Independent evolution of functional Pm3 resistance genes in wild tetraploid wheat and domesticated bread wheat

The Pm3 alleles of cultivated bread wheat confer gene for gene resistance to the powdery mildew fungus. They represent a particular case of plant disease resistance gene evolution, because of their recent origin and possible evolution after the formation of hexaploid wheat. The Pm3 locus is conserved in tetraploid wheat, thereby allowing the comparative evolutionary study of the same resistance locus in a domesticated species and in one of its wild ancestors. We have identified 61 Pm3 allelic sequences from wild and domesticated tetraploid wheat subspecies. The Pm3 sequences corresponded to 24 different haplotypes. They showed low sequence diversity, differing by only a few polymorphic sequence blocks that were further reshuffled between alleles by gene conversion and recombination. Polymorphic sequence blocks are different from the blocks found in functional Pm3 alleles of hexaploid wheat, indicating an independent evolution of the Pm3 loci in the two species. A new functional gene was identified in a wild wheat accession from Syria. This gene, Pm3k , conferred intermediate race-specific resistance to powdery mildew, and consists of a mosaic of gene segments derived from non-functional alleles. This demonstrates that Pm3 -based resistance is not very frequent in wild tetraploid wheat, and that the evolution of functional resistance genes occurred independently in wild tetraploid and bread wheat. The Pm3 sequence variability and geographic distribution indicated that diversity was higher in wild emmer wheat from the Levant area, compared with the accessions from Turkey. Further screens for Pm3 functional genes in wild wheat should therefore focus on accessions from the Levant region.     

Gene clusters and polycistronic transcription in eukaryotes

Sometimes genes are arranged nonrandomly on the chromosomes of eukaryotes. This review considers instances of gene clusters in which two genes or more are expressed from a single promoter. This includes cases in which a polycistronic pre-mRNA is processed to make monocistronic mRNAs in nematodes, as well as isolated examples of polycistronic mRNAs found in mammals, flies, and perhaps plants. BioEssays 20 :480–487, 1998. © 1998 John Wiley & Sons, Inc.     

Identification of interspecific hybrids among domesticated apple and its wild relatives

Potential interspecific hybrids are usually identified in natural populations by their proximity to interbreeding species or their intermediate phenotypes; hybridization can then be confirmed by comparing the genetic makeup of putative hybrids to pure species. In contrast, detecting interspecific hybridization and misclassifications in ex situ collections can be difficult because fine-scale geographic locations and species-specific phenotypic data are generally unavailable. Thus, there is little a priori information available to suggest which individuals might be hybrids. Instead, hybrids or misclassified individuals must be identified based on molecular data via population assignment and admixture detection programs. We have applied a variety of population assignment and admixture detection programs to over 400 samples of four closely related Malus species held in the US Department of Agriculture?CAgricultural Research Service National Plant Germplasm System that were genotyped at 19 simple sequence repeat loci. Our findings indicate that over 10?% of the samples of the wild species Malus sieversii and Malus orientalis and nearly 20?% of the samples of the wild species Malus sylvestris may be admixed or misclassified. The percentage of admixed or misclassified samples of the domesticated species, Malus × domestica, was much lower, at <5?%. These findings provide an illustration of how to detect hybridization and misclassification in ex situ collections using molecular data and, ultimately, should help to maximize the utility of the collections. In addition, the presence of wild-collected samples that show admixture with domesticated apple suggests that gene flow may be occurring from the crop into natural populations of the wild species.     

Polyphenol oxidase genes as integral part of the evolutionary history of domesticated tetraploid wheat

Studying and understanding the genetic basis of polyphenol oxidases (PPO)-related traits plays a crucial role in genetic improvement of crops.A tetraploid wheat collection (T. turgidum ssp., TWC) was analyzed using the 90K wheat SNP iSelect assay and phenotyped for PPO activity. A total of 21,347 polymorphic SNPs were used to perform genome-wide association analysis (GWA) in TWC and durum wheat sub-groups, detecting 23 and 85 marker-trait associations (MTA). In addition, candidate genes responsible for PPO activity were predicted. Based on the 23 MTAs detected in TWC, two haplotypes associated with low and high PPO activity were identified. Four SNPs were developed and validated providing one reliable marker (IWB75732) for marker assisted selection. The 23 MTAs were used to evaluate the genetic divergence (F_ST > 0.25) between the T. turgidum subspecies, providing new information important for understanding the domestication process of Triticum turgidum ssp. and in particular of ssp. carthlicum.     

Inference of miRNA targets using evolutionary conservation and pathway analysis

Background

MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast, functional annotations are available only for a very small fraction of these miRNAs, and even in these cases only partially.

Results

We developed a general Bayesian method for the inference of miRNA target sites, in which, for each miRNA, we explicitly model the evolution of orthologous target sites in a set of related species. Using this method we predict target sites for all known miRNAs in flies, worms, fish, and mammals. By comparing our predictions in fly with a reference set of experimentally tested miRNA-mRNA interactions we show that our general method performs at least as well as the most accurate methods available to date, including ones specifically tailored for target prediction in fly. An important novel feature of our model is that it explicitly infers the phylogenetic distribution of functional target sites, independently for each miRNA. This allows us to infer species-specific and clade-specific miRNA targeting. We also show that, in long human 3' UTRs, miRNA target sites occur preferentially near the start and near the end of the 3' UTR. To characterize miRNA function beyond the predicted lists of targets we further present a method to infer significant associations between the sets of targets predicted for individual miRNAs and specific biochemical pathways, in particular those of the KEGG pathway database. We show that this approach retrieves several known functional miRNA-mRNA associations, and predicts novel functions for known miRNAs in cell growth and in development.

Conclusion

We have presented a Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of functional sites for each miRNA, and assigns a posterior probability to each putative target site. The results presented here indicate that our general method achieves very good performance in predicting miRNA target sites, providing at the same time insights into the evolution of target sites for individual miRNAs. Moreover, by combining our predictions with pathway analysis, we propose functions of specific miRNAs in nervous system development, inter-cellular communication and cell growth. The complete target site predictions as well as the miRNA/pathway associations are accessible on the ElMMo web server.     

A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica

Lack of introgression or divergent selection may be responsible for the maintenance of phenotypic differences between sympatric populations of crops and their wild progenitors. To distinguish between these hypotheses, amplified fragment length polymorphism markers were located on a molecular linkage map of Phaseolus vulgaris relative to genes for the domestication syndrome and other traits. Diversity for these same markers was then analyzed in two samples of wild and domesticated populations from Mesoamerica. Differentiation between wild and domesticated populations was significantly higher in parapatric and allopatric populations compared to sympatric populations. It was also significantly higher near genes for domestication compared to those away from these genes. Concurrently, the differences in genetic diversity between wild and domesticated populations were strongest around such genes. These data suggest that selection in the presence of introgression appears to be a major evolutionary factor maintaining the identity of wild and domesticated populations in sympatric situations. Furthermore, alleles from domesticated populations appear to have displaced alleles in sympatric wild populations, thus leading to a reduction in genetic diversity in such populations. These results also provide a possible experimental framework for assessing the long-term risk of transgene escape and the targeting of transgenes inside the genome to minimize the survival of these transgenes into wild populations following introduction by gene flow.This article is dedicated to the memory of Epimaki M. K. Koinange.     

Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat

All forms of domesticated tetraploid wheat (Triticum turgidum, genomes AABB) are nearly monomorphic for restriction fragment length polymorphism (RFLP) haplotype a at the Xpsr920 locus on chromosome 4A (Xpsr920-A1a), and wild tetraploid wheat is monomorphic for haplotype b. The Xpsr920-A1a/b dimorphism provides a molecular marker for domesticated and wild tetraploid wheat, respectively. Hexaploid wheat (Triticum aestivum, genomes AABBDD) is polymorphic for the 2 haplotypes. Bacterial artificial chromosome (BAC) clones hybridizing with PSR920 were isolated from Triticum urartu (genomes AA), Triticum monococcum (genomes AmAm), and T. turgidum ssp. durum (genomes AABB) and sequenced. PSR920 is a fragment of a putative ATP binding cassette (ABC) transporter gene (designated ABCT-1). The wheat ABCT-1 gene is more similar to the T. urartu gene than to the T. monococcum gene and diverged from the T. urartu gene about 0.7 MYA. The comparison of the sequence of the wheat A genome BAC clone with that of the T. urartu BAC clone provides the first insight into the microsynteny of the wheat A genome with that of T. urartu. Within 103 kb of orthologous intergenic space, 37 kb of new DNA has been inserted and 36 kb deleted leaving 49.7% of the region syntenic between the clones. The nucleotide substitution rate in the syntenic intergenic space has been 1.6 x 10(-8) nt(-1) year(-1), which is, respectively, 4 and 3 times as great as nucleotide substitution rates in the introns and the third codon positions of the juxtaposed gene. The RFLP is caused by a miniature inverted transposable element (MITE) insertion into intron 18 of the ABCT-A1 gene. Polymerase chain reaction primers were developed for the amplification of the MITE insertion site and its sequencing. The T. aestivum ABCT-A1a haplotype is identical to the haplotype of domesticated tetraploid wheat, and the ABCT-A1b haplotype is identical to that of wild tetraploid wheat. This finding shows for the first time that wild tetraploid wheat participated in the evolution of hexaploid wheat. A cline of the 2 haplotype frequencies exists across Euro-Asia in T. aestivum. It is suggested that T. aestivum in eastern Asia conserved the gene pool of the original T. aestivum more than wheat elsewhere.     

Evidence for domesticated and wild populations of Saccharomyces cerevisiae

Saccharomyces cerevisiae is predominantly found in association with human activities, particularly the production of alcoholic beverages. S. paradoxus, the closest known relative of S. cerevisiae, is commonly found on exudates and bark of deciduous trees and in associated soils. This has lead to the idea that S. cerevisiae is a domesticated species, specialized for the fermentation of alcoholic beverages, and isolates of S. cerevisiae from other sources simply represent migrants from these fermentations. We have surveyed DNA sequence diversity at five loci in 81 strains of S. cerevisiae that were isolated from a variety of human and natural fermentations as well as sources unrelated to alcoholic beverage production, such as tree exudates and immunocompromised patients. Diversity within vineyard strains and within saké strains is low, consistent with their status as domesticated stocks. The oldest lineages and the majority of variation are found in strains from sources unrelated to wine production. We propose a model whereby two specialized breeds of S. cerevisiae have been created, one for the production of grape wine and one for the production of saké wine. We estimate that these two breeds have remained isolated from one another for thousands of years, consistent with the earliest archeological evidence for wine-making. We conclude that although there are clearly strains of S. cerevisiae specialized for the production of alcoholic beverages, these have been derived from natural populations unassociated with alcoholic beverage production, rather than the opposite.     

Allozyme variation in domesticated annual sunflower and its wild relatives

 The annual sunflower (Helianthus annuus L.) is a morphologically and genetically variable species composed of wild, weedy, and domesticated forms that are used for ornament, oilseed, and edible seeds. In this study, we evaluated genetic variation in 146 germplasm accessions of wild and domesticated sunflowers using allozyme analysis. Results from this survey showed that wild sunflower exhibits geographically structured genetic variation, as samples from the Great Plains region of the central United States were genetically divergent from accessions from California and the southwestern United States. Sunflower populations from the Great Plains harbored greater allelic diversity than did wild sunflower from the western United States. Comparison of genetic variability in wild and domesticated sunflower by principal coordinate analysis showed these groups to be genetically divergent, in large part due to differences in the frequency of common alleles. Neighbor-Joining analyses of domesticated H. annuus, wild H. annuus and two closely related wild species (H. argophyllus T. & G. and H. petiolaris Nutt.) showed that domesticated sunflowers form a genetically coherent group and that wild sunflowers from the Great Plains may include the most likely progenitor of domesticated sunflowers. Received: 2 December 1996/Accepted: 4 April 1997     

Microsatellite markers application on domesticated silkworm and wild silkworm

Abstract Twenty-seven sets of simple sequence repeat (SSR) primers were developed through hybridizing of (CA)n, (CT)n and (GT)n and sequencing the positive clones in libraries constructed by using p50 silkworm strain. Of those primer pairs, 26 sets of SSR primers amplified well in two regional wild silkworm strains. Ten domesticated silkworm strains and two regional wild silkworm strains were used for comparing the polymorphisms and for constructing a phylogenetic tree employing the UPGAM method. The result showed that the genetic distances within Japanese strains are closer than those of Chinese strains. And this result also implies that Japanese strains diverged from domesticated silkworm later than Chinese strains. According to the clustering result, the domesticated silkworm is firstly clustered in one class, but could be classified into two groups. Within a strain, the individual polymorphism of wild silkworm was significantly higher in abundance than those of domesticated silkworm. The S SR primers of domesticated silkworm could be used in genetic studies for wild silkworm.     

Detecting hybridization between wild species and their domesticated relatives

The widespread occurrence of free-ranging domestic or feral carnivores (dogs, cats) or ungulates (pigs, goats), and massive releases of captive-reproduced game stocks (galliforms, waterfowl) is raising fear that introgressive hybridization with wild populations might disrupt local adaptations, leading to population decline and loss of biodiversity. Detecting introgression through hybridization is problematic if the parental populations cannot be sampled (unlike in classical stable hybrid zones), or if hybridization is sporadic. However, the use of hypervariable DNA markers (microsatellites) and new statistical methods (Bayesian models), have dramatically improved the assessment of cryptic population structure, admixture analyses and individual assignment testing. In this paper, I summarize results of projects aimed to identify occurrence and extent of introgressive hybridization in European populations of wolves (Canis lupus), wildcats (Felis silvestris), rock partridges and red-legged partridges (Alectoris graeca and Alectoris rufa), using genetic methods. Results indicate that introgressive hybridization can be locally pervasive, and that conservation plans should be implemented to preserve the integrity of the gene pools of wild populations. Population genetic methods can be fruitfully used to identify introgressed individuals and hybridizing populations, providing data which allow evaluating risks of outbreeding depression. The diffusion in the wild of invasive feral animals, and massive restocking with captive-reproduced game species, should be carefully controlled to avoid loss of genetic diversity and disruption of local adaptations.     

The mycoflora of domesticated and wild bees (Apoidea)

Fungi including yeasts are common in the honey stomachs and provisions of diverse bees. They may be parasites, commensals or mutualistic. Yeasts, singly or in association with bacteria, are pioneer colonizers during a microbial succession in larval cells of many subterranean bees. They are followed by fungi such asAspergillus, Penicillium, Emericellopsis, Sartorya, Pseudoarachniotus, Gymnoascus, Carpenteles andFusarium. Aspergillus flavus andSaccharomyces spp. are pathogenic to many species of bees, and fungi are the main cause of declining alkali bee populations. There are 124 species of fungi, including 36 new records, associated with Apoidea; 49 species are associated with alkali bees.Cooperative investigations of the Plant Sciences Research (L. R. Batra) and Entomology (G. E. Bohart) Divisions, Agricultural Research Service, U.S. Department of Agriculture, and the Utah Agricultural Experiment Station, Logan, Utah.     

The structure of wild and domesticated emmer wheat populations,gene flow between them,and the site of emmer domestication

The domestication of emmer wheat (Triticum turgidum spp. dicoccoides, genomes BBAA) was one of the key events during the emergence of agriculture in southwestern Asia, and was a prerequisite for the evolution of durum and common wheat. Single- and multilocus genotypes based on restriction fragment length polymorphism at 131 loci were analyzed to describe the structure of populations of wild and domesticated emmer and to generate a picture of emmer domestication and its subsequent diffusion across Asia, Europe and Africa. Wild emmer consists of two populations, southern and northern, each further subdivided. Domesticated emmer mirrors the geographic subdivision of wild emmer into the northern and southern populations and also shows an additional structure in both regions. Gene flow between wild and domesticated emmer occurred across the entire area of wild emmer distribution. Emmer was likely domesticated in the Diyarbakir region in southeastern Turkey, which was followed by subsequent hybridization and introgression from wild to domesticated emmer in southern Levant. A less likely scenario is that emmer was domesticated independently in the Diyarbakir region and southern Levant, and the Levantine genepool was absorbed into the genepool of domesticated emmer diffusing from southeastern Turkey. Durum wheat is closely related to domesticated emmer in the eastern Mediterranean and likely originated there. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.