Patent Abstract:
the present invention relates to the selection of sunflower genotypes with high oleic acid content in seed oil . the invention concerns more particularly molecular markers useful for a rapid and easy selection of sunflower lines and then sunflower hybrids capable of producing seeds having high oleic acid content .

Detailed Description:
the present invention relates to pervenets mutation specific molecular markers located in a 29 kb region , a map thereof is represented on fig2 . this region carrying these molecular markers is divided in 3 sequences , from 5 ′ to 3 ′: sequence n1 having 6 . 662 kb : δ12hos / δ12lor common part carrying a δ12 - desaturase gene ( seq id no : 1 ); sequence n2 : ho specific insertion ; ( this sequence has been partially sequenced ( seq id no : 2 ); sequence n3 : the 3 ′ adjacent part of the ho specific insertion fragment . the molecular marker of the invention comprises the isolated nucleic acid seq id no 3 having 872 bp or a sequence having a high degree of homology with sequence seq id no 3 . said nucleic acid sequence is a part of sequence seq id no : 4 having 3026 bp and being identified as sequence n1 / 2 on fig2 . the marker having seq id no : 3 is located between 2154 bp and 3026 bp of seq id no : 4 . in the present description , a high degree of homology denotes a homology ( ratio of the identical nucleotides to the total number of nucleotides ) of at least 85 %, and preferably 90 %, for the nucleotide sequences when they are aligned according to the maximum homology by the optimal sequence alignment method of align . this method is used especially in the gcg software of devereux et al . ( 9 ). the invention also relates to the isolated nucleic acid fragments having 10 - 30 bp and which hybridize with seq n2 ( seq id no : 2 ). said fragments are particularly useful tools as primers for nucleic acid amplification , for example pcr amplification . the invention also relates to the primer pairs useful for nucleic acid amplification , which comprise : 1 ) as the first member of the pair a nucleic acid fragment having 1 to 30 bp and which hybridises with sequence n1 ( seq id no 1 ) and 2 ) as the second member of the pair a nucleic acid fragment having 10 to 30 bp and which hybridises with seq id no : 2 . in the present description , acid nucleic sequences codes end by a number whereas acid nucleic fragments useful as primers end by f or r depending on they are designed forward or reverse , respectively . these references are reported on the map of the 29 kb region ( fig2 ). the invention also relates to the isolated ssr nucleic acid sequence seq id no 10 having 45 bp with 16 tta repeat microsallelites tta . this sequence involving a polymorphism associated with the pervenets mutation may be used in selection programs for rapidly identifying the locus of the pervenets mutation . said ssr sequence is located in the intron of the oleate - desaturase gene besides the pervenets insertion . therefore , said ssr sequence is very useful for mapping the oleate - desaturase gene in the genome of sunflower plants to be selected . the invention also concerns the molecular marker specific for mapping the oleate - desaturase gene in the genome of the sunflower to be selected which comprises the nucleic acid sequence seq id no 10 or a sequence having a high degree of homology with sequence seq id no 10 . the invention also concerns the isolated nucleic acid fragments seq id no 11 and seq id no 12 . said fragments are useful as primers for amplifying the above ssr sequence : all the isolated nucleic acid sequences and fragments of the invention may be obtained by chemical synthesis following the conventional methods well known by the person skilled in the art . the invention also relates to a process for selecting sunflower having seeds with a high content of oleic acid which comprises the steps of : extracting the genomic dna ; amplifying said genomic dna by means of primer pair , said pair being constituted with a first member of nucleic acid fragment having 10 to 30 bp , which hybridises with sequence n1 ( seq id no : 1 ) and a second member of nucleic acid fragment having 10 to 30 bp , which hybridises with sequence n2 ( seq id no : 2 ); hybridizing the amplified dna fragment with the labelled sequence seq id no 3 and isolating the genotypes giving a positive hybridisation signal . this process allows the selection of genotypes having the pervenets mutation without needing to determine the oleic acid content of the seeds , which considerably reduces the selection time . following an advantageous embodiment of this process , the pervenets mutation is firstly mapped in most of progenies ( most of sunflower line couples display polymorphism for the ssr ) by a process comprising the steps of : extracting the genomic dna ; amplifying said genomic dna by means of primers seq id no 11 and seq id no 12 ; isolating the clones having a dna fragment length which is different from a reference clone without the pervenets mutation . the thus selected clones have the pervenets mutation and are used as such in the above invention process . examples of the primer pairs useful in the invention process are the : isolated nucleic acid fragments seq id no : 5 and seq id no : 6 as first member of said pair , and isolated nucleic acid fragments seq id no : 7 to seq id no : 9 as second member of said pair . the invention also relates to the molecular marker constituted by the isolated nucleic sequence seq id no : 13 having 763 bp , which is common to lo and ho regions and located over the insertion point of the pervenets mutation . the insertion point is located between the bp 83 and bp 366 of seq id no : 13 . the invention also relates to the isolated nucleic acid fragments having 10 - 30 bp and which hybridise with seq id no : 13 . said fragments are also useful tools as primers for nucleic acid amplification , for example for pcr amplification . the invention also relates to the process for amplifying the region across the insertion pervenets mutation site both in lo and ho genotypes . said process comprises the steps of : extracting the genomic dna ; amplifying said genomic dna by means of primer pair , said pair being constituted with a first member of nucleic acid fragments having 10 to 30 bp which hybridises with sequence n1 ( seq id no : 13 ). in all the invention processes , the amplification step may be carried out by any nucleic amplification method known by the person skilled in the art , for example by the well - known pcr amplification method . a 6662 kb region carrying the δ12hos and δ12lor common part in rha 345 ho line ( seq n1 ) was cloned , sequenced and characterized . it was shown that it carries a putative functional δ12 - desaturase gene ( seq n1 - δ12 ). indeed , the tataaa and caat consensus promoter elements are present at positions − 92 bp and − 42 bp upstream the + 1 transcriptional point , respectively . because of its sequence and its position , the aagtaa sequence , 16 nt before the end of the transcribed part , corresponds to a poly - a signal aataaa , except for one nucleotide . the δ12 - desaturase gene is interrupted by a 1686pb intron between nt 83 and nt 1767 upstream the + 1 transcriptional point . the consensus splicing sites gt and ag are present at the intron extremities . a 16 repeats of a tta ssr motive is revealed in the intron sequence between nt 784 and 832 upstream the + 1 transcriptional point . using primer pairs enabling this ssr amplification ( seq n1 - 1f and seq n1 - 1r ), size polymorphism at this locus in a set of 42 ho and lo genotypes was tested ( table 1 ). pcr amplification leads to 237 / 240 / 243 bp fragments corresponding to 15 / 16 / 17 ssr repeats , respectively . in the 174 individuals segregating population already studied ( 7 ), a strict co - segregation between the ssr polymorphism of the ho parental line ( 16 motifs ) and the δ12hos allele ( example 2 ) was revealed . so , this ssr sequence displays a polymorphism tightly linked to the pervenets mutation . consequently , it can be used to map the locus of the δ12 - desaturase gene in sunflower genome in most of crosses . moreover , it may be used in selection programs for fast screening of genotypes carrying the pervenets mutation by pcr method . the invention relates to this ssr nucleic acid sequence present in seq id n1 and seq id n1 - δ12 . the invention also relates to sequences having a high degree of homology with sequence seq id n1 or n1 - δ12 and nucleic acid fragments that can be used as pcr primers to amplify the ssr motive such as seq id n1 - 1f and seq id n1 - 1r leading to a pcr fragment carrying the 15 , 16 or 17 tta motives . in order to select molecular markers corresponding to the pervenets mutation itself , parts of the 7 . 9 kb ecori ho specific fragment that should carry the pervenets mutation was cloned , sequenced and characterized . primer pairs on both side of the 5 ′ pervenets mutation insertion point : seq id n1 - 2f located on seq n1 and seq id n2 - 1r located on the seq n2 and designed in δ12 - desaturase cdna were selected . because of their positions , these primers lead to a 3026 bp pcr amplification fragment only in rha 345 ho genotype compared to lo4 and other lo genotypes . subsequently , we cloned sequenced and characterised this pcr fragments carrying the 5 ′ pervenets mutation insertion point ( seq id n1 / 2 ) was cloned , sequenced and characterized . the organisation of this sequence is , from 5 ′ to 3 ′: a 2576 bp ho / lo common region the 5 ′ insertion point ho specific δ12 - desaturase gene like sequence : part of the intron ( 239 bp ) and part of the coding region ( 211 bp ). based on this characterisation , new primers were computed ( seq id n1 - 3f located on seq id n1 , seq id n2 - 2r and seq id n2 - 3r designed on δ12 - desaturase cdna sequence ). these primer pair combinations lead to ho specific amplification fragments of about 870 bp ( seq id n1 - 3f + seq id n2 - 1r ), 1000 bp ( seq id n1 - 3f + seq id n2 - 2r ) and 1400 bp ( seq id n1 - 3f + seq id n2 - 3r ) in pcr experiments involving 42 ho and lo genotypes ( example 1 ). in the 174 recombinant inbred line population , a strict co - segregation between the seq id n1 - 3f + n2 - 1r ho specific fragment and the δ12hos allele ( example 2 ) was revealed . the invention relates to seq n1 / 2 ( seq id no : 1 ) corresponding to part of the δ12 - desaturase ho specific fragment , and sequences having a high degree of homology with seq n1 / 2 ( seq id no : 1 ). the invention also relates to nucleic acid fragments which can be used as pcr primers to amplify genomic region having a high degree of homology with seq id n1 / 2 such as combinations of seq id n1 - 2f or seq id n1 - 3f with seq id n2 - 1r , seq id n2 - 2r and seq id n2 - 3r . these primer pair combinations enable to obtain fragment lengths of 3026 bp ( sequence n1 - 2f + sequence n2 - 1r ), 870 bp ( sequence n1 - 3f + sequence n2 - 1r ), 1000 bp ( sequence n1 - 3f + sequence n2 - 2r ) and 1400 bp ( sequence n1 - 3f + sequence n2 - 3r ), respectively . those primer sequences are coded : as above - mentioned the invention also relates to a sequence common to lo and ho regions which is localised over the insertion point of the pervenets mutation . this sequence seq id no : 13 was isolated by rage pcr and the sequences of the cloned lo and ho fragments clearly displays the break - up at the insertion point . primer pairs were defined to amplify across the insertion pervenets mutation point . a fragment of 170 bp ( seq id no : 14 and seq id no : 15 ) a fragment of 160 bp ( seq id no : 16 and seq id no : 17 ) a fragment of 170 bp ( seq id no : 18 and seq id no : 19 ) a fragment of 170 bp ( seq id no : 18 and seq id no : 20 ) we also demonstrated that sunflower carries also a duplicated sequence at a second locus but where there is no insertion . thus , the use of these primer pair combinations always revealed these short fragments whatever the lo or ho genotypes . however , this region enables to further characterize revertant mutant that still carry a short insertion that cannot silence the wild desaturase gene , since these were still lo . combination of primers amplifying the ssr , the δ12hos allele and the sequence across the insertion site will boost improvement of sunflower with high oleic oil content . troubles faced by breeders to improved hoac sunflower are mainly due to the instability of the pervenets mutation that seems to disappear for two reasons : 1 ) there is a reversion , corresponding to a deletion in the insertion ( several have been characterized ) that may lead to the lo phenotype when the silencing mechanism is stopped . 2 ) there is a suppressor that prevents the silencing mechanism and consequently , the phenotype is lo . for the reversion the combination of the markers ( ssr , δ12hos allele and that across the insertion site ) enables to unravel what happened . since there is no genetic recombination between the ssr locus and the δ12hl locus , the ssr allele will be always linked ( in the same phasis ) to the δ12hl allele that was present . if it reverts the δ12lor allele will be found linked to the incorrect ssr allele . moreover , when the reversion leaves a small dna fragment in the insertion site , it is possible to directly detect it with the primer pairs described that amplify the sequence over the insertion site . changes in the length of the insertion were found in twelve out of 174 recombinant inbred lines . thus it is frequent and may disturb the expected frequency ratio for ho / lo . in the progenies , ten individuals carried the ssr of the ho parent ( rha345 ) linked with a modified insertion . once corrected the ho lo ratio fits the mendelian proportion that was distorted since ten lo progenies were in fact revertant . the suppressor is detected when the presence of the δ12hos allele does not lead to the ho phenotype . fig1 δ12hos and δ12lor physical maps established according to ecori and / or hindiii rflp profiles revealed with the δ12 - desaturase cdna ( 8 ). fig2 outcome map of the 29 kb region with seq positions in ho genotypes ( b ) and in lo genotypes ( a ). fig3 ho specific pcr amplifications in a set of ho and lo genotypes using primer pair combination seq id n1 - 3f + seq id n 2 - 1r ( a ), seq id n1 - 3f + seq id n 2 - 2r ( b ), seq id n1 - 3f + seq id n 2 - 3r ( c ). 42 ho and lo genotypes to test ssr and other pcr amplification polymorphisms were selected from different public and private institutes in order to represent a wide sunflower genetic diversity . the ho rha345 and the lo lo4 genotypes ( table 1 ) were used for long pcr experiments . the ( lo ) line 83hr4 ( inra ), male - sterilized by gibberellin , was crossed with the ( ho ) line rha345 ( usa ) in the inra nursery during the summer of 1996 . nine f 1 hybrid seeds were obtained and the f 1 plants were inter - crossed to produce a f 2 generation in a greenhouse during the following winter . 174 f 6 progenies were obtained from these f 1 plants . these progenies were used to determine 18 : 1 content separately on half of a cotyledon of five seeds for each f 6 family . these seeds were sown in jiffypots and after 6 days in a greenhouse they were transferred to the field . for each f 6 family , plant number 2 in the field was selected for molecular characterizations ( rflp and pcr genotyping ). 83hr4 and rha345 parental lines were included as controls . δ12 - desaturase cdna used in the following example has 1458 bp and is similar to the complete δ12 - desaturase cdna deposited in the genbank under n o u91341 and described by hongtrakul et al ( 5 ). oil composition measurement and 18 : 1 content determination were performed on half a cotyledon using gas chromatography as described by conte et al . ( 10 ). the dna was extracted from 5 g of ground leaves in liquid nitrogen according to the method disclosed by gentzbittel ( 11 ). after the addition of 9 ml of a sodium sulphate solution ( 28 mg / ml ) prepared in the buffer ctab 2 × ( ctab 2 % ( w / v ), tris - hcl 10 mm ph8 , na 2 edta 100 mm ph8 , nacl 1 . 4 m , pvp 1 % ( w / v )), the mixture was incubated at 65 ° c . for 30 minutes . five ml of chloroform / isoamylic alcohol ( 24 / 1 , v / v ) was added before centrifugation at 10 . 000 rpm , 10 min . the supernatant was recovered and incubated at 37 ° c . for 30 min after the addition of 500 mg rnase a , then for one hour also at 37 ° c . after the addition of 4 mg of proteinase k . one ml of ctab 10 × ( ctab 10 % ( w / v ), nacl 0 . 7 m ) and 7 ml of chloroform / isoamylic alcohol ( 24 / 1 , v / v ) was added before centrifugation at 10 . 000 rpm , 10 min . the supernatant was recovered in a precipitation buffer , the volume of which corresponds to two volumes of the supernatant ( ctab 1 % ( w / v ), tris - hcl 50 mm ph8 , edta 100 mm ph8 ). after centrifugation at 12 . 000 rpm , for 15 min ., the pellet was recovered and dissolved in 3 ml of te high buffer ( tris - hcl 10 mm ph8 , na 2 edta 1 mm ph8 , nacl 1m ) and two volumes of 95 % cold ethanol , before a further centrifugation at 12 , 000 rpm , for 15 min . the pellet containing the dna was dissolved in 1 ml of te 0 . 1 × ( tris - hcl 1 mm ph8 , na 2 edta 0 . 1 mm ). the amount of dna is determined using an absorbance spectrophotometer ( do ) at 260 nm . eight μg of dna of each genotype were restricted with ecori and / or hindiii enzymes according to the provider recommendations ( boehringer ). eight enzyme units per μg of dna were used and each restriction reaction was carried out at 37 ° c . for 6 hours . the restriction products were separated by gel electrophoresis on agarose 0 . 8 % ( w / v ) gel in the 0 . 5 × tbe buffer ( tris - hcl 45 mm ph8 , boric acid 45 mm , edta ph8 1 mm ) at 1 v / cm for 16 hours . the gel was then colored in etbr bath ( 1 μg / ml ). the migration profiles were made visible under uv light ( at 312 nm ). after 30 min of partial depurination of the dna by a 0 . 25 n hcl solution , the samples were transferred onto a nylon membrane ( appligene ). the transfer was made under reduced pressure at 60 mbar during 2 hours using a vacuum transfer apparatus ( appligene ). a 0 . 4 n naoh solution was used as a transfer solution . the membranes were then washed in a 2 × ssc solution ( nacl 3m , sodium citrate 0 . 3 m ph 7 ). the dna was fixed on the membranes by incubation at 80 ° c . for two hours . the membranes were stocked at 4 ° c . until using them for hybridization . the radioactive labelling of the probes was carried out by the random primer elongation in the presence of a desoxyribonucleotide labelled by a radioactive isotype , α 32 p - dctp according to the method described by feinberg and volgelstein ( 12 ). the prehybridization and the hybridization were carried out in the same buffer containing sds 7 % ( w / v ), sodium phosphate buffer 0 . 5 m ( ph 7 . 2 ), edta 1 mm ( ph 8 ), stirring at 62 ° c . for 1 hour ( prehybridization ) and 12 hours ( hybridization ). two washes for 10 min . at 60 ° c . were carried out using a buffer containing sds 1 % ( w / v ), sodium phosphate buffer 40 mm ( ph 7 . 2 ), edta 1 mm ( ph 8 ) according to methods described by sambrook et al . ( 13 ). the conditions of na + molarity and of temperature determine stringence conditions high enough to ensure specific hybridizations . an autoradiographic film was then exposed to the membrane at − 70 ° c . for a duration , which depends on the intensity of the radioactive signals emitted by the membrane . each pcr amplification was carried out starting from 80 ng of genomic dna in a final volume of 30 μl containing tris - hcl 10 mm ( ph 8 . 3 ); kcl 50 mm , mgcl 2 1 . 5 mm ; dntps 200 μm ; 1 μm of each primer , taq polymerase 1u ( sigma ). the amplifications were carried out using a ptc 100 thermocycler ( mj research ) according to the following program : the amplification products were then either separated by electrophoresis on agarose gel or purified in order to be cloned and sequenced . the electrophoresis was carried out on 1 . 2 % ( w / v ) agarose gel in tbe 0 . 5 × buffer ( 10 v / cm ) for two hours . purification of the amplification products was carried out with the wizard pcr prep dna purification systems kit ( promega ). the amplification using the ssr primers was carried out using 40 ng of genomic dna in a final volume of 25 μl containing tris - hcl 10 mm ( ph 8 . 3 ), kcl 50 mm , mgcl 2 1 . 5 mm , dntps 200 μm , 1 μm of each primer ; taq polymerase 1u ( sigma ). the amplifications were carried out using a ptc 100 thermocycler ( mj research ) according to the following program : amplification product were loaded onto 6 % denaturing polyacrylamide gels containing 7 . 5 m urea , 6 % acrylamide and 1 × tbe buffer ( tris - hci 90 mm ph8 , boric acid 90 mm , edta ph8 2 mm ). gels were run in a 1 × tbe buffer for 90 min at 60v . ssr amplifications were visualized by sliver staining with a commercial kit from promega . in order to amplify pcr fragment from genomic dna longer than 2 kb , we used the expend long template pcr system from roche applied science . the long pcr were made according to the provider instructions . diversity analysis with the ho specific pcr fragment across the insertion pervenets point the pervenets mutation was labelled by ho specific pcr amplifications across the 5 ′ insertion point using designed primer pair combinations ( seq id n1 - 3f located on seq id n1 with seq id n2 - 1r , - 2r or - 3r designed on δ12 - desaturase cdna sequence ). forty - two ho and lo genotypes were used for these pcr experiments . these genotypes were previously genotyped using δ12 - desaturase cdna as a probe to reveal rflps . all the ho genotypes displayed the δ12hos allele whereas the lo genotypes displayed the δ12lor one ( 6 ). pcr amplification products of about 870 bp ( seq id n1 - 3f + seq id n2 - 1r ), 1000 bp ( seq id n1 - 3f + seq id n2 - 2r ) and 1400 bp ( seq id n1 - 3f + seq id n2 - 3r ) were specifically revealed in ho genotypes carrying the pervenets mutation ( fig3 a , b and c , respectively ). all the 42 genotypes were categorized into lo or ho without any error according to these ho specific pcr amplifications . the recombinant inbred line families were obtained by crossing the lines 83hr4 ( lo ) by rha 345 ( ho ) according to the method described above . using δ12 - desaturase as a probe to reveal rflp , we showed that the rha 345 ho parent line carries the δ12hos allele whereas the 83hr4 lo parental line displayed the δ12lor allele . in the 174 recombinant inbred line population , the δ12hos / δ12lor alleles segregated as 78 / 96 . the pervenets mutation was labelled by the 870 bp pcr fragment across the 5 ′ insertion point and by the polymorphism of the ssr locus located on the δ12 - desaturase gene intron . moreover this ssr polymorphism labelled the δ12 - desaturase gene itself . 870 bp ho specific pcr amplification : we used designed primer pair combination seq id n1 - 3f with seq id n2 - 1r : in the 174 recombinant inbred line population , it leads to pcr amplification of about 870 bp only in genotypes carrying the δ12hos allele and thus the pervenets mutation . amplification of the ssr sequence : the ssr polymorphism between rha 345 and 83hr4 parental line was revealed by pcr amplification using the primer pair seq id n1 - 1f / seq id n1 - 1r . this pcr amplification leads to 237 bp ( 15 ssr motives ) and 240 bp ( 16 ssr motives ) in 83hr4 and rha 345 , respectively . the segregation of this ssr polymorphism was tested in the 174 recombinant inbred line population . all the genotypes carrying the δ12hos allele displayed the ho rha 345 ssr polymorphism ( 16 ssr motives ) whereas genotypes carrying the δ12lor allele displayed the lo 83hr4 ssr polymorphism ( 15 ssr motives ). pcr methods with these primer pairs enabling to amplify either the pervenets mutation itself or the ssr locus , lead to distinguish between genotypes carrying the pervenets mutation and genotypes without the mutation . consequently , the ssr sequence and the ho pcr specific fragment may be used in selection programs to identify genotypes carrying the pervenets mutation . moreover , the ssr polymorphism can be used to map the δ12 - desaturase gene . 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