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Molecular mapping of the male-sterile, female-sterile mutant gene (st8) in soybean.

Soybean male-sterile, female-sterile mutant genes have been identified by genetic and cytological studies. The St8 gene has been identified as an asynaptic mutation resulting in male and female sterility. This mutant gene was derived from a gene-tagging study using the soybean w4-mutable line. In this report we identified the genetic map position of st8 via restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers. The St8 gene mutation was located between RFLP marker E107 and SSR markers Satt132, Sct_065, and Satt414 on molecular linkage group J and linked to each by 7.8 cM and 3.4 cM, respectively.

Chromosome Mapping↗

A deletion affecting several gene candidates is present in the Evergrowing peach mutant.

Evergrowing (EVG) peach is one of only two described mutants affecting winter dormancy in woody perennial species. EVG peach does not set terminal buds, cease new leaf growth, nor enter into a dormant resting phase in response to winter conditions. The EVG mutation segregates in F2 progeny as a single recessive nuclear gene. A local molecular genetic linkage map around EVG was previously developed using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers, and a bacterial artificial chromosome (BAC) contig that contains the EVG mutation was assembled. A MADS box coding open reading frame (ORF) was found in a BAC of this contig and used as a probe. The probe detected a polymorphism between the wild-type and mutant genomes, and the polymorphism is indicative of a deletion in EVG peach. The EVG gene region contained six potential MADS-box transcription factor sequences, and the deletion in EVG affected at least four of these. The deletion was bracketed using RFLP analysis, which showed that it is contained within a segment of the genome no greater than 180 kb.

Base Sequence↗

Characterization and molecular mapping of genes determining semidwarfism in barley.

The semidwarf trait is desired in cereal breeding programs for increased lodging resistance. We characterized 27 brachytic (brh) semidwarf mutants in barley (Hordeum vulgare L.) and located the genes on barley chromosome linkage maps. All brachytic genes were transferred into the two-rowed cultivar Bowman by backcrossing four to seven times and selecting for semidwarf plants. The brachytic lines were evaluated for 10 phenotypic traits: plant height, awn, peduncle, and rachis internode length, leaf length and width, lodging, grain yield, number of kernels per spike, and kernel weight. We intercrossed the lines to determine which mutants were at independent loci and which were alleles at the same locus. F2 populations from 18 brh semidwarfs were constructed for genetic mapping using simple sequence repeat (SSR) markers. The brachytic semidwarf near-isogenic lines were significantly shorter than their normal counterparts and most had lower yields (16/27); shorter awns (26/27), peduncles (26/27), and rachis internodes (24/27); and reduced kernel weight (22/27). Twelve of the lines had shorter penultimate leaves and 15 had reduced lodging. Four lines had increased kernels per spike, while one had fewer kernels per spike. Allelism tests and mapping comparisons indicated that the 27 semidwarfs comprise 18 independent genetic loci. SSR mapping placed these loci in five of the seven barley chromosomes. Knowledge of the effects and locations of these brachytic semidwarf genes will help barley breeders select appropriate lines for barley improvement.

Chromosome Mapping↗

Chloroplast DNA variation confirms a single origin of domesticated sunflower (Helianthus annuus L.).

Although sunflower was long thought to be the product of a single domestication in what is now the east-central United States, recent archaeological and genetic evidence have suggested the possibility of an independent origin of domestication, perhaps in Mexico. We therefore used hypervariable chloroplast simple-sequence repeat markers to search for evidence of a possible Mexican origin of domestication. This work resulted in the identification of 45 chloroplast haplotypes from 26 populations across the range of wild sunflower as well as 3 haplotypes from 15 domesticated lines, representing both primitive and improved cultivars. The 3 domesticated haplotypes were characterized by 1 primary haplotype (found at a frequency of 6.7% in the wild) as well as 2 rare haplotypes, which are most likely the products of mutation or introgression. One of these rare haplotypes was not observed in the wild, bringing the total number of haplotypes identified to 46. A principal coordinate analysis revealed the presence of 3 major haplotype clusters, one of which contained the primary domesticated haplotype, the 2 rare domesticated variants, as well as haplotypes found across much of the range of wild sunflower. The Mexican haplotypes, on the other hand, fell well outside of this cluster. Although our data do not provide insight into the specific location of sunflower domestication, the relative rarity of the primary domesticated haplotype in the wild, combined with the dissimilarity between this haplotype and those found in the Mexican populations surveyed, provides further evidence that the extant domesticated sunflowers are the product of a single domestication event somewhere outside of Mexico.

Cluster Analysis↗

EST databases as a source for molecular markers: lessons from Helianthus.

Expressed sequence tag (EST) databases represent a potentially valuable resource for the development of molecular markers for use in evolutionary studies. Because EST-derived markers come from transcribed regions of the genome, they are likely to be conserved across a broader taxonomic range than are other sorts of markers. This paper describes a case study in which the publicly available cultivated sunflower (Helianthus annuus) EST database was used to develop simple sequence repeat (SSR) markers for use in the genetic analysis of a rare sunflower species, Helianthus verticillatus, as well as the more widespread Helianthus angustifolius. EST-derived SSRs were found to be more than 3 times as transferable across species as compared with anonymous SSRs (73% vs. 21%, respectively). Moreover, EST-SSRs whose primers were located within protein-coding sequence were more readily transferable than those derived from untranslated regions, and the former loci were no less variable than the latter. The utility of existing EST databases as a means for facilitating population genetic analyses in plants was further explored by cross-referencing publicly available EST resources against available lists of rare or invasive flowering plant taxa. This survey revealed that more than one-third of all plant-derived EST collections of sufficient size could conceivably serve as a source of EST-SSRs for the analysis of rare, endangered, or invasive plant species worldwide.

Asteraceae↗

Genetic analysis of 4 new mutants at the unstable k2 Mdh1-n y20 chromosomal region in soybean.

In soybean (Glycine max (L.) Merr.), a chromosomal region defined by 3 closely linked loci, k2 (tan-saddle seed coat), Mdh1-n (malate dehydrogenase 1 null), and y20 (yellow foliage), is highly mutable. A total of 31 mutants have been reported from this region. In this study, a mutation with tan-saddle seed coat was found from bulk-harvested seed of cultivar Kenwood. Genetic analysis established that this tan-saddle seed coat mutation is allelic to the k2 locus and inherited as a recessive gene. Simple sequence repeat analysis showed that this mutant is not a contaminant from other existing k2 mutants. The mutant was named Kenwood-k2. To test for genetic instability at the k2 Mdh1-n y20 chromosomal region, Kenwood-k2 was crossed reciprocally with cultivars Harosoy and Williams. No new mutants were found in F2 families. In the genetic instability tests of T239 (k2) with cultivar Williams, 3 new mutants with yellow foliage (y20) and malate dehydrogenase 1 null (Mdh1-n) were identified. In the genetic instability tests of T261 (k2 Mdh1-n) with cultivar Williams, no new mutants were found. The Kenwood-k2 and the 3 yellow-foliage, malate dehydrogenase 1-null mutants provide additional genetic materials to study chromosomal aberrations in this mutable/unstable chromosomal region.

Alleles↗

p53 tumor suppressor gene status and the degree of genomic instability in sporadic colorectal cancers.

BACKGROUND: Genomic instability reflects the propensity and the susceptibility of the genome to acquire multiple alterations and, in turn, is believed to be a driving force behind multistep carcinogenesis. Although the molecular basis of genomic instability in sporadic colorectal cancers remains largely a mystery, mutation of the p53 tumor suppressor gene (also known as TP53) has been proposed to play an integral role in this process. However, a dilemma exists in that p53 mutation appears to be a late event in the progression of sporadic colorectal tumors, whereas genomic instability, serving as a facilitator of tumor progression, is envisioned as occurring early in this process. PURPOSE: We evaluated the relationship between p53 mutation and the major form of genomic instability in sporadic colorectal tumors, namely, that involving DNA breakage, which leads to chromosomal translocations, insertions, deletions, and gene amplification. METHODS: Fifty-eight sporadic colorectal tumors that had been previously evaluated for genomic instability were analyzed for p53 mutations. These tumors were from consecutively diagnosed patients. Genomic instability was quantified by use of inter-simple sequence repeat polymerase chain reaction analysis that employed (CA)8RG and (CA)8RY primers (R = purine [A or G]; Y = pyrimidine [C or T]); a genomic instability index (a measure of the number of alterations in tumor DNA in comparison with normal DNA, expressed as a percent) was calculated for each tumor. Mutation of the p53 gene in exons 5-9 was determined by use of single-strand conformational polymorphism-polymerase chain reaction analysis and DNA sequencing. Chi-squared analysis was used to determine the statistical significance of differences between groups of tumors. Reported P values are two-sided. RESULTS: p53 mutations were identified in 29 (50%) of the 58 tumors. The median genomic instability index value was 3.3%. Nineteen (65.5%) of the 29 tumors with p53 mutations had genomic instability indices that were less than the median value (range, 0%-2.6%); the remaining 10 (34.5%) tumors had genomic instability indices that were greater than the median (range, 3.9%-13.0%). Eleven (37.9%) of the 29 tumors with wild-type p53 genes had genomic instability indices that were less than the median value (range, 0%-2.6%), whereas the remaining 18 tumors had genomic instability indices above the median (range, 3.9%-11.7%). There was a statistically significant association between a lesser degree of genomic instability and the presence of p53 mutations (P = .032). CONCLUSIONS AND IMPLICATIONS: Tumors with no or minimal evidence of genomic instability are more likely to harbor p53 mutations than tumors with evidence of substantial genomic instability. p53 mutations play an important role in the development of cancers but do not appear to initiate or promote genomic instability in sporadic colorectal tumors.

Chromosome Aberrations↗

Genetic analysis of rooting ability of transplanted rice (Oryza sativa L.) under different water conditions.

In order to assess the benefits of superior rooting ability of rice (Oryza sativa L.) for growth after transplanting under water-limiting conditions, genetic differences in the rooting ability of rice seedlings 30 d after sowing, with their visible roots either pruned or not pruned, were quantified by several root parameters 4 d after transplanting (DAT), under flooded or non-flooded paddy fields (four treatments in total), together with production traits at maturity. Ninety-eight recombinant inbred lines from the two japonica ecotypes, a lowland variety Otomemochi, and an upland variety Yumenohatamochi, were genotyped with 107 simple sequence repeat (SSR) markers. Otomemochi in general produced more adventitious roots, partitioned a greater proportion of biomass to roots, and had a greater increment of root dry weight (DeltaRW) at 4 DAT than Yumenohatamochi, but these variety differences were less clear under non-flooded conditions without root pruning. Several quantitative trait loci (QTLs) associated with rooting ability were identified mainly in chromosomes 1, 4, and 6 across the four treatments or in combined analysis. On the other hand, QTLs for DeltaRW around RM2357 in chromosome 5 and for maximum new root length in RM215-RM205 in chromosome 9 were found only under root pruning treatments and under non-flooded conditions without root pruning, respectively. Greater DeltaRW was associated with higher head dry weight per hill at maturity only in the non-flooded and root-pruning treatments. This study suggests the importance of rooting ability after transplanting and, possibly, other mechanisms for adaptation to non-flooded conditions.

Oryza↗

Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites.

The L1 Ta subfamily of long interspersed elements (LINEs) consists exclusively of human-specific L1 elements. Polymerase chain reaction-based screening in nonhuman primate genomes of the orthologous sites for 249 human L1 Ta elements resulted in the recovery of various types of sequence variants for approximately 12% of these loci. Sequence analysis was employed to capture the nature of the observed variation and to determine the levels of gene conversion and insertion site homoplasy associated with LINE elements. Half of the orthologous loci differed from the predicted sizes due to localized sequence variants that occurred as a result of common mutational processes in ancestral sequences, often including regions containing simple sequence repeats. Additional sequence variation included genomic deletions that occurred upon L1 insertion, as well as successive mobile element insertions that accumulated within a single locus over evolutionary time. Parallel independent mobile element insertions at orthologous loci in distinct species may introduce homoplasy into retroelement-based phylogenetic and population genetic data. We estimate the overall frequency of parallel independent insertion events at L1 insertion sites in seven different primate species to be very low (0.52%). In addition, no cases of insertion site homoplasy involved the integration of a second L1 element at any of the loci, but rather largely involved secondary insertions of Alu elements. No independent mobile element insertion events were found at orthologous loci in the human and chimpanzee genomes. Therefore, L1 insertion polymorphisms appear to be essentially homoplasy free characters well suited for the study of population genetics and phylogenetic relationships within closely related species.

Animals↗

Microsatellites within genes: structure, function, and evolution.

Recently, increasingly more microsatellites, or simple sequence repeats (SSRs) have been found and characterized within protein-coding genes and their untranslated regions (UTRs). These data provide useful information to study possible SSR functions. Here, we review SSR distributions within expressed sequence tags (ESTs) and genes including protein-coding, 3'-UTRs and 5'-UTRs, and introns; and discuss the consequences of SSR repeat-number changes in those regions of both prokaryotes and eukaryotes. Strong evidence shows that SSRs are nonrandomly distributed across protein-coding regions, UTRs, and introns. Substantial data indicates that SSR expansions and/or contractions in protein-coding regions can lead to a gain or loss of gene function via frameshift mutation or expanded toxic mRNA. SSR variations in 5'-UTRs could regulate gene expression by affecting transcription and translation. The SSR expansions in the 3'-UTRs cause transcription slippage and produce expanded mRNA, which can be accumulated as nuclear foci, and which can disrupt splicing and, possibly, disrupt other cellular function. Intronic SSRs can affect gene transcription, mRNA splicing, or export to cytoplasm. Triplet SSRs located in the UTRs or intron can also induce heterochromatin-mediated-like gene silencing. All these effects caused by SSR expansions or contractions within genes can eventually lead to phenotypic changes. SSRs within genes evolve through mutational processes similar to those for SSRs located in other genomic regions including replication slippage, point mutation, and recombination. These mutational processes generate DNA changes that should be connected by DNA mismatch repair (MMR) system. Mutation that has escaped from the MMR system correction would become new alleles at the SSR loci, and then regulate and/or change gene products, and eventually lead to phenotype changes. Therefore, SSRs within genes should be subjected to stronger selective pressure than other genomic regions because of their functional importance. These SSRs may provide a molecular basis for fast adaptation to environmental changes in both prokaryotes and eukaryotes.

Codon↗

Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms.

Sequences of spacers and group I introns in plant chloroplast genomes have recently been shown to be very effective in phylogenetic reconstruction at higher taxonomic levels and not only for inferring relationships among species. Group II introns, being more frequent in those genomes than group I introns, may be further promising markers. Because group II introns are structurally constrained, we assumed that sequences of a group II intron should be alignable across seed plants. We designed universal amplification primers for the petD intron and sequenced this intron in a representative selection of 47 angiosperms and three gymnosperms. Our sampling of taxa is the most representative of major seed plant lineages to date for group II introns. Through differential analysis of structural partitions, we studied patterns of molecular evolution and their contribution to phylogenetic signal. Nonpairing stretches (loops, bulges, and interhelical nucleotides) were considerably more variable in both substitutions and indels than in helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of four mutational hotspots accounting for less than 18% of sequence length, which are located in loops of domains I and IV, all sequences could be aligned unambiguously across seed plants. Microstructural changes predominantly occurred in loop regions and are mostly simple sequence repeats. An indel matrix comprising 241 characters revealed microstructural changes to be of lower homoplasy than are substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD data set proved effective in testing between alternative hypotheses on the basal nodes of the angiosperm tree. Within angiosperms, group II introns offer phylogenetic signal that is intermediate in information content between that of spacers and group I introns on the one hand and coding sequences on the other.

Base Sequence↗

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria).

The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from this continent with the sweet potato by Polynesian voyagers around A.D. 1,000. To test the hypothesis of an American origin for the Polynesian bottle gourd, we developed seven markers specific to bottle gourd (two chloroplast and five nuclear). The nuclear markers were developed using a new technique where polymorphic inter simple sequence repeat (ISSR) markers are converted into single-locus polymerase chain reaction and sequencing markers--an approach that will be useful for developing markers in other taxa. All seven markers were sequenced in 36 cultivars of bottle gourd from Asia, the Americas, and Polynesia. The results support a dual origin for the Polynesian bottle gourd: the chloroplast markers are exclusively of Asian origin, but the nuclear markers show alleles originating in both the Americas and Asia. Because hybridization of Polynesian bottle gourds with post-European introductions cannot be excluded, ancient DNA from archaeological material will be useful for further elucidating the prehistoric movements of this species in Polynesia. This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole.

Cell Nucleus↗

Variation in the extent of microsatellite instability in human cell lines with defects in different mismatch repair genes.

Mismatch repair deficiency results in the elevation of mutation rates in tumors, which is especially pronounced in simple repeat sequences (microsatellites). We have investigated the relationship between microsatellite mutagenesis and certain combinations of mutations in mismatch repair genes, using a frameshift reversion assay to determine the spontaneous mutation rates of a dinucleotide microsatellite in two cancer cell lines, HCT116, which has defects in hMLH1 and hMSH3, and HEC-1-A, which has defects in hPMS2 and hMSH6. We found a 10-fold difference in mutation rates between these two cell lines. In addition, a mutant hPMS2 allele, PMS134, which has been reported to have a dominant negative effect, was expressed in mismatch repair-proficient telomerase-immortalized hTERT-1604 fibroblasts and mutation rates were determined. Expression of PMS134 did not elevate mutation rates in hTERT-1604. Combined, these results suggest that mutations in different mismatch repair genes can lead to varying degrees of microsatellite instability. It is also likely that there is heterogeneity in the mutations that are acquired in the absence of mismatch repair, such that some mismatch repair-defective cancer cells also contain mutations in other genes coding for proteins involved in the maintenance of genetic stability.

Base Pair Mismatch↗

Use of microsatellite DNA polymorphisms on mouse chromosome 11 for in vitro analysis of thymidine kinase gene mutations.

The mouse lymphoma (L5178Y tk+/- 3.7.2C) in vitro mutagenesis assay can measure the genotoxic effects of a wide variety of chemical agents by inactivation of a single functional thymidine kinase (tk-1) gene. We have previously demonstrated, using cytogenetic and molecular techniques, that the types of molecular lesions associated with tk-1 gene inactivation span a wide range similar to that seen in tumor cells at specific oncogene and tumor suppressor gene loci. We have identified, using polymerase chain reaction techniques, 21 microsatellite, or 'simple sequence repeat', polymorphisms between chromosomes 11a and 11b in 3.7.2C cells. These microsatellite polymorphisms span virtually the entire chromosome, from mapping positions of 3-78 centiMorgans (cM) from the centromere, thus providing landmarks to study loss of genetic material across the entire chromosome. Four of the microsatellite polymorphisms lie within 12 cM of tk-1, and provide a means of mapping loss of genetic material in the immediate vicinity of tk-1, a capability that we have not previously had in the mouse lymphoma assay. Loss of alleles (i.e. loss of heterozygosity) is an important feature of tumor development, having to do with tumor suppressor gene expression. Therefore, the ability to detect loss of heterozygosity in the mouse lymphoma assay will make the assay an extremely valuable tool in the detection of agents capable of inducing loss of heterozygosity.

Animals↗

Hypermutability at a poly(A/T) tract in the human germline.

Poly(A/T) tracts are abundant simple sequence repeats (SSRs) within the human genome. They constitute part of the coding sequence of a variety of genes, encoding polylysine stretches that are important for protein function. Assessment of poly(A/T) tract stability is also used to identify microsatellite unstable colorectal cancers, which are characteristic of tumours defective in DNA mismatch repair. Despite their importance, little is known about the stability of poly(A/T) SSRs in the human germline. We have determined the stability of a paradigm poly(A/T) tract, BAT-40, by study of population allele frequencies, mutation frequency in families and mutation frequency in sperm DNA. We show that the locus is polymorphic, with a level of heterozygosity of 59.7%. Germline mutation was observed in 13 of 187 germline transmissions (7.0%) in 10 families suggesting BAT-40 is unstable in the germline. Further evidence for germline instability at BAT-40 was provided by small pool PCR analysis of matched blood and sperm DNA templates, revealing a significantly elevated frequency of mutation in the germline (P < 0.001). These findings provide insight into poly(A/T) tract stability in the germline. They also have relevance to the study of gene expression and to determination of microsatellite instability in tumours.

AT Rich Sequence↗

Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers.

We describe a technique, sequence-tagged microsatellite profiling (STMP), to rapidly generate large numbers of simple sequence repeat (SSR) markers from genomic or cDNA. This technique eliminates the need for library screening to identify SSR-containing clones and provides an approximately 25-fold increase in sequencing throughput compared to traditional methods. STMP generates short but characteristic nucleotide sequence tags for fragments that are present within a pool of SSR amplicons. These tags are then ligated together to form concatemers for cloning and sequencing. The analysis of thousands of tags gives rise to a representational profile of the abundance and frequency of SSRs within the DNA pool, from which low copy sequences can be identified. As each tag contains sufficient nucleotide sequence for primer design, their conversion into PCR primers allows the amplification of corresponding full-length fragments from the pool of SSR amplicons. These fragments permit the full characterisation of a SSR locus and provide flanking sequence for the development of a microsatellite marker. Alternatively, sequence tag primers can be used to directly amplify corresponding SSR loci from genomic DNA, thereby reducing the cost of developing a microsatellite marker to the synthesis of just one sequence-specific primer. We demonstrate the utility of STMP by the development of SSR markers in bread wheat.

Australia↗

Targeted development of informative microsatellite (SSR) markers.

We describe a novel approach, selectively amplified microsatellite (SAM) analysis, for the targeted development of informative simple sequence repeat (SSR) markers. A modified selectively amplified microsatellite polymorphic loci assay is used to generate multi-locus SSR fingerprints that provide a source of polymorphic DNA markers (SAMs) for use in genetic studies. These polymorphisms capture the repeat length variation associated with SSRs and allow their chromosomal location to be determined prior to the expense of isolating and characterising individual loci. SAMs can then be converted to locus-specific SSR markers with the design and synthesis of a single primer specific to the conserved region flanking the repeat. This approach offers a cost-efficient and rapid method for developing SSR markers for predetermined chromosomal locations and of potential informativeness. The high recovery rate of useful SSR markers makes this strategy a valuable tool for population and genetic mapping studies. The utility of SAM analysis was demonstrated by the development of SSR markers in bread wheat.

Alleles↗

Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci.

There is a lack of information on how individual microsatellite loci differ with respect to their mutation properties. Such variation will have an important bearing on our understanding of the ubiquitous occurrence of simple repeat sequences in eukaryotic genomes and on deriving proper mutation models that can be incorporated into genetic distance estimates. We genotyped approximately 100 families of the bird barn swallow (Hirundo rustica) for two hypervariable (heterozygosity >95%) microsatellite markers: HrU6, an (AAAG)n tetranucleotide repeat, and HrU10, an (AAGAG)n pentanucleotide repeat. A total of 27 germline mutation events were documented, corresponding to mutation rates of 0.57% (HrU6) and 1.56% (HrU10). The mutation rate increased with allele size, at approximately 0.1% per repeat unit over the observed range of allele sizes (approximately 10-100 repeat units). Single repeat unit changes dominated, with 21/27 mutations representing the gain or loss of one repeat unit. There was no clear difference in the number of gains versus losses nor was there an effect of allele size on the magnitude or direction of mutation. Unexpectedly, the mutation rate of females (maternally transmitted mutations) was 2.5-5 times higher than that of males. Contrasting these observations with mutation data from other microsatellite loci reveals differences not only in the mutation rate, but also in the magnitude, direction and effect of sex on mutation. Thus, microsatellite mutation and evolution may be viewed as a dynamic and variable process.

Animals↗