Showing papers in "Journal of Heredity in 2005"
TL;DR: A new software package entitled ‘‘Alleles In Space’’ (AIS) is developed, which has the ability to perform joint analyses of interindividual spatial and genetic information that can be applied at virtually any spatial scale.
Abstract: Genetic analyses of natural populations have historically relied on statistical procedures based on the concept that distinct ‘‘populations’’ of a species exist across a landscape. Invariably, commonly used analyses reduce to approaches that treat collections of individuals (‘‘populations’’) as independent/causative variables and allele frequencies as dependent/ response variables. Examples of these procedures include Wright’s FST and its variants (Excoffier et al. 1992; Nei 1973; Slatkin 1995; Weir and Cockerham 1984), contingency table procedures (Raymond and Rousset 1995; Roff and Bentzen 1989), and measures of genetic distances among populations (e.g., Nei 1972, 1978; Reynolds et al. 1983). These analyses qualitatively or explicitly test null hypotheses of homogeneity of allele frequencies between or among populations. Although almost universally applied, the analyses mentioned above are not necessarily appropriate in many situations. For example, highly mobile organisms such as large mammals or birds can occupy continuous habitats over large spatial scales. Plants may also occupy large continuous habitats, as can species inhabiting marine or aquatic systems. In these cases, objectively designating groups of individuals at population levels for use in genetic analyses may prove difficult, if not impossible. Clearly, an important consideration in these situations is the spatial extent of the ‘‘populations’’ that are chosen for analyses. If groups of organisms are defined over larger than appropriate spatial scales, resulting measures of genetic differentiation may actually provide ambiguous or misleading results (Miller et al. 2002). To address many of these issues, I have developed a new software package entitled ‘‘Alleles In Space’’ (AIS). This program, rather than implementing methodology that relies on arbitrary groupings of individuals, instead has the ability to perform joint analyses of interindividual spatial and genetic information that can be applied at virtually any spatial scale. These approaches specifically lend themselves to analyses of genetic data when one or a few individuals are sampled from large numbers of collection sites. Moreover, the program is designed to handle a wide variety of genetic data types, including codominant marker systems, dominant marker systems, and DNA sequences. Thus AIS will likely be useful for elucidation of patterns in diverse study types ranging from local analyses of genetic structure, phylogeographical studies, and studies encompassing aspects of the emerging field of landscape genetics (Manel et al. 2003).
561 citations
TL;DR: Overall, theory and empirical evidence gathered to date suggest that ecological selection is a major factor promoting homoploid hybrid speciation, with the strongest evidence coming from genetic studies.
Abstract: Our understanding of homoploid hybrid speciation has advanced substantially since this mechanism of species formation was codified 50 years ago. Early theory and research focused almost exclusively on the importance of chromosomal rearrangements, but it later became evident that natural selection, specifically ecological selection, might play a major role as well. In light of this recent shift, we present an evaluation of ecology's role in homoploid hybrid speciation, with an emphasis on the genetics underlying ecological components of the speciation process. We briefly review new theoretical developments related to the ecology of homoploid hybrid speciation; propose a set of explicit, testable questions that must be answered to verify the role of ecological selection in homoploid hybrid speciation; discuss published work with reference to these questions; and also report new data supporting the importance of ecological selection in the origin of the homoploid hybrid sunflower species Helianthus deserticola. Overall, theory and empirical evidence gathered to date suggest that ecological selection is a major factor promoting homoploid hybrid speciation, with the strongest evidence coming from genetic studies.
353 citations
TL;DR: The demonstration that targeted expression of one and the same master control gene, that is, Pax6 can induce the formation of ectopic eyes in both insects and vertebrates necessitates a reconsideration of the dogma of a polyphyletic origin of the various eye types in all the animal phyla.
Abstract: Recent experiments on the genetic control of eye development have opened up a completely new perspective on eye evolution. The demonstration that targeted expression of one and the same master control gene, that is, Pax6 can induce the formation of ectopic eyes in both insects and vertebrates, necessitates a reconsideration of the dogma of a polyphyletic origin of the various eye types in all the animal phyla. The involvement of Pax6 and six1 and six3 genes, which encode highly conserved transcription factors, in the genetic control of eye development in organisms ranging from planarians to humans argues strongly for a monophyletic origin of the eye. Because transcription factors can control the expression of any target gene provided it contains the appropriate gene regulatory elements, the conservation of the genetic control of eye development by Pax6 among all bilaterian animals is not due to functional constraints but a consequence of its evolutionary history. The prototypic eyes postulated by Darwin to consist of two cells only, a photoreceptor and a pigment cell, were accidentally controlled by Pax6 and the subsequent evolution of the various eye types occurred by building onto this original genetic program. A hypothesis of intercalary evolution is proposed that assumes that the eye morphogenetic pathway is progressively modified by intercalation of genes between the master control genes on the top of the hierarchy and the structural genes like rhodopsin at the bottom. The recruitment of novel genes into the eye morphogenetic pathway can be due to at least two different genetic mechanisms, gene duplication and enhancer fusion.In tracing back the evolution of eyes beyond bilaterians, we find highly developed eyes in some box-jellyfish as well as in some Hydrozoans. In Hydrozoans the same orthologous six genes (six1 and six3) are required for eye regeneration as in planarians, and in the box jellyfish Tripedalia a pax B gene, which may be a precursor of Pax6, was found to be expressed in the eyes. In contrast to the adults, which have highly evolved eyes, the Planula larva of Tripedalia has single- celled photoreceptors similar to some unicellular protists. For the origin of photoreceptor cells in metazoa, I propose two hypotheses, one based on cellular differentiation and a more speculative one based on symbiosis. The former assumes that photoreceptor cells originated from a colonial protist in which all the cells were photosensitive and subsequent cellular differentiation to give rise to photoreceptor cells. The symbiont hypothesis, which I call the Russian doll model, assumes that photosensitivity arose first in photosynthetic cyanobacteria that were subsequently taken up into red algae as primary chloroplasts. The red algae in turn were taken up by dinoflagellates as secondary chloroplasts and in some species evolved into the most sophisticated eye organelles, as found, for example, in some dinoflagellates like Erythropsis and Warnovia, which lack chloroplasts. Because dinoflagellates are commonly found as symbionts in cnidarians, the dinoflagellates may have transferred their photoreceptor genes to cnidarians. In cnidarians such as Tripedalia the step from photoreceptor organelles to multicellular eyes has occurred. These two hypotheses, the cellular differentiation and the symbiont hypothesis, are not mutually exclusive and are the subject of further investigations.
208 citations
TL;DR: It is concluded that eye degeneration in cavefish may be caused by adaptive evolution and pleiotropy, and a key discovery is that Hedgehog midline signaling is expanded and inhibits eye formation by inducing lens apoptosis in Cavefish embryos.
Abstract: The evolutionary mechanisms responsible for eye degeneration in cave-adapted animals have not been resolved. Opposing hypotheses invoking neural mutation or natural selection, each with certain genetic and developmental expectations, have been advanced to explain eye regression, although little or no experimental evidence has been presented to support or reject either theory. Here we review recent developmental and molecular studies in the teleost Astyanax mexicanus, a single species consisting of a sighted surface-dwelling form (surface fish) and many blind cave-dwelling forms (cavefish), which shed new light on this problem. The manner of eye development and degeneration, the ability to experimentally restore eyes, gene expression patterns, and comparisons between different cavefish populations all provide important clues for understanding the evolutionary forces responsible for eye degeneration. A key discovery is that Hedgehog midline signaling is expanded and inhibits eye formation by inducing lens apoptosis in cavefish embryos. Accordingly, eyes could have been lost by default as a consequence of natural selection for constructive traits, such as feeding structures, which are positively regulated by Hh signaling. We conclude from these studies that eye degeneration in cavefish may be caused by adaptive evolution and pleiotropy.
207 citations
TL;DR: Although written primarily as a program for research purposes, the new version of MolKin (version 2.0) improves the user’s environment and offers a number of features that may be of interest to teachers and students for developing an indepth understanding of concepts related to population genetic analysis.
Abstract: Recently different studies have formalized the way in which it is possible to obtain coancestry coefficients from molecular information (Caballero and Toro 2002; Eding and Meuwissen 2001) by applying Malecot’s (1948) definition of kinship to marker genes, though referring it to identity-by-state instead of identity-by-descent (Caballero and Toro 2002). The molecular coancestry between two individuals, i and j, is the probability that two randomly sampled alleles from the same locus in two individuals are identical by state. Because of its straightforward relationship with genealogical coancestry, this parameter has been shown to have interesting properties that may be used for conservation purposes (Eding et al. 2002; Toro et al., 2002; 2003). Moreover, molecular coancestry can be used to assess genetic diversity within and between populations (Eding and Meuwissen 2001). Using simulated data, Eding and Meuwissen (2001) showed that molecular coancestry has some interesting properties, namely that average kinship between populations becomes constant very quickly after population fission, causing between-population diversity to remain constant. This property allows researchers using molecular coancestry information to study the genetic relationships between populations (Alvarez et al. 2005; Caballero and Toro 2002; Fabuel et al. 2004). Despite the utility of molecular coancestry for conservation worth and evolutionary studies, no computer routines are available to facilitate the use of molecular coancestry information. MolKin (version 2.0) is a population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation. A previous version of MolKin (version 1.0) was available on request for research purposes (Alvarez et al. 2005). Following Bennewitz and Meuwissen (2005), who have recently suggested that bootstrapping could significantly improve kinship estimates, the main change included in the present version of MolKin (version 2.0) is the inclusion of a bootstrapping procedure to compute, when needed, molecular coancestry coefficients and most genetic distances calculated by MolKin with the corresponding standard errors. Following Felsenstein (1985), the bootstrapping procedure implemented in MolKin (version 2.0) involves creating new datasets by randomly sampling individuals with replacement, so that the resulting datasets have the same size as the original, but some genotypes have been left out and others are duplicated. The random variation of the results from analyzing these bootstrapped datasets can be shown statistically to be typical of the variation that you would get from collecting new datasets. Although written primarily as a program for research purposes, the new version of MolKin (version 2.0) improves the user’s environment and offers a number of features that may be of interest to teachers and students for developing an indepth understanding of concepts related to population genetic analysis.
191 citations
TL;DR: Results strongly indicate that conclusions from studies on clonal organisms derived using markers showing low polymorphism, including microsatellites, should be reassessed using appropriate polymorphic markers.
Abstract: The increasing use of molecular tools to study populations of clonal organisms leads us to question whether the low polymorphism found in many studies reflects limited genetic diversity in populations or the limitations of the markers used. Here we used microsatellite datasets for two sea grass species to provide a combinatory statistic, combined with a likelihood approach to estimate the probability of identical multilocus genotypes (MLGs) to be shared by distinct individuals, in order to ascertain the efficiency of the markers used and to optimize cost-efficiently the choice of markers to use for deriving unbiased estimates of genetic diversity. These results strongly indicate that conclusions from studies on clonal organisms derived using markers showing low polymorphism, including microsatellites, should be reassessed using appropriate polymorphic markers.
180 citations
TL;DR: Although the primary role of the DEF/GLO subfamily appears to be in specifying the stamens and inner perianth, several examples of potential sub- and neofunctionalization are observed.
Abstract: DEFICIENS (DEF) and GLOBOSA (GLO) function in petal and stamen organ identity in Antirrhinum and are orthologs of APETALA3 and PISTILLATA in Arabidopsis. These genes are known as B-function genes for their role in the ABC genetic model of floral organ identity. Phylogenetic analyses show that DEF and GLO are closely related paralogs, having originated from a gene duplication event after the separation of the lineages leading to the extant gymnosperms and the extant angiosperms. Several additional gene duplications followed, providing multiple potential opportunities for functional divergence. In most angiosperms studied to date, genes in the DEF/GLO MADS-box subfamily are expressed in the petals and stamens during flower development. However, in some angiosperms, the expression of DEF and GLO orthologs are occasionally observed in the first and fourth whorls of flowers or in nonfloral organs, where their function is unknown. In this article we review what is known about function, phylogeny, and expression in the DEF/GLO subfamily to examine their evolution in the angiosperms. Our analyses demonstrate that although the primary role of the DEF/GLO subfamily appears to be in specifying the stamens and inner perianth, several examples of potential sub- and neofunctionalization are observed.
158 citations
TL;DR: Chromosome identities were assigned to 15 linkage groups of the RFLP joinmap developed from four intraspecific cotton (Gossypium hirsutum L.) populations with different genetic backgrounds (Acala, Delta, and Texas Plains) as mentioned in this paper.
Abstract: Chromosome identities were assigned to 15 linkage groups of the RFLP joinmap developed from four intraspecific cotton (Gossypium hirsutum L.) populations with different genetic backgrounds (Acala, Delta, and Texas Plains). The linkage groups were assigned to chromosomes by deficiency analysis of probes in the previously published joinmap, based on genomic DNA from hypoaneuploid chromosome substitution lines. These findings were integrated with QTL identification for multiple fiber and yield traits. Overall results revealed the presence of 63 QTLs on five different chromosomes of the A subgenome (chromosomes-03, � 07, � 09, � 10, and � 12) and 29 QTLs on the three different D subgenome (chromosomes-14 Lo, � 20, and the long arm of � 26). Linkage group-1 (chromosome-03) harbored 26 QTLs, covering 117 cM with 54 RFLP loci. Linkage group-2, (the long arm of chromosome-26) harbored 19 QTLs, covering 77.6 cM with 27 RFLP loci. Approximately 49% of the putative 92 QTLs for agronomic and fiber quality traits were placed on the above two major joinmap linkage groups, which correspond to just two different chromosomes, indicating that cotton chromosomes may have islands of high and low meiotic recombination like some other eukaryotic organisms. In addition, it reveals highly recombined and putative gene abundant regions in the cotton genome. QTLs for fiber quality traits in certain regions are located between two RFLP markers with an average of less than one cM (0.4;0.6 Mb) and possibly represent targets for map-based cloning. Identification of chromosomal location of RFLP markers common to different intra- and interspecificpopulations will facilitate development of portable framework markers, as well as genetic and physical mapping of the cotton genome.
133 citations
TL;DR: Molecular evidence is presented by an analysis of nuclear ribosomal DNA data that dogroses are complex allopolyploids resulting from multiple hybridization events and that the pentaploid Caninae genome originated from different members of nondogroses and the now extinct Protocaninae.
Abstract: The European dogroses (Rosa sect. Caninae (DC.) Ser.) are characterized by a unique meiosis system ("canina-meiosis"), which controls the heterogamous development of tetraploid egg cells and haploid pollen grains resulting in a pentaploid somatic status. This permanent anorthoploidy is supposed to have originated by a hybridization event in the postglacial period. In this study we present molecular evidence by an analysis of nuclear ribosomal DNA data that dogroses are complex allopolyploids resulting from multiple hybridization events. As previously described, the nrITS-1 region does not undergo concerted evolution in dogroses. Thus, different ITS-1 sequences persist within single individuals. Secondary structure predictions do not point to the existence of pseudogenes within these ITS-1 types. Our data suggest that the pentaploid Caninae genome originated from different members of nondogroses and the now extinct Protocaninae.
112 citations
TL;DR: The distribution of haplotypes indicates sheep appear to have the weakest population structure and the highest rate of intercontinental dispersal of any domestic animal reported to date.
Abstract: Sequence variation present within the mitochondrial genome was used to investigate genetic diversity within sheep breeds from Asia and Europe. Comparison of 2027 bp of sequence from 121 animals revealed 44 phylogenetically informative nucleotide positions and a single insertion/deletion. A total of 57 haplotypes were observed which formed two distinct clades. Type A haplotypes were found in breeds from Asia (India, Indonesia, Mongolia, and Tibet), while type B haplotypes were observed at the highest frequency in breeds sourced from Europe (nine breeds from Austria, Aland, Finland, Spain, and northwestern Russia). The distribution of haplotypes indicates sheep appear to have the weakest population structure and the highest rate of intercontinental dispersal of any domestic animal reported to date. Only 2.7% of the sequence variation observed was partitioned between continents, which is lower than both goat (approximately 10%) and cattle (approximately 50%). Diagnostic restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) tests which distinguish type A and B haplotypes were used to test an additional 223 animals from 17 breeds of European and Asian origin. A mixture of the two lineages was found in every breed except Suffolk and the Indian Garole, indicating introgression has played a major part during breed development and subsequent selection.
111 citations
TL;DR: The transfer of "reduced height genes" (Rht genes) from Japanese wheat varieties to wheat varieties in Europe and their influence on the increase of the total wheat production in the last century are described.
Abstract: Wheat is the main crop and often a strategic crop in many European countries. From a historical perspective, we describe the transfer of "reduced height genes" (Rht genes) from Japanese wheat varieties to wheat varieties in Europe and their influence on the increase of the total wheat production in the last century. Historic pathways of Rht genes were influenced directly or indirectly by wheat breeders exchanging seed samples and by some governments importing large quantities of wheat during historically critical periods for their countries.
TL;DR: It is shown that genome-wide heterozygosity is poorly estimated not only by allozymes but also by microsatellite loci and by single-nucleotide polymorphisms (SNPs) so that associations between fitness (or other phenotypes) andheterozygosity should be established firmly on causative factors and not on simple correlations.
Abstract: Coltman and Slate (2003) recently performed a meta-analysis on studies that investigated the association between genetic variation at microsatellite loci and phenotypic trait variation. One factor not explicitly addressed in their meta-analysis is the actual estimation of genome-wide heterozygosity via molecular markers. Many authors still associate marker-estimated heterozygosity with genome-wide heterozygosity, despite allozyme-based evidence that such correlations are usually very weak or nonexistent. Here, we show that genome-wide heterozygosity is poorly estimated not only by allozymes but also by microsatellite loci and by single-nucleotide polymorphisms (SNPs). Thus, associations between fitness (or other phenotypes) and heterozygosity should be established firmly on causative factors and not on simple correlations.
TL;DR: The results provide very strong evidence that the specific nucleotide variants of feline TYR (chromosome D1) are causative of the siamese and burmese alleles of the albino locus, as well as nucleotideVariant 1 of TYRP1 (chromOSome D4) as specifying the chocolate (b) and cinnamon (b(l) allele of the B locus.
Abstract: The genes encoding enzymes of the tyrosinase family are strong candidates for coat color variation in mammals. To investigate their influence in domestic cat coat color, we determined the complete nucleotide coding sequence of the domestic cat genes tyrosinase (TYR)—a plausible candidate gene for the albino (C) locus, and tyrosinase related protein 1 (TYRP1)—a candidate gene for the brown (B) locus. Sequence variants between individuals exhibiting variation in pigmentation were submitted to association studies. In TYR, two nonsynonymous substitutions encoding TYR-G301R and TYR-G227W were associated with the siamese and burmese phenotypes of the albino locus, respectively. TYRP1 was mapped on chromosome D4 within 5 cM of a highly polymorphic microsatellite, previously found to be fixed in a cat breed selected for the chocolate (b) allele of the B locus, which reinforced TYRP1 as a candidate gene for the B locus in the domestic cat. Two DNA polymorphisms, one leading to a TYRP1-A3G substitution in the signal peptide and another to an in-frame insertion TYRP1-421ins17/18 caused by a donor splice site mutation in intron 6, were associated with the chocolate (b) allele. A premature UAG stop codon at position 100 of TYRP1 was associated with a second allele of the B locus, cinnamon (b l ). The results provide very strong evidence that the specific nucleotide variants of feline TYR (chromosome D1) are causative of the siamese (c s ) and burmese (c b ) alleles of the albino locus, as well as nucleotide variants of TYRP1 (chromosome D4) as specifying the chocolate (b) and cinnamon (b l ) alleles of the B locus.
TL;DR: The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide an extremely powerful system for the unique identification of Eucalyptus individuals for fingerprinting purposes and parentage testing.
Abstract: We report the genetic analysis of 192 unrelated individuals of an elite breeding population of Eucalyptus grandis (Hill ex Maiden) with a selected set of six highly polymorphic microsatellite markers developed for species of the genus Eucalyptus. A full characterization of this set of six loci was carried out generating allele frequency distributions that were used to estimate parameters of genetic information content of these loci, including expected heterozygosity, polymorphism information content (PIC), power of exclusion, and probability of identity. The number of detected alleles per locus ranged from 6 to 33, with an average of 19.8 +/- 9.2. The average expected heterozygosity was 0.86 +/- 0.11 and the average PIC was 0.83 +/- 0.16. Using only three loci, it was possible to discriminate all 192 individuals. The overall probability of identity considering all six EMBRA microsatellite markers combined was lower than 1 in 2 billion. An analysis of the sample size necessary to estimate expected heterozygosity with minimum variance indicated that at least 64 individuals have to be genotyped to characterize this parameter with adequate accuracy for most microsatellites in Eucalyptus. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide an extremely powerful system for the unique identification of Eucalyptus individuals for fingerprinting purposes and parentage testing.
TL;DR: Isolation of Architeuthis DNA from an ingested tentacle and the presence of chitin fragments indicate cannibalism occurs in giant squid, and polymerase chain reaction-based methods for detection of DNA in the prey remains and amorphous slurry from an ArchiteUTHis gut sample were explored.
Abstract: Giant squids (Architeuthis sp.) remain mysterious; they have evaded observation and are rarely taken from their deep sea habitat. Information on the diet of Architeuthis is scarce due to the limited number of specimens with morphologically recognizable remains in their digestive tracts. We explored the use of polymerase chain reaction (PCR)-based methods for detection of DNA in the prey remains and amorphous slurry from an Architeuthis gut sample. The DNA region amplified varied in size, allowing separation of fish and squid components. Sequence comparisons identified fish prey as Macruronus novaezelandiae. Isolation of Architeuthis DNA from an ingested tentacle and the presence of chitin fragments indicate cannibalism occurs in giant squid. Denaturing gradient gel electrophoresis was used to screen for less common DNA types, revealing a high frequency of PCR-generated false alleles, but no additional prey species.
TL;DR: In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds and the high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out.
Abstract: In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.
TL;DR: This study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.
Abstract: A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.
TL;DR: This investigation attempted to develop a high-density genetic map of the Rps8 region and identify closely linked SSR markers for marker-assisted selection of this invaluable gene, and bulk segregant analysis revealed that the RPS8 gene maps closely to the disease resistance gene-rich Rps3 region.
Abstract: Root and stem rot is one of the major diseases of soybean. It is caused by the oomycete pathogen Phytophthora sojae. A series of resistance genes (Rps) have been providing soybean with reasonable protection against this pathogen. Among these genes, Rps8, which confers resistance to most P. sojae isolates, recently has been mapped. However, the most closely linked molecular marker was mapped at about 10 cM from Rps8. In this investigation, we attempted to develop a high-density genetic map of the Rps8 region and identify closely linked SSR markers for marker-assisted selection of this invaluable gene. Bulk segregant analysis was conducted for the identification of SSR markers that are tightly linked to Rps8. Polymorphic SSR markers selected from the Rps8 region failed to show cosegregation with Phytophthora resistance. Subsequently, bulk segregant analysis of the whole soybean genome and mapping experiments revealed that the Rps8 gene maps closely to the disease resistance gene-rich Rps3 region.
TL;DR: The cluster analysis provided evidence suggesting hybridization among Powell amaranth, redroot pigweed, and smooth pigweed and further investigations using molecular analysis of the ribosomal internal transcribed spacer region from atypical plants supported this notion.
Abstract: Weedy Amaranthus species frequently cause economically significant reductions in crop yields. Accurate identification of Amaranthus species is important for efficient weed control, but Amaranthus species can interbreed, which might cause difficulty when identifying hybrid-derived specimens. To determine which of several economically important weedy Amaranthus species are most genetically similar, and thus most likely to produce viable hybrids, we performed amplified fragment length polymorphism (AFLP)-based unweighted pair group method with arithmetic mean (UPGMA) analysis on 8 of these species, with 141 specimens representing 98 accessions. The analysis grouped the specimens into four principal clusters composed of Palmer amaranth (Amaranthus palmeri S. Wats.) and spiny amaranth (Amaranthus spinosus L.); Powell amaranth (Amaranthus powellii S. Wats.), redroot pigweed (Amaranthus retroflexus L.), and smooth pigweed (Amaranthus hybridus L.); waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and sandhills amaranth (Amaranthus arenicola I.M. Johnst.); and tumble pigweed (Amaranthus albus L.). The cluster analysis provided evidence suggesting hybridization among Powell amaranth, redroot pigweed, and smooth pigweed. Further investigations using molecular analysis of the ribosomal internal transcribed spacer region from atypical plants supported this notion. Three species, Palmer amaranth, sandhills amaranth, and waterhemp, are dioecious; nevertheless, the Palmer amaranth and waterhemp-sandhills amaranth clusters were distinct from each other. The Palmer amaranth-spiny amaranth cluster included a cluster of Palmer amaranth and two clusters of spiny amaranth, a monoecious species. Thus the dioecious species Palmer amaranth and waterhemp may not necessarily hybridize with each other more readily than they would to one or more of the monoecious Amaranthus species.
TL;DR: This review discusses how COMMD1 functions as a regulator of not only copper homeostasis but also sodium transport and the NF-kappaB signaling pathway and outlines the possible mechanisms through whichCOMMD1 exerts these newly identified functions.
Abstract: Copper is an essential transition metal but is toxic in excess; therefore, its metabolism needs to be tightly regulated. Defects in the regulation of copper can lead to various disorders characterized by copper deficiency or copper excess. Recently, we characterized the COMMD1 (previously MURR1) gene as the defective gene in canine copper toxicosis. The molecular functions of COMMD1 remain unknown, but significant progress has been made in identifying the cellular processes in which COMMD1 participates, through the identification of proteins interacting with COMMD1. This review discusses how COMMD1 functions as a regulator of not only copper homeostasis but also sodium transport and the NF-kappaB signaling pathway. We outline the possible mechanisms through which COMMD1 exerts these newly identified functions.
TL;DR: Although RAPD markers are generally considered dominant, it is possible to identify a few codominant markers that behave like restriction fragment length polymorphism (RFLP) markers that may be helpful in rapidly screening out hybrids in crops where cross-pollination is a problem.
Abstract: Three controlled crosses were carried out involving Mentha arvensis and Mentha spicata [M. spicata CIMAP/C30 x M. spicata CIMAP/C33 (cv. Neera); M. arvensis CIMAP/C18 x CIMAP/C17 (cv. Kalka); and M. arvensis CIMAP/C17 x M. spicata CIMAP/C33]. The parents were subjected to random amplified polymorphic DNA (RAPD) analysis with 80 primers, and polymorphic primers were tested for detecting coinherited RAPD profiles among the progeny of these crosses. Of 50 seedlings tested from each intraspecific cross, all demonstrated dominant profiles with the selected RAPD primers except the detected hybrid from respective crosses. Coinherited markers could be detected with the primers OPJ 01, MAP 06, OPT 08, and OPO 20 for M. arvensis; OPJ 05, OPJ 14, OPO 19, and OPT 09 for M. spicata; and OPJ 07, OPJ 10, OPJ 11, OPJ 14, and OPO 02 for the cross M. arvensis x M. spicata. In our amplified fragment length polymorphism (AFLP) analysis, 40 coinherited marker fragments were identified for the cross involving M. arvensis, 32 for the cross involving M. spicata, and 41 for the interspecific cross between M. arvensis and M. spicata. In all crosses, similarity values between the parents were less than those between the parents and the hybrids. Although RAPD markers are generally considered dominant, it is possible to identify a few codominant markers that behave like restriction fragment length polymorphism (RFLP) markers. This molecular marker system may be helpful in rapidly screening out hybrids in crops where cross-pollination is a problem.
TL;DR: This preliminary study revealed that some alleles are breed specific (or rare in the dog population), with some representing the major allele in the breeds concerned, and some representingThe level of polymorphism was high--all genes were found to have allelic variants--leading to amino acid changes and pseudogenization of some allele in a number of cases.
Abstract: Olfactory receptors, to which odorant molecules specifically bind, are encoded by the largest gene family yet identified in the mammalian genome. We investigated additional polymorphism due to the possible existence of multiple alleles dispersed in different dog breeds by carrying out a survey of the sequences of 16 olfactory receptor genes in a sample of 95 dogs of 20 different breeds. The level of polymorphism was high--all genes were found to have allelic variants--leading to amino acid changes and pseudogenization of some alleles in a number of cases. This preliminary study also revealed that some alleles are breed specific (or rare in the dog population), with some representing the major allele in the breeds concerned.
TL;DR: While FoxP2 appears to be under strong functional constraints in mammals and birds, it is found that there is no evidence for its role during the evolution of vocal learning in nonhuman animals as in humans.
Abstract: FoxP2 is the first identified gene that is specifically involved in speech and language development in humans. Population genetic studies of FoxP2 revealed a selective sweep in recent human history associated with two amino acid substitutions in exon 7. Avian song learning and human language acquisition share many behavioral and neurological similarities. To determine whether FoxP2 plays a similar role in song-learning birds, we sequenced exon 7 of FoxP2 in multiple song-learning and nonlearning birds. We show extreme conservation of FoxP2 sequences in birds, including unusually low rates of synonymous substitutions. However, no amino acid substitutions are shared between the song-learning birds and humans. Furthermore, sequences from vocal-learning whales, dolphins, and bats do not share the human-unique substitutions. While FoxP2 appears to be under strong functional constraints in mammals and birds, we find no evidence for its role during the evolution of vocal learning in nonhuman animals as in humans.
TL;DR: Comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of reared environment.
Abstract: Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment.
TL;DR: Analysis of DNA from four divergent chicken breeds screened for single nucleotide polymorphisms in the cGH gene shows that G+1705A was significantly associated with body weight at all ages measured, shank length at three of four Ages measured, and average daily gain within weeks 0 to 4.
Abstract: The chicken growth hormone (cGH) gene plays a crucial role in controlling growth and metabolism, leading to potential correlations between cGH polymorphisms and economic traits. In this study, DNA from four divergent chicken breeds were screened for single nucleotide polymorphisms (SNPs) in the cGH gene using denaturing high-performance liquid chromatography and sequencing. A total of 46 SNPs were identified, of which 4 were in the 5# untranslated region, 1 in the 3# untranslated region, 5 in exons (two of which are nonsynonymous), with the remaining 36 in introns. The nucleotide diversity in the cGH gene (h 5 2.7 � 10 � 3 ) was higher than that reported for other chicken genes, even within the same breeds. The associations of five of these SNPs and their haplotypes with chicken growth and carcass traits were determined using polymerase chain reaction–restriction fragment length polymorphism analysis in a F2 resource population cross of two of the four chicken breeds (White Recessive Rock and Xinghua). This analysis shows that, among other correlations, Gþ1705A was significantly associated with body weight at all ages measured, shank length at three of four ages measured, and average daily gain within weeks 0 to 4. Thus, this cGH polymorphism, or another polymorphism that is in linkage disequilibrium with Gþ1705A, appears to correspond to a significant growth-related quantitative trait locus difference between the two breeds used to construct the resource population.
TL;DR: The results suggest that Northern Iberian ponies--which are phenotypically close to British ponies, especially Exmoor--are the result of an introgression rather than population replacement, which supports the close genetic relationship between the ancestral mare populations of the Iberia Peninsula and Northern Africa.
Abstract: Despite a number of recent studies that have focused on the origin of domestic horses, genetic relationships between major geographical clusters still remain poorly understood. In this study we analyzed a 296 bp mtDNA fragment from the HVI region of 171 horses representing 11 native Iberian, Barb, and Exmoor breeds to assess the maternal phylogeography of Iberian horses. The mtDNA haplogroup with a CCG motif (nucleotide position 15,494 to 15,496) was the most frequent in Iberian and Barb breeds (0.42 and 0.57, respectively), regardless of geographic location or group of breeds. This finding supports the close genetic relationship between the ancestral mare populations of the Iberian Peninsula and Northern Africa. Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population subdivision based on maternal lineages. Our results also suggest that Northern Iberian ponies—which are phenotypically close to British ponies, especially Exmoor—are the result of an introgression rather than population replacement.
TL;DR: Although some degree of dominance was observed for high-defensive behavior in one of the four sets of crosses involving European paternity, most of the dominance effects reported in the literature appear to be the result of paternal effects.
Abstract: The defensive behavior of 52 hybrid honeybee (Apis mellifera L.) colonies from four sets of crosses was studied and compared with that of European and Africanized bee colonies. Colonies containing F1 hybrid workers were obtained through reciprocal crosses between European and Africanized bees. The total number of stings deposited by workers in a moving leather patch in 1 min was recorded. In each of the four sets of crosses, bees from hybrid colonies of Africanized paternity left more stings in leather patches than bees from hybrid colonies of European paternity. Results strongly suggest paternal effects of African origin increasing the defensive behavior of hybrid colonies. Although some degree of dominance was observed for high-defensive behavior in one of the four sets of crosses involving European paternity, most of the dominance effects reported in the literature appear to be the result of paternal effects. Several hypotheses to explain this phenomenon, as well as the implications of these effects on the fitness and breeding of honeybees are discussed.
TL;DR: Noninvasive DNA analysis methods using fecal samples for identification of the species and sex of four small sympatric carnivores living on the Tsushima Islands of Japan could be a valuable tool in the management and conservation of the four carnivore species occurring on theTsushima Islands.
Abstract: Fecal analysis is a useful tool for the investigation of food habits and species identity in mammals. However, it is generally difficult to identify the species based on the morphological features and contents of feces deposited by mammals of similar body size. Therefore we developed noninvasive DNA analysis methods using fecal samples for identification of the species and sex of four small sympatric carnivores living on the Tsushima Islands of Japan: the leopard cat (Felis bengalensis), Japanese marten (Martes melampus), Siberian weasel (Mustela sibirica), and feral cat (Felis catus). Based on DNA sequence data from previous phylogenetic studies, we designed species-specific primers for polymerase chain reaction (PCR) amplification of the partial mitochondrial cytochrome b gene (112-347 bp) to identify the species and primers for the partial SRY gene (135 bp) to determine the sex. Due to the adjustment of PCR conditions, those specific DNA fragments were successfully amplified and then applied for species and sex identification. Nucleotide sequences obtained from the PCR products corresponded with cytochrome b sequences of the carnivore species expected. The protocol developed could be a valuable tool in the management and conservation of the four carnivore species occurring on the Tsushima Islands.
TL;DR: A crossbreed pedigree for mapping quantitative trait loci for hip dysplasia in dogs by crossing dysplastic Labrador Retrievers and normal Greyhounds is developed and it is shown that one advantage to using a crossBreed pedigree is the increased marker informativeness in the backcross/F2 population relative to the founder populations.
Abstract: Recent advances in genomics resources and tools are facilitating quantitative trait locus mapping. We developed a crossbreed pedigree for mapping quantitative trait loci for hip dysplasia in dogs by crossing dysplastic Labrador Retrievers and normal Greyhounds. We show that one advantage to using a crossbreed pedigree is the increased marker informativeness in the backcross/F2 population relative to the founder populations. We also discuss three factors that affect the detection power in the context of this crossbreed pedigree: being able to detect and correct genotyping errors, increasing marker density for chromosomes with a sparse coverage, and adding individuals to the mapping population as soon as they become available.
TL;DR: The theories proposed to explain centromere repositioning in mammals are examined in light of evidence gained in human studies and in the presented data from the marsupial model species Macropus eugenii, the tammar wallaby.
Abstract: The centromere is a cytologically defined entity that possesses a conserved and restricted function in the cell: it is the site of kinetochore assembly and spindle attachment. Despite its conserved function, the centromere is a highly mutable portion of the chromosome, carrying little sequence conservation across taxa. This divergence has made studying the movement of a centromere, either within a single karyotype or between species, a challenging endeavor. Several hypotheses have been proposed to explain the permutability of centromere location within a chromosome. This permutability is termed "centromere repositioning" when described in an evolutionary context and "neocentromerization" when abnormalities within an individual karyotype are considered. Both are characterized by a shift in location of the functional centromere within a chromosome without a concomitant change in linear gene order. Evolutionary studies across lineages clearly indicate that centromere repositioning is not a rare event in karyotypic evolution and must be considered when examining the evolution of chromosome structure and syntenic order. This paper examines the theories proposed to explain centromere repositioning in mammals. These theories are interpreted in light of evidence gained in human studies and in our presented data from the marsupial model species Macropus eugenii, the tammar wallaby.