K R Tobutt

Publications (21)54.71 Total impact

• Article: The myrobalan (Prunus cerasifera L.): a useful diploid model for studying the molecular genetics of self-incompatibility in plums

  B. G. Sutherland, R. Cerovič, T. P. Robbins, K. R. Tobutt
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  ABSTRACT: A series of PCR methods were used to detect S-RNase alleles and SFB alleles and to determine S-genotypes in 25 accessions of myrobalan (Prunus cerasifera L.). Firstly, primers flanking the polymorphic second intron were used to identify S-RNases in agarose gels. These primers amplified one or two bands per accession in 25 accessions. Then consensus primers were designed for amplifying the polymorphic first intron, unique to Prunus S-RNases, for automated fluorescent detection. Each accession produced one or two peaks. New primers were then developed to amplify the intron in the SFB gene, for detection by fluorescence. Cross-referencing PCR bands and peaks indicated 15 S-alleles were present in the 25 accessions. Cloning, sequencing and comparison with published data indicated that the amplified products were S-RNase alleles. Sequence information was used to design primers specific for each S-RNase. Full and consistent S-genotypes were obtained by cross-comparing PCR data for 23 of the 25 accessions, and two accessions appeared to have a single allele. Pollen-tube microscopy indicated function of some but not all of the S-alleles sequenced.
  Euphytica 04/2012; 166(3):385-398. · 1.55 Impact Factor
• Article: Primers amplifying a range of Prunus S‐alleles

  B. G. Sutherland, T. P. Robbins, K. R. Tobutt, W.E. Weber
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  ABSTRACT: Although various consensus polymerase chain reaction (PCR) primers have been reported for identifying Prunus S-alleles, they have been developed from and optimized on a limited set of alleles, which may limit their applicability to a broader allele range. To develop a primer set for use across the genus, degenerate consensus primers were designed from conserved regions of 27 S-RNase sequences available from five Prunus species. The primers were tested in 15 previously genotyped cultivars of cherry, almond and apricot, representing alleles S1 to S6 in each crop and also Sc in apricot. Comparisons were made with previously published primers tested in the same 15 cultivars under reported reaction conditions. The new primers generated an amplification product for each of the 19 S-alleles whereas those previously available amplified no more than 14. The primers will be useful for genotyping and genetic studies in cultivars and wild populations.
  Plant Breeding 06/2008; 123(6):582 - 584. · 1.60 Impact Factor
• Article: The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map.

  D J Sargent, G Cipriani, S Vilanova, D Gil-Ariza, P Arús, D W Simpson, K R Tobutt, A Monfort
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  ABSTRACT: We have identified a set of plants (the bin set) to permit "selective" or "bin" mapping using the diploid strawberry mapping population FV x FN, derived from the F2 cross F. vesca 815 x F. nubicola 601, which has been used to develop the Fragaria reference map. The bin set consists of 8 plants: the F. vesca 815 parent, the F1 hybrid individual, and 6 seedlings of the F2 population. This bin set divides the 578 cM of the diploid Fragaria genome into 46 bins, the largest mapping bin being 26 cM in length and the average bin size being 12.6 cM. To validate the FV x FN bin set, we used it to locate 103 loci into bins on the FV x FN map. These loci comprised 61 previously described SSRs, 38 new SSRs developed in this investigation from Fragaria x ananassa genomic DNA, EST and gene sequences, and 4 ripening-related genes developed for Prunus. The 103 markers were located to bins on all 7 linkage groups of the Fragaria map and a new mapping bin was identified with the novel markers, demonstrating that the map covers the majority of the diploid Fragaria genome and that the 6 bin-set seedlings selected were appropriate for bin mapping using this progeny.
  Genome 03/2008; 51(2):120-7. · 1.65 Impact Factor
• Article: The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera.

  D J Sargent, A Rys, S Nier, D W Simpson, K R Tobutt
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  ABSTRACT: We have developed 46 primer pairs from exon sequences flanking polymorphic introns of 23 Fragaria gene sequences and one Malus sequence deposited in the EMBL database. Sequencing of a set of the PCR products amplified with the novel primer pairs in diploid Fragaria showed the products to be homologous to the sequences from which the primers were originally designed. By scoring the segregation of the 24 genes in two diploid Fragaria progenies FV x FN (F. vesca x F. nubicola F(2)) and 815 x 903BC (F. vesca x F. viridis BC(1)) 29 genetic loci at discrete positions on the seven linkage groups previously characterised could be mapped, bringing to 35 the total number of known function genes mapped in Fragaria. Twenty primer pairs, representing 14 genes, amplified a product of the expected size in both Malus and Prunus. To demonstrate the applicability of these gene-specific loci to comparative mapping in Rosaceae, five markers that displayed clear polymorphism between the parents of a Malus and a Prunus mapping population were selected. The markers were then scored and mapped in at least one of the two additional progenies.
  Theoretical and Applied Genetics 02/2007; 114(2):373-84. · 3.30 Impact Factor
• Source

  Available from: Daniel James Sargent

  Article: An enhanced microsatellite map of diploid Fragaria.

  D J Sargent, J Clarke, D W Simpson, K R Tobutt, P Arús, A Monfort, S Vilanova, B Denoyes-Rothan, M Rousseau, K M Folta, N V Bassil, N H Battey
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  ABSTRACT: A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. x ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F2 mapping population (FVxFN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes of known function, for comparative mapping purposes within Rosaceae.
  Theoretical and Applied Genetics 06/2006; 112(7):1349-59. · 3.30 Impact Factor
• Article: Improved discrimination of self‐incompatibility S‐RNase alleles in cherry and high throughput genotyping by automated sizing of first intron polymerase chain reaction products

  T. Sonneveld, T. P. Robbins, K. R. Tobutt
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  ABSTRACT: A novel polymerase chain reaction (PCR) approach to determine and confirm the self-incompatibility (S) genotype of cherries is reported. The method involves PCR amplification with a new pair of consensus primers that immediately flank the first intron of cherry S-RNases, one of which is fluorescently labelled. Fluorescent amplification products range from 234 to c. 460 bp and can be sized accurately on an automated sequencer. Thirteen S alleles reported in sweet cherry can be distinguished, except for S2 and S7, which have an amplification product of exactly the same size. S13, which is also amplified, gives a microsatellite-like trace which shows minor intra-allelic length variation. This method gives fast and accurate results and should be especially useful for medium/high-throughput genotyping of wild and cultivated cherries.
  Plant Breeding 05/2006; 125(3):305 - 307. · 1.60 Impact Factor
• Article: Isolation of S-locus F-box alleles in Prunus avium and their application in a novel method to determine self-incompatibility genotype.

  S P Vaughan, K Russell, D J Sargent, K R Tobutt
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  ABSTRACT: This study characterises a series of 12 S-locus haplotype-specific F-box protein genes (SFB) in cherry (Prunus avium) that are likely candidates for the pollen component of gametophytic self-incompatibility in this species. Primers were designed to amplify 12 SFB alleles,including the introns present in the 50 untranslated region;sequences representing the S-alleles S1, S2, S3, S4, S40, S5,S6, S7, S10, S12, S13 and S16 were cloned and characterized. [The nucleotide sequences reported in this paper have been submitted to the EMBL/GenBank database under the following accession numbers: PaSFB1(AY805048), PaSFB2 (AY805049), PaSFB3 (AY805057),PaSFB4 (AY649872), PaSFB40 (AY649873), PaSFB5(AY805050), PaSFB6 (AY805051), PaSFB7 (AY805052),PaSFB10 (AY805053), PaSFB12 (AY805054), PaSFB13(AY805055), PaSFB16 (AY805056).] Though the coding regions of six of these alleles have been reported previously,the intron sequence has previously been reported only for S6. Analysis of the introns revealed sequence and length polymorphisms. A novel, PCR-based method to genotype cultivars and wild accessions was developed which combines fluorescently labelled primers amplifying the intron of SFB with similar primers for the first intron of S-RNase alleles. Intron length polymorphisms were then ascertained using a semi-automated sequencer. The convenience and reliability of this method for the determination of the self-incompatibility (SI) genotype was demonstrated both in sweet cherry cultivars representing alleles S1 to S16 and in individuals from a wild population encompassing S-alleles S17 to S22. This method will greatly expedite SI characterisation in sweet cherry and also facilitate large-scale studies of self-incompatibility in wild cherry and other Prunus populations.
  Theoretical and Applied Genetics 04/2006; 112(5):856-66. · 3.30 Impact Factor
• Article: Inheritance and interactions of incompatibility alleles in the tetraploid sour cherry.

  R I Bosković, B Wolfram, K R Tobutt, R Cerović, T Sonneveld
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  ABSTRACT: Three progenies of sour cherry (Prunus cerasus) were analysed to correlate self-(in)compatibility status with S-RNase phenotype in this allotetraploid hybrid of sweet and ground cherry. Self-(in)compatibility was assessed in the field and by monitoring pollen tube growth after selfing. The S-RNase phenotypes were determined by isoelectric focusing of stylar proteins and staining for RNase activity and, for the parents, confirmed by PCR. Seedling phenotypes were generally consistent with disomic segregation of S-RNase alleles. The genetic arrangements of the parents were deduced to be 'Köröser' (self-incompatible) S1S4.S(B) S(D), 'Schattenmorelle' (self-compatible) S6S13.S(B)S(B), and clone 43.87 (self-compatible) S4S13.S(B)S(B), where "." separates the two homologous genomes. The presence of S4 and S6 alleles at the same locus led to self-incompatibility, whereas S13 and S(B) at homologous loci led to self-compatibility. The failure of certain heteroallelic genotypes in the three crosses or in the self-incompatible seedlings indicates that S4 and S6 are dominant to S(B). However, the success of S13S(B) pollen on styles expressing corresponding S-RNases indicates competitive interaction or lack of pollen-S components. In general, the universal compatibility of S13S(B) pollen may explain the frequent occurrence of S13 and S(B) together in sour cherry cultivars. Alleles S(B) and S(D), that are presumed to derive from ground cherry, and S13, presumably from sweet cherry, were sequenced. Our findings contribute to an understanding of inheritance of self-(in)compatibility, facilitate screening of progenies for self-compatibility and provide a basis for studying molecular interactions in heteroallelic pollen.
  Theoretical and Applied Genetics 02/2006; 112(2):315-26. · 3.30 Impact Factor
• Source

  Available from: inbo.be

  Article: Determining self-incompatibility genotypes in Belgian wild cherries.

  B De Cuyper, T Sonneveld, K R Tobutt
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  ABSTRACT: ABSTRACT The self-incompatibility (S) genotypes of a collection of 65 Belgian accessions of wild cherry, selected within two populations and planted in a seed orchard, were determined using polymerase chain reaction (PCR) methods. Initially, DNA extracts were amplified with consensus primers that amplify across the second intron of the S-ribonuclease gene which shows considerable length polymorphism. The provisional genotypes deduced were checked with the appropriate allele-specific primers for the known alleles S(1) to S(16). Putative new alleles were subjected to PCR with consensus primers amplifying across the first intron. Six new alleles, S(17) to S(22), were thus indicated on the basis of the estimated lengths of the first and second intron PCR products. Examples of these alleles were partially sequenced and were indeed mutually distinct and different from the known alleles. The incompatibility genotypes of all 65 accessions were determined and one triploid individual was found. Seventeen alleles were detected in all. Allele frequencies differed between samples and the expected total number of alleles in the underlying populations was estimated. The wild cherry populations differed significantly with respect to allelic frequencies from sweet cherry cultivars; alleles S(4) and S(5), which are moderately frequent in sweet cherry, were absent from the wild cherry accessions. The knowledge of the S genotypes will be useful for studying the gene flow within the seed orchard and these approaches should also be informative in wild populations.
  Molecular Ecology 05/2005; 14(4):945-55. · 5.52 Impact Factor
• Article: A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria.

  D J Sargent, T M Davis, K R Tobutt, M J Wilkinson, N H Battey, D W Simpson
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  ABSTRACT: Diploid Fragaria provide a potential model for genomic studies in the Rosaceae. To develop a genetic linkage map of diploid Fragaria, we scored 78 markers (68 microsatellites, one sequence-characterised amplified region, six gene-specific markers and three morphological traits) in an interspecific F2 population of 94 plants generated from a cross of F.vesca f. semperflorens x F. nubicola. Co-segregation analysis arranged 76 markers into seven discrete linkage groups covering 448 cM, with linkage group sizes ranging from 100.3 cM to 22.9 cM. Marker coverage was generally good; however some clustering of markers was observed on six of the seven linkage groups. Segregation distortion was observed at a high proportion of loci (54%), which could reflect the interspecific nature of the progeny and, in some cases, the self-incompatibility of F. nubicola. Such distortion may also account for some of the marker clustering observed in the map. One of the morphological markers, pale-green leaf (pg) has not previously been mapped in Fragaria and was located to the mid-point of linkage group VI. The transferable nature of the markers used in this study means that the map will be ideal for use as a framework for additional marker incorporation aimed at enhancing and resolving map coverage of the diploid Fragaria genome. The map also provides a sound basis for linkage map transfer to the cultivated octoploid strawberry.
  Theoretical and Applied Genetics 12/2004; 109(7):1385-91. · 3.30 Impact Factor
• Article: Identification of incompatibility alleles in the tetraploid species sour cherry.

  K R Tobutt, R Bosković, R Cerović, T Sonneveld, D Ruzić
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  ABSTRACT: The incompatibility genetics of sour cherry ( Prunus cerasus), an allotetraploid species thought to be derived from sweet cherry (diploid) and ground cherry (tetraploid), were investigated by test crossing and by analysis of stylar ribonucleases which are known to be the products of incompatibility alleles in sweet cherry. Stylar extracts of 36 accessions of sour cherry were separated electrophoretically and stained for ribonuclease activity. The zymograms of most accessions showed three bands, some two or four. Of the ten bands seen, six co-migrated with bands that in sweet cherry are attributed to the incompatibility alleles S(1), S(3), S(4), S(6, ) S(9) and S(13). 'Cacanski Rubin', 'Erdi Botermo B', 'Koros' and 'Ujfehertoi Furtos', which showed bands apparently corresponding to S(1) and S(4), were test pollinated with the sweet cherry 'Merton Late' ( S(1) S(4)). Monitoring pollen tube growth, and, in one case, fruit set, showed that these crosses were incompatible and that the four sour cherries indeed have the alleles S(1) and S(4). Likewise, test pollination of 'Marasca Piemonte', 'Marasca Savena' and 'Morello, Dutch' with 'Noble' ( S(6) S(13)) showed that these three sour cherries have the alleles S(6) and S(13). S(13) was very frequent in sour cherry cultivars, but is rare in sweet cherry cultivars, whereas with S(3) the situation is reversed. It was suggested that the other four bands are derived from ground cherry and one of these, provisionally attributed to S(B), occurred frequently in a small set of ground cherry accessions surveyed. Analysing some progenies from sour by sweet crosses by S allele-specific PCR and monitoring the success of some sweet by sour crosses were informative. They indicated mostly disomic inheritance, with sweet cherry S alleles belonging to one locus and, presumably, the ground cherry alleles to the other, and helped clarify the genomic arrangement of the alleles and the interactions in heteroallelic pollen.
  Theoretical and Applied Genetics 04/2004; 108(5):775-85. · 3.30 Impact Factor
• Article: Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers.

  T Sonneveld, K R Tobutt, T P Robbins
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  ABSTRACT: PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S(1) to S(6) S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S(13), these also amplified S(7) to S(14) and an allele previously referred to as S(x), which we now label S(16). The genomic PCR products were cloned and sequenced. The partial sequence of S(11) matched that of S(7) and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S(7) to S(16), so that allele-specific primers are now available for all 13 S alleles of cherry (S(8), S(11) and S(15) are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S(3) S(16)), comprising 'Rodmersham Seedling' and 'Strawberry Heart', and Group XXIV (S(6) S(12)), comprising 'Aida' and 'Flamentiner'. Four new self-compatibility genotypes, S(3) S(3)', S(4)' S(6), S(4)' S(9) and S(4)' S(13), were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.
  Theoretical and Applied Genetics 11/2003; 107(6):1059-70. · 3.30 Impact Factor
• Article: Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers

  T. Sonneveld, K.R. Tobutt, T.P. Robbins
  [show abstract] [hide abstract]
  ABSTRACT: PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S1 to S6 S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S13, these also amplified S7 to S14 and an allele previously referred to as Sx, which we now label S16. The genomic PCR products were cloned and sequenced. The partial sequence of S11 matched that of S7 and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S7 to S16, so that allele-specific primers are now available for all 13 S alleles of cherry (S8, S11 and S15 are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S3S16), comprising ''Rodmersham Seedling'' and ''Strawberry Heart'', and Group XXIV (S6S12), comprising ''Aida'' and ''Flamentiner''. Four new self-compatibility genotypes, S3S3, S4S6, S4S9 and S4S13, were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.
  Theoretical and Applied Genetics 09/2003; 107(6):1059-1070. · 3.30 Impact Factor
• Source

  Available from: oxfordjournals.org

  Article: Polylink: to support two-point linkage analysis in autotetraploids.

  Y He, X Xu, K R Tobutt, M S Ridout
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  ABSTRACT: Polylink runs under Microsoft Windows (95 or later). It performs various calculations that are useful for investigating two-point linkage analysis for autopolyploids, based on the random chromosome pairing model. These include calculation of offspring phenotypic probabilities as functions of the recombination fraction, calculation of theoretical standard errors for the maximum likelihood estimator of and numerical computation of maximum likelihood estimates. It also includes simulation facilities. AVAILABILITY: Polylink is free and available from Xiangming Xu via email
  Bioinformatics 09/2001; 17(8):740-1. · 5.47 Impact Factor
• Article: Cloning of six cherry self-incompatibility alleles and development of allele-specific PCR detection

  T. Sonneveld, T. P. Robbins, R. Bošković, K. R. Tobutt
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  ABSTRACT: Reverse transcription of stylar RNA from three cherry cultivars representing six self-incompatibility (S) alleles, Early Rivers (S 1 S 2 ), Napoleon (S 3 S 4 ) and Colney (S 5 S 6 ), followed by 3′ RACE using degenerate primers based on conserved regions of Prunus S ribonucleases (S RNases), gave six classes of partial putative S RNase clones. These were sequenced, and specific primers were designed for each class and, by using them in genomic PCR on 28 cultivars previously genotyped, we were able to assign the classes to individual S alleles. The primers for S 3 amplified the allele reported previously as S 8 , and a controlled cross showed that these two alleles are functionally the same. Analysis of three cherry progenies using the specific primers showed cosegregation with stylar S RNases for all six clones. This confirmed that the clones indeed represent cherry S RNases. The allele-specific primers for S 5 presented here provide the first PCR test for true S 5 . In a fourth progeny, the amplification product of a mutant S 4 allele, S 4 ′, cosegregated with self-compatibility. Sixteen cultivars were genotyped for the first time using the allele-specific primers. Thus, this approach will be valuable for genotyping cultivars and seedlings that have the alleles S 1 –S 6 and for detecting self-compatible seedlings from vegetative material. The sequences of five of the S RNases, including S 5 , were completed by 5′ RACE.
  Theoretical and Applied Genetics 04/2001; 102(6):1046-1055. · 3.30 Impact Factor
• Article: An isoenzyme marker linked to the incompatibility locus in cherry

  R. Bošković, K. Russell, K. R. Tobutt, M. S. Ridout
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  ABSTRACT: Analysis of two cherry progenies from semi-compatible crosses for the esterase enzyme system showed extremely distorted segregation ratios for Est-5. Analysis of two progenies from compatible crosses for esterase and for stylar ribonuclease proved that Est-5 is linked with the incompatibility locus S. The recombination fraction is 4%. About a fifth of some 50 cultivars or selections genotyped for Est-5 were heterozygous. The various heterozygotes could provide ’testers’ for the presence in cultivars of unknown genotype of 8 of the 11 known S alleles. A seedling suitable for testing S 9 has been identified and crosses have been made to raise testers for S 10 and S 11 . Isoenzyme analysis of the four progenies for glutamate oxaloacetate transaminase, and of one of them for isocitrate dehydrogenase, showed no evidence for the linkage of Got-1 or Idh-2 with S, contrary to a previous report. Estimation of linkage with S in semi-compatible crosses is discussed.
  Theoretical and Applied Genetics 01/2000; 100(3):512-518. · 3.30 Impact Factor
• Article: Inheritance of stylar ribonucleases in cherry progenies, and reassignment of incompatibility alleles to two incompatibility groups

  R. Bošković, K. Russell, K.R. Tobutt
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  ABSTRACT: Stylar proteins were extracted from parents and seedlings of six progenies of cherry (Prunus avium), separated using isoelectric focusing, and the gels stained for ribonuclease activity. The zymogram of each plant showed two main ribonuclease bands in the region pI 8.3 to 9.6. Progenies from crosses of parents with one band in common segregated into just two classes, whereas progenies from crosses of parents with no common bands segregated into four classes, the two types of segregation corresponding to those expected from semi-compatible and fully-compatible crosses respectively. This behaviour was consistent either with the ribonuclease locus being tightly linked with the self-incompatibility, S, locus, or else with the S locus coding for the ribonuclease variants. Evidence favouring the latter hypothesis is discussed. An apparently anomalous segregation led us to assign to ‘Bradbourne Black’ a genotype different from that previously reported, and analysis of some other cultivars in the same incompatibility group, Group VII, led us to conclude the genotype of this group is S3S5, and not S4S5 as previously reported. Correspondingly, we suggest the genotype of Group V is S4S5, and not S3S5. Five new S alleles, S7, S8, S9, S10 and S11 were proposed in parental cultivars and selections that had not previously been assigned a genotype.
  Euphytica 04/1997; 95(2):221-228. · 1.55 Impact Factor
• Article: LINKEM: A Program for Genetic Linkage Analysis

  C. J. Vowden, M S Ridout, K R Tobutt
• Article: Development of "universal" gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae

  D. J. Sargent, A. Marchese, D. W. Simpson, W. Howad, F. Fernandez-Fernandez, A. Monfort, P. Arus, K. M. Evans, K. R. Tobutt
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  ABSTRACT: including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage maps for these species, with a view to marker-assisted selection to assist breeding programs and, recently, in the development of transferable markers to permit syntenic comparisons of maps of different rosaceous genera. In this investigation, a set of Malus cDNA sequences were downloaded from the European Molecular Biology Laboratory database. The sequences were aligned with homologous full-length Arabidopsis genomic DNA sequences to identify putative intron-exon junctions and conserved flanking exon sequences. Primer pairs were designed from the conserved exon sequences flanking predicted intron-exon junctions in the Malus cDNA sequences. These were used to amplify products by polymerase chain reaction from the parents of the Malus mapping progeny "Fiesta" * "Totem." Eleven loci, representing ten genes (39%), were polymorphic in the "Fiesta" * "Totem" population and mapped to seven Malus linkage groups. Transferability to other rosaceous genera was high, with primer pairs representing 85% of genes, amplifying products from Fragaria and primer pairs representing 85% of genes, amplifying products from Prunus genomic DNA. These primers were screened in the Fragaria and Prunus mapping bin sets and 38% of the genes were successfully located on both maps. Analysis of the markers mapped in more than one rosaceous genus revealed patterns of synteny between genera, while a comparison with the physical positions of homologous genes on the Arabidopsis genome revealed high sequence conservation but only fragmentary patterns of macrosynteny.
  Tree Genetics and Genomes. 5(1):133-145.
• Article: Development of "universal" gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae

  D. J. Sargent, A. Marchese, D. W. Simpson, W. Howad, F. Fernandez-Fernandez, A. Monfort, P. Arus, K. M. Evans, K. R. Tobutt
  [show abstract] [hide abstract]
  ABSTRACT: including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage maps for these species, with a view to marker-assisted selection to assist breeding programs and, recently, in the development of transferable markers to permit syntenic comparisons of maps of different rosaceous genera. In this investigation, a set of Malus cDNA sequences were downloaded from the European Molecular Biology Laboratory database. The sequences were aligned with homologous full-length Arabidopsis genomic DNA sequences to identify putative intron-exon junctions and conserved flanking exon sequences. Primer pairs were designed from the conserved exon sequences flanking predicted intron-exon junctions in the Malus cDNA sequences. These were used to amplify products by polymerase chain reaction from the parents of the Malus mapping progeny "Fiesta" * "Totem." Eleven loci, representing ten genes (39%), were polymorphic in the "Fiesta" * "Totem" population and mapped to seven Malus linkage groups. Transferability to other rosaceous genera was high, with primer pairs representing 85% of genes, amplifying products from Fragaria and primer pairs representing 85% of genes, amplifying products from Prunus genomic DNA. These primers were screened in the Fragaria and Prunus mapping bin sets and 38% of the genes were successfully located on both maps. Analysis of the markers mapped in more than one rosaceous genus revealed patterns of synteny between genera, while a comparison with the physical positions of homologous genes on the Arabidopsis genome revealed high sequence conservation but only fragmentary patterns of macrosynteny.
  Tree Genetics and Genomes. 5(1):133-145.