The Journal of heredity

Published by Oxford University Press (OUP)
Online ISSN: 0022-1503
Publications
Phenotypic reactions to Phomopsis seed infection of parents and an F 2 population from AP 350 Â PI 80837 inoculated with Phomopsis longicolla in the field and genotypes of F 2 plants based on SSR markers 
Article
Resistance to Phomopsis seed decay (PSD) in soybean (Glycine max [L.] Merr.) could provide dependable control of this important disease that affects seed quality. Studies have shown that single dominant genes that are allelomorphically different confer low levels of PSD in MO/PSD-0259 and PI 80837. The objectives of this research were to identify simple sequence repeat (SSR) markers linked to genes for PSD resistance in PI 80837 and MO/PSD-0259 and to associate the resistance genes to known linkage groups. Crosses were made between the PSD-susceptible cultivar Agripro 350 and each of the resistant lines MO/PSD-0259 and PI 80837. F(2) populations from each cross were grown and inoculated in the field. Individual plant reactions were characterized by determining the levels of seed infection, and DNA of F(2) plants was extracted for SSR analysis and mapping. F(2) segregation data showed that different single dominant genes condition PSD resistance in MO/PSD-0259 and PI 80837. Resistance in PI 80837 was linked to Sat_177 (4.3 cM) and Sat_342 (15.8 cM) on molecular linkage group (MLG) B2. In MO/PSD-0259, resistance was linked to Sat_317 (5.9 cM) and Sat_120 (12.7 cM) on MLG F. These data support work by Berger and Minor (Berger RD, Minor HC. 1999. An restriction fragment length polymorphism (RFLP) marker associated with resistance to Phomopsis seed decay in soybean PI 417479. Crop Sci 39:800-805.) in which PSD resistance in PI 417479, the resistant parent used to develop MO/PSD-0259, was associated with RFLP marker A708 on MLG F. These SSR markers should be useful in selection for resistant genotypes in breeding programs.
 
Article
Genetic analysis of a (BN x ACI)ACI backcross for the biochemical markers Es-1 and Es-2 (linkage group V) and a microsatellite marker of Ucp (chromosome 19) revealed linkage between these three loci. This linkage relationship confirms that in the rat linkage group V genes are located on chromosome 19. Genetic analysis of a (BN x LEW)LEW backcross showed that Hp is linked to Ucp, thus indicating that the Hp locus is also located on chromosome 19. These results substantiate the linkage homology of RNO 19, MMU 8, and HSA 16.
 
Article
Estimating population parameters from polymorphism frequency data requires neutral genetic markers. Any departure from neutrality may invalidate the inferences drawn from such analyses. We recently discussed the possibility of identifying markers that show deviation from neutral expectations in pairwise comparisons of diverging populations. We are now releasing a user-friendly software package that implements all the necessary steps to identify the signature of selection among molecular markers in a set of polymorphism data. This software can be downloaded free of charge at http://www.univ-montp2.fr/~genetix/detsel/detsel.html.
 
Article
We developed MBP (version 1.0), a software package for optimizing maize (Zea mays L.) breeding procedures based on doubled haploid lines. This software accounts for both recurrent selection and the development of hybrid parent lines. Based on quantitative genetic model calculations, MBP (version 1.0) maximizes the expected genetic gain per year as a function of various genetic parameters and operational variables under the restriction of a given annual breeding budget. Exact formulae for the prediction of the effective population size are implemented, which allows to optimize breeding procedures under limited relative annual loss of genetic variance.
 
Article
Acknowledgments: We thank the European Science Foundation for supporting the visit of JT to Aarhus (grant no. ESF-POBI/95Y), the Danish Natural Science Research council for supporting parts of the project (grant no. 9701412 to VL). Dept. of Genetics and Ecology, Aarhus University, Ny Munkegade, Bldg. 540, DK{8000 Aarhus C, Denmark, Phone: (+45)8942-3268, Fax: (+45)86127191, e-mail: volker.loeschcke@biology.aau.dk Running title. POPDIST: A Genetic Distance Program Key words and phrases. Genetic distance, genetic identity, program 1 Abstract In this note we announce the release of POPDIST version 1.1.1. This is a program to calculate genetic distance and identity measures, includ- ing the measure of Tomiuk and Loeschcke, which also allows calculation of genetic similarity measures for comparisons involving polyploid and parthenogenetic populations. The program is available for free from the Internet as C source code, or compiled for the Macintosh, MS Windows 95, and various brands of UNIX. 2 POPDIST is a program for the calculation of various population genetic dis- tance and identity measures. It uses an input,le format that is similar to the input format used by the GENEPOP software (Raymond and Rousset 1995), and,les created for GENEPOP for diploid populations are read unmodied,by
 
Article
Recent evolution of separate sexes in flowering plants provides unparalleled opportunities for understanding the early stages of sex chromosome evolution, including their origin from autosomes. Moreover, the transition from combined to separate sexes can be associated with speciation via polyploidization in angiosperms, suggesting that genome doubling/merger may facilitate sterility mutations required for sex chromosome formation. To gain insight into the origin of sex chromosomes in a polyploid plant, we doubled the simple sequence repeat (SSR) density and increased genome coverage in a genetic map of octoploid Fragaria virginiana, a species purported to have a "proto-sex" chromosome, where limited recombination occurs between 2 linked "loci" carrying the male- and female-sterility mutations. Incorporation of almost 3 times the number of SSR markers into the current map facilitated complete characterization of the F. virginiana proto-sex chromosome, revealing its largely autosomal nature and the location of the sex-determining region toward the distal end. Furthermore, extensive synteny between our genetic map and a map involving diploid hermaphroditic congeners allowed assignment of linkage groups to homeologous groups, identification of the proto-sex chromosome's autosomal homoeolog, and detection of a putative rearrangement near the sex-determining region. Fine mapping and additional comparative work will shed light on the intriguing possibility that rearrangements during polyploidization were involved in the evolution of sex chromosomes in Fragaria.
 
Basic properties of the 20 microsatellite markers developed in this study
Article
Species of Eucalyptus are keystone species for ecological studies in their natural ranges and are extensively planted in the tropical and subtropical regions of the world to supply high-quality woody biomass for various applications. We report the development of a selected set of 20 dinucleotide and trinucleotide repeat microsatellites derived from Eucalyptus expressed sequence tags (ESTs). These microsatellites were selected for full transferability and homogeneous rate of polymorphism across species. They were evaluated for individual fingerprinting, parentage testing, and intraspecific population structure analyses in 6 of the most extensively studied and planted species worldwide, representing key phylogenetic sections of the largest subgenus Symphyomyrtus. This set of markers provides exceptional resolution for population genetics and molecular breeding applications in the genus Eucalyptus. As they were developed from conserved transcribed regions, the transferability and polymorphism of these microsatellites will most likely extend to the other 300 or more species within the same subgenus.
 
SSR electropherograms of sample 80A for the loci Mh35-2 (A), Mh57 (B), and Mh80 (C) showing scores (1–10) applied to peaks in the SSR profiles using the MANUAL scoring routine (see text). Peaks identified automatically (AUTO) are marked with asterisks and those scored additionally in SEMI mode by þ.  
Neighbor joining (NJ) dendrograms for SEMI (left) and MANUAL 8 routines (right; different scales). Numbers at branches are bootstrap values .50% (NJ search with 100 000 replicates in PAUP). Context data are coded in the sample tag (with letters A, B, and D referring to plots) and color of the boxes (sex): The 12 MLLs from Elisenhain consist of 5 males (gray) and 7 females (blank); the numbers of merigenets assigned to these MLLs are listed in brackets. Female 3 (marked by asterisk, different unsupported position in both trees) includes a nonflowering merigenet and a single female sample allowing for sex determination in the former.  
Characteristics of 8 polymorphic SSR loci isolated from Mercurialis huetii and used for genet discrimination in decaploid M. perennis
Number of MLLs (bars) and of conflicts (diamonds) with merigenet (white), sex (gray), and plot information (black) obtained for 0–25 tolerated fragment differences for 54 analyzed samples of Mercurialis perennis using 8 SSR loci and 4 different peak-scoring routines: (A) AUTO, (B) SEMI, (C) MANUAL 8, and (D) MANUAL 4. Light bars mark 14 MLLs and no conflicts with context; arrows mark the minimum number of differing fragments that can be tolerated without conflicts.  
Locus accumulation curve for the AUTO (A) and SEMI scoring mode (B), applying thresholds of 7 and 4 different fragments for MLL identity, respectively. Shown are (A, B) mean numbers of differentiated MLLs with standard deviations (solid lines) and combinations of loci performing best and poorest (upper and lower dotted lines, respectively) and the resulting mean sex (C) and plot (D) conflicts per sample for AUTO (triangles) and SEMI (circles) routine, with standard deviations in solid and dotted lines, respectively.
Article
For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as amplified fragment length polymorphisms (AFLPs). In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from 4 different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within 1 MLL, all analyses revealed the same 14 MLLs without conflicting with merigenet, sex, or plot assignment. For semiautomatic scoring, a combination of as few as 2 of the 4 most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.
 
The geographic range of Cyprogenia stegaria populations sampled in the Ohio and Tennessee River systems. The symbol (d) indicates sampling sites.
Minimum-spanning network between haplotypes of Cyprogenia stegaria . Nodes represent haplotypes, with the size of each node representing the number of individuals that share that haplotype. Numbers used to denote haplotypes follow Table 3. Cross-bars reflect the number of mutational events between specific haplotype pairs; a clear line connecting 2 circles represents a single event. For n . 4 mutational events, numbers next to interrupted lines are used to indicate the number of mutations. Colors used to indicate population(s) of origin of haplotypes: Green d , Rolling Fork s , Licking d , and Clinch d ; and with C. aberti haplotypes h for comparison. 
Article
We report on multiple patterns of differentiation and connectivity in the fanshell pearlymussel (Cyprogenia stegaria), based on different markers. Knowledge of genetic variation and genetic connectivity among remaining populations of this federally endangered species is needed to initiate implementation of the species recovery plan. We collected tissue samples from 96 specimens from the Green, Rolling Fork, and Licking Rivers, tributaries to the Ohio River, and the Clinch River, a tributary to the Tennessee River, providing broad coverage of the current distributional range of the species. Results from 7 nuclear DNA microsatellite markers suggested minimal population-level differentiation, whereas a mitochondrial DNA (mtDNA) marker (ND1) exhibited significant differentiation between C. stegaria in the Clinch River and the Ohio River populations. The ND1 data also confirm the existence of 2 distinct mtDNA lineages in the genus that transcends species boundaries. Further analyses suggest that the disproportionally strong signal from 2 very divergent ND1 lineages possibly masks finer-grained structure in the Ohio River population, based on one of the mtDNA lineages only. We recommend further sampling to confirm the absence of one lineage from the upper Clinch River drainage and suggest that provisional management guidelines should limit reciprocal exchanges among C. stegaria populations from the Clinch River and those in the Ohio River system.
 
Validation of the sequencing-based method to determine the relative contribution of the homeologs using 2 methods. (A) Example (gene S H 3-66) for measure of proportion of SNP haplotypes in amplicons from 3 types of genomic DNA: Coffea arabica Caturra (tetraploid, 1/2 E a , 1/2 C a ), H855 triploid hybrid C. arabica  C. canephora (2/3 C a þ C, 1/3 E a ), and Arabusta tetraploid hybrid from a cross between C. arabica and ''tetraploid'' C. canephora (3/4 C a þ C, 1/4 E a ). (B) The relative proportion of 2 types of the SNP in amplicons from different mixed BAC DNA solutions (0.84 E a /0.16 C a , 0.63 E a /0.37 C a , and 0.36 E a /0.64 C a ) and C. arabica var. Caturra (tetraploid, 1/2 E a , 1/2 C a ) for 3 genes: S H 3-66, S H 3-76, and S H 3-81. In the 2 figures, the values obtained were compared with the theoretical ratio curve.
Homeologous genes investigated, SNP, and pairs of oligonucleotides used to study their relative contribution to the transcriptome of Coffea arabica
Representation of the average relative homeologous expression of 13 genes (E a /E a þ C a ) in different organs and for 2 growth condition (A, warm; B, cold).
Article
Allopolyploidy is considered as a major factor contributing to speciation, diversification, and plant ecological adaptation. In particular, the expression of duplicate genes (homeologs) can be altered leading to functional plasticity and to phenotypic novelty. This study investigated the influence of growing temperatures on homeologous gene expression in Coffea arabica L., a recent allopolyploid involving 2 closely related diploid parental species. The relative expression of homeologs of 13 genes all located in the same genomic region was analyzed using an SNP ratio quantification method based on dideoxy-terminated sequences of cDNA amplicons. The relative expression of homeologous genes varied depending on the gene, the organ, and the growing condition. Nevertheless, expression of both homeologs was always detected (i.e., no silencing). Although the growing conditions were suitable for one or other of the parental species, neither subgenome appeared preferentially expressed. Furthermore, relative homeologous expression showed moderate variations across organs and conditions and appeared uncorrelated between adjacent genes. These results indicate the absence of signs of subfunctionalization suggesting C. arabica has not undergone noticeable diploidization. Furthermore, these results suggest that the expression of homeologous genes in C. arabica is regulated by a shared trans-regulation mechanism acting similarly on the 2 subgenomes and that the observed biases in the relative homeolog expression may result from cis fine-scale factors.
 
Article
The seagrass Zostera marina is widely distributed in coastal regions throughout much of the northern hemisphere, forms the foundation of an important ecological habitat, and is suffering population declines. Studies in the Atlantic and Pacific oceans indicate that the degree of population genetic differentiation is location dependent. San Francisco Bay, California, USA, is a high-current, high-wind environment where rafting of seed-bearing shoots has the potential to enhance genetic connectivity among Z. marina populations. We tested Z. marina from six locations, including one annual population, within the bay to assess population differentiation and to compare levels of within-population genetic diversity. Using 7 microsatellite loci, we found significant differentiation among all populations. The annual population had significantly higher clonal diversity than the others but showed no detectible differences in heterozygosity or allelic richness. There appears to be sufficient input of genetic variation through sexual reproduction or immigration into the perennial populations to prevent significant declines in the number and frequency of alleles. In additional depth comparisons, we found differentiation among deep and shallow portions in 1 of 3 beds evaluated. Genetic drift, sweepstakes recruitment, dispersal limitation, and possibly natural selection may have combined to produce genetic differentiation over a spatial scale of 3-30 km in Z. marina. This implies that the scale of genetic differentiation may be smaller than expected for seagrasses in other locations too. We suggest that populations in close proximity may not be interchangeable for use as restoration material.
 
Article
A new recessive mutation, spasmodic (spd), producing behavior that mimics that of the neurological mutation spastic (spa) with rapid tremors, stiff posture, and difficulty in righting, arose spontaneously in strain A/HeJ at the Jackson Laboratory in 1979. It is not an allele of spa and linkage tests show that this mutation is located close to vestigial tail (vt) near the center of chromosome 11. Additional genetic tests show that it is not an allele of trembler (Tr), shaker-2 (sh-2), nor vibrator (vb), all neurological mutations located in the same region of chromosome 11. No differences were observed in the levels of the major CNS and PNS myelin proteins or lipids of spd/spd mice versus littermate controls, suggesting that, unlike several closely linked mutations, the spd mutation does not affect myelination. Pharmacological studies reported here show that aminooxyacetic acid improves the behavioral abnormalities of affected spd/spd mice in the same way it improves the behavior of affected spa/spa mice. However, unlike the spa/spa mice, there are no changes in the postsynaptic receptors for glycine, GABA, or benzodiazepines in spd/spd mice.
 
Marker* mapped relative to the T16Ad breakpoint in band B5 on motue chromosome 11 
Article
To contribute to the physical gene map of mouse chromosome 11 (MMU11) and to extend the mapping resources available for this chromosome, we have produced mouse x rat somatic cell hybrids containing only bands B5 to E of MMU11. Characterization of the hybrids by polymerase chain reaction (PCR) amplification and Southern blot analyses of MMU11 markers revealed two hybrids, T16Ad14B and T16Ad19A, that had selectively retained the 3(11) translocation product containing distal MMU11 (bands B5-E). Cytogenetic analysis of the hybrid T16Ad14B by fluorescence in situ hybridization (FISH) and conventional G-banding confirmed the presence of the 3(11) translocation chromosome. Mapping of markers in both the T16Ad14B and T16Ad19A hybrids localized the T16Ad translocation breakpoint between the proximal markers Atplb2 and Acrb and the more distal markers Scya2 and Mpo. Loci for D11Mit5, Rpo2-1, Trp53, Glut4, Acrb, and Atplb2 could all be localized proximal to the T16Ad breakpoint in band B5, between bands B1 and B5 on MMU11.
 
Article
One of the most frequent chromosomal translocations in human beings is 11q/22q, which results in the "partial trisomy of 22q syndrome." However, the breakpoint on the long arms of chromosomes 11 and 22 is still a matter of controversy. In the present study, we have used chromosomes from lymphocytes of a neonate who happened to have this classical abnormality, and by R-banding prometaphase chromosomes with acridine orange it has been possible to establish that the translocation between chromosomes 11 and 22 resulted from 3:1 meiotic maternal nondisjunction. A detailed analysis of the chromosome regions involved in this translocation revealed that the breakpoints on chromosomes 11 and 22 were at 11q23.3 and 22q11.1, respectively.
 
Article
The karyotype of the human cell line, J-111, has been studied employing R-banding by fluorescence using acridine orange technique (RFA). The model chromosome number of this line was 112. All human chromosomes except the Y were present in each metaphase. Twenty-one marker chromosomes were distinguished and their possible origins were investigated. Of these, twelve were consistently present in all cells. Nine markers were highly variable. Four typical marker chromosomes of HeLa cells were found and their origins were identified, indicating that the line is a HeLa contaminant. The reverse banding patterns of all marker chromosomes are presented and the value of the RFA technique is discussed.
 
Article
Testes and brain tissue of Japanese quail ( Coturnix japonica ) from a heavy strain and a randombred strain were assayed for density of [125I]iodomelatonin binding sites ( B max ) and their binding affinity ( K d ). The fact that iodomelatonin and melatonin have similar biological action suggests that the [125I]iodomelatonin binding sites are putative melatonin receptors. The heavy strain has lower fertility, higher early embryonic mortality, and lower hatchability than the randombred strain. Although the testes of the heavy males were significantly heavier than those of the randombred males, their testes had significantly fewer melatonin binding sites per milligram of protein as well as relative to total testis protein. There was no difference in the K d of these binding sites between the two strains. B max and K d of brain tissue of the two strains were not different. Our results suggest a direct relationship between the pineal and the gonads. Selection for fast growth rate may significantly affect the direct regulatory role of melatonin on gonadal function via changes in the sensitivity of the reproductive organ (downregulation) to the action of melatonin.
 
Article
Mesenchymal dysplasia (mes) is a new autosomal recessive mouse mutation that alters normal growth of mesenchyme-derived tissues and provides a new mouse model for studying connective tissue development and defects. Mutants are characterized by preaxial polydactyly of all four feet, a shortened face, wide set eyes, domed head, and a shortened kinky tail. Multiple skeletal defects are seen in alizarin-stained specimens. Histologically, areas of mineralization are found in tendons. Mutants also have increased musculature in the shoulders and hips and decreased peritoneal fat. Salivary glands, testes, and kidneys are smaller than in littermates. Mesenchymal dysplasia has been mapped to mouse chromosome (Chr) 13. These mapping crosses also confirmed that the Purkinje cell degeneration (pcd) mutation is on Chr 13.
 
Article
A minisatellite sequence in the first intron of the rat renin gene showed five-allelic polymorphism in 11 inbred rat strains. A new allelic variant, which was thought to be generated in the germ line, was observed in 136 animals of two sets of backcross progenies originating from parental strains with different alleles. These facts suggested that the minisatellite is genetically unstable. A linkage analysis using the backcross progenies confirmed the assignment of renin locus (REN) on linkage group (LG) X at a site between FH (fumarate hydratase) and PEPC (peptidase) loci. Fluorescence in situ hybridization allowed mapping of the renin gene on rat chromosome 13q13.
 
Article
Professionals in genetics, medicine, and biology education have in recent years called for placing greater emphasis on human genetics in the education of the nation's citizenry. Since a large collegiate audience for such education is found in the general biology classroom, we elected to analyze 13 current and widely used general biology textbooks to determine their human genetics content. The analyses revealed that from 6.68 to 15.51 percent of the books' pages were devoted to genetics, but only 0.75 to 3.44 percent of the pages dealt specifically with human genetics. The number of human genetic traits discussed in the books ranged from four to 24, with a mean of 15.77. Nine different chromosome aberrations were cited, with Down, Klinefelter, and Turner syndromes being mentioned most often. Twenty autosomal dominant, fifteen autosomal recessive, and seven X-linked traits were used as examples in the various textbooks. Most frequently cited single-gene conditions were the ABO blood groups, sickle cell anemia, phenylketonuria, hemophilia, and red/green colorblindness. The books varied considerably in the emphasis given to social applications of medical genetics. Based on the findings of this study, we offer several recommendations for the improvement of the human genetics content of general biology textbooks and courses.
 
Article
A mutant characterized by small size, short snout, short middle and inner metatarsals and hallux, low vigor, and poor reproduction appeared in F2 from a cross of BALB/c in 1965. It proved recessive and was named dumpy, with symbol dpy. After some 10 years of maintenance, the stock showed much improved vigor and reproduction, but it is not carried on a pure-strain background. Linkage was found with satin (sa) in linkage group XIV, chromosome 13. Data from female heterozygotes gave about 16 percent crossing over, and from males about 10 percent. Three-point tests involving XtJ showed the map order XtJ-sa-dpy, again with sex difference in crossing over, confirming results of studies by others for this region of chromosome 13.
 
Article
beta-Carbolines, such as methyl beta-carboline-3-carboxylate (beta-CCM), attach to the benzodiazepine receptors in the brain, but have effects completely opposite to those of benzodiazepines: beta-CCM is a convulsant at high doses, an anxiogenic at moderate doses, and enhances learning at low doses. The aim of this work was to detect some of the chromosomal segments involved in the regulation of beta-CCM-induced seizures. The method used was a derivation of the classical use of linkage-testing strains. We tested several strains and some of their intercrosses and back-crosses. For two of these strains, we obtained significant results showing that genes located on chromosomes 4 and 13, provisionally termed respectively Bis1 and Bis2, were involved in the regulation of beta-carboline-induced seizures. Testing of these two strains with two other convulsant agents (pentylenetetrazol, which acts at the picrotoxine site of the GABA receptor complex, and strychnine, which acts at the glycinergic receptor) provided evidence that the genes implicated are not involved in general seizure processes but specifically in beta-CCM-induced seizures.
 
Article
As-1 is the putative structural locus for murine arylsulfatase B, and Lth-1 determines the presence or absence of a 35 000 dalton acidic liver protein. As-1 and Lth-1 were found to be closely linked using recombinant inbred (RI) strains. Both loci were found to have been cotransferred with the pearl (pe) coat color mutation (chromosome 13) in the B6.C3H pe/pe congenic strain. The linkage relationships between pe, Lth-1, and As-1 were further defined in a backcross. On the basis of the RI data, the congenic strain result, and the backcross data, the following genetic distances were estimated: pe--As-1, 7.1 +/- 4.0 cM; As-1--Lth-1, 2.5 +/- 1.0 cM; and pe--Lth-1, less than 6.9 cM. As-1 and Lth-1 are the first biochemically defined loci to be added to the chromosome 13 linkage map.
 
Article
Bilateral cataracts observed in the eyes of a 13/N guinea pig and one of her two offspring led to studies to determine the nature of this cataract and its possible heritability. The cataract was determined to be of the nuclear type, was congenital, and apparently transmitted by a single autosomal dominant gene. The cataractous condition of the mother had no effect on the percentage of litters containing stillborns. The cataractous condition of the offspring had no effect on their viability in utero, i.e., there was no greater incidence of stillborns among cataractous than among non-cataractous offspring. The birthweights of the cataractous animals were lower, but not significantly, than those of their non-cataractous littermates; however, the survivability to weaning of the cataractous offspring was reduced significantly when compared to their non-cataractous siblings.
 
Article
This paper reports the identification of a carrier of two different balanced chromosomal translocations (45,XX,-13,-14, + t(13q;14q), t(6;8) (p11;p12]. Ascertainment occurred during family studies following prenatal diagnosis performed because of advanced maternal age. Family pedigree and past reproductive difficulties also are reviewed, and the theoretical probability of producing a phenotypically normal offspring is explored. We are unaware of previously published observations in which two different balanced autosomal translocations are found in the same individual.
 
Article
In the chromosome survey of Maryland boys, a 15 year old white male was found to have a 5/14 translocation. Skeletal examination was normal and showed a bone age of 19 years. Clinical examination was unremarkable and cardiac and neurological functions were within normal limits. The boy's height was in the 10th percentile range, and his weight above the 97th percentile range at 15 years and 9 months. Clinical examination of other balanced carrier members of the family was within normal limits. The dermal patterns of the translocation carrier individuals were not markedly different from the chromosomally normal individuals. The segregation pattern of the loci for the MNS blood group system and PGM1 suggests that there may be some basis for assigning these loci to the translocation chromosomes.
 
Article
A lymphocyte clone with a 45, XY karyotype with a 14/14 tandem translocation marker, the frequency of which is time-variable, has been observed in an ataxia telangiectasia patient. Cells with the marker chromotosome were not observed in fibroblasts cultures derived from a skin biopsy, nor was the marker observed in leukocyte cultures from the patient's two affected sibs.
 
Locus names, target regions, fragment sizes, annealing temperatures (T a ), and primer sequences for cattle Y chromosome
AMOVA for cattle Y chromosome haplotypes
Article
DNA samples from 307 males of 13 Portuguese native cattle breeds, 57 males of the 3 major exotic breeds in Portugal (Charolais, Friesian, and Limousin), and 5 Brahman (Bos indicus) were tested for 5 single nucleotide polymorphisms, 1 “indel,” and 7 microsatellites specific to the Y chromosome. The 13 Y-haplotypes defined included 3 previously described patrilines (Y1, Y2, and Y3) and 10 new haplotypes within Bos taurus. Native cattle contained most of the diversity with 7 haplotypes (H2Y1, H3Y1, H5Y1, H7Y2, H8Y2, H10Y2, and H12Y2) found only in these breeds. H6Y2 and H11Y2 occurred in high frequency across breeds including the exotics. Introgression of Friesian cattle into Ramo Grande was inferred through their sharing of haplotype H4Y1. Among the native breeds, Mertolenga had the highest haplotype diversity (0.68 ± 0.07), Brava de Lide was the least differentiated. The analyses of molecular variance showed significant (P < 0.0001) differences between breeds with more than 64% of the total genetic variation found among breeds within groups and 33–35% within breeds. The detection of INRA189-104 allele in 8 native breeds suggested influence of African cattle in breeds of the Iberian Peninsula. The presence in Portuguese breeds of Y1 patrilines, also found in aurochs, could represent more ancient local haplotypes.
 
Article
New techniques allow fast genotyping of large numbers of single-nucleotide polymorphisms (SNPs) of the genome. These techniques are used to map disorders with complex inheritance patterns and require large study groups. Linkage analysis of monogenetic traits exploits close family relationships between relatively small numbers of cases and controls. Linkage studies are typically performed with a set of microsatellite markers spaced at 10 cM. We were interested to test whether SNP typing could be applied in genome-wide linkage analysis because of the speed of the procedure. White spotting in Boxer dogs was chosen as a model because it is a semidominant trait, allowing the assignment of locus genotypes to each phenotyped dog. A set of just more than 1500 SNPs were typed in 5 families with heterozygous parents and offspring that included 11 white, 6 brown, and 19 spotted dogs. Multipoint linkage analysis was performed and a LOD score of 12.1 was obtained on canine chromosome 20. The CFA20 region was the only region with a positive LOD score. The gene MITF, coding for a transcription factor implicated in Waardenburg syndrome in humans, is located in the region close to a SNP that is in apparent linkage disequilibrium with the white spotting locus. Thus, MITF is a likely candidate for involvement in white spotting in boxers. We conclude that SNPs, spaced at an average distance of 1.6 Mb, are highly informative in linkage analysis of monogenic traits and are a powerful alternative to microsatellite markers.
 
Article
Six partially developed 15I5-B-congenic lines of chickens were used to assess the genetic influence on the developmental expression of selected epitopes of two avian developmental antigen systems: chicken fetal antigen (CFA) and chicken adult antigen (CAA). Both CFA and CAA are serologically and molecularly complex hematopoietic antigen systems, yet little is known about genetic influences on their expression. Using polyclonal rabbit anti-CFA, only slight variations in overall CFA expression on peripheral erythrocytes were observed during neonatal development; no consistent trend was evident. In contrast, analysis with monoclonal antibody 10C6 revealed that the incidence of CFA determinant 8 (CFA8) on erythrocytes of the early neonate was significantly reduced in line 15I5 compared with lines .6-2, .7-2 and .15I-5; line .C-12 also exhibited a reduced CFA8 incidence at hatching. Likewise, the CAA epitope detected by monoclonal antibody 3F12 was found to appear at a slower rate on erythrocytes from lines 15I5 and .C-12 than on those of other lines. Similar results were obtained using the anti-CAA monoclonal 4C2 where reduced expression was found in lines 15I5, .C-12, and .P-13. Results of complement-mediated cytolysis using the positive control 9F9 monoclonal antibody suggested that observed genetic differences were not due to inherent differences in erythroid cytolytic sensitivity. Neither could the results be explained by the incidence of circulating reticulocytes vs. mature erythrocytes within the lines. Rather, the results suggest that different genetic lines of chickens vary in the developmental kinetics of definitive erythrocyte subpopulations bearing specific phenotypes defined by monoclonal antibodies. These findings are discussed in light of previous observations using these B-congenic lines.
 
Cytogenomic model of chicken microchromosome 16. Molecular, cytogenetic, and genomics data available to date were used to develop a model for GGA 16 chromosome architecture and organization inclusive of p and q arms, telomeres, centromere, a 2° constriction, AT-and GC-rich regions, and gene complex order of the NOR, MHCY, and MHC-B on the q arm inclusive of a large physical distance between the NOR/MHC-Y and-B.
Article
Here we present a high-resolution cytogenomic analysis of chicken microchromosome 16. We established the location of the major histocompatibility complex (MHC)-B and -Y subregions relative to each other and to the nucleolus organizer region (NOR) encoding the 18S–5.8S–28S ribosomal DNA. To do so, we employed multicolor fluorescence in situ hybridization using large-insert bacterial artificial chromosome clones with fully sequenced inserts or repetitive sequence probes specific for the subregion of interest. We show that the MHC-Y and -B regions are located on the same side of the NOR, rather than opposite ends, as previously proposed. On the q arm, the MHC-Y is closely adjacent to the NOR, whereas the MHC-B is distal near the q-terminus. A relatively large GC-rich region separates the 2 MHC subregions and includes a specialized structure, a secondary constriction. We propose that the GC-rich large physical distance is the basis for the lack of genetic linkage between the NOR and MHC-B and between the MHC-Y and -B. An integrated model for GGA 16 is presented that incorporates gene complex order in the context of key architectural features including p and q arms, primary (centromere) and secondary constrictions, telomeres, as well as AT- and GC-rich regions.
 
Article
We have studied the effects of wild-derived (Rb7) and laboratory-derived (Rb1) Robertsonian translocations involving chromosome 17 on t-complex determined transmission ratio distortion and crossing-over suppression in mice. The Rb7 chromosome is significantly unlike all other wild-type chromosome 17s tested, while Rb1 is not. t0/Rb7 males are uniformly extremely high distorters (greater than 96 percent) while th2/Rb7 males are uniformly extremely low distorters. t0/Rb7 animals allow genetic recombination in the centromere to t-lethal region interval. These observations could be explained if the Rb7 chromosome contains one or more t-like regions.
 
Article
Chondrodystrophy in turkeys is a lethal condition produced by an autosomal allele, ch. Mutants are characterized by very short and thick legs, shortened wings, globular head with parrot beak, and a protruding abdomen. Classification of ch/ch embryos may be accurately made at 12 days incubation, prior to which limited appendicular development precludes distinction from normal or heterozygous birds. Death caused by the mutant allele occurs between 24 and 28 days; some embryos are alive but unpipped at time of hatch. Analysis of the pattern of embryonic mortality for the stock carrying the ch allele revealed a 16–17-day lethal factor that appears to be independent of chondrodystrophy. Of 52 females mated to Ch/ch males, 41 were determined to be Ch/ch; 32 of these heterozygous females exhibited normal embryonic mortality patterns. Nine hens, in addition to being Ch/ch, displayed a significant increase in embryo death between 15 and 18 days, peaking sharply at 17 days. Of the 11 females determined to be Ch/ch, five showed the same 15 to 18 day pattern of mortality observed for the nine Ch/ch females.
 
Article
The protamines are small, arginine-rich nuclear proteins that replace histones and transition proteins late in the haploid phase of spermatogenesis in mammals. The two mouse genes encoding protamines--Prm-1 and Prm-2--have been molecularly cloned and mapped to mouse chromosome 16 (MMU 16). A cDNA clone of mouse Prm-1 that hybridized to the corresponding human gene was used to analyze a panel of somatic cell hybrids made between human lymphoblasts and the E36 hamster cell line. The human gene, which we have designated PRM 1, was syntenic with human chromosome 16 (HSA 16) and discordant with all other human chromosomes. Linkage analysis in the mouse was accomplished using the backcross (Czech II x BALB/c Pt) x Czech II to map Prm-1 and Prm-2 to a position near the 5' terminus of MMU 16. No recombination between Prm-1 and Prm-2 was observed among 89 progeny of the Czech II x BALB/c cross or among 94 progeny of the backcross (CBA/J x BALB/cJ) x BALB/cJ, demonstrating that the two loci are separated by less than 1.6 cM on MMU 16. This tight linkage may be of functional significance, as Prm-1 and Prm-2 are among a limited number of genes known to be expressed postmeiotically in male haploid germ cells.
 
Population names, codes, country of origin, and PC values
Two multidimensional scalling plot illustrating the DA genetic distances among 18 cattle breeds.
Genetic distances (D A ) estimates between the 18 studied breeds ALI ASM ASV SAY TUD ALE BAR MAR MER MIR AUB GAS SAL AVI BRU MOR PIR
Synthetic genetic maps of Iberian peninsula representing 28% of the total genetic variation. (A) and (B) are the interpolated values of the first and second PCs, respectively. The PC values are grouped in isopleths and ranked according the color tonalities, dark color: high values; light color: lower values. Black dots represent the geographic coordinate used for each population.
Article
The origin of Iberian cattle has been suggested by some authors to be the product of European and north African cattle entrances during the last few thousands of years. However, these hypotheses were mainly based on morphological similarities. This study analyzed 889 unrelated individuals from 15 representative Iberian breeds and 3 French breeds for 16 microsatellite loci. Statistical tests were used to calculate interpopulation genetic distances (D(A)) and principal components analysis (PCA). To visualize the geographical distribution of the genetic differentiation between Iberian cattle breeds, data from the PCA analysis were used to construct synthetic maps. Genetic similarity among neighboring Iberian breeds is mainly caused by gene flow. However, recent demographic fluctuations and reproductive isolation in Alistana, Mirandesa, and Tudanca has increased genetic drift, which may be the main cause for the relatively high differentiation of these populations. The synthetic maps constructed with the first and second PCs revealed (1) a large differentiation between Northern Iberian breeds rather than between more geographically distant breeds, and (2) a clear east-west gradient that may be related with the model of demic diffusion of agriculture. Finally, we detected no strong evidence for an African genetic influence in the Iberian cattle breeds analyzed in this study.
 
Article
Trisomy mapping is a powerful method for assigning genes to chicken microchromosome 16 (GGA 16). The single chicken nucleolar organizer region (NOR), the 2 major histocompatibility complex regions (MHC-Y and MHC-B), and CD1 genes were all previously assigned to GGA 16 using trisomy mapping. Here, we combined array comparative genomic hybridization with trisomy mapping to screen unassigned genomic scaffolds (consigned temporarily to chrUn_random) for sequences originating from GGA 16. A number of scaffolds mapped to GGA 16. Among these were scaffolds that contain genes for olfactory (OR) and cysteine-rich domain scavenger (SRCR) receptors, along with a number of genes that encode putative immunoglobulin-like receptors and other molecules. We used high-resolution cytogenomic analyses to confirm assignment of OR and SRCR genes to GGA 16 and to pinpoint members of these gene families to the q-arm in partially overlapping regions between the centromere and the NOR. Southern blots revealed sequence polymorphism within the OR/SRCR region and linkage with the MHC-Y region, thereby providing evidence for conserved linkage between OR genes and the MHC within birds. This work localizes OR genes to the vicinity of the chicken MHC and assigns additional genes, including immune defense genes, to GGA 16.
 
Article
Qualitative analysis of C-band heteromorphisms was carried out in 200 infants (100 males and 100 females) in Delhi, India. Partial inversions minor and half inversions were observed as modal levels for chromosomes 1 and 9 in both sexes. No chromosome 16 with a C-band inversion was observed in the present investigation. A significantly higher incidence of percent inversions for chromosomes 1 and 9 was observed in males than in females. The frequency of heterozygous inversion level combinations for chromosome pairs 1 and 9 were remarkably higher than homozygous combinations both in males and females. Our results are compared with the other reported studies, and the possible role of these heteromorphisms in ethnic/racial variation and in developmental disturbances are discussed.
 
Article
Earlier studies have shown two types of mitochondrial DNA in Spanish honeybees (Apis mellifera iberica): a western European or A. m. mellifera type, which predominates in northern Spain, and a north African or A. m. intermissa type, which predominates in southern Spain. Adult workers from 28 colonies sampled in northern and southern Spain were surveyed for polymorphisms at eight allozyme loci. Polymorphisms were found in Mdh1 (two alleles) and Pgm (five alleles). Three of the Pgm alleles have not been described previously. The frequencies of Mdh1 alleles in northern and southern samples are significantly different: Mdh1(80) = 0.94 in the north and 0.75 in the south. The frequencies of Pgm alleles in northern and southern samples do not differ significantly. The Hk allele (Hk100) found in all Spanish samples is the same as that found in other European populations. The results are consistent with the presence of a hybrid zone between African and west European honeybee subspecies in the Iberian peninsula or north Africa. The high number and frequency of novel Pgm alleles in the Spanish bees resembles the "rare allele" phenomenon observed in other hybrid populations.
 
Genetic distance of transcribed versus genomic DNA portions of LCR16u 
Article
An unexpected finding of the human genome was the large fraction of the genome organized as blocks of interspersed duplicated sequence. We provide a comparative and phylogenetic analysis of a highly duplicated region of 16p12.2, which is composed of at least four different segmental duplications spanning in excess of 160 kb. We contrast the dispersal of two different segmental duplications (LCR16a and LCR16u). LCR16a, a 20 kb low-copy repeat sequence A from chromosome 16, was shown previously to contain a rapidly evolving novel hominoid gene family (morpheus) that had expanded within the last 10 million years of great ape/human evolution. We compare the dispersal of this genomic segment with a second adjacent duplication called LCR16u. The duplication contains a second putative gene family (KIAA0220/SMG1) that is represented approximately eight times within the human genome. A high degree of sequence identity (approximately 98%) was observed among the various copies of LCR16u. Comparative analyses with Old World monkey species show that LCR16a and LCR16u originated from two distinct ancestral loci. Within the human genome, at least 70% of the LCR16u copies were duplicated in concert with the LCR16a duplication. In contrast, only 30% of the chimpanzee loci show an association between LCR16a and LCR16u duplications. The data suggest that the two copies of genomic sequence were brought together during the chimpanzee/human divergence and were subsequently duplicated as a larger cassette specifically within the human lineage. The evolutionary history of these two chromosome-specific duplications supports a model of rapid expansion and evolutionary turnover among the genomes of man and the great apes.
 
Article
The secondary constriction regions (h) of chromosomes 1, 9, and 16 stained deep red by RBA (R-bands by BrdU using Giemsa)--a useful tool for demonstrating the constitutive heterochromatic heteromorphisms in these regions. The unusual staining pattern of bands p 12 to q11 of chromosome 3, which is late replicating, also is reported. The extended deep red region does not correspond to C-banding on chromosome 3. This technique does not require sequential banding by QFQ and CBG for detecting the h-region heteromorphisms.
 
Article
Dense incisors (din) is a new autosomal recessive mutation in the mouse that interferes with complete eruption of the incisors. The initial eruption of incisors through the gingiva does not differ in mutants and normal littermates, but subsequent further eruption of incisors is arrested in mutants. Radiographic examinations show that, because the incisors do not erupt, continued dentin formation gradually occludes the pulp chambers of these teeth creating a dense incisor. The arrested eruption of the incisor results in an anterior open bite. The pleiotropic phenotype of din/din mutant mice also includes small body size, reduced ear pinna size, and coat color dilution. The din mutation was mapped to Chr 16 near the pituitary transcription factor gene Pit1, but din is not a mutation in Pit 1.
 
Inferred gene network for (a) 16S rRNA and (b) COI rRNA.
(a) Geographic versus genetic distance for 16S rRNA. Solid circles indicate genetic distance between Eldridge Road population and others. (b) Geographic versus genetic distance for COI.
Article
We used 16S ribosomal RNA (rRNA) and cytochrome c oxidase subunit I (COI) sequence data to investigate the population structure in the centipede Craterostigmus tasmanianus Pocock, 1902 (Chilopoda: Craterostigmomorpha: Craterostigmidae) and to look for possible barriers to gene flow on the island of Tasmania, where C. tasmanianus is a widespread endemic. We first confirmed a molecular diagnostic character in 28S rRNA separating Tasmanian Craterostigmus from its sister species Craterostigmus crabilli (Edgecombe and Giribet 2008) in New Zealand and found no shared polymorphism in this marker for the 2 species. In Tasmania, analysis of molecular variance analysis showed little variation at the 16S rRNA and COI loci within populations (6% and 13%, respectively), but substantial variation (56% and 48%, respectively) among populations divided geographically into groups. We found no clear evidence of isolation by distance using a Mantel test. Bayesian clustering and gene network analysis both group the C. tasmanianus populations in patterns which are broadly concordant with previously known biogeographical divisions within Tasmania, but we did not find that genetic distance varied in a simple way across cluster boundaries. The coarse-scale geographical sampling on which this study was based should be followed in the future by sampling at a finer spatial scale and to investigate genetic structure within clusters and across cluster boundaries.
 
Phylogenetic networks of the mtDNA 16S rRNA gene region for (A) chimpanzee, (B) bonobo, and (C) gorilla. Numbers designate individuals of Table 2. D and X designate sequences determined by Horai et al. (1995) and Xu and Arnason (1996), respectively. Edge lengths are proportional to the number of nucleotide differences. Arrows indicate the edges in which roots are probably located. 
Phylogenetic tree of the mtDNA 16S rRNA gene region for chimpanzee, bonobo, and gorilla. The tree was rooted by using the midpoint rooting method. 
Phylogenetic tree of the mtDNA 16S rRNA gene region for gibbons. 
Phylogenetic tree of the eight gibbon species. UPGMA was used. (A) When all three H. pileatus individuals were included. (B) When H. pileatus no. 3 which was closely related to H. concolor was eliminated from the comparison. 
Article
We determined nucleotide sequences of the 16S rRNA gene of mitochondrial DNA (mtDNA) (about 1.6 kb) for 35 chimpanzee, 13 bonobo, 10 gorilla, 16 orangutan, and 23 gibbon individuals. We compared those data with published sequences and estimated nucleotide diversity for each species. All the ape species showed higher diversity than human. We also constructed phylogenetic trees and networks. The two orangutan subspecies were clearly separated from each other, and Sumatran orangutans showed much higher nucleotide diversity than Bornean orangutans. Some gibbon species did not form monophyletic clusters, and variation within species was not much different from that among species in the subgenus Hylobates.
 
Top-cited authors
Francois Rousset
  • Université de Montpellier
Jerome Goudet
  • University of Lausanne
Roeland E Voorrips
  • Wageningen University & Research
Luc Baudouin
  • Cirad - La recherche agronomique pour le développement
Sylvain Piry
  • French National Institute for Agriculture, Food, and Environment (INRAE)