Human phosphoglycolate phosphatase (PGP) E.C.3.1.3.18: Linkage analysis

Summary Linkage data on phosphoglycolate phosphatase (PGP) E.C.3.1.3.18 and 26 other human genetic markers are presented. One hundred and one families from the southwestern area of Germany were tested. Close linkage between PGP and the following markers could be ruled out: AB0, acP, ADA, GPT, PGM₁, GLO, HLA, and PGM₃. There is some evidence for possible linkage with MNSs, Rh, Gm and EsD. Family segregation data confirm the hypothesis formerly established by Barker and Hopkinson: three common alleles PGP¹, PGP² and PGP³ at an autosomal locus PGP.Supported by the Deutsche ForschungsgemeinschaftSupported by DAAD and Portuguese Inst. for Scientific Research (INIC)     

Genetic linkage relations of the sixth component of complement (C6)

Summary Linkage relations between the C6 and 33 other genetic marker loci have been analyzed in Norwegian pedigrees, including 114 matings with 388 informative children, by use of the MOSM computer program. No suggestion of linkage was found. Very close or close linkage (<0.06) has been ruled out for males between C6 and the following 19 marker loci: GPT, HLA+Bf, Rh, C3, Hp, PGM ₃, Km, Gm, Fy, Gc, AB0, Jk, GLO ₁, K, MNSs, PTC, ACP ₁, PGM ₁ and Pi. For several of the relations even loose linkage is unlikely.     

Red cell enzymes of the Pongidae

Summary The red cell enzymes acid phosphatase, adenylate kinase, adenosine deaminase and phosphoglucomutase were analyzed by horizontal starch gel electrophoresis in 43 members of the family Pongidae: Pongo pygmaeus (n=10), Gorilla g. gorilla (n=8), Pan troglodytes (n=22) and Pan paniscus (n=3).In all the Pongidae a red cell acid phosphatase zymogram corresponding to the phenotype B in man was found. The adenylate kinase corresponded to the human phenotype AK 1. All the Pongidae showed the same homozygous adenosine deaminase phenotype which was different from the zymograms in man and was designated ADA ape. In all Pongidae the allele PGM ₁ ¹ was present, in addition in Gorilla g. gorilla a second allele was demonstrated, PGM ₁ ^Go . In Pan troglodytes a second allele, PGM ₁ ^Pan was recognized. In Pongo pygmaeus and Gorilla g. gorilla the PGM₂ patterns differed in their migration rates from PGM₂ 1 in man. In one individual of the species Pan troglodytes a PGM₂ zymogram was found resembling the heterozygous phenotype PGM₂ 3–1, PGM ₂ ¹ PGM ₂ ³, (type Palmer) in man. In all the other individuals of the species Pan troglodytes and in those of the species Pan paniscus the PGM₂ zymogram corresponded to the phenotype PGM₂ 1 in man.

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Zusammenfassung Bei 43 Vertretern der Familie Pongidae, Pongo pygmaeus (n=10), Gorilla g. gorilla (n=8), Pan troglodytes (n=22) und Pan paniscus (n=3), wurden die Erythrocytenenzyme saure Phosphatase, Adenylatkinase, Adenosindeaminase und Phosphoglucomutase mit der horizontalen Stärkegelelektrophorese analysiert. Bei allen Pongiden fanden wir eine saure Phosphatase, die dem Phänotyp B des Menschen entsprach, und eine Adenylatkinase, die dem Phänotyp AK 1 des Menschen glich. Alle Pongiden besaßen das gleiche, einem homozygoten Phänotyp entsprechende Adenosindeaminase-Zymogramm, das sich von den Zymogrammen des Menschen unterschied; wir bezeichnen diesen Phänotyp mit ADA ape. Bei allen Pongiden kommt das Allel PGM ₁ ¹ vor, bei Gorilla g. gorilla zusätzlich ein zweites Allel, PGM ₁ ^Go , und bei Pan troglodytes ein zweites Allel, PGM ₁ ^Pan . Die PGM₂-Zymogramme von Pongo pygmaeus und Gorilla g. gorilla unterschieden sich in ihrer elektrophoretischen Wandergeschwindigkeit vom Phänotyp PGM₂ 1 des Menschen. Bei einem Individuum der Species Pan troglodytes fanden wir ein heterozygotes PGM₂-Zymogramm, das an den heterozygoten Phänotyp PGM₂ 3–1, PGM ₂ ¹ PGM ₂ ³ (Typ Palmer) des Menschen erinnerte, bei allen übrigen Individuen der Species Pan troglodytes und bei denen der Species Pan paniscus ein homozygotes PGM₂-Zymogramm, das dem Phänotyp PGM₂ 1 des Menschen entsprach.

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Supported by the Deutsche Forschungsgemeinschaft.     

Localization of genes on human chromosomes by studies of human-Chinese hamster somatic cell hybrids

Summary About 75 man-Chinese hamster hybrid clones were analysed for their human chromosome complement and simultaneously tested for human enzyme markers. Correlation of the presence of chromosomes and enzyme activity revealed assignments of the PGD linkage group to chromosome 1, ME₁, PGM₃ and IPO-B to 6, LDH-A to 11, LDH-B to 12 and IPO-A to 21.The assignment of PGM₃ puts the HL-A loci on chromosome 6. Segregation of the enzymes of the PGD linkage group was demonstrated in a clone which had retained a deleted chromosome 1. Subclones of this line indicate that the loci for PGD and PGM₁ are situated on the short arm or proximal part of the long arm of 1 and the locus for Pep-C on the long arm.

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Zusammenfassung Etwa 75 Hybrid-Zellklone Mensch/Chinesischer Hamster wurden in bezug auf den menschlichen Anteil ihres Chromosomensatzes analysiert und gleichzeitig auf menschliche Enzym-Marker untersucht. Die Korrelation zwischen Anwesenheit von Chromosomen und Enzym-Markern ließ die Folgerung zu, daß die PGD-Koppelungsgruppe auf Chromosom 1, ME₁, PGM₃ und IPO-B auf Nr. 6, LDH-A auf 11, LDH-B auf 12 und IPO-A auf Chromosom 21 gelegen ist.Die Lokalisation von PGM₃ läßt die Folgerung zu, daß auch die HL-A-loci auf Chromosom 6 lokalisiert sind. Aufspaltung der Enzyme der PGD-Koppelungsgruppe konnte an einem Klon dargestellt werden, der ein deletiertes Chromosom 1 enthielt. Die Subklone dieser Linie zeigen, daß die loci für PGD und PGM₁ auf dem kurzen Arm oder dem proximalen Teil des langen Arms von Chromosom Nr. 1 liegen, während der locus für Pep-C auf dem langen Arm gelegen ist.

     

Characterization and molecular genetic mapping of microsatellite loci in pepper

Microsatellites or simple sequence repeats are highly variable DNA sequences that can be used as informative markers for the genetic analysis of plants and animals. For the development of microsatellite markers in Capsicum, microsatellites were isolated from two small-insert genomic libraries and the GenBank database. Using five types of oligonucleotides, (AT)₁₅, (GA)₁₅, (GT)₁₅, (ATT)₁₀ and (TTG)₁₀, as probes, positive clones were isolated from the genomic libraries, and sequenced. Out of 130 positive clones, 77 clones showed microsatellite motifs, out of which 40 reliable microsatellite markers were developed. (GA) _n and (GT) _n sequences were found to occur most frequently in the pepper genome, followed by (TTG) _n and (AT) _n . Additional 36 microsatellite primers were also developed from GenBank and other published data. To measure the information content of these markers, the polymorphism information contents (PICs) were calculated. Capsicum microsatellite markers from the genomic libraries have shown a high level of PIC value, 0.76, twice the value for markers from GenBank data. Forty six microsatellite loci were placed on the SNU-RFLP linkage map, which had been derived from the interspecific cross between Capsicum annuum TF68 and Capsicum chinense Habanero. The current SNU2 pepper map with 333 markers in 15 linkage groups contains 46 SSR and 287 RFLP markers covering 1,761.5 cM with an average distance of 5.3 cM between markers.Communicated by J. Dvorak     

Mapping the genome of rapeseed (Brassica napus L.). I. Construction of an RFLP linkage map and localization of QTLs for seed glucosinolate content

A linkage map of the rapeseed genome comprising 204 RFLP markers, 2 RAPD markers, and 1 phenotypic marker was constructed using a F₁ derived doubled haploid population obtained from a cross between the winter rapeseed varieties Mansholt's Hamburger Raps and Samourai. The mapped markers were distributed on 19 linkage groups covering 1441 cM. About 43% of these markers proved to be of dominant nature; 36% of the mapped marker loci were duplicated, and conserved linkage arrangements indicated duplicated regions in the rapeseed genome. Deviation from Mendelian segregation ratios was observed for 27.8% of the markers. Most of these markers were clustered in 7 large blocks on 7 linkage groups, indicating an equal number of effective factors responsible for the skewed segregations. Using cDNA probes for the genes of acyl-carrier-protein (ACP) and -ketoacyl-ACP-synthase I (KASI) we were able to map three and two loci, respectively, for these genes. The linkage map was used to localize QTLs for seed glucosinolate content by interval mapping. Four QTLs could be mapped on four linkage groups, giving a minimum number of factors involved in the genetic control of this trait. The estimated effects of the mapped QTLs explain about 74% of the difference between both parental lines and about 61.7 % of the phenotypic variance observed in the doubled haploid mapping population.     

Towards an integrated linkage map of common bean 2. Development of an RFLP-based linkage map

Summary A restriction fragment length polymorphism (RFLP)-based linkage map for common bean (Phaseolus vulgaris L.) covering 827 centiMorgans (cM) was developed based on a F₂ mapping population derived from a cross between BAT93 and Jalo EEP558. The parental genotypes were chosen because they exhibited differences in evolutionary origin, allozymes, phaseolin type, and for several agronomic traits. The segregation of 152 markers was analyzed, including 115 RFLP loci, 7 isozyme loci, 8 random amplified polymorphic DNA (RAPD) marker loci, and 19 loci corresponding to 15 clones of known genes, 1 virus resistance gene, 1 flower color gene, and 1 seed color pattern gene. Using MAPMAKER and LINKAGE-1, we were able to assign 143 markers to 15 linkage groups, whereas 9 markers remained unassigned. The average interval between markers was 6.5 cM; only one interval was larger than 30 cM. A small fraction (9%) of the markers deviated significantly from the expected Mendelian ratios (121 or 31) and mapped into four clusters. Probes of known genes belonged to three categories: seed proteins, pathogen response genes, and Rhizobium response genes. Within each category, sequences homologous to the various probes were unlinked. The I gene for bean common mosaic virus resistance is the first disease resistance gene to be located on the common bean genetic linkage map.     

Isoelectric focusing of red cell phosphoglucomutase (E.C.:2.7.5.1) at the PGM1 locus in a French-Canadian population

Summary Phosphoglucomutase₁ (PGM₁) polymorphism was studied in a French-Canadian population of Québec city, Canada by means of a low voltage (max 500 V) isoelectric focusing (IEF) procedure on vertical polyacrylamide gel slabs. Frequencies of the four common PGM₁ genes estimated from the phenotype distribution in 308 unrelated individuals were PGM ₁ ¹⁺ , 0.61 (±0.02); PGM ₁ ^1- , 0.13 (±0.01); PGM ₁ ¹⁺ , 0.61 (±0.02); PGM ₁ ^1- , 0.18 (±0.02); and PGM ₁ ¹⁺ , 0.61 (±0.02); PGM ₁ ^1- , 0.08 (±0.01). The segregation patterns observed in 154 families, which included 31 different mating types and 353 children, confirmed a Mendelian inheritance of four autosomal genes. The distribution of the PGM₁ phenotypes observed or expected in a Hardy-Weinberg equilibrium was compared with that of other populations. A significant (P<0.001) difference was found between the Québec population and a Black population from Keneba, Gambia, West-Africa.     

Multipoint linkage analysis in X-linked Alport syndrome

Summary In order to localize the gene for the X-linked form of Alport syndrome (ATS) more precisely, we performed restriction fragment length polymorphism analysis with nine different X-chromosomal DNA markers in 107 members of twelve Danish families segregating for classic ATS or progressive hereditary nephritis without deafness. Two-point linkage analysis confirmed close linkage to the markers DXS17(S21) (Z _max = 4.44 at = 0.04), DXS94(pXG-12) (Z _max=8.07 at =0.04), and DXS101(cX52.5) (Z _max=6.04 at =0.00), and revealed close linkage to two other markers: DXS88(pG3-1) (Z _max =6.36 at =0.00) and DXS11(p22–33) (z _max=3.45 at =0.00). Multipoint linkage analysis has mapped the gene to the region between the markers DXS17 and DXS94, closely linked to DXS101. By taking into account the consensus map and results from other studies, the most probable order of the loci is: DXYS1(pDP34)-DXS3(p19-2)-DXS17-(ATS, DXS101)-DXS94-DXS11-DXS42(p43-15)-DXS51(52A). DXS88 was found to be located between DXS17 and DXS42, but the order in relation to the ATS locus and the other markers used in this study could not be determined.     

RAPD-based genetic linkage map of blueberry derived from a cross between diploid species (Vaccinium darrowi and V. elliottii)

An initial genetic linkage map for blueberry has been constructed from over 70 random amplified polymorphic DNA (RAPD) markers that segregated 11 in a testcross population of 38 plants. The mapping population was derived from a cross between two diploid blueberry plants: the F₁ interspecific hybrid (Vaccinium darrowi Camp x V. elliottii Chapm.) and another V. darrowi plant. The map currently comprises 12 linkage groups (in agreement with the basic blueberry chromosome number) and covers a total genetic distance of over 950cM, with a range of 3–30cM between adjacent markers. The use of such a map for identifying molecular markers linked to genes controlling chilling requirement and cold hardiness is discussed.     

Molecular marker analysis of Helianthus annuus L. 2. Construction of an RFLP linkage map for cultivated sunflower

A detailed linkage map of Helianthus annuus was constructed based on segregation at 234 RFLP loci, detected by 213 probes, in an F₂ population of 289 individuals (derived from a cross between the inbred lines HA89 and ZENB8). The genetic markers covered 1380 centiMorgans (cM) of the sunflower genome and were aranged in 17 linkage groups, corresponding to the haploid number of chromosomes in this species. One locus was found to be unlinked. Although the average interval size was 5.9 cM, there were a number of regions larger than 20 cM that were devoid of markers. Genotypic classes at 23 loci deviated significantly from the expected ratios (121 or 31), all showing a reduction in the ZENB8 homozygous class. The majority of these loci were found to map to four regions on linkage groups G, L and P.     

Analyse der Koppelung zwischen dem HL-A-System und anderen Loci

Zusammenfassung Die Koppelung der HL-A-Gene mit den Loci ABO, Rh, MNSs, P, Fy, Jk, K, SEP, PGM ₁, AK, ADA, GPT, Hp, Gm, Inv, Gc, Pt und Se wurde mit Hilfe der Lod-score-Methode untersucht. Es wurde dabei kein Hinweis für eine enge Koppelung zwischen den HL-A-Loci und den anderen Genorten gefunden.

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Analysis of the linkage between the HL-A loci and the genes of other markers

Summary The linkage of the HL-A genes with the loci ABO, Rh, MNSs, P. Fy, Jk, K, acP, PGM ₁, AK, ADA, GPT, Hp, Gm, Inv, Gc, Pt and ABH secretion was analyses using the lod-score method. There was no evidence for a close linkage between the HL-A loci and the genes of the other markers.

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National Blood Group Reference Laboratory (WHO), National Tissue Typing Reference Laboratory (Council of Europe)     

Population studies on human phosphoglucomutase-1 thermostability polymorphism

Summary The electrophoretic and thermostability polymorphisms of the PGM ₁ locus were examined in about 700 Czechoslovakians (Prague) and 3000 Italians. The Italian sample consisted of individuals from Pavia (Northern Italy), Viareggio and Rome (Central Italy) and Naples (Southern Italy). The eight PGM ₁ alleles, PGM ₁ ^1Str , PGM ₁ ^1Sts , PGM ₁ ^1Ftr , PGM ₁ ^1Fts , PGM ₁ ^2Str , PGM ₁ ^2Sts , PGM ₁ ^2Ftr , PGM ₁ ^2Fts , have been considered as combinations of mutations at three different sites, 1/2 S/F and tr/ts, within the PGM ₁ gene and their frequencies discussed in terms of linkage disequilibrium between these sites. All pairwise differences between the samples were significant except for Pavia-Viareggio and Viareggio-Rome. The frequencies of the PGM ₁ ^ts alleles have been found to range from 0.0981 (Prague) to 0.0546 (Naples) and can be ordered according to a North-South cline.This paper is dedicated to Professor Giuseppe Montalenti in occasion of his 80th birthday     

Population genetic studies in three Chinese minorities

Three minority ethnic groups from China (Mongolians, Koreans, Zhuang) were examined with respect to the genetic markers GLO, GPT, ACP, ESD, 6-PGD, PGM₁ subtypes, C3, and TF. Significant variations were noted for the gene frequencies of GLO, GPT, ESD, sub PGM₁ between Zhuang and Mongolians; for GPT, ACP, ESD, sub PGM₁ between Zhuang and Koreans; and for GLO between Mongolians and Koreans.     

A genetic map of Prunus based on an interspecific cross between peach and almond

A genetic linkage map of Prunus has been constructed using an interspecific F₂ population generated from self-pollinating a single F₁ plant from a cross between a dwarf peach selection (54P455) and an almond cultivar Padre. Mendelian segregations were observed for 118 markers including 1 morphological (dw), 6 isozymes, 12 plum genomic, 14 almond genomic and 75 peach mesocarp specific cDNA markers. One hundred and seven markers were mapped to 9 different linkage groups covering about 800 cM map distance, and 11 markers remained unlinked. Three loci identified by three cDNA clones, PC8, PC5 and PC68.1, were tightly linked to the dw locus in linkage group 5. Segregation distortion was observed for approximately one-third of the markers, perhaps due to the interspecific nature and the reproductive (i.e. self-incompatibility) differences between peach and almond. This map will be used for adding other markers and genes controlling important traits, identifying the genomic locations and genetic characterizing of the economically important genes in the genus Prunus, as well as for markerassisted selection in breeding populations. Of particular interest are the genes controlling tree growth and form, and fruit ripening and mesocarp development in peach and almond.     

A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers

A genetic linkage map of papaya (Carica papaya L.) was constructed using randomly amplified polymorphic DNA (RAPD) markers and a F₂ population derived from a University of Hawaii UH breeding line 356 x Sunrise cross. A total of 596 10-mer primers were screened, and 96 polymorphisms were detected. At LOD 4.0, 62 of these markers mapped to 11 linkage groups comprising 999.3 cM. About 80% of the markers conformed to expected Mendelian segregation ratios. We have mapped the locus that determines sex to a 14-cM region flanked by RAPD markers. The results demonstrate the usefulness of RAPD markers for developing a basic genetic linkage map in papaya.Journal series No. 4146 of the Hawaii Institute of Tropical Agriculture and Human Resources     

Genetic linkage mapping in peach using morphological,RFLP and RAPD markers

We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F₂ individuals derived from the self-fertilization of four F₁ individuals of a cross between New Jersey Pillar and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh color, and flower petal color, size and number. The segregation of 65 markers, comprising 46 RFLP loci, 12 RAPD loci and seven morphological loci, was analyzed. Low-copy genomic and cDNA probes were used in the RFLP analysis. The current genetic map for the WV family contains 47 markers assigned to eight linkage groups covering 332 centi Morgans (cM) of the peach nuclear genome. The average distance between two adjacent markers is 8 cM. Linkage was detected between Pillar (Pi) and double flowers (Dl) RFLP markers linked to Pi and flesh color () loci were also found. Eighteen markers remain unassigned. The individuals analyzed for linkage were not a random sample of all F₂ trees, as an excess of pillar trees were chosen for analysis. Because of this, Pi and eight other markers that deviated significantly from the expected Mendelian ratios (e.g., 121 or 31) were not eliminated from the linkage analysis. Genomic clones that detect RFLPs in the WV family also detect significant levels of polymorphism among the 34 peach cultivars examined. Unique fingerprint patterns were created for all the cultivars using only six clones detecting nine RFLP fragments. This suggests that RFLP markers from the WV family have a high probability of being polymorphic in crosses generated with other peach cultivars, making them ideal for anchor loci. This possibility was examined by testing RFLP markers developed with the WV family in three other unrelated peach families. In each of these three peach families respectively 43%, 54% and 36% of RFLP loci detected in the WV family were also polymorphic. This finding supports the possibility that these RFLP markers may serve as anchor loci in many other peach crosses.     

Genetic analysis of RFLPs, GATA microsatellites and RAPDs in a cross between L. esculentum and L. pimpinellifolium

A population of 257 BC₁ plants was developed from a cross between an elite processing line of tomato (Lycopersicon esculentum cvM82-1-7) and the closely related wild species L. pimpinellifolium (LA1589). The population was used to construct a genetic linkage map suitable for quantitative trait locus (QTL) analysis to be conducted in different backcross generations. The map comprises 115 RFLP, 3 RAPD and 2 morphological markers that span 1279 cM of the tomato genome with an average distance between markers of 10.7 cM. This map is comparable in length to that of the highdensity RFLP map derived from a L. esculentum x L. pennellii F₂ population. The order of the markers in the two maps is also in good agreement, however there are considerable differences in the distribution of recombination along the chromosomes. The segregation of six GATA-containing loci and 47 RAPD markers was also analyzed in subsets of the population. All of the microsatellite loci and 35 (75%) of the RAPDs mapped to clusters associated with centromeric regions.     

Theobroma cacao L.: a genetic linkage map and quantitative trait loci analysis

A genetic linkage map of Theobroma cacao (cocoa) has been constructed from 131 backcross trees derived from a cross between a single tree of the variety Catongo and an F1 tree from the cross of Catongo by Pound 12. The map comprises 138 markers: 104 RAPD loci, 32 RFLP loci and two morphologic loci. Ten linkage groups were found which cover 1068 centimorgans (cM). Only six (4%) molecular-marker loci show a significant deviation from the expected 11 segregation ratio.The average distance between two adjacent markers is 8.3 cM. The final genome-size estimates based on two-point linkage data ranged from 1078 to 1112 cM for the cocoa genome. This backcross progeny segregates for two apparently single gene loci controlling (1) anthocyanidin synthesis (Anth) in seeds, leaves and flowers and (2) self-compatibility (Autoc). The Anth locus was found to be 25 cM from Autoc and two molecular markers co-segregate with Anth. The genetic linkage map was used to localize QTLs for early flowering, trunk diameter, jorquette height and ovule number in the BC₁ generation using both single-point ANOVA and interval mapping. A minimum number of 2–4 QTLs (P<0.01) involved in the genetic expression of the traits studied was detected. Coincident map locations of a QTL for jorquette height and trunk diameter suggests the possibility of pleiotropic effects in cocoa for these traits. The combined estimated effects of the different mapped QTLs explained between 11.2% and 25.8% of the phenotypic variance observed in the BC₁ population.     

Genetic analysis using trans-dominant linked markers in an F2 family

Trans-dominant linked markers pairs (trans referring to the repulsion linkage phase) provide a model for inferring the F₂ progeny genotype based upon both the conditional probabilities of F₂ genotypes, given the F₂ phenotype, and prior information on marker arrangement. Prior information of marker arrangement can be readily obtained from a linkage analysis performed on marker segregation data in a family resulting by crossing the F₁ individual to a tester parent or else can be obtained directly from the gametes of the F₁, or from recombinant inbred lines. We showed that a trans-dominant linked marker (TDLM) pair can be recoded as a co-dominant megalocus when the recombination fraction, r₁, for apair of TDLMs is less than 0.05. We obtained a maximum-likelihood estimator (MLE) of the recombination frequency, r₂, between a TDLM pair and a co-dominant marker in an F₂ family using the EM algorithm. The MLE was biased. Mean bias increased as r₁ and r₂ increased, and decreased as sample size increased. The information content for r₂ was compared to the information content of dominant and co-dominant markers segregating in an F₂ family. It was almost identical with two co-dominant markers when r₁0.01 and r₂0.05. For larger values of r₁, (0.05r₁0.15) a TDLM pair provided 75%–66% of the information content of two co-dominant markers. Although dominant markers can be converted to co-dominant markers by a laborious process of cloning, sequencing, and PCR, TDLM pairs could easily substitute for co-dominant markers in order to detect quantitative trait loci (QTLs) and estimate gene action in an F₂ family.