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PubMed1995

An aphid-resistance locus is tightly linked to the nematode-resistance gene, Mi, in tomato.

Tomato lines from diverse breeding programs were evaluated in the field for resistance to a natural infestation of the potato aphid, Macrosiphum euphorbiae, in Davis, CA. It was noted that all lines that carried the nematode-resistance gene, Mi, displayed aphid resistance. A greenhouse assay for aphid resistance was developed to investigate this relationship. Association of nematode and aphid resistances in near-isogenic lines suggested that these traits are tightly linked. Analysis of an F2 population segregating for nematode resistance indicated that aphid resistance segregated as a single major locus genetically linked to Mi. The name Meu1 is proposed for this locus. It is likely that Meu1 was introduced into tomato along with Mi from the wild species Lycopersicon peruvianum. The presence of aphid resistance in the line Motelle, which contains a very small region of introgressed DNA, and the lack of recombinants suggest that Meu1 is tightly linked to Mi or possibly is the same gene. The map-based strategy currently being used to clone Mi should be applicable to cloning Meu1.

Journal Article↗

PubMed1996

The estrogen receptor locus is associated with a major gene influencing litter size in pigs.

Identification of individual major genes affecting quantitative traits in livestock species has been limited to date. By using a candidate gene approach and a divergent breed cross involving the Chinese Meishan pig, we have shown that a specific allele of the estrogen receptor (ER) locus is associated with increased litter size. Female pigs from synthetic lines with a 50% Meishan background that were homozygous for this beneficial allele produced 2.3 more pigs in first parities and 1.5 more pigs averaged over all parities than females from the same synthetic lines and homozygous for the undesirable allele. This beneficial ER allele was also found in pigs with Large White breed ancestory. Analysis of females with Large White breed background showed an advantage for females homozygous for the beneficial allele as compared to females homozygous for the other allele of more than 1 total pig born. Analyses of growth performance test records detected no significant unfavorable associations of the beneficial allele with growth and developmental traits. Mapping of the ER gene demonstrated that the closest known genes or markers were 3 centimorgans from ER. To our knowledge, one of these, superoxide dismutase gene (SOD2), was mapped for the first time in the pig. Analysis of ER and these linked markers indicated that ER is the best predictor of litter size differences. Introgression of the beneficial allele into commercial pig breeding lines, in which the allele was not present, and marker-assisted selection for the beneficial allele in lines with Meishan and Large White background have begun.

Animals↗

PubMed1997

Genetics and the origin of bird species.

External (environmental) factors affecting the speciation of birds are better known than the internal (genetic) factors. The opposite is true for several groups of invertebrates, Drosophila being the outstanding example. Ideas about the genetics of speciation in general trace back to Dobzhansky who worked with Drosophila. These ideas are an insufficient guide for reconstructing speciation in birds for two main reasons. First, speciation in birds proceeds with the evolution of behavioral barriers to interbreeding; postmating isolation usually evolves much later, perhaps after gene exchange has all but ceased. As a consequence of the slow evolution of postmating isolating factors the scope for reinforcement of premating isolation is small, whereas the opportunity for introgressive hybridization to influence the evolution of diverging species is large. Second, premating isolation may arise from nongenetic, cultural causes; isolation may be affected partly by song, a trait that is culturally inherited through an imprinting-like process in many, but not all, groups of birds. Thus the genetic basis to the origin of bird species is to be sought in the inheritance of adult traits that are subject to natural and sexual selection. Some of the factors involved in premating isolation (plumage, morphology, and behavior) are under single-gene control, most are under polygenic control. The genetic basis of the origin of postmating isolating factors affecting the early development of embryos (viability) and reproductive physiology (sterility) is almost completely unknown. Bird speciation is facilitated by small population size, involves few genetic changes, and occurs relatively rapidly.

Animals↗

PubMed1997

Oat-maize chromosome addition lines: a new system for mapping the maize genome.

Novel plants with individual maize chromosomes added to a complete oat genome have been recovered via embryo rescue from oat (Avena sativa L., 2n = 6x = 42) x maize (Zea mays L., 2n = 20) crosses. An oat-maize disomic addition line possessing 21 pairs of oat chromosomes and one maize chromosome 9 pair was used to construct a cosmid library. A multiprobe (mixture of labeled fragments used as a probe) of highly repetitive maize-specific sequences was used to selectively isolate cosmid clones containing maize genomic DNA. Hybridization of individual maize cosmid clones or their subcloned fragments to maize and oat genomic DNA revealed that most high, middle, or low copy number DNA sequences are maize-specific. Such DNA markers allow the identification of maize genomic DNA in an oat genomic background. Chimeric cosmid clones were not found; apparently, significant exchanges of genetic material had not occurred between the maize-addition chromosome and the oat genome in these novel plants or in the cloning process. About 95% of clones selected at random from a maize genomic cosmid library could be detected by the multiprobe. The ability to selectively detect maize sequences in an oat background enables us to consider oat as a host for the cloning of specific maize chromosomes or maize chromosome segments. Introgressing maize chromosome segments into the oat genome via irradiation should allow the construction of a library of overlapping fragments for each maize chromosome to be used for developing a physical map of the maize genome.

Chromosome Mapping↗

PubMed1999

Plant genetic resources: what can they contribute toward increased crop productivity?

To feed a world population growing by up to 160 people per minute, with >90% of them in developing countries, will require an astonishing increase in food production. Forecasts call for wheat to become the most important cereal in the world, with maize close behind; together, these crops will account for approximately 80% of developing countries' cereal import requirements. Access to a range of genetic diversity is critical to the success of breeding programs. The global effort to assemble, document, and utilize these resources is enormous, and the genetic diversity in the collections is critical to the world's fight against hunger. The introgression of genes that reduced plant height and increased disease and viral resistance in wheat provided the foundation for the "Green Revolution" and demonstrated the tremendous impact that genetic resources can have on production. Wheat hybrids and synthetics may provide the yield increases needed in the future. A wild relative of maize, Tripsacum, represents an untapped genetic resource for abiotic and biotic stress resistance and for apomixis, a trait that could provide developing world farmers access to hybrid technology. Ownership of genetic resources and genes must be resolved to ensure global access to these critical resources. The application of molecular and genetic engineering technologies enhances the use of genetic resources. The effective and complementary use of all of our technological tools and resources will be required for meeting the challenge posed by the world's expanding demand for food.

Agriculture↗

PubMed1999

Chromosome regions between centromeres and proximal crossovers are the physical sites of major effect loci for yield in potato: genetic analysis employing meiotic mutants.

Meiotic mutant (2n) gametes formed by first-division restitution without crossover (FDR-NCO) are expected to be superior to FDR with crossover (FDR-CO) because they transmit to the progeny, without disruption by recombination, almost 100% of the parental genotype. FDR-CO transfers approximately 80% of the parental heterozygosity and a large fraction of the epistatic interactions. Another genetic expectation associated with both FDR gametes is their equivalence for the phenotypic expression of traits controlled by genes residing between centromeres and proximal crossover sites. This set of unique cytogenetic features of FDR mutants was employed here as a tool to infer physical location of quantitative trait loci controlling total tuber yield (TTY) in potato. Two assays were conducted to verify the superiority of FDR-NCO over FDR-CO gametes for TTY by using progenies from 4x-2x factorial crosses. Male clones were 2n-pollen producers by either FDR-CO or FDR-NCO mechanisms. Compared with the 4x parents, TTY of the progenies ranged from 41% to 175% (i.e., high-parent heterosis). However, no significant TTY differences were observed between FDR-CO and FDR-NCO families. In addition, the size of variance components of males was smaller than females and near zero. Our results reinforce the hypothesis that genes controlling yielding ability have a predominant physical location between centromeres and proximal chiasmata. Quantitative trait loci in chromosome regions with reduced levels of recombination may provide a partial explanation for the slow progress in increasing TTY through conventional 4x-4x crosses and for the often high degree of heterosis obtained by introgressing genetic diversity via 4x-2x crosses in potato.

Journal Article↗

PubMed2001

Ancient origin of pathogen recognition specificity conferred by the tomato disease resistance gene Pto.

We have investigated the origin of the Pto disease resistance (R) gene that was previously identified in the wild tomato species Lycopersicon pimpinellifolium and isolated by map-based cloning. Pto encodes a serine-threonine protein kinase that specifically recognizes strains of Pseudomonas syringae pv. tomato (Pst) that express the avirulence gene avrPto. We examined an accession of the distantly related wild species Lycopersicon hirsutum var. glabratum that exhibits avrPto-specific resistance to Pst. The Pst resistance of L. hirsutum was introgressed into a susceptible Lycopersicon esculentum background to create the near-isogenic line 96T133-3. Resistance to Pst(avrPto) in 96T133-3 was inherited as a single dominant locus and cosegregated with a restriction fragment length polymorphism detected by the Pto gene. This observation suggested that a member of the Pto gene family confers Pst(avrPto) resistance in this L. hirsutum line. Here we report the cloning and characterization of four members of the Pto family from 96T133-3. One gene (LhirPto) is 97% identical to Pto and encodes a catalytically active protein kinase that elicits a hypersensitive response when coexpressed with avrPto in leaves of Nicotiana benthamiana. In common with the Pto kinase, the LhirPto protein physically interacts with AvrPto and downstream members of the Pto signaling pathway. Our studies indicate that R genes of the protein kinase class may not evolve rapidly in response to pathogen pressure and rather that their ability to recognize specific Avr proteins can be highly conserved.

Base Sequence↗

PubMed2003

Evolution in Darwin's finches: a review of a study on Isla Daphne Major in the Galápagos archipelago.

This paper reviews research pertaining to the problem of speciation of the finches on the Galápagos archipelago carried out by assistants, several colleagues, Peter Grant and myself. I give a brief history of the radiation, examine the process of divergence by natural selection over time, and then consider the nature of the reproductive barrier to gene flow between closely related species. Fluctuating climatic conditions have produced a continuously changing ecological landscape and altered feeding conditions for the finches over the last 30 years. Finch populations tracked these changes by natural selection and evolutionary responses to the main events. At each event significant morphological change occurred from one generation to the next generation. As a consequence of these accumulated changes, the mean bill shape and body size of the Geospiza fortis and G. scandens populations differed markedly from 1973 to 2002. Song, a learned culturally transmitted trait, acted as a barrier to reproduction between these species. Rare incidences of misimprinting on song led to hybridization and introgression. Low levels of gene flow from one species to another increased genetic variation on which selection acted. Although the major driving force of diversification was ecological change, the process of diversification involved a subtle interplay between ecology, genetic evolution and learned culturally transmitted traits. An important message for conservation is that neither the environment nor species are fixed entities, therefore a wise strategy for conserving endangered species should keep them capable of further change.

Journal Article↗

PubMed2005

The interaction of Schistosoma haematobium and S. guineensis in Cameroon.

Interactions between schistosomes are complex with some different species being able to mate and hybridize. The epidemiology of schistosomiasis in specific areas of South West Cameroon has evolved remarkably over 30 years as a result of hybridization between Schistosoma guineensis and S. haematobium. Morphological and biological data suggest that S. haematobium replaced S. guineensis in areas of Cameroon through introgressive hybridization. Data are reported on the use of single stranded conformational polymorphism (SSCP) analysis of the nuclear ribosomal second internal transcribed spacer (ITS2) of individual schistosomes from hybrid zones of Cameroon. The data show that since 1990 S. haematobium has completely replaced S. guineensis in Loum, with S. haematobium and the recombinants still present in 2000. This study illustrates the complexities of the dynamics between S. haematobium and S. guineensis in South West Cameroon.

Animals↗

PubMed2005

Molecular cloning, expression and mapping analysis of a novel cytosolic ascorbate peroxidase gene from tomato.

Ascorbate peroxidase (APX, EC 1.11.1.11) plays a major role in H(2)O(2)-scavenging in plants and can help to avoid reactive oxygen species (ROS) damage. A new cytosolic APX gene was cloned from tomato (designated LecAPX2) by RACE-PCR. The full-length cDNA of LecAPX2 contained a complete open reading frame (ORF) of 753 bp, which encoding 250 amino acid residues. Homology analysis of LecAPX2 showed a 94% identity with potato cAPX gene and 92% identity with another tomato cAPX gene (APX20), the deduced amino acid showed 88% homology with APX20 protein and 75-92% identity with cAPX from other plants such as potato, tobacco, broccoli, spinach, pea, rice, etc. LecAPX2 revealed the existence of a haem peroxidase and plant APX family signatures. Northern blot analysis showed that LecAPX2 was constitutively expressed in root, stem, leaf, flower and fruit of tomato, whereas the expression levels were different. LecAPX2 was mapped to 6-A using 75 tomato introgression lines (ILs), each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii.

Amino Acid Sequence↗

PubMed2002

Importance of hybridization between indigenous and nonindigenous freshwater species: an overlooked threat to North American biodiversity.

Biodiversity of North American freshwaters is among the greatest in the world. However, due to extensive habitat degradation, pollution, and introductions of nonindigenous species, this biodiversity is also among the most endangered. Unlike habitat degradation and pollution, nonindigenous species represent a permanent loss of biodiversity because their removal or control is often impossible. Most species introduced into nonnative North American ranges, however, are not from Eurasia but have been introduced from geographically isolated regions within North America. Although the ecological effects of introduced species have been widely documented, the effects of hybridization, especially between closely related species, represents an equally serious mechanism of extinction but is much less studied. Identification of which species are likely to hybridize after contact is of critical importance to prevent the further loss of native species. Molecular phylogenetics serves as a powerful tool to identify freshwater species at risk of introgression, if we can assume that genetic distance is a good predictor of the potential for hybridization. Although not a thorough review of all cases of hybridization, this article documents the extent and effects of hybridization in fishes, crayfishes, mussels, and other invertebrates in light of the currently accepted phylogenetic relationships. We suggest this approach may be the first step in addressing the potential threat of hybridization between many of the closely related species in North American fresh waters.

Animals↗

PubMed2006

Utility of nuclear allele networks for the analysis of closely related species in the genus Carabus, subgenus Ohomopterus.

Nuclear DNA sequence data for diploid organisms are potentially a rich source of phylogenetic information for disentangling the evolutionary relationships of closely related organisms, but present special phylogenetic problems owing to difficulties arising from heterozygosity and recombination. We analyzed allelic relationships for two nuclear gene regions (phosphoenolpyruvate carboxykinase and elongation factor-1a), along with a mitochondrial gene region (NADH dehydrogenase subunit 5), for an assemblage of closely related species of carabid beetles (Carabus subgenus Ohomopterus). We used a network approach to examine whether the nuclear gene sequences provide substantial phylogenetic information on species relationships and evolutionary history. The mitochondrial gene genealogy strongly contradicted the morphological species boundary as a result of introgression of heterospecific mitochondria. Two nuclear gene regions showed high allelic diversity within species, and this diversity was partially attributable to recombination between various alleles and high variability in the intron region. Shared nuclear alleles among species were rare and were considered to represent shared ancestral polymorphism. Despite the presence of recombination, nuclear allelic networks recovered species monophyly more often and presented genetic differentiation patterns (low to high) among species more clearly. Overall, nuclear gene networks provide clear evidence for separate biological species and information on the phylogenetic relationships among closely related carabid beetles.

Alleles↗

PubMed2005

Phylogenetic relationships, divergence time estimation, and global biogeographic patterns of calopterygoid damselflies (odonata, zygoptera) inferred from ribosomal DNA sequences.

The calopterygoid superfamily (Calopterygidae + Hetaerinidae) is composed of more than twenty genera in two families: the Calopterygidae (at least 17) and the Hetaerinidae (at least 4). Here, 62 calopterygoid (ingroup) taxa representing 18 genera and 15 outgroup taxa are subjected to phylogenetic analysis using the ribosomal 18S and 5.8S genes and internal transcribed spacers (ITS1, ITS2). The five other families of calopterid affinity (Polythoridae, Dicteriadidae, Amphipterygidae, Euphaeidae, and Chlorocyphidae) are included in the outgroup. For phylogenetic inference, we applied maximum parsimony, maximum likelihood, and the Bayesian inference methods. A molecular phylogeny combined with a geographic analysis produced a well-supported phylogenetic hypothesis that partly confirms the traditional taxonomy and describes distributional patterns. A monophyletic origin of the calopterygoids emerges, revealing the Hetaerinid clade as sister group to the Calopterygidae sensu strictu. Within Calopterygidae, seven clades of subfamily rank are recognized. Phylogenetic dating was performed with semiparametric rate smoothing by penalized likelihood, using seven reference fossils for calibration. Divergence time based on the ribosomal genes and spacers and fossil constraints indicate that Calopteryginae (10 genera, approximately 50% of all Calopterygid taxa studied here), Vestalinae (1 genus), and Hetaerinidae (1 genus out of 4 studied here) started radiating around 65 Mya (K/T boundary). The South American Iridictyon (without distinctive morphology except for wing venation) and Southeast Asian Noguchiphaea (with distinctive morphology) are older (about 86 My) and may be survivors of old clades with a Gondwanian range that went extinct at the K/T boundary. The same reasoning (and an even older age, ca. 150 My) applies to the amphipterygids Rimanella and Pentaphlebia (South America-Africa). The extant Calopterygidae show particular species and genus richness between west China and Japan, with genera originating between the early Oligocene and Pleistocene. Much of that richness probably extended much wider in preglacial times. The Holarctic Calopteryx, of Miocene age, was deeply affected by the climatic cooling of the Pliocene and by the Pleistocene glaciations. Its North American and Japanese representatives are of Miocene and Pliocene age, respectively, but its impoverished Euro-Siberian taxa are late Pliocene-Pleistocene, showing reinvasion, speciation, and introgression events. The five other calopterid families combine with the Calopterygidae and Hetaerinidae to form the monophyletic cohort Caloptera, with Polythoridae, Dicteriadidae, and Amphipterygidae sister group to Calopterygoidea. The crown node age of the latter three families has an age of about 157 My, but the Dicteriadidae and Polythoridae themselves are of Eocene age, and the same is true for the Euphaeidae and Chlorocyphidae. The cohort Caloptera itself, with about 197 My of age, goes back to the early Jurassic.

Animals↗

PubMed1998

Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets.

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.

Animals↗

PubMed1999

Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae).

Cladistic analyses of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences from 55 samples corresponding to 34 taxa in the genus Armeria reveal that ITS sequence diversity among and within species utterly conflicts with patterns of morphological similarity. Three facts are apparent from the results here reported: (1) different samples of a single subspecies, A. villosa subsp. longiaristata, appear in three of the five major clades; (2) samples of at least one of the six subspecies of A. villosa appear in four of the five major clades; and (3) the composition of major clades shows greater congruence with the geographic origin of plants than with the traditional systematic arrangement based primarily on morphology. Specifically, the clades here termed Ia, II, III, and IV each encompass terminals restricted to geographically delimited areas. There are alternative explanations for the ITS pattern, but the most likely one is that nucleotide positions supporting the major clades are due, in some of the samples, to concerted evolution following horizontal transfer (gene flow) rather than to recency of common ancestry. This interpretation is consistent with previous systematic and experimental evidence and implies that reticulation in Armeria may be extensive. Harlan and de Wet (1963, Evolution 17:497-501) proposed the compilospecies concept to account for situations in which a genetically "aggressive" species captures portions of the genome of other sympatric species by means of extensive introgression. Evidence of extensive reticulation, ecological diversification, and geographic pattern indicates that A. villosa may fit the compilospecies concept, which is here supported on molecular grounds for the first time.

Base Sequence↗

PubMed2000

Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold).

Populations of the jumping spider Habronattus pugillis Griswold isolated on nearby mountain ranges in southern Arizona are differentiated in many features of the males (color, shape, and orientation of setae on face; shape of carapace; markings of palpi and legs; motions during courtship behavior). These features are (mostly) consistent within a range and different between ranges. The concentration of differences in male courtship behavior and body parts exposed to the female during courtship and correlations between form and courtship behavior suggest sexual selection was involved in the differentiation. A phylogenetic analysis of the populations yields a tree that for the most part groups geographic neighbors, but the history of H. pugillis populations may not be adequately described by a tree. Geographic proximity of apparent convergences suggests that populations from at least some of the mountain ranges acquired characteristics through introgression. Lowering of the woodland habitat during the last glacial period probably brought some populations into contact, but it is not clear whether the interrange woodlands would have provided corridors for extensive mixing.

Altitude↗

PubMed1973

Evidence for the linkage of the IGC H locus to a gene controlling the idiotypic specificity of anti-p-azophenylarsonate antibodies in strain A mice.

Anti-p-azophenylarsonate (anti-Ar) antibodies elicited in all strain A/J mice tested share one or more idiotypic specificities. These specificities are also found in the anti-Ar antibodies of mice of the closely related strain, AL/N, but not in those of BALB/c mice. Anti-Ar antibodies were elicited in congenic mice in which the IgC(H) locus of AL/N mice, which controls allotypic markers in the constant regions of heavy chains, had been introgressively backcrossed for nine generations onto a BALB/c background; the mice were then rendered homozygous for the AL/N allotypic determinant. On the average, these antibodies were quantitatively equivalent, with respect to content of the cross-reactive idiotype, to those of AL/N mice. This indicates that the gene controlling the idiotype is closely linked to the IgC(H) locus. Since idiotype must be a function of V region sequences, the results suggest close linkage of V(H) and C(H) genes. The cross-reactive idiotype was found in nearly all F(1) mice (C57/BL x A/J or BALB/c x A/J) tested.

Animals↗

PubMed2004

The T allele of a single-nucleotide polymorphism 13.9 kb upstream of the lactase gene (LCT) (C-13.9kbT) does not predict or cause the lactase-persistence phenotype in Africans.

The ability to digest the milk sugar lactose as an adult (lactase persistence) is a variable genetic trait in human populations. The lactase-persistence phenotype is found at low frequencies in the majority of populations in sub-Saharan Africa that have been tested, but, in some populations, particularly pastoral groups, it is significantly more frequent. Recently, a CT polymorphism located 13.9 kb upstream of exon 1 of the lactase gene (LCT) was shown in a Finnish population to be closely associated with the lactase-persistence phenotype (Enattah et al. 2002). We typed this polymorphism in 1,671 individuals from 20 distinct cultural groups in seven African countries. It was possible to match seven of the groups tested with groups from the literature for whom phenotypic information is available. In five of these groups, the published frequencies of lactase persistence are >/=25%. We found the T allele to be so rare that it cannot explain the frequency of the lactase-persistence phenotype throughout Africa. By use of a statistical procedure to take phenotyping and sampling errors into account, the T-allele frequency was shown to be significantly different from that predicted in five of the African groups. Only the Fulbe and Hausa from Cameroon possessed the T allele at a level consistent with phenotypic observations (as well as an Irish sample used for comparison). We conclude that the C-13.9kbT polymorphism is not a predictor of lactase persistence in sub-Saharan Africans. We also present Y-chromosome data that are consistent with previously reported evidence for a back-migration event into Cameroon, and we comment on the implications for the introgression of the -13.9kb*T allele.

Alleles↗