Comparing the distribution of RAPD and RFLP markers in a high density linkage map of sugar beet.

The distribution of RAPD markers was compared with that of RFLP markers in a high density linkage map of sugar beet. The same mapping population of 161 F2 individuals was used to generate all the marker data. The total map comprises 160 RAPD and 248 RFLP markers covering 508 cM. Both the RAPD and the RFLP markers show a high degree of clustering over the nine linkage groups. The pattern is compatible with a strong distal localization of recombination in the sugar beet. It leads generally to one major cluster of markers in the centre of each linkage group. In regions of high marker density, dominant RAPD markers present in either linkage phase and codominant RFLP markers are subclustered relative to each other. This phenomenon is shown to be attributable to: (i) effects of the mapping procedure when dominant and codominant data are combined, (ii) effects of the mapping procedure when dominant data in both linkage phases are combined, and (iii) genuine differences in the way RAPD and RFLP markers are recruited.     

A linkage map of sugar beet (Beta vulgaris L.)

Summary We have established a first linkage map for beets based on RFLP, isozyme and morphological markers. The population studied consisted of 96 F₂ individuals derived from an intraspecific cross. As was expected for outbreeding species, a relatively high degree of polymorphism was found within sugar beet; 47% of the DNA markers were polymorphic for the chosen population. The map consists of 115 independent chromosomal loci designated by 108 genomic DNA probes, 6 isozyme and one morphological marker. The loci cover 789 cM with an average spacing of 6.9 cM. They are dispersed over nine linkage groups corresponding to the haploid chromosome number of Beta species. Eighteen markers (15.4%) showed distorted segregation which, in most instances, can be explained by gametic selection of linked lethal loci. The application of the linkage map in sugar beet breeding is discussed.     

RFLP linkage map of asparagus.

A population resulting from a double pseudotestcross of two outbred-derived asparagus (Asparagus officinalis L.) clones was evaluated by RFLP (restriction fragment length polymorphism) analysis to produce individual maps of the male and female parents. An asparagus PstI genomic library was created and used as the source of probes. Scoring of bands was done by examining SDRFs (single dose restriction fragments) that are present in one parent and absent in the other and segregate 1:1 in the progeny. The data were analyzed as a backcross population; inversion or recoding allowed for the detection of repulsion phase linkage. The male parent map consisted of 33 loci in 10 groups, while the female parent map had 48 loci arranged in 14 groups. Segregation distortion was minimal (5%), and 17% of the markers were found to be unlinked. Loci of the configuration a/b x a/b and a/c x b/c were used to bridge seven homologous linkage groups between the two parents. The sex locus was not found to be associated with any linkage group. Key words : RFLP, bridge loci, repulsion phase linkage, double pseudotestcross.     

An extended map of the sugar beet genome containing RFLP and RAPD loci

An updated map of sugar beet (Beta vulgaris L. ssp. vulgaris var altissima Doell) is presented. In this genetic map we have combined 248 RFLP and 50 RAPD loci. Including the loci for rhizomania resistance Rr1, hypocotyl colour R and the locus controlling the monogerm character M, 301 loci have now been mapped to the nine linkage groups covering 815 cM. In addition, the karyotype of some of the Beta vulgaris chromosomes has been correlated with existing RFLP and RAPD linkage maps.     

An RFLP linkage map of Lycopersicon peruvianum

In order to map genes determining resistance to bacterial canker in tomato, backcrosses were made between a resistant and a susceptible Lycopersicon peruvianum accession. The linkage study with RFLP markers yielded a genetic map of L. Peruvianum. This map was compared to that derived from a L. esculentum x L. pennellii F₂ population, based on 70 shared RFLP markers. The maps showed a good resemblance in both the order of markers and the length of the chromosomes, with the exception of just one relocated marker on chromosome 9. Because backcrosses were made with the F₁, either as the pollen parent or as the pistil parent, linkage maps from male and female meioses could be estimated. It was concluded that recombination at male meiosis was reduced, and that gametophytic selection for parental genotypes at more than one locus per chromosome might be partly responsible for the reduction of the estimated male map length.     

RFLP linkage map and genome analysis of Saccharum spontaneum.

An RFLP linkage map of the wild sugarcane species Saccharum spontaneum L. (2n = 8x = 40-128) was constructed, comprising 216 loci, detected by 116 DNA probes, and distributed over 44 linkage groups. At a density of at least one marker every 25-cM interval, the coverage of the genome was estimated as 86%. For the generation of RFLP markers, probes were surveyed from seven DNA libraries: three sugarcane cDNA, one oat cDNA, one rice cDNA, and one barley cDNA, as well as one sugarcane genomic. Sixty-two maize genomic clones that were previously mapped on maize were used to initiate a comparative map between the sugarcane, sorghum, and maize genomes. Based on the RFLP segregation data, we conclude that this species is an autopolyploid, with an estimated genome size of 2107 cM.     

A linkage map with RFLP and isozyme markers for almond

Inheritance and linkage studies were conducted with seven isozyme genes and 120 RFLPs in the F₁ progeny of a cross between almond cultivars Ferragnes and Tuono. RFLPs were detected using 57 genomic and 43 cDNA almond clones. Eight of the cDNA probes corresponded to known genes (extensin, prunin (2), -tubulin, endopolygalacturonase, oleosin, actin depolymerizing factor and phosphoglyceromutase). Single-copy clones were found more frequently in the cDNA (65%) than in the genomic libraries (26%). Two maps were elaborated, one with the 93 loci heterozygous in Ferragnes and another with the 69 loci heterozygous in Tuono. Thirty-five loci were heterozygous in both parents and were used as bridges between both maps. Most of the segregations (91%) were of the 11 or 1111 types, and data were analyzed as if they derived from two backcross populations. Eight linkage groups covering 393 cM in Ferragnes and 394 in Tuono were found for each map. None of the loci examined in either map was found to be unlinked. Distorted segregation ratios were mainly concentrated in two linkage groups of the Ferragnes map.     

A genetic linkage map of human chromosome 5 with 60 RFLP loci.

A genetic map of human chromosome 5 that contains 60 restriction fragment length polymorphism (RFLP) loci in one linkage group has been constructed. Segregation data using these markers and 40 large multigenerational families supplied by the Centre d'Etude du Polymorphisme Humain have been collected. Linkage analyses were performed with the program package CRI-MAP; using odds greater than 1000:1, 30 RFLP loci could be placed on the map. This genetic map spans 289 cM sex-equal, 353 cM in females, and 244 cM in males. While the relative rate of recombination for female meioses is nearly twice that of males over much of the chromosome, several instances of statistically significant excess male recombination were observed. The order of probes on the genetic map has been confirmed by their physical order as determined by somatic cell hybrid lines containing deletions of normal chromosome 5. There is concordance between the physical positions of markers and their genetic positions. Our most distal probes on the genetic map are cytologically localized to the most distal portions of the chromosome. This suggests that our genetic map spans most of chromosome 5.     

Molecular characterization of UV-treated sugar beet somaclones using RFLP markers

Sugar beet plants regenerated from UV-treated calluses were examined by restriction fragment length polymorphism (RFLP) analysis to determine the extent of somaclonal variation occurring at the DNA level. In total, 50 random sugar beet DNA sequences were used to screen 42 somaclones for genetic alterations. Three polymorphisms were detected among the 7 644 alleles analysed. From these data a mutation frequency of 0.03 ± 0.02% per allele was estimated. This frequency is in agreement with similar studies of somaclonal DNA variation using molecular markers and lies in the upper range of the spontaneous gene mutation frequencies found in plants. The two probegenotype combinations showing independent polymorphisms, were further analysed using the restriction enzymes Bam HI, Eco RI, Eco RV and Hind III. Both polymorphisms are likely to result from structural rearrangements rather than from point mutations. Differences in methylation among 10 of the investigated somaclones were tested for by comparing Hpa II and Msp I generated RFLP patterns. The somaclones showed extensive methylation, but no differences in their degree of methylation. Cytological analysis revealed 34 diploid, 8 tetraploid, but no aneuploid plants.     

A RFLP linkage map of Sorghum bicolor (L.) Moench

A RFLP linkage map of sorghum composed principally of markers detected with sorghum low-copy-number nuclear DNA clones has been constructed. The map spans 1789 cMs and consists of 190 loci grouped into 14 linkage groups. The 10 largest linkage groups consist of from 10 to 24 markers and from 103 to 237 cMs, and the other 4 linkage groups consist of from 2 to 5 markers and from 7 to 62 cMs. The map was derived in Sorghum bicolor ssp. bicolor by analysis of a F₂ population composed of 50 plants derived from a cross of IS 3620C, a guinea line, and BTx 623, an agronomically important inbred line derived from a cross between a zera zera (a caudatum-like sorghum) and an established kafir line. The restriction fragment length polymorphism (RFLP) frequency detected in this population using polymerase chain reaction (PCR)-amplifiable low-copy-number sorghum clones and five restriction enzymes was 51%. A minimal estimate of the number of clones that detect duplicate sequences is 11 %. Null alleles occurred at 13% of the mapped RFLP loci.     

An RFLP linkage map of Upland cotton, Gossypium hirsutum L.

 Ninety-six F₂.F₃ bulked sampled plots of Upland cotton, Gossypium hirsutum L., from the cross of HS46×MARCABUCAG8US-1-88, were analyzed with 129 probe/enzyme combinations resulting in 138 RFLP loci. Of the 84 loci that segregated as co-dominant, 76 of these fit a normal 1 :  2 : 1 ratio (non-significant chi square at P=0.05). Of the 54 loci that segregated as dominant genotypes, 50 of these fit a normal 3: 1 ratio (non-significant chi square at P=0.05). These 138 loci were analyzed with the MAPMAKER∖ EXP program to determine linkage relationships among them. There were 120 loci arranged into 31 linkage groups. These covered 865 cM, or an estimated 18.6% of the cotton genome. The linkage groups ranged from two to ten loci each and ranged in size from 0.5 to 107 cM. Eighteen loci were not linked. Received: 31 March 1998 / Accepted: 29 April 1998     

Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris spp.)

A set of informative simple sequence repeat markers has been identified for use in the marker-assisted breeding of Beta vulgaris. Highly enriched small insert genomic libraries were constructed, consisting of 1536 clones (with inserts of between 250–900 bp). Screening the clones with CA, CT, CAA, CATA and GATA nucleotide-repeat probes revealed positive hybridisation to over 50% of the clones. Of these 340 were sequenced. Primer pairs were designed for sequences flanking the repeats and, of these, 57 pairs revealed length polymorphism with 12 Beta accessions. Heterozygosity levels of the SSR loci ranged from 0.069 to 0.809. Heterozygosity levels were found to be similar to those detected employing RFLP probes with the same accessions. Phenetic analysis using the markers, indicated relationships in accordance with known pedigrees. Twenty three of the SSR markers were polymorphic in one or both of two F₂ mapping populations, and were placed relative to a framework of RFLP probes. The markers are distributed over all nine linkage groups of sugar beet. Received: 14 July 1999 / Accepted: 27 October 1999     

Genetic linkage map in sour cherry using RFLP markers

 Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunus cerasus L., 2n=4x=32) cultivars, Rheinische Schattenmorelle (RS) and Erdi Botermo (EB), were constructed from 86 progeny from the cross RS×EB. The RS linkage map consists of 126 single-dose restriction fragment (SDRF, Wu et al. 1992) markers assigned to 19 linkage groups covering 461.6 cM. The EB linkage map has 95 SDRF markers assigned to 16 linkage groups covering 279.2 cM. Fifty three markers mapped in both parents were used as bridges between both maps and 13 sets of homologous linkage groups were identified. Homoeologous relationships among the sour cherry linkage groups could not be determined because only 15 probes identified duplicate loci. Fifty nine of the markers on the linkage maps were detected with probes used in other Prunus genetic linkage maps. Four of the sour cherry linkage groups may be homologous with four of the eight genetic linkage groups identified in peach and almond. Twenty one fragments expected to segregate in a 1 : 1 ratio segregated in a 2 : 1 ratio. Three of these fragments were used in the final map construction because they all mapped to the same linkage group. Six fragments exhibited segregation consistent with the expectations of intergenomic pairing and/or recombination. Received: 1 April 1998 / Accepted: 9 June 1998     

Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps

 Three RFLP maps, as well as several RAPD maps have been developed in common bean (Phaseolus vulgaris L.). In order to align these maps, a core linkage map was established in the recombinant inbred population BAT93×Jalo EEP558 (BJ). This map has a total length of 1226 cM and comprises 563 markers, including some 120 RFLP and 430 RAPD markers, in addition to a few isozyme and phenotypic marker loci. Among the RFLPs mapped were markers from the University of California, Davis (established in the F₂ of the BJ cross), University of Paris-Orsay, and University of Florida maps. These shared markers allowed us to establish a correspondence between the linkage groups of these three RFLP linkage maps. In total, the general map location (i.e., the linkage group membership and approximate location within linkage groups) has been determined for some 1070 markers. Approaches to align this core map with other current or future maps are discussed. Received: 10 March 1998 / Accepted: 22 April 1998     

Development of an RFLP linkage map in diploid peanut species

An RFLP linkage map of peanut has been developed for use in genetic studies and breeding programs aimed at improving the cultivated species (Arachis hypogaea L.). An F₂ population derived from the interspecific hybridization of two related diploid species in the sectionArachis (A. stenosperma ×A. cardenasii) was used to construct the map. Both random genomic and cDNA clones were used to develop the framework of the map. In addition, three cDNA clones representing genes coding for enzymes involved in the lipid biosynthesis pathway have been mapped in peanut. Of the 100 genomic and 300 cDNA clones evaluated, 15 and 190, respectively, revealed polymorphisms among the parents of our mapping population. Unfortunately, a large number of these produced complex banding patterns that could not be mapped. Of the 132 markers analyzed for segregation, 117 are distributed among 11 linkage groups, while 15 have not yet been associated with any other marker. A total map distance of approximately 1063 cM has been covered to-date.     

Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome

Sugar beet (Beta vulgaris) is an important root crop for sucrose production. A study was conducted to find a new abundant source of microsatellite (SSR) markers in order to develop marker assistance for breeding. Different sources of existing microsatellites were used and new ones were developed to compare their efficiency to reveal diversity in mapping population and mapping coverage. Forty-one microsatellite markers were isolated from a B. vulgaris ssp maritima genomic library and 201 SSRs were extracted from a B. vulgaris ssp vulgaris library. Data mining was applied on GenBank B. vulgaris expressed sequence tags (ESTs), 803 EST-SSRs were identified over 19,709 ESTs. Characteristics, polymorphism and cross-species transferability of these microsatellites were compared. Based on these markers, a high density genetic map was constructed using 92 F₂ individuals from a cross between a sugar and a table beet. The map contains 284 markers, spans over 555 cM and covers the nine chromosomes of the species with an average markers density of one marker every 2.2 cM. A set of markers for assignation to the nine chromosomes of sugar beet is provided.     

Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.).

A microsatellite-based high-density linkage map for oil palm (Elaeis guinensis Jacq.) was constructed from a cross between two heterozygous parents, a tenera palm from the La Mé population (LM2T) and a dura palm from the Deli population (DA10D). A set of 390 simple sequence repeat (SSR) markers was developed in oil palm from microsatellite-enriched libraries and evaluated for polymorphism along with 21 coconut SSRs. A dense and genome-wide microsatellite framework as well as saturating amplified fragments length polymorphisms (AFLPs) allowed the construction of a linkage map consisting of 255 microsatellites, 688 AFLPs and the locus of the Sh gene, which controls the presence or absence of a shell in the oil palm fruit. An AFLP marker E-Agg/M-CAA132 was mapped at 4.7 cM from the Sh locus. The 944 genetic markers were distributed on 16 linkage groups (LGs) and covered 1,743 cM. Our linkage map is the first in oil palm to have 16 independent linkage groups corresponding to the plants 16 homologous chromosome pairs. It is also the only high-density linkage map with as many microsatellite markers in an Arecaceae species and represents an important step towards quantitative trait loci analysis and physical mapping in the E. guineensis species.     

Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions

Key message

Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection.

Abstract

Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.     

RFLP markers for sugar beet breeding: chromosomal linkage maps and location of major genes for rhizomania resistance, monogermy and hypocotyl colour

An RFLP linkage map for the nine chromosomes of sugar beet (Beta vulgaris L. ssp. vulgaris var. altissima Doell) was constructed by using a segregating population from a cross between two plants which were heterozygous for several agronomically interesting characters. One hundred and eleven RFLP loci have been mapped to nine linkage groups using 92 genomic markers. The current RFLP map covers a total length of 540 cM. Evidence for the existence of a major gene for rhizomania resistance (Rr1) is given, together with its map position on linkage group IV in the interval between loci GS44 and GS28a. The presence of an RFLP fragment at the GS3d locus is, until now, the best molecular marker for rhizomania-resistant genotypes in segregating populations of sugar beet; GS3d is linked to Rr1 with 6.7 cM. The gene MM, controlling the polygerm/monogerm seed type, has been mapped on linkage group IX in a distal position at 4.2 cM from the locus GS7. The gene R controlling the hypocotyl colour maps to linkage group VII and does not recombine with the RFLP locus GS42. The inheritance of a group of RFLP loci revealed the possible presence of a translocation in the population used to establish the map. The data presented are discussed in relation to the possibility of using RFLP markers in sugar beet breeding.