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PubMed2002

QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice ( Oryza sativa) using microsatellite markers.

Rice ( Oryza sativa) cultivar development currently faces the task of overcoming yield plateaus, which is difficult due to the narrow genetic base of breeding programs. Oryza glumaepatula is a diploid wild relative of cultivated rice, native to Central and South America, and is therefore a potential source of alleles of agronomic importance to rice breeding programs. We studied 11 agronomic traits in BC(2)F(2) families of the interspecific cross Oryza sativa x O. glumaepatula. Transgressive lines which are almost isogenic to the elite recurrent O. sativa parent were identified for most of these traits. Quantitative trait locus (QTL) analysis was performed by single-point and interval mapping using a molecular map based on 157 microsatellite and STS markers. Marker regions accounting for 14.5 to 72.9% of a phenotypic variation trait were identified in 9 of the 12 rice chromosomes. Positive QTL effects from O. glumaepatula were observed in chromosomal regions associated with tillering and panicle-number traits.

Journal Article↗

PubMed2002

Development of isothiocyanate-enriched broccoli, and its enhanced ability to induce phase 2 detoxification enzymes in mammalian cells.

Broccoli florets contain low levels of 3-methylsuphinylpropyl and 4-methylsulphinylbutyl glucosinolates. Following tissue disruption, these glucosinolates are hydrolysed to the corresponding isothiocyanates (ITCs), which have been associated with anticarcinogenic activity through a number of physiological mechanisms including the induction of phase II detoxification enzymes and apoptosis. In this paper, we describe the development of ITC-enriched broccoli through the introgression of three small segments of the genome of Brassica villosa, a wild relative of broccoli, each containing a quantitative trait locus (QTL), into a broccoli genetic background, via marker-assisted selection and analysis of glucosinolates in the florets of backcross populations. Epistatic and heterotic effects of these QTLs are described. The ITC-enriched broccoli had 80-times the ability to induce quinone reductase (a standard assay of phase II induction potential) when compared to standard commercial broccoli, due both to an increase in the precursor glucosinolates and a greater conversion of these into ITCs.

Anticarcinogenic Agents↗

PubMed2006

Evidence of natural hybridization and introgression between Vasconcellea species (Caricaceae) from southern Ecuador revealed by chloroplast, mitochondrial and nuclear DNA markers.

BACKGROUND AND AIMS: Vasconcellea x heilbornii is believed to be of natural hybrid origin between V. cundinamarcensis and V. stipulata, and is often difficult to discriminate from V. stipulata on morphological grounds. The aim of this paper is to examine individuals of these three taxa and of individuals from the closely related species V. parviflora and V. weberbaueri, which all inhabit a hybrid zone in southern Ecuador. METHODS: Molecular data from mitochondrial, chloroplast and nuclear DNA from 61 individuals were analysed. KEY RESULTS: Molecular analysis confirmed occasional contemporary hybridization between V. stipulata, V. cundinamarcensis and V. x heilbornii and suggested the possible involvement of V. weberbaueri in the origin of V. x heilbornii. In addition, the molecular data indicated unidirectional introgression of the V. cundinamarcensis nuclear genome into that of V. stipulata. Several of the individuals examined with morphology similar to that of V. stipulata had genetic traces of hybridization with V. cundinamarcensis, which only seems to act as pollen donor in interspecific hybridization events. Molecular analyses also strongly suggested that most of the V. x heilbornii individuals are not F(1) hybrids but instead are progeny of repeated backcrosses with V. stipulata. CONCLUSIONS: The results of the present study point to the need for re-evaluation of natural populations of V. stipulata and V. x heilbornii. In general, this analysis demonstrates the complex patterns of genetic and morphological diversity found in natural plant hybrid zones.

Caricaceae↗

PubMed2000

Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny.

A backcrossed population (BC(4)F(2)) derived from a cross between a japonica rice variety, Nipponbare, as the recurrent parent and an indica rice variety, Kasalath, as the donor parent showed a long-range variation in days to heading. Quantitative trait loci (QTL) analysis revealed that two QTL, one on chromosome 3, designated Hd6, and another on chromosome 2, designated Hd7, were involved in this variation; and Hd6 was precisely mapped as a single Mendelian factor by using progeny testing (BC(4)F(3)). The nearly isogenic line with QTL (QTL-NIL) that carries the chromosomal segment from Kasalath for the Hd6 region in Nipponbare's genetic background was developed by marker-assisted selection. In a day-length treatment test, the QTL-NIL for Hd6 prominently increased days to heading under a 13.5-hr day length compared with the recurrent parent, Nipponbare, suggesting that Hd6 controls photoperiod sensitivity. QTL analysis of the F(2) population derived from a cross between the QTL-NILs revealed existence of an epistatic interaction between Hd2, which is one of the photoperiod sensitivity genes detected in a previous analysis, and Hd6. The day-length treatment tests of these QTL-NILs, including the line introgressing both Hd2 and Hd6, also indicated an epistatic interaction for photoperiod sensitivity between them.

Chromosome Mapping↗

PubMed2006

Hybridization in coral reef fishes: introgression and bi-directional gene exchange in Thalassoma (family Labridae).

Hybrids in coral reef fishes have traditionally been described based on external features using meristic characters and colouration to identify putative parental contributors. This study utilised molecular genetic techniques to verify hybrid status and identify putative parental species for five hybrid specimens (Labridae: Thalassoma) collected from Holmes Reef in the Coral Sea. Phylogenetic analyses support hybrid origins of the specimens. Mitochondrial COI gene, nuclear S7 (intron 1) and nuclear copy of mitochondrial (NUMT) D-loop region corroborate the identity of T. quinquevittatum as the maternal and T. jansenii as the paternal contributor. Backcrossing to parental species by hybrids and bi-directional gene exchange between the Holmes Reef populations of T. jansenii and T. quinquevittatum was detected, suggesting that hybrids are fertile and able to reproduce successfully. F(1) hybrids display a mixture of the colouration attributes of the two parental species, but subsequent backcrossed individuals were unrecognisable as hybrids and displayed colouration of either parental species. A large numerical imbalance exists between the putative parental species at Holmes Reef, with T. quinquevittatum outnumbering T. jansenii by approximately 25:1. In this case study, hybridization appears to be driven by ecological rather than evolutionary factors.

Animals↗

PubMed2004

Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass.

Recent molecular phylogenetic studies of polyploid plants have successfully clarified complex patterns of reticulate evolution. In this study of Elymus repens, an allohexaploid member of the wheat tribe Triticeae, chloroplast and nuclear DNA data reveal an extreme reticulate pattern, revealing at least five distinct gene lineages coexisting within the species, acquired through a possible combination of allohexaploidy and introgression from both within and beyond the Triticeae. Earlier cytogenetic studies of E. repens suggested that Hordeum (genome H) and Pseudoroegneria (St) were genome donors to E. repens. Chloroplast DNA data presented here (from the rpoA gene and from the region between trnT and trnF) identify three potential maternal genome donors (Pseudoroegneria, Thinopyrum, and Dasypyrum), and information from previous molecular work suggests that, of these, Pseudoroegneria is the most likely maternal donor. Nuclear starch synthase gene data indicate that both Hordeum and Pseudoroegneria have contributed to the nuclear genome of E. repens, in agreement with cytogenetic data. However, these data also show unexpected contributions from Taeniatherum, and from two additional donors of unknown identity. One of the sequences of unknown origin falls within the Triticeae, but is not closely associated with any of the sampled diploid genera. The second falls outside of the clade containing Triticeae and its outgroup Bromus, suggesting the acquisition of genetic material from a surprisingly divergent source. Bias toward the amplification of certain starch synthase variants has complicated attempts to thoroughly sample from within individuals, but the data clearly indicate a complex pattern of reticulate evolution, consistent not only with allohexaploidy, but also with introgression from unexpectedly divergent sources.

Base Sequence↗

PubMed2005

Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation.

The current study is the first installment of an effort to explore the secondary gene pool for the enhancement of Upland cotton (Gossypium hirsutum L.) germplasm. We developed advanced-generation backcross populations by first crossing G. hirsutum cv. Tamcot 2111 and G. barbadense cv. Pima S6, then independently backcrossing F(1) plants to the G. hirsutum parent for three cycles. Genome-wide mapping revealed introgressed alleles at an average of 7.3% of loci in each BC(3)F(1) plant, collectively representing G. barbadense introgression over about 70% of the genome. Twenty-four BC(3)F(1) plants were selfed to generate 24 BC(3)F(2) families of 22-172 plants per family (totaling 2,976 plants), which were field-tested for fiber elongation and genetically mapped. One-way analysis of variance detected 22 non-overlapping quantitative trail loci (QTLs) distributed over 15 different chromosomes. The percentage of variance explained by individual loci ranged from 8% to 28%. Although the G. barbadense parent has lower fiber elongation than the G. hirsutum parent, the G. barbadense allele contributed to increased fiber elongation at 64% of the QTLs. Two-way analysis of variance detected significant (P<0.001) among-family genotype effects and genotypexfamily interactions in two and eight regions, respectively, suggesting that the phenotypic effects of some introgressed chromosomal segments are dependent upon the presence/absence of other chromosomal segments.

Analysis of Variance↗

PubMed2006

Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm.

Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.

Alleles↗

PubMed2000

Kalilo plasmids are a family of four distinct members with individual global distributions across species.

Kalilo is a linear 9-kb plasmid, isolated originally from Hawaiian strains of the heterothallic fungus Neurospora intermedia. Its properties include terminal inverted repeats, two ORFs coding for a presumptive DNA and an RNA polymerase, and the ability to cause senescence in its original host and in the closely related species Neurospora crassa. We have examined natural isolates alleged to contain plasmids homologous to kalilo. Most of these isolates do in fact contain plasmids with so close an identity to kalilo as to be certain relatives. We found a new case of kalilo in Neurospora tetrasperma from Moorea-Tahiti, and a new case of LA-kalilo (previously found only in N. tetrasperma) in N. crassa from Haiti. A previously unreported, substantially shorter, kalilo variant has been found in three geographically separate isolates of the heterothallic species Neurospora discreta. Therefore, if the previously reported kalilo variant from the genus Gelasinospora is included, in all there are four members of the kalilo plasmid family. The main differences between these plasmids are in the terminal inverted repeats (TIRs). The phylogeny of the TIR sequences is largely congruent with that of nuclear DNA in the species in which they are found, suggesting that the plasmids are related by vertical descent throughout the evolution of these species. However, there are two cases of a plasmid found in a heterothallic and a pseudohomothallic species in the same global area; these cases might have arisen from more recent horizontal transmission or introgression.

Base Sequence↗

PubMed1991

Differential susceptibility to a trematode parasite among genotypes of the Mytilus edulis/galloprovincialis complex.

We show that parasitism by the trematode Prosorhynchus squamatus in parental and introgressed Mytilus edulis/galloprovincialis (Bivalvia) mussels occurs in individuals with a predominantly M. edulis genome. This result suggests that the restricted specificity of P. squamatus is dependent on genetic factor(s) present in M. edulis. Because of its strong pathogenic effects (i.e. total castration and possible death), this parasite may be a source of intense selection against M. edulis genomes when they are present in a site. As a consequence, it may favour the geographic extension of the M. galloprovincialis genome. Previous studies have indicated that, in hybrid zones, recombinant genotypes are more susceptible to parasitic infections than either parental genotype. We demonstrate that this is not the case for the M. edulis/M. galloprovincialis system, and that the parental genotype alone determines susceptibility.

Alleles↗

PubMed1997

Endosperm balance number manipulation for direct in vivo germplasm introgression to potato from a sexually isolated relative (Solanum commersonii Dun.).

Diploid (2n = 2x = 24) Solanum species with endosperm balance number (EBN) = 1 are sexually isolated from diploid 2EBN species and both tetraploid (2n = 4x = 48, 4EBN) and haploid (2n = 2x = 24, 2EBN) S. tuberosum Group Tuberosum. To sexually overcome these crossing barriers in the diploid species S. commersonii (1EBN), the manipulation of the EBN was accomplished by scaling up and down ploidy levels. Triploid F1 hybrids between an in vitro-doubled clone of S. commersonii (2n = 4x = 48, 2EBN) and diploid 2EBN clones were successfully used in 3x x 4x crosses with S. tuberosum Group Tuberosum, resulting in pentaploid/near pentaploid BC1 progenies. This provided evidence of 2n (3x) egg formation in the triploid female parents. Two selected BC1 pentaploid hybrids were successfully backcrossed both as male and as female parents with S. tuberosum Group Tuberosum. The somatic chromosome number varied greatly among the resulting BC2 progenies, which included hyperaneuploids, but also a number (4.8%) of 48-chromosome plants. The introgression of S. commersonii genomes was confirmed by the presence of S. commersonii-specific randomly amplified polymorphic DNA markers in the BC2 population analyzed. The results clearly demonstrate the feasibility of germplasm introgression from sexually isolated diploid 1EBN species into the 4x (4EBN) gene pool of the cultivated potato using sexual hybridization. Based on the amount and type of genetic variation generated, cumbersomeness, general applicability, costs, and other factors, it would be interesting to compare the approach reported here with other in vitro or in vivo, direct or indirect, approaches previously reported.

Journal Article↗

PubMed2004

Consomic rat model systems for physiological genomics.

A consomic rat strain is one in which an entire chromosome is introgressed into the isogenic background of another inbred strain using marker-assisted selection. The development and physiological screening of two inbred consomic rat panels on two genetic backgrounds (44 strains) is well underway. Consomic strains enable one to assign traits and quantitative trait loci (QTL) to chromosomes by surveying the panel of strains with substituted chromosomes. They enable the rapid development of congenic strains over a narrow region and enable one to perform F2 linkage studies to positionally locate QTL on a single chromosome with a fixed genetic background. These rodent model systems overcome many of the problems encountered with segregating crosses where even if linkage is found, each individual in the cross is genetically unique and the combination of genes cannot be reproduced or studied in detail. For physiologists, consomics enable studies to be performed in a replicative or longitudinal manner to elucidate in greater detail the sequential expression of genes responsible for the observed phenotypes of these animals. They often provide the best available inbred control strains for physiological comparisons with the parental strains and they enable one to assess the impact of a causal gene region in a genome by allowing comparisons of the effect of replacement of a specific chromosome on a disease susceptible or a resistant genomic background. Consomic rat strains are proving to be a unique scientific resource that can greatly extend our understanding of genes and their role in the regulation of complex function and disease.

Animals↗

PubMed2004

Differentiation in a geographical mosaic of plants coevolving with ants: phylogeny of the Leonardoxa africana complex (Fabaceae: Caesalpinioideae) using amplified fragment length polymorphism markers.

Comprising four allopatric subspecies that exhibit various grades of ant-plant interactions, from diffuse to obligate and symbiotic associations, the Leonardoxa africana complex (Fabaceae, Caesalpinioideae) provides a good opportunity to investigate the evolutionary history of ant-plant mutualisms. A previous study of the L. africana complex based on chloroplast DNA noncoding sequences revealed a lack of congruence between clades suggested by morphological and plastid characters. In this study, we analysed phylogenetic relationships within the L. africana complex using a Bayesian probability approach on amplified fragment length polymorphism markers. The results reported permit partial validation of the four subspecies of L. africana previously defined by morphological and ecological markers. Incongruences between phylogenies based on chloroplast DNA and amplified fragment length polymorphism markers are discussed in the light of morphological and ecological data, and confronted with hypotheses of convergence, lineage sorting and introgression.

Analysis of Variance↗

PubMed2004

Application of chromosomal substitution techniques in gene-function discovery.

A consomic rat strain is one in which an entire chromosome is introgressed into the isogenic background of another inbred strain using marker assisted selection. The development and initial physiologic screening of two inbred consomic rat panels on two genetic backgrounds (44 strains) is well underway. The primary uses of consomic strains are: (1) to assign traits and quantitative trait loci (QTL) to chromosomes by surveying the panel of strains with substituted chromosomes; (2) to rapidly develop congenic strains over a narrow region using several approaches described in this review and perform F2 linkage studies to positionally locate QTL in a fixed genetic background. In addition, consomic strains overcome many of the problems encountered with segregating crosses where, even if linkage is found, each individual in the cross is genetically unique and the combination of genes cannot be reproduced or studied in detail. Consomic strains provide greater statistical power to detect linkage than traditional F2 crosses because of their fixed genetic backgrounds, and can produce sufficient numbers of genetically identical rats to validate the relationship between a trait and a particular chromosome. These strains allow studies to be performed in a replicative or longitudinal manner to elucidate in greater detail the sequential changes responsible for the observed phenotypes of these animals, and they enable one to assess the impact of a causal gene region in a genome by allowing comparisons of the effect of replacement of a specific chromosome upon a disease susceptible or resistant genomic background. Consomics can be used to quickly develop multiple chromosome substitution models to investigate gene-gene interactions of complex traits or diseases. Finally, they often provide the best available inbred control strain for particular physiological comparisons with the inbred parental strains. Consomic rat strains are proving to be a unique scientific resource that greatly extends our understanding of genes and complex normal and pathological function.

Animals↗

PubMed2004

Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula.

A long-standing issue in marine biology is identifying spatial scales at which populations of sessile adults are connected by planktonic offspring. We examined the genetic continuity of the acorn barnacle Balanus glandula, an abundant member of rocky intertidal communities of the northeastern Pacific Ocean, and compared these genetic patterns to the nearshore oceanography described by trajectories of surface drifters. Consistent with its broad dispersal potential, barnacle populations are genetically similar at both mitochondrial (cytochrome oxidase I) and nuclear (elongation factor 1-alpha) loci across broad swaths of the species' range. In central California, however, there is a striking genetic cline across 475 km of coastline between northern and southern populations. These patterns indicate that gene flow within central California is far more restricted spatially than among other populations. Possible reasons for the steep cline include the slow secondary introgression of historically separated populations, a balance between diversifying selection and dispersal, or some mix of both. Geographic trajectories of oceanic drifters closely parallel geographical patterns of gene flow. Drifters placed to the north (Oregon; approximately 44 degrees N) and south (Santa Barbara, California; approximately 34 degrees N) of the cline disperse hundreds of kilometers within 40 days, yet over the long-term their trajectories never overlapped. The lack of communication between waters originating in Oregon and southern California probably helps to maintain strong genetic differentiation between these regions. More broadly, the geographical variation in gene flow implies that focusing on species-level averages of gene flow can mask biologically important variance within species which reflects local environmental conditions and historical events.

Animals↗

PubMed1997

Multiregional introgressions inferred from the mitochondrial DNA phylogeny of a hybridizing species complex of gobiid fishes, genus Tridentiger.

Partial sequences of the cytochrome b gene (402 bp) in mtDNA were determined for brackishwater gobiid fishes, genus Tridentiger, collected from geographically distant locations in the Japanese Archipelago, and their interspecific and geographic variations were analyzed and compared. Contrary to the results of a previous allozyme analysis which revealed the existence of considerable genetic divergence (Nei's genetic distance > 0.5) between T. obscurus and T. brevispinis, the mtDNA haplotypes (mitotypes) of these two species were very similar and could not be distinguished by any of the neighbor-joining, maximum-likelihood or parsimony analyses. Hybrid individuals between the two species were also found, with several mitotypes being shared by both species and their hybrids. The phylogenetic relationships of mitotypes were divided into three subgroups, the geographical distributions of the latter being allied to geographical features of the Archipelago. These results suggested the occurrence of multiregional introgression between the two species, with mitotypes transferring from one species to the other.

Animals↗

PubMed2001

Improving plant breeding with exotic genetic libraries.

Naturally occurring variation among wild relatives of cultivated crops is an under-exploited resource in plant breeding. Here, I argue that exotic libraries, which consist of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide plant breeders with an important opportunity to improve the agricultural performance of modern crop varieties. These libraries can also act as reagents for the discovery and characterization of genes that underlie traits of agricultural value.

Breeding↗

PubMed2001

Mapping of avirulence genes in Phytophthora infestans with amplified fragment length polymorphism markers selected by bulked segregant analysis.

In this study we investigated the genetic control of avirulence in the diploid oomycete pathogen Phytophthora infestans, the causal agent of late blight on potato. The dominant avirulence (Avr) genes matched six race-specific resistance genes introgressed in potato from a wild Solanum species. AFLP markers linked to Avr genes were selected by bulked segregant analysis and used to construct two high-density linkage maps, one containing Avr4 (located on linkage group A2-a) and the other containing a cluster of three tightly linked genes, Avr3, Avr10, and Avr11 (located on linkage group VIII). Bulked segregant analysis also resulted in a marker linked to Avr1 and this allowed positioning of Avr1 on linkage group IV. No bulked segregant analysis was performed for Avr2, but linkage to a set of random markers placed Avr2 on linkage group VI. Of the six Avr genes, five were located on the most distal part of the linkage group, possibly close to the telomere. The high-density mapping was initiated to facilitate future positional cloning of P. infestans Avr genes.

Chromosome Mapping↗