollinae Beta B. corol/iflora B. trigyna B. lomatogona B. macrorhyza B. intermedia B. maritima B. maritima B. maritima B. maritima B. maritima B. maritima B. maritima B. maritima var. maritima Origin of variety Rosenhof, Germany Rosenhof, Germany Rosenhof, Germany East Germany Turkish Beltsville, MD Turkish Turkish INRA Colmar, France Universite LilIe, France INRA Colmar, France INRA Colmar, France INRA Colmar, France Collection Deleplanque INRA Colmar, France INRA Dijon, France Author Reference Chr. & Sm. Moq. Moq. Zoss. Waldst. Fisch. Stev. Bunge Arcang. Arcang. Arcang. Arcang. Arcang. Arcang. Arcang. Arcang. WB 21, H 2148 WB 20, F 3977 WB 22, F 3981 WB 12 WB 8, G 2377 WB 5, G 2362 G 2365, A 1326 F 3971 H 2151 I 9001 F 3494 F 3954 F 4001 F 3903 H 2151 F 3997 I ~ ....0 :; " 1::. ~ [FJ c ""~ I:l:I "' :l ~ ~ '" ;:l :r - t~ 'Z. 0 '"" Q. N 48 Journal of Sugar Beet Research Vol 31 No 1 and 2 of enzyme per g DNA at 37°C for 2.5 h. Submarine agarose gel elec trophoresis or vertical 6070 polyacrylamide gels were used in TAE buf fer (Maniatis et al., 1982). Cloning of DNA fragments and data analysis of distances are given in Santoni and Berville (1992b). Every probe corresponding to a unique fragment (25ng) or to total DNA (200ng) was labelled using the Random Primed DNA or the nick translation DNA labelling kit of Boehringer, using 20ttCi of 32p_ aCTP (3,000Cilmmol). Sequences of the chosen cloned monomers were obtained by the enzymatic chain-termination procedure with 35S-')IATP and the Multiwell Sequencing kit from Amersham (Sanger et al., 1977). Se quence recovery from GenBank and EMBL databases was perform ed using the GCG program (Devereux et al., 1984). Sequence analysis was performed according to Wilburg and Lipman (1983). All other methods, cited, but not used by ourselves, are describ ed in the referenced articles. RESULTS AND DISCUSSION Moderately repeated, tandemly arranged sequences were cloned first from B. corolliflora; they correspond to satellite DNAs. Two novel sequences were found. The pBCE cloned fragment is about 258 bp long and is about 46% AT rich (Fig. 1). The degree of repetition of the BCESAT family is about 2,000 copies per haploid genome. pBCE contains several direct or inverted repeats (Fig. lA). The AluI and EcoRI patterns are shown for two species in Fig. 2. The EcoRI polymorphism in various species is displayed in Fig. 3. The copy number determination in a wide range of species is displayed in Fig. 4. Incomplete restriction, due to variable DNA methylation within species, is likely. The pBCA sequence is shown in Fig. lB. The pBCA fragment used as a probe for AluI restricted DNA from B. trigyna and B. lomatogona displays several signals at 160, 320 and 480bp, thus sug gesting a tandem array of fragments (Fig. 5). The BCASAT family contains about 15,000 motifs of 150bp and represents about 0.02% of the haploid genome. The EcoRI polymorphism from various species is displayed Fig. 6. The Beta, Corollinae and Procumbentes species are differentiated. The pBVE and pBVA DNA fragments reveal two highly repeated sequence families. BVESAT and BVBSAT families have been found in the section Beta. The PTS family (BPESAT) has been found in the section Procumbentes (Schmidt et al., 1991). BVESAT and BPESAT share homologies at medium stringency. However, at high January.June 1994 Possible Use of RFLP in Repeated Sequence Families 49 1 ~ CCTTCGAAGG CCAAAATCGG ACCAAAATGG CCTTCATTTA CCCAAAATGG 51 100 GTTTCAAAGC ATATGAGTGA ACTTTAATTG ACTCTTATAG TTATATATGT 101 150 ACCTATTATA ACTATATATG ACCTAACATG TGGCTAAATG CGCGAAACTA 151 161 AGTCAAA TGA G A 1 ~ CTAGCTCTTC CAGAGTGGTA TCTCACTGAT GGCTCGGGCC CCCCGGAAGC 51 100 CTTCTTCGCC TTCCACCTAA GCTGCGCAGG AAAAGCCCAA AGCCAATCCC 101 150 AGGGAACAGT AAAGCTTCAT AGGGTCTTTC TGTCCAGGTG CAGGTAGTCC 151 200 GCATCTTCAC AGACATGTCT ATTTCACCGA GTTTCTCTCC GAGACAGTGC 201 250 CCAGATCGTT ACGCCTTTCG TGCGGGTCGG AACTTACCCG ACAAGGAATT 251 258 TCGCTACC B Figure 1. A = Sequences of the pBCE fragment. B = Sequences of the pBCA fragment. stringency, BVESAT and BPESAT are perfectly distinguished. It is worth noting that Jung et al. (1990) and Schmidt et al. (1991) have found highly repeated sequences when looking for B. procumbens specific DNA probes. Surprisingly we were not able to clone a highly repeated DNA family in the section Corollinae. The pBCASAT1, pBCESATl, and pBVESATl-4 sequences are registered in the EMBL data bank under numbers X69916, X69917, and X69918, respectively. Dispersed repeated sequences were searched in the three Beta sections without success. There is no specific strategy for cloning such sequences, which might explain why we failed to clone them. However, the number of clones checked in this way is not large enough to draw a definitive conclusion. DNA fragments used to reveal polymorphisms in unique se quences enabled Pillen et al. (1992) to construct a linkage map of sugar beet with 108 RFLP loci, six isozymes and a morphological trait. The loci cover 789 cM with an average spacing of 6.9 cM. This Journal of Sugar Beet Research 50 Vol 31 No 1 and 2 map is to be enlarged by public institutes and by companies. We have previously reported results on ribosomal DNA probes which reveal polymorphisms in moderately repeated sequences (Santoni and Berville, 1992a). The polymorphisms in the rDNA genes are larger in B. maritima L. than in sugar beet. Several unit types exist in wild forms differing either in size (lOA, 10.7, 11, and 11.3 kb 4.2 2 3 4 4.2 1.618 1.618 0.516 0.516 0.258 0.258 Figure 2. Autoradiogram of the Southern transfer of restricted beet total DNA, electrophoresed in 0.8 070 agarose and hybridized with the pBCEl insert. MW markers: lkb and 123bp ladders from Bethesda Research Laboratories. A: B. trigyna, lane 1: AluI; lane 2: EcoRI; B: B. maritima F3903, lane 3: AluI; lane 4: EcoRI. January.June 1994 51 Possible Use of RFLP in Repeated Sequence Families or in sequences for the intergenic spacer (IGS) carrying 1,2 or 3 EcoRI sites 0.3 kb apart. Several length variable units of each type have been detected. They all represent less than 15070 of the units. In sugar beet we have found the 11 kb unit carrying 3 EcoRI sites in the IGS. Although sugar beet varieties have been introgressed by wild beet such as B. maritima, the corresponding expected rDNA alleles were not found in sugar beet or other cultivated beet varieties. We here suggest that the rDNA locus is linked to a major characteristic found in cultivated beets, and, therefore, wild alleles from B. maritima are eliminated because the plants carrying wild alleles do not display the correct characteristic. I,b 1 2 3 4 5 6 7 8 9 JO 11 12 13 14 15 I{b 11.6 11.6 10.5 8.37 10.5 8.37 6.0 6.0 1.75 1.75 1.63 1.63 516 394 Figure 3. Characterization of BCESAT moderately repeated family. Autoradiogram of EcoRI restricted beet nuclear DNA electrophoresed in 0.80/0 agarose gel and stained with ethidium bromide, transferred to nylon membrane and then probed with the pBCE fragnc :lt. For the following lanes, 12g DNA per lane was hydrolyzed with 60U of rc iction enzyme. Lane I: sugar beet 059; lane 2: table beet albin a FD 020; lane 3: B. maritima FD 010; lane 4: sugar beet 59; lane 5: B. maritima 19001; lane 6: table beet Crapaudine H2099; lane 7: B. webbiana; lane 8: B. maritima F3494; lane 9: B. trigyna G2377; lane 10: B. lomatogona G2362; lane 11: Petunia hybridaTlvl; lane 12: B. maritima F3903; lane 13: B. corollijlora WBI2; lane 14: B. macrocarpa; lane IS: PCR pBCE amplification. 52 Journal of Sugar Beet Research ____ pg ___ 0.11 A II . i, ng"------_ 10 2050 0.10.5 1 10 20 .~ I• • _ B Vol 31 No 1 and 2 • • • •-i • • I • " ••••• • •••• • ••••• •••• •••• I I I I 2 3 4 5 ) I 6 7 pBCE 5~g 0.5~g I 8 9 10 11 Figure 4. Determination of copy numbers for the BCESAT families. Dots were hybridiz ed with the pBCEI insert. A: dots of pBVEI insert (ng or pg). B: dots of total DNA (g); lane I: Petunia; lanes 2 and 3: sugar beet 59 and 059; lane 4: B. maritima F3903; lane 5: table beet Albina; lane 6: B. corol/iflora; lane 7: B. lomatogona; lane 8: B. maritima 19001; lane 9: B. maritima F3954; lane 10: table beet Crapaudine H2099; lane 11: B. webbiana. ~ :.:: ~ .....~ ~ ~ ~ kb ~ ~ :.:: ? .~ ~ ~ kb 0.483 0.322 0.483 0.322 0.161 0.161 Figure S. Autoradiogram of the Southern transfer of Alul restricted beet total DNA, electrophoresed in 0.8070 agarose, transferred to nylon membranes, and hybridized with the pBCAI insert. Lane I: Ikb ladder from BRL; lane 2: B. trigyna; lane 3: B. lomatogona. January.June 1994 Possible Use of RFLP in Repealed Sequence Families 53 kb kb 10.5 8.37 - - 10.5 - 8.37 6.0 - - 6.0 1.75 1.63 - Figure 6. Characterizationof the BCASAT moderately repeated family. Autoradiogram of EcoRl restricted beet nuclear DNA electrophoresed in 0.8070 agarose gel and stained with ethidium bromide, transferred to nylon membrane and then probed with the pBCA fragment. For the following lanes, 12g DNA per lane were hydrolyzed with 60U of restriction enzyme. Lane I: B. atriplicijolia; lane 2: table beet Crapaudine Vilmorin; lane 3: B. maritima F3494; lane 4: sugar beet 059; lane 5: B. maritima FDOIO; lane 6: sugar beet 59; lane 7: table beet H2099; lane 8: B. trigyna G2377; lane 9: sugar beet 059; lane 10: B. maritima F3995; lane 11: B. procumbens; lane 12: B. maritima F4001; lane 13: B. maritima F3903; lane 14: B. maritima 19001; lane 15: table beet albina; lane 16: B. maritima F3960; lane 17: B. webbiana; lane 18: MW marker Raoul. CONCLUSIONS Sugar beet linkage maps are necesssary to speed up efficient beet breeding. Many morphological and physiological traits are being map ped to enable breeders to split and recombine allele blocks in order to obtain better associations. Selection assisted by molecular markers should be used to introduce disease resistance genes from wild rela tives. DNA fragments used to reveal polymorphisms in tandemly ar ranged moderately repeated sequences identify polymorphisms suitable for use, as are RFLP in unique sequences. Examples are taken from our preceding work on RFLP in ribosomal DNA. Polymor phisms in the rDNA will allow mapping this gene family in a cross 54 Journal of Sugar Beet Research Vol 31 Noland 2 between the two B. vulgaris and B. maritima subspecies. However, the rDNA is assigned to the chromosome carrying a satellite (Chr I of sugar beet). Pillen et a!. (1992) clearly established that linkage group I carries major physiological functions and, because of the satellite, the rDNA locus also. The 5S DNA genes were not studied, but this family is likely to provide a mark for another chromosome. The efficacy of each sort of molecular marker is given for several applications (Table 2). DNA fragments used to reveal polymorphisms in unique se quences and cDNA have been found to be conserved in related plant species and particularly in beets (Nagamine et a!., 1989). The com parison of genotypes involves the computing of molecular similarities into genetic distances. There are several methods possible to calculate genetic distances. Each method takes into account the common presence of fragments, the common absence, the distances through correspondence analysis, etc. Each method establishes a specific distance between genotypes. Consequently, the aggregation of distances or similarities, which leads to a tree called a phenogram, using either the Joining or the UPGMA methods displays several phenograms. A phenogram is not a phylogram since it is unroated and there is no possibility of checking which is the best phenogram corresponding to the true phylogeny. The use of RFLP in phylogeny involves analysing data with methods based upon weighted markers, such as parsimony, in order to screen for the best suitable tree, or segmentation analysis to detect groups and subgroups which may possibly correspond to taxa. DNA fragments used to reveal polymorphisms in highly repeated sequences have been shown to vary considerably both in size and in sequence between distantly related species of Beta or within other genera, but have been shown to be highly conserved in closely related species. Moreover, they have resulted in species groupings consistent with the major taxonomic divisions delineated by botanists. Those repeated sequences were obtained from two different Beta sections. The differentiation, recognition and identification of RFLP in unique sequences if lines and varieties have been approached in several species because of the importance of varietal protection and to iden tify homogeneity. RFLP in unique sequences do not appear as the most convenient tool for such uses since numerous probes have to be checked, and, moreover, the greater the number of genotypes analyzed the greater the number of probes needed. Consequently the cost is prohibitive. In contrast, the polymorphisms found in highly and moderately repeated sequences might offer a simpler, less expen sive method. The variability of macrosatellite DNA has been found Table 2. Classification of molecular markers as tools according to use for applications in plant breeding. 'Yes' means possible; 'Poorly' means difficult or expensive; 'Potent' means fruitful; 'Partially' means some risk to use. PFGE means pulse field gel electrophoresis. 'No' means no guarantee for results. Taxonomy Cytogenetic studies Chromosome phylogeny karyotype organisation :: e; '::Z. ".".. ... '-0 '-0 Applications Tools ..".. Genetic maps Variety identification ~ c:;; s;: "~ Isozymes no no no yes yes poor Polypeptides yes no no yes yes poor :e "'l Isozymes no no no yes yes poor :i' RFLP unique cDNA and g DNA poor no no yes yes poor RFLP moderately rDNA, 5S DNA yes partially yes partially yes partially yes yes poor """ RFLP highly macrosatellite yes potent yes potent yes potent in interspecific prospect crosses in PFGE r" -= ~ ... Q. [fJ M inisatellite no no yes yes yes VNTR or microsatellite no yes yes yes yes RAPD unique no no no yes yes poor RAPD repeated yes yes yes yes yes ":: .Q """" ~ g, ~. '" '" 56 Journal of Sugar Beet Research Vol 31 No 1 and 2 for humans and mice under long blocks of repeats revealed by PFGE, and they represent only a few loci (Mar<;:ais et aI., 1991). The varia tion in size is quite large (420 kb to 2,650 kb). The segregation of polymorphisms has been found to be Mendelian and no recombina tion event was detected after 150 cycles of meiosis. Therefore, these sequences constitute highly polymorphic, centromeric markers, which can be used in linkage analysis and to compare lines through PFGE using few macrosatellite probes. In contrast, RFLP probes targeting unique sequences usually require numerous probes. ACKNOWLEDGEMENTS Thanks are due to l. P. Denisot for enabling us to access the beet wild form collection and to 1. Delbut for his expertise in photography. LITERATURE CITED Barocka, K.H. 1966. Die Sektion Corollinae der Gattung Beta (Toumef) L. Z. Pflanzenzucht. 56: 379-388. Devereux l., P. Haeberli and O. Smithies. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12: 387-395. Fritzsche, K., M. Mezlaff, R. Melzer and R. Hagemann. 1987. 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Hum. Genet. 86: 311-316. January-June 1994 Possible Use of RFLP in Repeated Sequence Families 57 Nagamine, T., G. A. Todd, K. P. McKann, H. 1. Newbury and B. V. Ford-Lloyd. 1989. Use of restriction fragment length polymor phism to fingerprint beets at the genotype and species levels. Theor. Appl. Genet. 78: 847-851. Pillen, K., G. Steinrucken, G. Wricke, R. G. Hermann and C. Jung. 1992. A linkage map of sugar beet (Beta vulgaris L.). Theor. Appl. Genet. 84: 129- 135. Sanger, F., Nicklen S. and A. R. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. (USA) 74: 5463-5467. Santoni, S., P. Faivre-Rampant, E. Moreau and A. Berville. 1991. Rapid control of purity for the cytoplasm of male-sterile seed stocks by means of a dot hybridization assay. Mol. Cell. Probes 5: 1-9. Santoni, S. and A . Berville. 1992a. Characterization of the nuclear ribosomal DNA units and phylogeny of Beta L. wild forms and cultivated beets. Theor. Appl. Genet. 83: 533-542. Santoni, S. and A. Berville. 1992b. Two different satellite DNAs in Beta vulgaris L.: evolution, quantification, and distribution in the genus. Theor. Appl. Genet. 84: 1009-1016. Santoni, S. and A. Berville. 1992c. Evidences for gene exchanges bet ween sugar beet (B. vulgaris L.) and wild beets: consequence for transgenic sugar beets. Plant Mol. BioI. 20: 578-580. Schmidt, T and M . Metzlaff. 1991. Cloning and characterization of a Beta vulgaris satellite DNA family. Gene 101: 247-250. Schmidt, T, C. J ung and M. Metzlaff. 1991. Distribution and evolution of two satellite DNAs in the genus Beta. Theor. Appl. Genet. 82: 793-799. Wilburg, W. 1. and D. 1. Lipman. 1983. Description of part of the method used in FSTPSCAN. Proc. Natl. Acad. Sci. (USA), 60: 726-730.