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PubMed1993

Characterizations of candidate genes for IDD susceptibility from the diabetes-prone NOD mouse strain.

The nucleotide sequences of the NOD and C57BL/6J alleles of Glut-2, Sod-2, and Il-2 were determined by RT-PCR sequencing. Each of these loci is located in intervals that strongly correlated with susceptibility to diabetes in an (NOD/Uf x C57BL/6J)F1 x NOD/Uf backcross. No significant variations in the alleles of Glut-2 at 16 cM on Chromosome (Chr) 3 or Sod-2 at 8 cM on Chr 17 were detected. However, the Il-2 allele in NOD at 20 cM on Chr 3 was found to differ from that in C57BL/6J by a complex mutation involving the contraction of a simple sequence repeat (SSR). Il-2 in NOD differs from the allele in C57BL/6J via a complex mutation involving a deletion of four CAG codons from the SSR together with a length-compensatory four-codon duplication of a segment 5' from the SSR. Two nonsynonymous mutations in the coding region 5' to the SSR were also detected. Only these two allelic forms of Il-2 were detected in a survey of 13 standard inbred lines and 4 wild mouse strains. We propose to designate these alleles as Il-2a (for alleles such as C57BL/6J that contain 12 CAG repeats) and Il-2b (for alleles such as NOD), which occurred in a variety of standard inbred strains and in all four wild Mus musculus domesticus tested. The distribution of these Il-2 alleles among inbred strains correlated with the detection of Chr 3 as an interval effecting diabetes susceptibility in three separate genetic crosses.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed1994

Glucokinase gene in gestational diabetes mellitus: population association study and molecular scanning.

Mutations of the glucokinase gene result in early-onset familial Type 2 (non-insulin-dependent) diabetes mellitus, and several members of the mutant glucokinase kindreds were originally diagnosed as having gestational diabetes. This study examined the glucokinase gene in 270 American Black women, including 94 with gestational diabetes whose diabetes resolved after pregnancy (gestational diabetes only), 77 with gestational diabetes who developed Type 2 diabetes after pregnancy (overt diabetes), and 99 normal control subjects who were recruited during the peripartum period. Two simple sequence repeat polymorphisms flanking either end of the glucokinase gene were evaluated. No association was found between glucokinase alleles and gestational diabetes only or overt diabetes, after adjustment for multiple comparisons. To detect single base changes, all 11 exons and proximal islet and liver promoter regions were examined by polymerase chain reaction plus single-stranded conformational polymorphism analysis in 45 gestational diabetes only patients who had not yet developed Type 2 diabetes. Nine coding region variants were identified: Ala11 (GCC) to Thr11 (ACC) in islet exon 1, and 8 variants either in untranslated regions or in the third base of a codon. Four variant sites were found in introns, but none in splicing consensus sequences. Analysis of the promoter regions revealed two common variants, G-->A at islet -30 (24%), and G-->A at liver -258 (42%). The frequencies of the promoter variants, determined by allele specific polymerase chain reaction analysis, but did not differ among the three groups. Thus, no significant coding sequence glucokinase mutations were found in 90 alleles from 45 patients with gestational diabetes.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1995

Genetic mapping of the polycystic kidney gene, pcy, on mouse chromosome 9.

The murine polycystic kidney disease gene, pcy, is an autosomal recessive trait located on chromosome 9. To determine the genetic locus of pcy, 222 intraspecific backcross mice were obtained by mating C57BL/6FG-pcy and Mus molossinus. Restriction fragment length polymorphism analysis of 70 of the 222 backcross progeny showed that pcy, dilute coat color (d), and cholecystokinin (Cck) were located in the order d--pcy--Cck from the centromere. Simple sequence repeat length polymorphism analysis of DNA of all 222 backcross mice was carried out using four markers which were located near the central regions of d and Cck. One and eight recombinations were detected between D9Mit24 and pcy and between D9Mit16 and pcy, respectively. However, no recombinant was observed among pcy, D9Mit14, and D9Mit148. These findings strongly suggest that D9Mit14 and D9Mit148 are located near the pcy gene and are good markers for chromosomal walking to this gene.

Animals↗

PubMed1995

Differentiation of Fusarium sambucinum Fuckel sensu lato and related species by RAPD PCR.

DNA polymorphisms generated by the random amplified polymorphic DNA polymerase chain reaction (RAPD PCR) were used to analyse 41 isolates investigated in the European Fusarium sambucinum Project (EFSP). Employing ten arbitrary (10-mer) oigonucleotides and simple repeat sequences (M13, (GACA)4) as single primers, informative banding patterns typical for identifying European populations of Fusarium sambucinum Fuckel s. str., F. torulosum (Berk. & Curt.) Nirenberg and F. venenatum Nirenberg were obtained.

Base Sequence↗

PubMed1992

Generation and characterization of a human chromosome 9 cosmid library.

A cosmid library has been constructed from the hamster-human hybrid cell line PK-87-9, which contains chromosome 9 as its sole known human component. Ten thousand colonies were produced, of which approximately 200, or 2%, contain human material. Fifty of these 200 were regionally mapped by an Alu-primed PCR product hybridization procedure. These cosmids were localized to all regions of chromosome 9, but were especially concentrated in the distal portion of 9q. The map location derived by the Alu-primed PCR product hybridization procedure was compared to the map location derived by fluorescent in situ hybridization. Assignment of chromosomal location by the two methods was correspondent in all but a few cases. The presumptive presence of HTF islands was investigated for 130 cosmids by digestion with the restriction enzyme NotI. Twenty percent of cosmids contained at least one NotI site. A number of simple sequence repeat polymorphisms identified from the cosmid set were characterized and will provide a link between the genetic and physical maps for this chromosome.

Animals↗

PubMed1995

Analysis of aldehyde oxidase and xanthine dehydrogenase/oxidase as possible candidate genes for autosomal recessive familial amyotrophic lateral sclerosis.

Recently, point mutations in superoxide dismutase 1 (SOD1) have been shown to lead to a subset of autosomal dominantly inherited familial amyotrophic lateral sclerosis (ALS). These findings have led to the hypothesis that defects in oxygen radical metabolism may be involved in the pathogenesis of ALS. Therefore, we decided to analyze other enzymes involved in oxygen radical metabolism for possible involvement in other forms of ALS. We report here analysis of two genes encoding the molybdenum hydroxylases aldehyde oxidase (AO) and xanthine dehydrogenase/oxidase (XDH) for involvement in ALS. Of particular interest, one gene identified as encoding aldehyde oxidase is shown to map to 2q33, a region recently shown to contain a gene responsible for a familial form of ALS with autosomal recessive inheritance (FALS-AR). The AO gene appears to be located within 280,000 bp of simple sequence repeat marker D2S116, which shows no recombination with the FALS-AR locus. The AO gene is highly expressed in glial cells of human spinal cord. In addition, we mapped a gene for XDH to 2p22, a region previously shown to contain a highly homologous but different form of XDH. Neither of these XDH genes appears to be highly expressed in human spinal cord. This evidence suggests that AO may be a candidate gene for FALS-AR.

Aldehyde Oxidase↗

PubMed1996

Comparative diagnoses of twin zygosity by SSLP variant analysis, questionnaire, and dermatoglyphic analysis.

Zygosity diagnosis has been performed in 79 pairs of twins using three methods. Simple sequence repeat length polymorphism (SSLP) analysis allows an efficient classification (MZ or DZ) with only a few markers following a simplified technique of extraction and amplification. A method based on a full questionnaire completed by parents about twin similarity correctly classifies 97.46% of the pairs; 92.41% are correctly classified using only four questions as suggested by logistic regression analysis. The third method, using dermatoglyphic analyses, correctly classifies 86.76% of pairs. To lower the cost of DNA diagnosis we stress the possibility of limiting its use to pairs with scores in the overlap area between MZ and DZ twins with a validated questionnaire.

Child↗

PubMed1993

Four polymorphic markers on rat chromosome 12 form a single linkage group.

Four PCR-typable polymorphic markers were mapped to rat chromosome 12 by linkage analysis of F2 intercross progeny of Fischer (F344/N) and Lewis (LEW/N) rat strains. The markers formed a single linkage group, covering 27.7 cM, with the following order and distance between markers: plasminogen activator inhibitor (Planh)--0.0 cM--phosphoenolpyruvate carboxykinase-related sequence 2 (Pepckr2)--15.4 cM--anonymous marker (D12N155)--12.3 cM--serine dehydratase (Sdh). All markers were identified and genotyped by PCR analysis of simple sequence repeats. The gene encoding Planh was previously assigned to rat chromosome 12, which allowed us to assign the entire linkage group to this chromosome. These markers were highly polymorphic in 13 additional inbred rat strains (BUF/N, BN/SsN, WKY/N, MNR/N, LER/N, WBB1/N, WBB2/N, MR/N, LOU/MN, SHR/N, ACI/N, SR/Jr, and SS/Jr). These markers should be useful tools for further genetic studies in rats.

Animals↗

PubMed2006

QTL mapping of Fusarium moniliforme ear rot resistance in maize. 1. Map construction with microsatellite and AFLP markers.

To map the QTLs of Fusarium moniliforme ear rot resistance in Zea mays L., a total of 230 F2 individuals, derived from a single cross between inbred maize lines R15 (resistant) and Ye478 (susceptible), were genotyped for genetic map construction using simple sequence repeat (SSR) markers and amplified fragment length polymorphism (AFLP) markers. We used 778 pairs of SSR primers and 63 combinations of AFLP primers to detect the polymorphisms between parents, R15 and Ye478. From the polymorphic 30 AFLP primer combinations and 159 SSR primers, we scored 260 loci in the F2 population, among which 8 SSR and 13 AFLP loci could not be assigned to any of the linkage groups. An integrated molecular genetic linkage map was constructed by the remaining 151 SSR and 88 AFLP markers, which distributed throughout the 10 linkage groups of maize and spanned the genome of about 3463.5 cM with an average of 14.5 cM between two markers. On 4 chromosomes, we detected 5 putative segregation distortion regions (SDRs), including 2 new ones (SDR2 and SDR7). The other 3 SDRs were located near the regions where gametophyte genes were mapped, indicating that segregation distortion could be partially caused by gametophytic factors.

Chromosome Mapping↗

PubMed2006

Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification.

Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.

Breeding↗

PubMed1999

Evaluating a putative bottleneck in a population of bowhead whales from patterns of microsatellite diversity and genetic disequilibria.

A size-selected Balaena mysticetus genomic library was screened for clones containing simple sequence repeat, or microsatellite, loci. A total of 11 novel loci was identified. These loci were combined with a set of 9 published loci, for a total of 20 markers, and were scored across a sample of 108 bowhead whales from the Bering-Chukchi-Beaufort Seas population of bowhead whales. Genetic variability was measured in terms of polymorphism information content values and unbiased heterozygosity. From the latter, estimates of long-term effective population size were obtained. In addition, gametic phase disequilibrium among loci was investigated. Moderate to high levels of polymorphism were found overall, and the long-term effective size estimates were large relative to total population size. Tests of heterozygosity excess (Cornuet and Luikart 1996) and allele frequency distribution (Luikart et al. 1998) indicated that the possibility of a recent genetic bottleneck in the Bering-Chukchi-Beaufort Seas population of bowhead whales is highly unlikely. However, the fact that five loci displayed a statistically significant heterozygote deficiency remains to be explained.

Animals↗

PubMed2002

Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources.

Previously isolated tomato ( Lycopersicon esculentum) microsatellite markers were mainly clustered in the centromeric heterochromatin and not located in euchromatic regions. To achieve a more-uniform distribution of microsatellite markers for genome mapping purposes, a set of tomato microsatellite markers containing dinucleotide simple sequence repeats were developed by screening genomic libraries enriched for single-copy sequences, and screening the tomato EST database. The tomato microsatellites isolated in these ways were characterized by combinations of different types of repeated motifs and they were polymorphic in a set of L. esculentum varieties detecting up to four alleles. A total of 20 markers were placed on the genetic map of tomato. Interestingly, all markers isolated from genomic libraries enriched for single-copy sequences by PstI-pre-digestion mapped into the centromeric regions. The majority of markers derived from EST sequences contained predominantly AT microsatellites and were located in euchromatic regions.

Journal Article↗

PubMed2002

The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers.

Molecular markers were used to assess polymorphism between and within the genetic bases of coffee (i.e. Typica and Bourbon) spread from Yemen since the early 18th century that have given rise to most arabica cultivars grown world-wide. Eleven Coffea arabica accessions derived from the disseminated bases were evaluated by amplified fragment length polymorphism (AFLP) using 37 primer combinations and simple-sequence repeats (SSRs) produced by six microsatellites. Four cultivars growing in Yemen and 11 subspontaneous accessions collected in the primary centre of diversity of the species were included in the study in order to define their relationship with the accessions derived from the genetic bases of cultivars. One hundred and seven AFLP markers were used to calculate genetic distances and construct a dendrogram. The accessions derived from the disseminated bases were grouped separately, according to their genetic origin, and were distinguished from the subspontaneous accessions. The Yemen cultivars were classified with the Typica-derived accessions. Except for one AFLP marker, all AFLP and SSR markers present in the cultivated accessions were also detected in the subspontaneous accessions. Polymorphism among the subspontaneous accessions was much higher than among the cultivated accessions. It was very low within the genetic bases, confirming the historical documentation on their dissemination. The results enabled a discussion of the genetic diversity reductions that successively occurred during the dissemination of C. arabica from its primary centre of diversity.

Journal Article↗

PubMed2002

SSR analysis of genetic diversity among maize inbred lines adapted to cold regions of Japan.

Information regarding diversity and relationships among breeding material is necessary for hybrid maize ( Zea mays L.) breeding. Simple-sequence repeat (SSR) analysis of the 60 loci distributed uniformly throughout the maize genome was carried out for 65 inbred lines adapted to cold regions of Japan in order to assess genetic diversity among the inbred lines and to assign them to heterotic groups. The mean value (0.69) of the polymorphic-index content (PIC) for the SSR loci provided sufficient discrimination-ability for the assessment of genetic diversity among the inbred lines. The correlation between the genetic-similarity (GS) estimates and the coancestry coefficient was significant ( r = 0.70). The average-linkage (UPGMA) cluster analysis and principal-coordinate analysis (PCOA) for a matrix of the GS estimates showed that the Northern flint inbred lines bred in Japan were similar to a Canadian Northern flint inbred line CO12 and a European flint inbred line F283, and that dent inbred lines bred in Japan were similar to BSSS inbred lines such as B73. These associations correspond to the known pedigree records of these inbred lines. The results indicate that SSR analysis is effective for the assessment of genetic diversity among maize inbred lines and for the assignment of inbred lines to heterotic groups.

Journal Article↗

PubMed2002

A genetic linkage map for watermelon derived from a testcross population: ( Citrullus lanatus var. citroides x C. lanatus var. lanatus) x Citrullus colocynthis.

A genetic linkage map was constructed for watermelon using a testcross population [Plant Accession Griffin 14113 ( Citrullus lanatus var. citroides) x New Hampshire Midget (NHM; C. lanatus var. lanatus)] x U.S. Plant Introduction (PI) 386015 ( Citrullus colocynthis). The map contains 141 randomly amplified polymorphic DNA (RAPD) markers produced by 78 primers, 27 inter-simple sequence repeat (ISSR) markers produced by 17 primers, and a sequence-characterized amplified region (SCAR) marker that was previously reported as linked (1.6 cM) to race-1 Fusarium wilt [incited by Fusarium oxysporum Schlechtend.:Fr. f. sp. niveum (E.F.Sm.) W.C. Synder & H.N. Hans] resistance in watermelon. The map consists of 25 linkage groups. Among them are a large linkage group that contains 22 markers covering a mapping distance of 225.6 cM and six large groups each with 10-20 markers covering a mapping distance of 68.8 to 110.8 cM. There are five additional linkage groups consisting of 3-7 markers per group, each covering a mapping distance of 36.5 to 57.2 cM. The 13 remaining linkage groups are small, each consisting of 2-11 markers covering a mapping distance of 3.5-29.9 cM. The entire map covers a total distance of 1,166.2 cM with an average distance of 8.1 cM between two markers. This map is useful for the further development of markers linked to disease resistance and watermelon fruit qualities.

Journal Article↗

PubMed2002

Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat.

In hexaploid bread wheat ( Triticum aestivum L. em. Thell), ten members of the IWMMN ( International Wheat Microsatellites Mapping Network) collaborated in extending the microsatellite (SSR = simple sequence repeat) genetic map. Among a much larger number of microsatellite primer pairs developed as a part of the WMC ( Wheat Microsatellite Consortium), 58 out of 176 primer pairs tested were found to be polymorphic between the parents of the ITMI ( International Triticeae Mapping Initiative) mapping population W7984 x Opata 85 (ITMI pop). This population was used earlier for the construction of RFLP ( Restriction Fragment Length Polymorphism) maps in bread wheat (ITMI map). Using the ITMI pop and a framework map (having 266 anchor markers) prepared for this purpose, a total of 66 microsatellite loci were mapped, which were distributed on 20 of the 21 chromosomes (no marker on chromosome 6D). These 66 mapped microsatellite (SSR) loci add to the existing 384 microsatellite loci earlier mapped in bread wheat.

Journal Article↗

PubMed2002

Isolation and characterization of microsatellites in Brassica rapa L.

We report here the isolation and characterization of microsatellites, or simple sequence repeats (SSRs), in Brassica rapa. The size-fractionated genomic library was screened with (GA)(15) and (GT)(15) oligonucleotide probes. A total of 58 clones were identified as having the microsatellite repeats, and specific primer pairs were designed for 38 microsatellite loci. All primer pairs, except two, amplified fragments having the sizes expected from the sequences. Of the 36 primer pairs, 35 amplified polymorphic loci in 19 cultivars of B. rapa, while monomorphism was observed in only one primer pair. A total of 232 alleles was identified by the 36 primer pairs in 19 cultivars of B. rapa, and these primer pairs were examined also in nine Brassicaceae species. Most of the 36 primer pairs amplified the loci in the Brassicaceae species. Segregation of the microsatellites was studied in an F(2) population from a cross of doubled-haploid lines DH27 x G309. The microsatellites segregated in a co-dominant manner. These results indicate that the microsatellites isolated in this study were highly informative and could be useful tools for genetic analysis in B. rapa and other related species.

Journal Article↗

PubMed2002

Genetic mapping of a dominant gene conferring resistance to cassava mosaic disease.

Cassava mosaic disease (CMD) is the most-important disease of cassava ( Manihot esculenta) in Africa, and is a potential threat to Latin American (LA) cassava production. Although this viral disease is still unknown in LA, its vector - the whitefly - has recently been found. The disease is best controlled through host-plant resistance, which was first found in third backcross derivatives of an interspecific cross between cassava and Manihot glaziovii, and is thought to be polygenic. Recently, high levels of resistance were also found in several Nigerian cassava landraces. Classical genetic analysis and molecular genetic-mapping of the landraces showed that a major dominant gene confers this resistance. Bulk segregant analysis (BSA) was used to quickly identify a simple sequence repeat (SSR) marker linked to the CMD-resistance gene. The marker, SSRY28, is located on linkage group R of the male-parent-derived molecular genetic map. The gene, designated as CMD2, is flanked by the SSR and RFLP marker GY1 at 9 and 8 cM, respectively. To our knowledge, this is the first report of qualitative virus resistance in cassava, and of molecular markers that tag CMD resistance in cassava. We discuss the use of markers linked to CMD2 for marker-assisted breeding of CMD resistance in Latin America and for increasing the cost-effectiveness of resistance breeding in Africa.

Journal Article↗