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J F Wendel

Publications and source records attributed to J F Wendel.

33 records · Page 2Linked to original sources
PubMed1996

Hairpins create minute inversions in non-coding regions of chloroplast DNA.

Minute inversions (4 bp in length), associated with probable hairpin secondary structures, were inferred from comparative analysis of rpl16 intron sequences from the chloroplast genomes of Chusquea species and related bamboos (Poaceae). The inverted sequences, which appear to have arisen independently on several occasions, comprise entire loops of the putative hairpins. The process of inversion seems dependent upon the stem length of the hairpin and its estimated free energy of formation. A similar inversion was uncovered for other plants in a previously published data set for a different non-coding region of the chloroplast genome, suggesting that the inversional process may be a common feature of non-coding DNA evolution. Several implications for phylogenetic analysis are noted.

Base Sequence↗
PubMed1995

Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium).

Polyploidy is a prominent process in plant evolution; yet few data address the question of whether homeologous sequences evolve independently subsequent to polyploidization. We report on ribosomal DNA (rDNA) evolution in five allopolyploid (AD genome) species of cotton (Gossypium) and species representing their diploid progenitors (A genome, D genome). Sequence data from the internal transcribed spacer regions (ITS1 and ITS2) and the 5.8S gene indicate that rDNA arrays are homogeneous, or nearly so, in all diploids and allopolyploids examined. Because these arrays occur at four chromosomal loci in allopolyploid cotton, two in each subgenome, repeats from different arrays must have become homogenized by interlocus concerted evolution. Southern hybridization analysis combined with copy-number estimation demonstrate that this process has gone to completion in the diploids and to completion or near-completion in all allopolyploid species and that it most likely involves the entire rDNA repeat. Phylogenetic analysis demonstrates that interlocus concerted evolution has been bidirectional in allopolyploid species--i.e., rDNA from four polyploid lineages has been homogenized to a D genome repeat type, whereas sequences from Gossypium mustelinum have concerted to an A genome repeat type. Although little is known regarding the functional significance of interlocus concerted evolution of homeologous sequences, this study demonstrates that the process occurs for tandemly repeated sequences in diploid and polyploid plants. That interlocus concerted evolution can occur bidirectionally subsequent to hybidization and polyploidization has significant implications for phylogeny reconstruction, especially when based on rDNA sequences.

Base Sequence↗
PubMed1995

An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression.

The New World allopolyploid (AD-genome) cottons (Gossypium) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Africa-Asia (the A-genome) and the American tropics and subtropics (the D-genome). Phylogenetic analysis of sequence data from the ribosomal DNA internal transcribed spacer region (ITS1, 5.8S rRNA, ITS2) reveals two strongly supported clades, one corresponding to African species and the other containing all American D-genome species except Gossypium gossypioides, which occupies a basal position within the African clade. This placement conflicts with evidence from fertility relationships, morphology, cytogenetics allozymes, and cpDNA restriction site analysis, which specify a sister-species relationship for G. gossypioides and Gossypium raimondii, deeply embedded within the American D-genome clade. Several alternative explanations for this striking incongruence are considered. The most probable involves: (1) an ancient hybridization event, whereby G. gossypioides experienced contact with an A-genome, either at the diploid level or at the triploid level as a consequence of hybridization with a New World allopolyploid and (2) repeated backcrossing of the hybrid into the G. gossypioides lineage, thereby restoring a nearly pure D-genome, but in the process generating a recombinant ribosomal DNA. We suggest that this process may implicate G. gossypioides, rather than G. raimondii, as the closest living descendant of the ancestral D-genome parent of the allopolyploids. In addition, this example of cryptic, intergenomic introgression between species groups now occupying different hemispheres illustrates how ITS data may provide insights into genome composition and evolutionary history, especially when used in the context of a holistic view that encompasses information from a variety of sources.

Africa↗
PubMed1994

A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome.

We employ a detailed restriction fragment length polymorphism (RFLP) map to investigate chromosome organization and evolution in cotton, a disomic polyploid. About 46.2% of nuclear DNA probes detect RFLPs distinguishing Gossypium hirsutum and Gossypium barbadense; and 705 RFLP loci are assembled into 41 linkage groups and 4675 cM. The subgenomic origin (A vs. D) of most, and chromosomal identity of 14 (of 26), linkage groups is shown. The A and D subgenomes show similar recombinational length, suggesting that repetitive DNA in the physically larger A subgenome is recombinationally inert. RFLPs are somewhat more abundant in the D subgenome. Linkage among duplicated RFLPs reveals 11 pairs of homoelogous chromosomal regions-two appear homosequential, most differ by inversions, and at least one differs by a translocation. Most homoeologies involve chromosomes from different subgenomes, putatively reflecting the n = 13 to n = 26 polyploidization event of 1.1-1.9 million years ago. Several observations suggest that another, earlier, polyploidization event spawned n = 13 cottons, at least 25 million years ago. The cotton genome contains about 400-kb DNA per cM, hence map-based gene cloning is feasible. The cotton map affords new opportunities to study chromosome evolution, and to exploit Gossypium genetic resources for improvement of the world's leading natural fiber.

Biological Evolution↗
PubMed1993

Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.).

Copia-like retrotransposable elements were identified in allotetraploid cotton, Gossypium hirsutum, and two species representing its diploid progenitors, G. herbaceum and G. raimondii. These elements are present in high copy number in all three species. Because the two diploid genomic groups have been isolated on opposite sides of the world for 6-11 million years, horizontal transfer of elements between these species is highly unlikely. Elements were intensively sampled to generate a model of copia-like retrotransposable element evolution in systems where vertical transmission is the sole probable means of descent. Copia-like retrotransposon diversity is equally great in all three Gossypium species. Despite this high heterogeneity, analysis of 89 partial reverse transcriptase sequences resulted in the recognition of nine sharply differentiated retrotransposon lineages, each containing elements that share high sequence similarity. No evidence of horizontal transfer from other taxa was obtained. Phylogenetic analyses demonstrate that element topologies are incongruent with Gossypium phylogeny. Consideration of processes that obscure phylogenetic reconstruction of multigene families (including sampling error, variable degrees of orthology and paralogy, differential lineage age and lineage loss and/or proliferation) demonstrates that incongruence between organismal and retrotransposon trees is expected under conditions in which vertical processes are the sole means of transmission. Identification of closely related elements between species allowed rates of copia-like retrotransposon sequence evolution to be estimated as approximately 10(-9) nucleotide substitutions/site/year. These rates are consistent with the interpretation that these retrotransposons have been evolving under functional constraints for most of the time frame bracketed by the species studied. Extrapolation of these results to previous studies that sampled from more highly divergent taxa indicates that horizontal transfer need not be invoked to explain observed phylogenetic patterns.

Amino Acid Sequence↗
PubMed1989

New World tetraploid cottons contain Old World cytoplasm.

New World tetraploid cottons (Gossypium spp.) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Asia-Africa (the A genome) and the New World tropics and subtropics (the D genome). Despite intensive study, the identity of the parental diploids and the antiquity of polyploidization remain unresolved. In this study, variation in the maternally inherited chloroplast genome was assessed among species representing both of the parental genomes and the tetraploids. Approximately 560 restriction sites were assayed in each accession, representing sequence information for about 3200 nucleotides. The resulting maternal phylogeny has no convergent restriction site mutations and demonstrates that the cytoplasm donor for all tetraploid species was an A genome diploid with a chloroplast genome that is similar to Gossypium arboreum and Gossypium herbaceum. No mutational differences were detected between these two species, and few mutations distinguish the chloroplast genomes of A genome diploids from those of tetraploid taxa. In contrast to expectations based on extensive taxonomic, geographic, and genetic diversity, a surprisingly low level of sequence divergence has accumulated subsequent to polyploidization. Chloroplast genomes of tetraploid species are distinguished from each other by between one and six apparent point mutations. The data suggest that tetraploid cotton originated relatively recently, perhaps within the last 1-2 million years, with subsequent rapid evolution and diversification throughout the New World tropics.

Journal Article↗
PubMed1988

New isozyme systems for maize (Zea mays L.): aconitate hydratase, adenylate kinase, NADH dehydrogenase, and shikimate dehydrogenase.

Electrophoretic variation and inheritance of four novel enzyme systems were studied in maize (Zea mays L.). A minimum of 10 genetic loci collectively encodes isozymes of aconitate hydratase (ACO; EC 4.2.1.3.), adenylate kinase (ADK; EC 2.7.4.3), NADH dehydrogenase (DIA; EC 1.6.99.-), and shikimate dehydrogenase (SAD; EC 1.1.1.25). At least four loci are responsible for the genetic control of ACO. Genetic data for two of the encoding loci, Aco1 and Aco4, demonstrated that at least two maize ACOs are active as monomers. Analysis of organellar preparations suggests that ACO1 and ACO4 are localized in the cytosolic and mitochondrial subcellular fractions, respectively. Maize ADK is encoded by a single nuclear locus, Adk1, governing monomeric enzymes that are located in the chloroplasts. Two cytosolic and two mitochondrial forms of DIA were electrophoretically resolved. Segregation analyses demonstrated that the two cytosolic isozymes are controlled by separate loci, Dia1 and Dia2, coding for products that are functional as monomers (DIA1) and dimers (DIA2). The major isozyme of SAD is apparently cytosolic, although an additional faintly staining plastid form may be present. Alleles at Sad1 are each associated with two bands that cosegregate in controlled crosses. Linkage analyses and crosses with B-A translocation stocks were effective in determining the map locations of six loci, including the previously described but unmapped locus Acp4. Several of these loci were localized to sparsely mapped regions of the genome. Dia2 and Acp4 were placed on the distal portion of the long arm of chromosome 1, 12.6 map units apart. Dia1 was localized to chromosome 2, 22.2 centimorgans (cM) from B1. Aco1 was mapped to chromosome 4, 6.2 cM from su1. Adk1 was placed on the poorly marked short arm of chromosome 6, 8.1 map units from rgd1. Less than 1% recombination was observed between Glu1 (on chromosome 10) and Sad1. In contrast to many other maize isozyme systems, there was little evidence of gene duplication or of parallel linkage relationships for these allozyme loci.

Aconitate Hydratase↗
PubMed1987

Evidence for multilocus genetic control of preferential fertilisation in maize.

Genetic segregation was studied in more than 1900 seedlings of an F2 between the maize (Zea mays L.) inbred lines T232 and CM37. Significant segregation distortion was observed at 11 of 17 segregating allozyme loci and at a single morphological marker locus distributed on 7 of the 10 chromosomes in the genome. Deviations from genotypic class expectations were small for most loci, and averaged 7.7 per cent. Percent transmission of the allele contributed by T232 varied from 47.7 per cent to 53.3 per cent. The allele donated by T232 was significantly under-represented for loci on chromosomes 1 and 8, whereas the allele contributed by CM37 was deficient for nine of the ten segregating loci on chromosomes 2, 3, and 6. In all cases, the parental origin of the deficient allele was consistent for markers on a chromosome. Evidence is presented that suggests the aberrant ratios arose from linkage of the markers with genetic factors affecting prezygotic transmission, and that a minimum of 5 such factors were operative, one on each of chromosomes 1, 2, 3, 6, and 8. In contrast to the multi-locus and multi-chromosomal distorted segregation observed in the F2, all loci in backcross progenies fit Mendelian expectations. It is suggested that this discrepancy reflects variable environmental selection pressures on genes that influence aspects of gamete competition.

Alleles↗
PubMed1987

Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action.

Individual genetic factors which underlie variation in quantitative traits of maize were investigated in each of two F2 populations by examining the mean trait expressions of genotypic classes at each of 17-20 segregating marker loci. It was demonstrated that the trait expression of marker locus classes could be interpreted in terms of genetic behavior at linked quantitative trait loci (QTLs). For each of 82 traits evaluated, QTLs were detected and located to genomic sites. The numbers of detected factors varied according to trait, with the average trait significantly influenced by almost two-thirds of the marked genomic sites. Most of the detected associations between marker loci and quantitative traits were highly significant, and could have been detected with fewer than the 1800-1900 plants evaluated in each population. The cumulative, simple effects of marker-linked regions of the genome explained between 8 and 40% of the phenotypic variation for a subset of 25 traits evaluated. Single marker loci accounted for between 0.3% and 16% of the phenotypic variation of traits. Individual plant heterozygosity, as measured by marker loci, was significantly associated with variation in many traits. The apparent types of gene action at the QTLs varied both among traits and between loci for given traits, although overdominance appeared frequently, especially for yield-related traits. The prevalence of apparent overdominance may reflect the effects of multiple QTLs within individual marker-linked regions, a situation which would tend to result in overestimation of dominance. Digenic epistasis did not appear to be important in determining the expression of the quantitative traits evaluated. Examination of the effects of marked regions on the expression of pairs of traits suggests that genomic regions vary in the direction and magnitudes of their effects on trait correlations, perhaps providing a means of selecting to dissociate some correlated traits. Marker-facilitated investigations appear to provide a powerful means of examining aspects of the genetic control of quantitative traits. Modifications of the methods employed herein will allow examination of the stability of individual gene effects in varying genetic backgrounds and environments.

Chromosome Mapping↗
PubMed1984

Distorted segregation and linkage of alcohol dehydrogenase genes in Camellia japonica L. (Theaceae).

Alcohol dehydrogenase isozymes in Camellia japonica are encoded by two genes, Adh-1 and Adh-2. Both loci are expressed in seeds, and their products randomly associate into intragenic and intergenic dimers. Electrophoresis of leaf extracts reveals only the products of Adh-2. Formal genetic analysis indicated that the two Adh loci are tightly linked (combined estimate of r = 0.004). Most segregations fit expected Mendelian ratios, but in some families distorted segregation was observed at Adh-1, Adh-2, or both loci. The deficient progeny class varied across families, and in two apparent back-crosses three rather than two phenotypic classes were recovered. The mechanism underlying these distortions is not known, but evidence is presented that suggests that the phenomenon is genic or segmental in nature. Plausible hypotheses include linkage of the Adh structural genes with a gametophytic self-incompatibility locus, translocation heterozygosity involving the segment bearing Adh-1 and Adh-2, or a combination of these two mechanisms.

Alcohol Dehydrogenase↗
PubMedDate not supplied

Comparative development of fiber in wild and cultivated cotton.

One of the most striking examples of plant hairs is the single-celled epidermal seed trichome of cultivated cotton. The developmental morphology of these commercial "fibers" has been well-characterized in Gossypium hirsutum, but little is known about the pattern and tempo of fiber development in wild Gossypium species, all of which have short, agronomically inferior fiber. To identify developmental differences that account for variation in fiber length, and to place these differences in a phylogenetic context, we conducted SEM studies of ovules at and near the time of flowering, and generated growth curves for cultivated and wild diploid and tetraploid species. Trichome initiation was found to be similar in all taxa, with few notable differences in trichome density or early growth. Developmental profiles of the fibers of most wild species are similar, with fiber elongation terminating at about two weeks post-anthesis. In contrast, growth is extended to three weeks in the A- and F-genome diploids. This prolonged elongation period is diagnosed as a key evolutionary event in the origin of long fiber. A second evolutionary innovation is that absolute growth rate is higher in species with long fibers. Domestication of species is associated with a further prolongation of elongation at both the diploid and allopolyploid levels, suggesting the effects of parallel artificial selection. Comparative analysis of fiber growth curves lends developmental support to previous quantitative genetic suggestions that genes for fiber "improvement" in tetraploid cotton were contributed by the agronomically inferior D-genome diploid parent.

Agriculture↗
PubMedDate not supplied

The mitochondrial genome of allotetraploid cotton (Gossypium L.).

Knowledge of patterns of organellar inheritance are crucial for analyses of organellar genetics and population or phylogenetic analyses based on organellar genes. While it has previously been shown that chloroplast DNA is maternally inherited in cotton (Gossypium L.), no, studies have assessed the mitochondrial genome complement of the allotetraploid species of cotton or addressed inheritance of mitochondrial DNA. In this article we report Southern hybridization analyses that indicate that the AD-genome allotetraploid species have an A-genome-like mitochondrial genome and provide evidence that mitochondrial genomes are also maternally inherited in cotton.

Blotting, Southern↗
PubMedDate not supplied

Duplicated plastid and triplicated cytosolic isozymes of triosephosphate isomerase in maize (Zea mays L.).

We studied electrophoretic variation and inheritance of triosephosphate isomerase (TPI) isozymes in maize (Zea mays L.). In contrast to most diploid plants, in maize, TPI exists as multiple isozymes in both the plastid and cytosolic subcellular compartments. Phenotypes result from the overlay of two independent sets of isozymes and allozymes, representing the plastid (encoded by the nuclear genes Tpi1 and Tpi2) and cytosolic (encoded by Tpi3, Tpi4, and Tpi5) systems. All possible intragenic and intergenic dimeric enzymes are formed between polypeptides within each subcellular compartment. No heterodimers are formed between plastid and cytosolic polypeptides. Extensive surveys of accessions of land races and inbred lines revealed 22 allelic variants for the five loci. Most alleles have been formally validated by segregation analysis. We describe two null alleles at Tpi4, distinguished by their relative abilities to form intergenic heterodimers with polypeptides specified by Tpi3 and Tpi5. Linkage analyses and crosses with B-A translocation stocks were effective in determining the chromosome locations of all five loci. Duplicated genes for both the plastid and cytosolic isozymes were localized to genomic regions that possess numerous other redundant sequences. We placed Tpi1 on the long arm of chromosome 7, approximately 23 centimorgans (cM) distal to g11; we localized its duplicate--Tpi2--17 cM distal to v4 on the long arm of chromosome 2. The triplicate loci encoding cytosolic TPIs reside on chromosomes 3 and 8. Tpi4 is approximately equidistant (11 cM) from d1 and Lg3, near the centromere of chromosome 3. Tpi3 and Tpi5 are located on distal ends of the most poorly marked maize chromosome; Tpi3 is 29 cM distal to Idh 1 on 8L, and Tpi5 is on 8S or near the centromere on 8L. In contrast to most duplicated maize sequences, which often occur in parallel linkages on different chromosomes, Tpi3 and Tpi5 provide an example of intrachromosomal gene duplication. Several of the Tpi loci are located in sparsely mapped regions of the genome, and Tpi1 is the first isozyme marker for chromosome 7.

Alleles↗