Refinement of the Spinal Muscular Atrophy Locus by Genetic and Physical Mapping

We report the mapping and characterization of 12 microsatellite markers including 11 novel markers. All markers were generated from overlapping YAC clones that span the spinal muscular atrophy (SMA) locus. PCR amplification of 32 overlapping YAC clones shows that 9 of the new markers (those set in italics) map to the interval between the two previous closest flanking markers (D5S629 and D5S557): cen - D5S6 - D5S125 - D5S435 - D5S1407-D5S629-D5S1410-D5S1411/D5S1412-D5S1413-D5S1414-D5Z8-D5Z9-CATT1-D5Z10/D5Z6-D5S557-D5S1408-D5S1409-D5S637-D5S351-MAP1B-tel. Four of these new markers detect multiple loci in and out of the SMA gene region. Genetic analysis of recombinant SMA families indicates that D5S1413 is a new proximal flanking locus for the SMA gene. Interestingly, among the 40 physically mapped loci, the 14 multilocus markers map contiguously to a genomic region that overlaps, and perhaps helps define, the minimum genetic region encompassing the SMA gene(s).     

Use of Random Amplified Polymorphic DNA Markers for Mapping the Chickpea Genome

Three interspecific crosses were developed using Cicer arietinum (ICC 4918) as the female parent and wild Cicer species [C. reticulatum - JM 2100, JM 2106 and C. echinospermum - ICCW 44] as the male parent. Cicer arietinum (ICC 4918) × C. reticulatum (JM 2100) cross produced the largest number of F₂ plants and was chosen for linkage mapping using Random Amplified Polymorphic DNA (RAPD) primers. A partial linkage map was constructed based upon the segregation of 36 RAPD markers obtained by amplification using 35 primers. The linkage map consists of two linkage groups with 17 linked markers covering a total of 464.9 cM. Analyses also revealed association of three morphological traits with linked RAPD markers. Out of seven morphological traits tested for association with linked markers in the segregating plants, four Quantitative trait loci (QTL) were detected for the trait leaf length and three QTLs each for the traits leaf width and erect plant habit.     

Genetic and Physical Mapping of the Mouse Ulnaless Locus

The mouse Ulnaless locus is a semidominant mutation which displays defects in patterning along the proximal-distal and anterior-posterior axes of all four limbs. The first Ulnaless homozygotes have been generated, and they display a similar, though slightly more severe, limb phenotype than the heterozygotes. To create a refined genetic map of the Ulnaless region using molecular markers, four backcrosses segregating Ulnaless were established. A 0.4-cM interval containing the Ulnaless locus has been defined on mouse chromosome 2, which has identified Ulnaless as a possible allele of a Hoxd cluster gene(s). With this genetic map as a framework, a physical map of the Ulnaless region has been completed. Yeast artificial chromosomes covering this region have been isolated and ordered into a 2 Mb contig. Therefore, the region that must contain the Ulnaless locus has been defined and cloned, which will be invaluable for the identification of the molecular nature of the Ulnaless mutation.     

Genetic and Physical Mapping of the Dreher Locus on Mouse Chromosome 1

Mutations in the mouse dreher (dr) gene cause skeletal defects, hyperactivity, abnormal gait, deafness, white belly spotting, and hypoplasia of Müllerian duct derivatives. To map dr to high resolution, we utilized two crosses. Initially, we analyzed an intersubspecific intercross to construct a detailed genetic map of simple sequence length polymorphism markers within a 6.3-cM region surrounding the dr locus. Subsequently, we analyzed a second intersubspecific intercross segregating for the dr(6J) allele, which positioned dr within a 0.13-cM region between Rxrg and D1Mit370. A physical contig of BAC clones spanning the dr critical region was constructed, and eight potential dr candidate genes were excluded by genetic or physical mapping. Together these results lay the foundation for positional cloning of the dr gene.     

Human Adipose-Derived Mesenchymal Stem Cells as a New Model of Spinal and Bulbar Muscular Atrophy

Spinal and bulbar muscular atrophy (SBMA) or Kennedy''s disease is an X-linked CAG/polyglutamine expansion motoneuron disease, in which an elongated polyglutamine tract (polyQ) in the N-terminal androgen receptor (ARpolyQ) confers toxicity to this protein. Typical markers of SBMA disease are ARpolyQ intranuclear inclusions. These are generated after the ARpolyQ binds to its endogenous ligands, which promotes AR release from chaperones, activation and nuclear translocation, but also cell toxicity. The SBMA mouse models developed so far, and used in preclinical studies, all contain an expanded CAG repeat significantly longer than that of SBMA patients. Here, we propose the use of SBMA patients adipose-derived mesenchymal stem cells (MSCs) as a new human in vitro model to study ARpolyQ toxicity. These cells have the advantage to express only ARpolyQ, and not the wild type AR allele. Therefore, we isolated and characterized adipose-derived MSCs from three SBMA patients (ADSC from Kennedy''s patients, ADSCK) and three control volunteers (ADSCs). We found that both ADSCs and ADSCKs express mesenchymal antigens, even if only ADSCs can differentiate into the three typical cell lineages (adipocytes, chondrocytes and osteocytes), whereas ADSCKs, from SBMA patients, showed a lower growth potential and differentiated only into adipocyte. Moreover, analysing AR expression on our mesenchymal cultures we found lower levels in all ADSCKs than ADSCs, possibly related to negative pressures exerted by toxic ARpolyQ in ADSCKs. In addition, with proteasome inhibition the ARpolyQ levels increased specifically in ADSCKs, inducing the formation of HSP70 and ubiquitin positive nuclear ARpolyQ inclusions. Considering all of this evidence, SBMA patients adipose-derived MSCs cultures should be considered an innovative in vitro human model to understand the molecular mechanisms of ARpolyQ toxicity and to test novel therapeutic approaches in SBMA.     

Association between Ag1-CA Alleles and Severity of Autosomal Recessive Proximal Spinal Muscular Atrophy

The gene for autosomal recessive proximal spinal muscular atrophy (SMA) has been mapped to an 850-kb interval on 5q11.2-q13.3, between the centromeric D5S823 and telomeric D5S557 markers. We report a new complex marker, Ag1-CA, that lies in this interval, whose primers produce one, two, or rarely three amplification-fragment-length variants (AFLVs) per allele. Class I chromosomes are those which amplify a single AFLV allele, and class II chromosomes are those which amplify an allele with two or three AFLVs. Ag1-CA shows highly significant allelic association with type I SMA in both the French Canadian (Hôpital Sainte-Justine [HSJ]) and American (Ohio State University [OSU]) populations (P<.0001). Significant association between the Ag1-CA genotype and disease severity was also observed. Type I patients were predominantly homozygous for class I chromosomes (P=.0003 OSU; P=.0012 HSJ), whereas the majority of type II patients were heterozygous for class I and II chromosomes (P=.0014 OSU; P=.001 HSJ). There was no significant difference in Ag1-CA genotype frequencies between type III patients (P=.5 OSU; P=.25 HSJ) and the paired normal chromosomes from both carrier parents. Our results indicate that Ag1-CA is the most closely linked marker to SMA and defines the critical candidate-gene region. Finally, we have proposed a model that should be taken into consideration when screening candidate SMA genes.     

Physical Mapping of Genetic Markers on the Short Arm of Chromosome 5

The deletion of the short arm of chromosome 5 is associated with the cri-du-chat syndrome. In addition, loss of this portion of a chromosome is a common cytogenetic marker in a number of malignancies. However, to date, no genes associated with these disorders have been identified. Physical maps are the first step in isolating causative genes, and genes involved in autosomal recessive disorders are now routinely mapped through the identification of linked markers. Extensive genetic maps based upon polymorphic short tandem repeats (STRs) have provided researchers with a large number of markers to which such disorders can be genetically mapped. However, the physical locations of many of these STRs have not been determined. Toward the goal of integrating the human genetic maps with the physical maps, a 5p somatic cell hybrid deletion mapping panel that was derived from patients with 5p deletions or translocations was used to physically map 47 STRs that have been used to construct genetic maps of 5p. These data will be useful in the localization of disease genes that map to 5p and may be involved in the etiology of the cri-du-chat syndrome.     

Direct Visualization of the Highly Polymorphic RNU2 Locus in Proximity to the BRCA1 Gene

Although the breast cancer susceptibility gene BRCA1 is one of the most extensively characterized genetic loci, much less is known about its upstream variable number tandem repeat element, the RNU2 locus. RNU2 encodes the U2 small nuclear RNA, an essential splicing element, but this locus is missing from the human genome assembly due to the inherent difficulty in the assembly of repetitive sequences. To fill the gap between RNU2 and BRCA1, we have reconstructed the physical map of this region by re-examining genomic clone sequences of public databases, which allowed us to precisely localize the RNU2 array 124 kb telomeric to BRCA1. We measured by performing FISH analyses on combed DNA for the first time the exact number of repeats carried by each of the two alleles in 41 individuals and found a range of 6-82 copies and a level of heterozygosity of 98%. The precise localisation of the RNU2 locus in the genome reference assembly and the implementation of a new technical tool to study it will make the detailed exploration of this locus possible. This recently neglected macrosatellite could be valuable for evaluating the potential role of structural variations in disease due to its location next to a major cancer susceptibility gene.     

Identification, Characterization, and Physical Mapping of 14 Polymorphic Simple Sequence Repeat Markers on Human Chromosome 21

Fourteen new dinucleotide repeat polymorphisms specific for human chromosome 21 have been identified, mapped, and characterized. The average heterozygosity of all markers was 0.66. The average PIC value was 0.61. The markers were mapped by STS content mapping of YACs previously assigned to chromosome 21. The correlation of polymorphic genetic markers with substantially complete physical maps should facilitate the identification of loci of interest on chromosome 21.     

Spinal Muscular Atrophy and the Antiapoptotic Role of Survival of Motor Neuron (SMN) Protein

Spinal muscular atrophy (SMA) is a devastating and often fatal neurodegenerative disease that affects spinal motor neurons and leads to progressive muscle wasting and paralysis. The survival of motor neuron (SMN) gene is mutated or deleted in most forms of SMA, which results in a critical reduction in SMN protein. Motor neurons appear particularly vulnerable to reduced SMN protein levels. Therefore, understanding the functional role of SMN in protecting motor neurons from degeneration is an essential prerequisite for the design of effective therapies for SMA. To this end, there is increasing evidence indicating a key regulatory antiapoptotic role for the SMN protein that is important in motor neuron survival. The aim of this review is to highlight key findings that support an antiapoptotic role for SMN in modulating cell survival and raise possibilities for new therapeutic approaches.     

Physical Mapping of 49 Microsatellite Markers on Chromosome 19 and Correlation with the Genetic Linkage Map

We have regionally localized 49 microsatellite markers developed by Généthon using a panel of previously characterized somatic cell hybrids that retain fragments from chromosome 19. The tight correlation observed between the physical and the genetic orders of the microsatellites provide cytogenetic anchorages to the genetic map data. We propose a position for the centromere just above D19S415, from the study of two hybrids, each of which retains one of the two derivatives of a balanced translocation t(1;19)(q11;q11). Microsatellites, which can be identified by a standard PCR protocol, are useful tools for the localization of disease genes and for the establishment of YAC or cosmid contigs. These markers can also judiciously be used for the characterization of new hybrid cell line panels. We report such a characterization of 11 clones, 8 of which were obtained by irradiation-fusion. Using the whole hybrid panel, we were able to define the order of 12 pairs of genetically colocalized microsatellites. As examples of gene mapping by the combined use of microsatellites and hybrid cell lines, we regionally assigned the PVS locus between the 19q13.2 markers D19S417 and D19S423 and confirmed the locations of fucosyltransferase loci FUT1, FUT2, and FUT5.     

Genetic and Physical Mapping of Sex-Linked AFLP Markers in Nile Tilapia (Oreochromis niloticus)

Identification of the sex-determining genes of the Nile tilapia (Oreochromis niloticus) has important implications for commercial aquaculture. We previously identified an XX/XY sex-determining locus in this species within a 10-cM interval between markers GM201 and UNH995 on linkage group one (LG1). In order to refine this region, we developed new AFLP markers using bulked segregant analysis of the mapping families. We identified three AFLP markers that showed a sex-specific pattern of segregation. All three mapped near, but just outside, the previously identified sex-determining region on LG1. Hybridization of BAC clones containing these markers to chromosome spreads confirmed that the XX/XY sex-determining locus is on one of the small chromosomes in O. niloticus.     

Construction of a Genetic Map and Development of DNA Markers Linked to the Sex-Determining Locus in the Patagonian Pejerrey (Odontesthes hatcheri)

The process of sex differentiation in fishes is regulated by genetic and environmental factors. The sex of Patagonian pejerrey (Odontesthes hatcheri) appears to be under strong genotypic control (GSD) because the sex ratios are balanced (1:1) between 17°C and 23°C. However, sex ratios become female-biased at <15°C and male-biased at 25°C, which shows that this species also possesses some degree of temperature-dependent sex determination (TSD). Identification of the genetic sex of an individual will help elucidate the molecular basis of sex differentiation in this species. In this study, we used amplified fragment length polymorphism (AFLP) analysis to develop a genetic linkage map for both sexes and a sex-linked DNA marker for Patagonian pejerrey. The AFLP analysis of 23 male and 23 female progeny via 64 primer combinations produced a total of 153 bands. The genetic linkage map consisted of 79 markers in 20 linkage groups and 48 markers in 15 linkage groups for males and females, respectively. One AFLP marker tightly linked to the sex-determining locus was identified: the marker, ACG/CAA-217, amplified to the male-specific DNA fragment. Sequence analysis of this region revealed a single nucleotide polymorphism (SNP) between males and females, which was converted into a SNP marker. This marker provides genetic confirmation that the sex of Patagonian pejerrey is determined genetically and would be useful for the analysis of the molecular basis of GSD and TSD in this species.     

Suitability of Random Amplified Polymorphic DNA for Genetic Markers in the Aphid Parasitoid, Aphelinus asychis Walker

The repeatability, variability, transmission, and linkage relationships of random amplified polymerphic DNA (RAPD) fragments were examined using six inbred lines of the haplodiploid parasitoid, Aphelinus asychis, originally collected on one date from a single held in southern France. Repeatability of RAPD fragments could be adequately judged using two replicate amplifications of the same individual in the same amplification run. Thirty-one of 136 repeatable fragments generated by 14 primers were polymorphic among lines. Segregation ratios in Fz males did not differ from 1:1 and extrachromosomal transmission was not observed. However, 5 nonparental bands that would increase the apparent number of loci by 16.2% in outbreeding populations were detected in hybrid F₁ females. In addition, linkage analysis indicates that the 31 polymorphic bands represent 19 presence-absence loci and 6 biallelic, fragment length polymorphism (FLP) or FLP-like loci. Four linkage groups were detected. Our main conclusion is that RAPD polymerphisms cannot be used as genetic markers unless information identifying nonparental bands and FLP and FLP-like loci is obtained. This information can be obtained during the course of typical population surveys in haplodiploid species because of male haploidy. In diploid species though, crossing experiments or DNA hybridization tests to establish homology are necessary prior to working with unpedigreed populations.     

Quantitative Analyses of SMN1 and SMN2 Based on Real-Time LightCycler PCR: Fast and Highly Reliable Carrier Testing and Prediction of Severity of Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is a common autosomal recessive disorder in humans, caused by homozygous absence of the survival motor neuron gene 1 (SMN1). SMN2, a copy gene, influences the severity of SMA and may be used in somatic gene therapy of patients with SMA in the future. We present a new, fast, and highly reliable quantitative test, based on real-time LightCycler PCR that amplifies either SMN1 or SMN2. The SMN1 copies were determined and validated in 329 carriers and controls. The specificity of the test is 100%, whereas the sensitivity is 96.2%. The quantitative analysis of SMN2 copies in 375 patients with type I, type II, or type III SMA showed a significant correlation between SMN2 copy number and type of SMA as well as duration of survival. Thus, 80% of patients with type I SMA carry one or two SMN2 copies, and 82% of patients with type II SMA carry three SMN2 copies, whereas 96% of patients with type III SMA carry three or four SMN2 copies. Among 113 patients with type I SMA, 9 with one SMN2 copy lived <11 mo, 88/94 with two SMN2 copies lived <21 mo, and 8/10 with three SMN2 copies lived 33-66 mo. On the basis of SMN2 copy number, we calculated the posterior probability that a child with homozygous absence of SMN1 will develop type I, type II, or type III SMA.     

家蚕基因特异性CAPs标记获得及其分子系统学应用

选取家蚕attacin和alpha-amylase基因序列,设计特异性引物,在家蚕品系P50、C108和子一代 (F1) 中扩增。分别采用4种不同的限制性内切酶对扩增产物酶切,最后每个基因都获得了一个CAPs分子标记。依据所得的两个CAPs分子标记对12个品系的家蚕遗传多样性进行了初步研究,构建了其分子系统树。     

Genetic Mapping of the Cloned Subgroup A Avian Sarcoma and Leukosis Virus Receptor Gene to the TVA Locus

A chicken gene conferring susceptibility to subgroup A avian sarcoma and leukosis viruses (ASLV-A) was recently identified by a gene transfer strategy. Classical genetic approaches had previously identified a locus, TVA, that controls susceptibility to ASLV-A. Using restriction fragment length polymorphism (RFLP) mapping in inbred susceptible (TVA*S) and resistant (TVA*R) chicken lines, we demonstrate that in 93 F₂ progeny an RFLP for the cloned receptor gene segregates with TVA. From these analyses we calculate that the cloned receptor gene lies within 5 centimorgans of TVA, making it highly probable that the cloned gene is the previously identified locus TVA. The polymorphism that distinguishes the two alleles of TVA in these inbred lines affects the encoded amino acid sequence of the region of Tva that encompasses the viral binding domain. However, analysis of the genomic sequence encoding this region of Tva in randomly bred chickens suggests that the altered virus binding domain is not the basis for genetic resistance in the chicken lines analyzed.Avian sarcoma and leukosis viruses (ASLV) may be classified into several subgroups based on properties of the viral envelope proteins. Five major subgroups of ASLV (A to E) have been defined based on immunological reactivity of the viral envelope proteins, host range, and infection interference patterns (reviewed in reference 18). The subgroup specificity of the virus maps to the env gene, and distinct hypervariable regions within env have been shown to determine the viral subgroup (2, 3, 7, 8).Patterns of susceptibility of inbred chicken lines to infection with the various ASLV subgroups suggest that three loci control viral entry for the five major ASLV subgroups (11, 12, 15, 17). Dominant alleles at the TVA and TVC (TVA*S and TVC*S) loci confer susceptibility to subgroups A and C viruses, respectively. The TVB locus is more complex, with various alleles determining infection by subgroup B, D, and E viruses. TVA, TVB, and TVC appear to act at the level of viral entry into the cell; therefore, it has been assumed that the TV loci encode or control expression of the cellular receptors for ASLV (5, 13).Recently, a gene that confers susceptibility to subgroup A ASLV (ASLV-A) was cloned by a gene transfer strategy (1, 19). Molecular clones containing coding sequences for this gene relieve the block to viral entry when expressed in a number of mammalian cell lines (1, 19). The gene encodes a surface glycoprotein that has been shown to bind directly and specifically to the ASLV-A envelope protein (4, 9). In addition, binding of the receptor protein to ASLV-A envelope protein induces conformational changes in the viral glycoproteins that appear to be associated with viral entry (10). Finally, an antibody to the receptor protein specifically blocks infection of chicken cells by subgroup A viruses, suggesting that this gene encodes the normal ASLV-A receptor on chicken cells (1). Taken together, these results demonstrate that the cloned gene encodes a subgroup A virus receptor.Since it is clear that the cloned gene encodes an ASLV-A receptor, the protein supposed to be encoded by the classical TVA locus, we asked whether the identified receptor gene mapped to the TVA locus. In this paper we show that a restriction fragment length polymorphism (RFLP) of DNA from inbred chickens can be used to demonstrate that the cloned ASLV-A receptor gene maps to within 5 centimorgans (cM) of the TVA locus as defined by susceptibility to ASLV-A, making it highly probable that the cloned gene is TVA. In addition, analysis of the genomic sequences encoding the viral interaction domain of the receptor in both inbred and randomly bred chickens demonstrates that alterations in this region of the receptor are not responsible for the resistance phenotype.

TVA segregation analysis.

Inbred chicken lines homozygous for TVA alleles encoding either sensitivity (TVA*S) or resistance (TVA*R) were used to generate birds in which the TVA segregation pattern could be studied. Regional Poultry Research Lab lines 6₃ (TVA*S/*S TVB*S/*S) and 7₂ (TVA*R/*R TVB*R/*R) (6) were crossed, and the resulting heterozygous F₁ progeny were mated to generate 93 F₂ chicks. The susceptibility phenotype of the F₂ chicks was determined on the basis of tumor formation following subcutaneous injection of 500 focus-forming units (FFU) of subgroup A Bryan high-titer Rous sarcoma virus (RSV) (RAV-1) and 500 FFU of subgroup B Bryan high-titer RSV (RAV-2) into the right and left wing webs, respectively, of 4-week-old chicks. At 2, 3, and 4 weeks postinjection the wings were palpated to check for tumor development. Chicks were scored as positive for susceptibility (e.g., TVA*S/*S or TVA*S/*R) if a tumor of any size formed in the appropriate wing web.Table ​Table11 summarizes the distribution of susceptibility to subgroups A and B RSV in the F₂ chicks. Segregation of TVB yielded roughly the predicted frequency of susceptible (67 observed versus 70 expected) and resistant (26 observed versus 23 expected) progeny for a dominant locus (P > 0.05). In contrast, the distribution of subgroup A-susceptible and -resistant birds deviated significantly from the expected 3:1 ratio, with an excessive number of subgroup A-resistant chicks observed and a ratio of 2:1 (χ² = 3.4) (Table ​(Table1).1). Previous analysis of the segregation of TVA using the same chicken lines did not reveal an altered distribution of sensitive and resistant birds (6), suggesting that the bias seen here may be a chance deviation from the expected ratio. Segregation of two endogenous virus loci, ALVE2 (previously designated ev2) (carried by line 7₂) and ALVE3 (previously designated ev3) (carried by line 6₃), also gave roughly the expected 3:1 ratio in these F₂ chicks (data not shown). When the segregation bias in the ASLV-A-susceptible birds was accounted for, then susceptibility to subgroup A and B RSV segregated independently, as was expected since the TVA and TVB genes have been reported to be unlinked (6). Recent mapping studies also confirmed that TVA and TVB are found on different linkage groups (3a).

TABLE 1

Segregation of resistance and susceptibility to subgroup A and B viruses in F₂ progeny obtained by crossing lines 6₃ and 7₂