BACKGROUND: Legless lizards, the slow worms of the genus Anguis, are forming secondary contact zones within their Europe-wide distribution. METHODS: We examined 35 populations of A. fragilis and A. colchica to identify the level of morphological and genetic divergence in Poland. We applied a conventional study approach using metric, meristic, and categorial (coloration) features for a phenotype analysis, and two standard molecular markers, a mitochondrial (NADH-ubiquinone oxidoreductase chain 2; ND2) and a nuclear (V(D)J recombination-activating protein 1; RAG1) one. RESULTS: We found clear differences between A. fragilis and A. colchica in molecular markers and phenotype-in meristic features, e.g., ear opening, number of scales rows around the body, and higher than so far known diversity in ND2 and RAG1 haplotypes. The presence of five hybrids was detected in three populations in the Polish part of the European contact zone. In all hybrids, homozygous alleles of RAG1 were detected, which suggests a back-crossing within the genus. CONCLUSIONS: The ability to produce fertile offspring by A. fragilis x A. colchica hybrids shows inefficient mechanisms of reproductive isolation of the two legless lizards. The hybrids were indistinguishable from parental species in head proportions (principal components and discriminant analyses) but more resembling A. colchica in meristic traits.

• Klíčová slova
• Anguidae, Biogeography, Hybridization, Morphometrics, Speciation, Taxonomy,
• MeSH
• fenotyp MeSH
• genetická variace MeSH
• haplotypy genetika   MeSH
• homeodoménové proteiny MeSH
• ještěři * genetika   anatomie a histologie   MeSH
• reprodukční izolace MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Polsko MeSH
• Názvy látek
• homeodoménové proteiny MeSH
• RAG-1 protein MeSH Prohlížeč

Polyploidy, the result of whole genome duplication (WGD), is widespread across the tree of life and is often associated with speciation and adaptability. It is thought that adaptation in autopolyploids (within-species polyploids) may be facilitated by increased access to genetic variation. This variation may be sourced from gene flow with sister diploids and new access to other tetraploid lineages, as well as from increased mutational targets provided by doubled DNA content. Here, we deconstruct in detail the origins of haplotypes displaying the strongest selection signals in established, successful autopolyploids, Arabidopsis lyrata and Arabidopsis arenosa. We see strong signatures of selection in 17 genes implied in meiosis, cell cycle, and transcription across all four autotetraploid lineages present in our expanded sampling of 983 sequenced genomes. Most prominent in our results is the finding that the tetraploid-characteristic haplotypes with the most robust signals of selection were completely absent in all diploid sisters. In contrast, the fine-scaled variant 'mosaics' in the tetraploids originated from highly diverse evolutionary sources. These include widespread novel reassortments of trans-specific polymorphism from diploids, new mutations, and tetraploid-specific inter-species hybridization-a pattern that is in line with the broad-scale acquisition and reshuffling of potentially adaptive variation in tetraploids.

• MeSH
• Arabidopsis * genetika   MeSH
• diploidie MeSH
• genetická variace MeSH
• genom rostlinný MeSH
• haplotypy * genetika   MeSH
• meióza genetika   MeSH
• molekulární evoluce MeSH
• polyploidie * MeSH
• selekce (genetika) genetika   MeSH
• tetraploidie MeSH
• Publikační typ
• časopisecké články MeSH

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

• Klíčová slova
• adaptation, birds, ecological genetics, genomics/proteomics, molecular evolution, population genetics – empirical,
• MeSH
• genetická variace * MeSH
• haplotypy genetika   MeSH
• jednonukleotidový polymorfismus * MeSH
• Passeriformes genetika   klasifikace   MeSH
• populační genetika metody   MeSH
• rekombinace genetická MeSH
• selekce (genetika) MeSH
• zpěvní ptáci * genetika   klasifikace   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

• MeSH
• biotechnologie MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná genetika   MeSH
• genom rostlinný * genetika   MeSH
• haplotypy genetika   MeSH
• hybridizace genetická genetika   MeSH
• polyploidie * MeSH
• referenční standardy MeSH
• Saccharum * klasifikace   genetika   MeSH
• šlechtění rostlin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• DNA rostlinná MeSH

The aim of this study was to investigate the association between genotypes and haplotypes of OPN, and milk composition in dairy cows. A total of 317 Chinese Holstein cows were genotyped via DNA sequencing in this study. Three single nucleotide polymorphisms (SNPs), g.2916G > A, g.58675C > T and g.58899C > A, and eight haplotypes were identified. Of the eight possible haplotypes, four haplotypes i.e., Hap2 (ACC; 55.30%), Hap6 (GCC, 15.6%), Hap1 (ACA, 13.6%) and Hap4 (ATC, 5.70%), were considered to be major with a cumulative estimated frequency of >90%. Single markers (g.2916G > A and g.58899C > A) and Haplotype Hap6/4 were found to be associated with an increase in butter-fat percentage (p < 0.05). Taken together, our results provided evidence that polymorphisms in OPN are associated with milk composition, and could potentially be used for marker-assisted selection in Chinese Holstein cows.

• Klíčová slova
• Genetic variability, OPN gene, Single nucleotide polymorphism, haplotype, milk composition,
• MeSH
• genotyp MeSH
• haplotypy genetika   MeSH
• jednonukleotidový polymorfismus * genetika   MeSH
• mléko * MeSH
• sekvence nukleotidů MeSH
• skot genetika   MeSH
• zvířata MeSH
• Check Tag
• skot genetika   MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: With stage 5 chronic kidney disease (CKD5) more prevalent in the Czech Republic than in most European countries, genetic susceptibility is potentially implicated. METHODS: In a group of 1489 CKD5 kidney transplantation patients (93% with complete clinical characteristics; mean age 52.0 years, 37% females) and 2559 healthy controls (mean age 49.0 years, 51% females), we examined the prevalence of six APOL1 SNPs (rs73885319, rs71785313, rs13056427, rs136147, rs10854688 and rs9610473) and one newly detected 55-nucleotide insertion/deletion polymorphism. RESULTS: The rs73885319 and rs71785313 variants were monomorphic in the Czech Caucasian population. Genotype frequencies of the three SNPs examined (rs13056427, rs136147 and rs9610473) were almost identical in patients and controls (all P values were between 0.39 and 0.91). Minor homozygotes of rs10854688 were more common between the patients (13.2%) than in controls (10.7%) (OR [95% CI]; 1.32 [1.08-1.64]; P < 0.01). Prevalence of the newly detected 55-bp APOL1 deletion was significantly higher in CKD5 patients (3.0% vs. 1.7%; OR [95% CI]; 1.80 [1.16-2.80]; P < 0.01) compared to controls. Frequencies of some individual APOL1 haplotypes were borderline different between patients and controls. CONCLUSION: We found an association between rs10854688 SNP within the APOL1 gene and end-stage renal disease in the Czech Caucasian population. Further independent studies are required before a conclusive association between the newly detected APOL1 insertion/deletion polymorphism and CKD5 can be confirmed.

• Klíčová slova
• Apolipoprotein L1, Haplotype, Polymorphism, Renal failure,
• MeSH
• apolipoprotein L1 genetika   MeSH
• černoši genetika   MeSH
• cyklin-dependentní kinasa 5 genetika   MeSH
• dospělí MeSH
• genetická predispozice k nemoci * MeSH
• genetická variace * MeSH
• haplotypy genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mutace INDEL genetika   MeSH
• renální insuficience genetika   MeSH
• restrikční mapování MeSH
• rizikové faktory MeSH
• senioři MeSH
• studie případů a kontrol MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• APOL1 protein, human MeSH Prohlížeč
• apolipoprotein L1 MeSH
• CDK5 protein, human MeSH Prohlížeč
• cyklin-dependentní kinasa 5 MeSH

Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species' past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.

• Klíčová slova
• Y chromosome haplotypes, domestication, matrilineal inheritance, mitochondrial haplogroups, patrilineal inheritance,
• MeSH
• chromozom Y genetika   MeSH
• domestikace * MeSH
• fylogeneze MeSH
• genetická variace * MeSH
• haplotypy genetika   MeSH
• mitochondriální DNA genetika   MeSH
• ovce genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• mitochondriální DNA MeSH

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.

• MeSH
• Asijci genetika   MeSH
• etnicita genetika   MeSH
• genetická variace genetika   MeSH
• haplotypy genetika   MeSH
• jazyk (prostředek komunikace) MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé MeSH
• populační genetika metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Geografické názvy
• Indie etnologie   MeSH
• jihovýchodní Asie etnologie   MeSH
• Thajsko etnologie   MeSH

BACKGROUND: Approximately half of patients diagnosed with Graves' disease (GD) relapse within two years of thyreostatic drug withdrawal. It is then necessary to decide whether to reintroduce conservative treatment that can have serious side effects, or to choose a radical approach. Familial forms of GD indicate a significant genetic component. Our aim was to evaluate the practical benefits of HLA and PTPN22 genetic testing for the assessment of disease recurrence risk in the Czech population. METHODS: In 206 patients with GD, exon 2 in the HLA genes DRB1, DQA1, DQB1 and rs2476601 in the gene PTPN22 were sequenced. RESULTS: The risk HLA haplotype DRB1*03-DQA1*05-DQB1*02 was more frequent in our GD patients than in the general European population. During long-term retrospective follow-up (many-year to lifelong perspective), 87 patients relapsed and 26 achieved remission lasting over 2 years indicating a 23% success rate for conservative treatment of the disease. In 93 people, the success of conservative treatment could not be evaluated (thyroidectomy immediately after the first attack or ongoing antithyroid therapy). Of the examined genes, the HLA-DQA1*05 variant reached statistical significance in terms of the ability to predict relapse (p=0.03). Combinations with either both other HLA risk genes forming the risk haplotype DRB1*03-DQA1*05-DQB1*02 or with the PTPN22 SNP did not improve the predictive value. CONCLUSION: the DQA1*05 variant may be a useful prognostic marker in patients with an unclear choice of treatment strategy.

• Klíčová slova
• Graves’ disease, HLA variants, PTPN22 gene, genetic predictors, treatment,
• MeSH
• alely MeSH
• dospělí MeSH
• frekvence genu genetika   MeSH
• genetická predispozice k nemoci genetika   MeSH
• Gravesova nemoc genetika   MeSH
• haplotypy genetika   MeSH
• lidé MeSH
• MHC antigeny I. třídy genetika   MeSH
• recidiva MeSH
• retrospektivní studie MeSH
• tyrosinfosfatasa nereceptorového typu 22 genetika   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• MHC antigeny I. třídy MeSH
• PTPN22 protein, human MeSH Prohlížeč
• tyrosinfosfatasa nereceptorového typu 22 MeSH

OBJECTIVE: We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS: We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS: The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION: The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.

• Klíčová slova
• Central Europe, Neolithic, ancient DNA, human population, mitochondrial haplogroups,
• MeSH
• antropologie fyzická MeSH
• běloši genetika   MeSH
• dějiny starověku MeSH
• haplotypy genetika   MeSH
• lidé MeSH
• mitochondriální DNA genetika   MeSH
• starobylá DNA * MeSH
• Check Tag
• dějiny starověku MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• historické články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Polsko MeSH
• Názvy látek
• mitochondriální DNA MeSH
• starobylá DNA * MeSH