Recombination Landscape Divergence Between Populations is Marked by Larger Low-Recombining Regions in Domesticated Rye

The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, individuals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) individuals. By analyzing population structure among individuals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analyzed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye individuals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harboring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected during domestication to achieve more homogeneous populations for agricultural use.     

Localization of Human Ribosomal Gene DNA Probes on Barley Chromosomes

To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S–28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. As a control, wheat rDNA probe (clon pTa71) was taken. Hybridization of the wheat DNA probe revealed two major labelling sites on mitotic barley chromosomes 5I (7H) and 6I (6H), as well as several minor sites. With the human DNA probe, signals were detected in the major sites of the ribosomal genes on chromosomes 5I (7H) and 6I (6H) only when the chromosome preparations were obtained using an optimized technique with obligatory pepsin treatment followed by hybridization. Thus, this study demonstrates that physical mapping of plant chromosomes with human DNA probes that are 60 to 70% homologous to the plant genes is possible. It suggests principal opportunity for the FISH mapping of plant genomes using probes from human genome libraries, obtained in the course of the total sequencing of the human genomes and corresponding to the coding regions of genes with known functions.     

Genetic Divergence Detected by ISSR Markers and Characterization of Microsatellite Regions in Mytilus Mussels

The wide distribution of microsatellites in mussels of the Mytilus edulis complex (Mytilidae) enables the analysis of inter-simple-sequence repeat (ISSR) markers. The aim of this investigation was to assess genetic differentiation in six sampling localities distributed along the European Atlantic coast to expose the potential of these markers in genetic studies requiring the detection of low polymorphism and as a source of sequences for developing microsatellite markers. We detected low genetic structuring within each member of the Mytilus edulis complex. Nei and Li distances and AMOVA clustered the individuals studied into two groups. On the basis of these results two sampling localities coming from the M. edulis × M. galloprovincialis mosaic hybrid zone in Western Europe were assigned to one species. On the other hand, mussels of a sampling locality in the Baltic Sea were not significantly different from a pure M. edulis locality supporting an extensive introgression of M. edulis in these individuals. Finally, 148 microsatellites were found in the sequences of 51 ISSR markers, and two polymorphic microsatellite markers were developed.     

Worldwide Patterns of Ancestry,Divergence, and Admixture in Domesticated Cattle

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.     

Ecological Genetic Divergence of the Fungal Pathogen Didymella rabiei on Sympatric Wild and Domesticated Cicer spp. (Chickpea)

For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.Environmental heterogeneity and genetic variability in host populations are major factors distinguishing natural from agricultural habitats. These differences exert powerful selective forces on plants and their pathogens, shaping the biology of pathosystems, epidemiological patterns, and pathogenic fitness (11, 21). Plant pathogens are dependent upon the abiotic environment as well as on their host plants and are subjected to strong selective forces exerted by their hosts. This process is shaped especially (but not exclusively) by genetic variation at loci controlling differential host specificity, which may ultimately be an important driver in speciation (37, 48, 49).The Neolithic revolution and the adoption of farming have had a large impact on plant communities as well as their related pathogens (11, 34, 57). The long-term interplay between plant pathogens and their hosts and the resulting evolutionary trajectories may have different patterns in natural plant communities as compared to agro-ecosystems (12). One striking observation is that pathogens of natural plant populations, although prevalent, rarely cause the destruction of their hosts (21). Therefore, investigations of the epidemiological and biological differences between pathogen populations from wild and domesticated origins are of fundamental interest and are highly relevant to understanding disease patterns, parasite evolution, and host resistance in agricultural systems. Such studies are expected to be especially fruitful in the centers of origin of crop species, because these regions are generally considered to be pathogen centers of origin as well (40, 57).Throughout West Asia, wild cereals and legumes and their domesticated derivatives have been growing sympatrically since the beginning of Near Eastern farming systems (41, 61). Domesticated chickpea, Cicer arietinum L, is grown sympatrically with a number of annual and perennial Cicer relatives, including the immediate wild progenitor of domesticated chickpea, C. reticulatum Ladiz (39, 58). Following the Neolithic agricultural revolution in southeastern Turkey (41), the Near Eastern crop package spread in all directions throughout the east Mediterranean and reached the southern Levant within 1 millennium (2, 3). This “passage” of the cultigens, from their core region in southeast Turkey into the southern Levant, traversed populations of many of their wild progenitors and more distantly related wild relatives (e.g., wild barley, wild emmer wheat, wild bitter vetch, wild lentils, and wild peas), (2, 3). Presumably, these natural populations were infested by pathogens capable of infecting the domesticated forms (2, 20, 24).Domesticated chickpea differs from the Near Eastern founder crops in its seasonal growth pattern. While most founder crops have retained the autumnal germination/spring maturation cycle like their wild relatives, domesticated chickpea is a spring-sown crop, germinating and developing up to 4 months later than its wild relatives (1, 3). This shift of life cycle is puzzling since water availability in the Levant is a major yield-limiting factor and autumn-sown crops enjoy a substantial yield benefit. It has been recently hypothesized that this shift was driven by the extreme vulnerability of chickpea to Ascochyta blight during the rainy season and was the only means to secure stable yields in ancient times (3). Didymella rabiei (Kovachevski) var. Arx. (Anamorph: Ascochyta rabiei (Pass) Labr.) is one of the most destructive diseases of domesticated chickpea, affecting all above-ground parts of the plant. Secondary spread of D. rabiei conidia occurs through rain splash, and epidemic intensity is governed by rain frequency and quantity. As Ascochyta blight epidemics proceed, foci of diseased plants become visible. Unlike other Ascochyta diseases of legumes and Septoria diseases of cereals, Ascochyta blight of chickpea may cause total yield loss under the appropriate environmental conditions (43). Autumn-sown chickpea is severely affected by Ascochyta blight because the crop growth period coincides with the rainy season and optimum environmental conditions for pathogen development and spread (3, 56).Unlike the often massive stands of wild cereals, C. reticulatum has a very narrow and fragmented distribution (2, 8, 38). However, other wild annual Cicer taxa are more common across the region and can be found in close proximity to the domesticated crop (1, 8). In the southern Levant, domesticated chickpea is grown sympatrically, often just few meters apart from C. judaicum (27). C. judaicum grows in patchy distributions in stony/rocky habitats in Israel and neighboring territories, mostly in sites with annual precipitation of >480 mm and altitude of <900 m (6). Unlike C. judaicum, modern chickpea cropping in Israel spans large tracts of land employing a 5-year rotation in individual fields. Recently, D. rabiei isolates sampled from C. judaicum and isolates sampled from C. arietinum were studied and found to be better adapted to their respective original host than to the other Cicer species (26, 27). In addition, in vitro hyphal growth rate experiments exposed an adaptation to higher temperatures among isolates originating from C. arietinum compared to isolates from C. judaicum (26). Given that the natural growing season of C. judaicum occurs during the Levantine winter and that chickpea is a traditional spring-sown crop in the region, it is likely that the apparent adaptation to higher temperatures of D. rabiei isolates from domesticated chickpea may represent an ecological shift following the introduction of summer cropping practices in the Near East (3). These sympatric wild and domesticated pathosystems of Cicer/Ascochyta represent a unique opportunity for studying the genetic basis of the pathogen''s ecological adaptation and its association with pathogenic fitness. Such a system may also help to determine the role of ecological factors and pathogenic fitness in pathogenic divergence and the evolutionary relationships among pathogen populations in natural and human-directed agro-ecosystems (57).In this context, our underlying hypotheses were as follows: (i) isolates sampled from C. arietinum and C. judaicum are conspecific but represent genetically distinct populations; (ii) the temperature growth response of D. rabiei isolates from C. judaicum and C. arietinum has a heritable genetic basis; (iii) the temperature growth response plays an important role in the ongoing pathogen divergence process and, therefore, it is expected to have high heritability values; and (iv) the existence of two sympatric D. rabiei populations (demes) requires the action of one or more genetic isolation mechanisms. In accord with the above hypotheses, the aims of this study were (i) to assess the genetic differentiation between D. rabiei isolates originating from C. judaicum versus C. arietinum, (ii) to determine the genetic basis of temperature response and estimate its heritability, and (iii) to assess the relationship between temperature adaptation and pathogenic fitness among progeny from crosses between D. rabiei isolates from C. judaicum and C. arietinum on the two original hosts.     

Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus

Genomic regions that determine mating compatibility are subject to distinct evolutionary forces that can lead to a cessation of meiotic recombination and the accumulation of structural changes between members of the homologous chromosome pair. The relatively recent discovery of dimorphic mating-type chromosomes in fungi can aid the understanding of sex chromosome evolution that is common to dioecious plants and animals. For the anther-smut fungus, Microbotryum lychnidis-dioicae (= M. violaceum isolated from Silene latifolia), the extent of recombination cessation on the dimorphic mating-type chromosomes has been conflictingly reported. Comparison of restriction digest optical maps for the two mating-type chromosomes shows that divergence extends over 90% of the chromosome lengths, flanked at either end by two pseudoautosomal regions. Evidence to support the expansion of recombination cessation in stages from the mating-type locus toward the pseudoautosomal regions was not found, but evidence of such expansion could be obscured by ongoing processes that affect genome structure. This study encourages the comparison of forces that may drive large-scale recombination suppression in fungi and other eukaryotes characterized by dimorphic chromosome pairs associated with sexual life cycles.     

Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.     

The Genetic Basis of Morphological Diversity in Domesticated Goldfish

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A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30–75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.     

中国大麦矮秆种质资源的基因分析Ⅱ．矮秆基因的染色体定位

根据连锁遗传原理,利用全套染色体形态性状状标记系,对２０份中国大麦筹秆南资源的矮秆基因,进行了染色体定位,结果表明,１５份单基因矮杆中,有１份其矮秆基因与宽护颖基因w连锁,位于２（２Ｈ）染色体短臂上;１０份的矮秆基因与uz基因等等位,由３（３Ｈ）长臂携带;４份的矮秆基因与钩芒K ,锁位于４（４Ｈ）长臂上,５份双基因矮秆中,有３份的筹秆基因分别位于２（２Ｈ）短臂和４（４Ｈ）长 臂上;１份的筹秆基因各由其３（３Ｈ）和４（４Ｈ）长臂携带;其余１份的两对矮秆基因,１对与uz基因等位,由于３（３Ｈ）长臂携带,另１对则与宽护颖基因w连锁,位于２（２Ｈ）短臂之上。     

The Nature of Nucleotide Sequence Divergence between Barley and Maize Chloroplast DNA

Analysis of a 2175-base pair (bp) SmaI-HindIII fragment of barley chloroplast DNA revealed that rbcL (the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase) and atpB (the gene for the beta subunit of ATPase) are transcribed divergently and are separated by an untranscribed region of 155-166 bp. The rbcL mRNA has a 320-residue untranslated leader region, whereas the atpB mRNA has a 296- to 309-residue leader region. The sequence of these regions, together with the initial 113 bp of the atpB-coding region and the initial 1279 bp of the rbcL-coding region, is compared with the analogous maize chloroplast DNA sequences. Two classes of nucleotide differences are present, substitutions and insertions/deletions. Nucleotide substitutions show a 1.9-fold bias toward transitions in the rbcL-coding region and a 1.5-fold bias toward transitions in the noncoding region. The level of nucleotide substitutions between the barley and maize sequences is about 0.065/bp. Seventy-one percent of the substitutions in the rbcL-coding region are at the third codon position, and 95% of these are synonymous changes. Insertion/deletion events, which are confined to the noncoding regions, are not randomly distributed in these regions and are often associated with short repeated sequences. The extent of change for the noncoding regions (about 0.093 events/bp) is less than the extent of change at the third codon positions in the rbcL-coding region (about 0.135 events/bp), including insertion/delection events. Limited sequence analysis of the analogous DNA from a wild line ( Hordeum spontaneum) and a primitive Iranian barley (H. vulgare) suggested a low rate of chloroplast DNA evolution. Compared to spinach chloroplast DNA, the barley rbcL-atpB untranslated region is extremely diverged, with only the putative rbcL promoters and ribosome-binding site being extensively conserved.     

Silver Staining for Nucleolar Organizing Regions of Vertebrate Chromosomes

Refinements to a simple, one-step silver staining technique for nucleolar organizing regions are described. These include fixation of silver stained material with sodium thiosulfate and standardization of silver development conditions for different groups of vertebrates. The central advantages to the method are that it is rapid, reliable, simple, and inexpensive. Additional benefits include (i) consistent and uniform silver staining of nucleolar organizing regions, (ii) few reduced silver deposits elsewhere on the chromosomes or on the slides, (iii) generally unaltered chromosome morphology after silver treatment, and (iv) relative permanence of Permounted preparations. The method works equally well on chromosomes made from cell cultures and from solid tissues of live specimens.     

Genetic Divergence in Mandible Form in Relation to Molecular Divergence in Inbred Mouse Strains

Genetic divergence in the form of the mandible is examined in ten inbred strains of mice. Several univariate and multivariate genetic distance estimates are given for the morphological data and these estimates are compared to measures of genealogical and molecular divergence. Highly significant divergence occurs among the ten strains in all 11 mandible traits considered individually and simultaneously. Genealogical relationship among strains is highly correlated with genetic divergence in single locus molecular traits. However, the concordance between genealogical relationship and multivariate genetic divergence in morphology is much more complex. Whether there is a significant correlation between morphological divergence and genealogy depends upon the method of analysis and the particular genetic distance statistic being employed.     

野生大麦与栽培大麦醇溶蛋白遗传多样性比较

利用A-PAGE(acid-polyacrylamide gel electrophoresis)法对采自以色列的野生大麦的一个野生自然群体的15个系和来自世界不同国家的14份栽培大麦品种醇溶蛋白的遗传多样性进行了分析.结果表明:在所有的29份供试材料中,共发现52条相对迁移率不同的谱带.52条谱带的出现频率为3.44%～93.1%,多样性指数为0.066～0.368;以中国春醇溶蛋白为标准,ω区大麦醇溶蛋白的谱带数最多,其次是β区;野生大麦Shannon多样性指数依次为β区>ω区>α区>γ区,而栽培大麦Shannon多样性指数依次为ω区β>区>γ区>a区;野生大麦自然群体和栽培大麦品种间的遗传相似系数变幅相当,且聚类分析结果显示,野生大麦自然群体和来自全球不同区域栽培大麦品种间的醇溶蛋白遗传多样性同样丰富.以上结果说明,野生大麦中保存了较栽培大麦更为丰富的基因资源,今后栽培大麦的品质改良应该重视野生大麦资源的合理利用.     

Historical Divergence and Gene Flow in the Genus Zea

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last ~150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.     

Genetic Divergence among Regions Containing the Vulnerable Great Desert Skink (Liopholis kintorei) in the Australian Arid Zone

Knowledge of genetic structure and patterns of connectivity is valuable for implementation of effective conservation management. The arid zone of Australia contains a rich biodiversity, however this has come under threat due to activities such as altered fire regimes, grazing and the introduction of feral herbivores and predators. Suitable habitats for many species can be separated by vast distances, and despite an apparent lack of current geographical barriers to dispersal, habitat specialisation, which is exhibited by many desert species, may limit connectivity throughout this expansive region. We characterised the genetic structure and differentiation of the great desert skink (Liopholis kintorei), which has a patchy, but widespread distribution in the western region of the Australian arid zone. As a species of cultural importance to local Aboriginal groups and nationally listed as Vulnerable, it is a conservation priority for numerous land managers in central Australia. Analysis of mitochondrial ND4 sequence data and ten nuclear microsatellite loci across six sampling localities through the distribution of L. kintorei revealed considerable differentiation among sites, with mitochondrial F_ST and microsatellite F′_ST ranging from 0.047-0.938 and 0.257-0.440, respectively. The extent of differentiation suggests three main regions that should be managed separately, in particular the southeastern locality of Uluru. Current genetic delineation of these regions should be maintained if future intervention such as translocation or captive breeding is to be undertaken.