Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

• Klíčová slova
• comparative mapping, flowering time, parallel domestication,
• MeSH
• DNA rostlinná genetika   MeSH
• genetická variace MeSH
• genetické lokusy MeSH
• jedlá semena genetika   MeSH
• klonování DNA MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• párování bází genetika   MeSH
• rostlinné geny * MeSH
• rostlinné proteiny chemie   genetika   MeSH
• rýže (rod) genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA MeSH
• sekvenční delece MeSH
• sekvenční seřazení MeSH
• selekce (genetika) MeSH
• Setaria (rostlina) genetika   MeSH
• Sorghum genetika   MeSH
• terciární struktura proteinů MeSH
• zemědělství * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• rostlinné proteiny MeSH

The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F2 and F3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.

• Klíčová slova
• Plant height, QTL × QTL interaction, Quantitative Trait Locus (QTL), Segregation distortion, Sorghum domestication, Transgressive segregation,
• MeSH
• chromozomy rostlin genetika   MeSH
• domestikace * MeSH
• genom rostlinný genetika   MeSH
• kvantitativní znak dědičný * MeSH
• lokus kvantitativního znaku genetika   MeSH
• mapování chromozomů MeSH
• rostlinné geny genetika   MeSH
• semena rostlinná MeSH
• šlechtění rostlin metody   MeSH
• Sorghum anatomie a histologie   genetika   MeSH
• Publikační typ
• časopisecké články MeSH

The effects of gastrointestinal tract microbiota (GTM) on host physiology and health have been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M. m. musculus and M. m. domesticus). Sequenced individuals were selected according to a 2 × 2 experimental design: wild (14) vs. inbred origin (16) and M. m. musculus (15) vs. M. m. domesticus (15). We compared alpha diversity (i.e. number of operational taxonomic units - OTUs), beta diversity (i.e. interindividual variability) and microbiota composition across the four groups. We found no difference between M. m. musculus and M. m. domesticus subspecies, suggesting low effect of genetic differentiation between these two subspecies on GTM structure. Both inbred and wild populations showed the same level of microbial alpha and beta diversity; however, we found strong differentiation in microbiota composition between wild and inbred populations. Relative abundance of ~ 16% of OTUs differed significantly between wild and inbred individuals. As laboratory mice represent the most abundant model for studying the effects of gut microbiota on host metabolism, immunity and neurology, we suggest that the distinctness of laboratory-kept mouse microbiota, which differs from wild mouse microbiota, needs to be considered in future biomedical research.

• Klíčová slova
• Mus musculus, domestication, hybrid zone, metagenomics, microbiome, symbiosis,
• MeSH
• Bacteria klasifikace   MeSH
• divoká zvířata mikrobiologie   MeSH
• gastrointestinální trakt mikrobiologie   MeSH
• genetická variace * MeSH
• inbrední kmeny myší mikrobiologie   MeSH
• metagenom MeSH
• mikrobiota genetika   MeSH
• myši MeSH
• RNA ribozomální 16S genetika   MeSH
• taxonomické DNA čárové kódování MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

Faecal (at least 3 months before slaughtering) and organ examinations were carried out in 611 animals (497 dairy, 69 dual-purpose and 44 beef cattle) originating from eight paratuberculosis infected cattle herds. The diagnosis in cattle was established by routine intestinal culture (ileum and the adjacent lymph nodes) after slaughter. In selected 132 animals, post-mortem intensive culture was performed on tissue samples collected from the gastrointestinal tract (duodenum, jejunum, ileum, ileocecal valve, caecum, rectum) and the corresponding lymph nodes, submandibular, retropharyngeal, tracheobronchial, liver and supramammary lymph nodes, kidney, liver and spleen. In 251 (41.1%) of all 611 animals, Mycobacterium avium subspecies paratuberculosis could be isolated from the faeces; in 164 (65.7%) out of 251 shedding animals the infection was detected in the ileum and adjacent lymph nodes. The detection of M. paratuberculosis by routine intestinal culture of faecal culture positive animals varied from 46.0% in animals shedding 1 CFU (colony forming unit), to 94.7% in massive shedders. On the contrary, M. paratuberculosis was detected by routine intestinal culture in 92 (25.5%) of the 360 faecal culture negative animals. Shedding animals had significantly higher (P<0.01) number of organisms in their organs than non-shedding animals. During the intensive tissue cultivation from selected 132 animals, 72 (54.5%) of them were positive. For the negative animals, no significant difference was found between the detection rate in organs examined after slaughter with routine and intensive method. However, in the subgroup of tissue culture positive animals a highly significant difference (P<0.01) was found by intensive examination (83.0%) compared with the routine examination (60.4%). Out of 72 tissue culture positive animals 73.6% of them harboured M. paratuberculosis in the gastrointestinal tract, 16.7% in the gastrointestinal tract and the parenchymatous organs, tracheobronchial and mandibular lymph nodes. The rest of the 9.7% of the infection was detected in the lymph nodes of head and lungs. Our study concerning the distribution of M. paratuberculosis by intensive examinations revealed a minimum effect of breed and production type on localisation of the agent. Thus, the results suggest that in case of an active infection, M. paratuberculosis can be localised in different organs of animals irrespective of their breed or production type.

• MeSH
• feces mikrobiologie   MeSH
• kultivační techniky veterinární   MeSH
• lymfatické uzliny mikrobiologie   MeSH
• mlékárenství MeSH
• Mycobacterium avium subsp. paratuberculosis izolace a purifikace   MeSH
• nemoci skotu diagnóza   MeSH
• paratuberkulóza diagnóza   MeSH
• skot MeSH
• střeva mikrobiologie   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• skot MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

• MeSH
• alely MeSH
• chov zvířat metody   MeSH
• chov MeSH
• destičkový růstový faktor metabolismus   MeSH
• divoká zvířata genetika   MeSH
• druhová specificita MeSH
• fenotyp MeSH
• frekvence genu MeSH
• genetická variace MeSH
• genetika MeSH
• genomika MeSH
• genotyp MeSH
• jednonukleotidový polymorfismus MeSH
• mutace MeSH
• ovce domácí genetika   MeSH
• ovce MeSH
• sekvenční analýza DNA MeSH
• sekvenování celého genomu MeSH
• selekce (genetika) MeSH
• vazebná nerovnováha MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• destičkový růstový faktor MeSH

J subgroup avian leukosis virus (ALV-J) infects domestic chicken, jungle fowl, and turkey and enters the host cell through a receptor encoded by tvj locus and identified as Na+/H+ exchanger 1 (NHE1). The resistance to ALV-J in a great majority of examined galliform species was explained by deletions or substitutions of the critical tryptophan 38 in the first extracellular loop of NHE1, and genetic polymorphisms around this site predict the susceptibility or resistance of a given species or individual. In this study, we examined the NHE1 polymorphism in domestic chicken breeds and documented quantitative differences in their susceptibility to ALV-J in vitro. In a panel of chicken breeds assembled with the aim to cover the maximum variability encountered in domestic chickens, we found a completely uniform sequence of NHE1 extracellular loop 1 (ECL1) without any source of genetic variation for the selection of ALV-J-resistant poultry. In parallel, we studied the natural polymorphisms of NHE1 in wild ducks and geese because of recent reports on ALV-J positivity in feral Asian species. In anseriform species, we demonstrate a specific and highly conserved critical ECL1 sequence without any homologue of tryptophan 38 in accordance with the resistance of duck cells to prototype ALV-J. Last, we demonstrated that the new Asian strains of ALV-J have not evolved their envelope glycoprotein to the entry the duck cells. Our results contribute substantially to the current discussion of possible heterotransmission of ALV-J and its spill-over into the wild ducks and geese.

• MeSH
• divoká zvířata * MeSH
• genetická variace * MeSH
• hospodářská zvířata * MeSH
• kultivované buňky MeSH
• kur domácí MeSH
• kuřecí embryo MeSH
• molekulární sekvence - údaje MeSH
• Na(+)-H(+) antiport chemie   genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin MeSH
• zvířata MeSH
• Check Tag
• kuřecí embryo MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Na(+)-H(+) antiport MeSH

BACKGROUND: Trypanosomatids are parasitic flagellates well known because of some representatives infecting humans, domestic animals, and cultural plants. Many trypanosomatid species bear RNA viruses, which, in the case of human pathogens Leishmania spp., influence the course of the disease. One of the close relatives of leishmaniae, Leptomonas pyrrhocoris, has been previously shown to harbor viruses of the groups not documented in other trypanosomatids. At the same time, this species has a worldwide distribution and high prevalence in the natural populations of its cosmopolitan firebug host. It therefore represents an attractive model to study the diversity of RNA viruses. RESULTS: We surveyed 106 axenic cultures of L. pyrrhocoris and found that 64 (60%) of these displayed 2-12 double-stranded RNA fragments. The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. Only two of these species, a tombus-like virus and an Ostravirus, were earlier documented in L. pyrrhocoris. In addition, there were four new species of Leishbuviridae, the family encompassing trypanosomatid-specific viruses, and a new species of Qinviridae, the family previously known only from metatranscriptomes of invertebrates. Currently, this is the only qinvirus with an unambiguously determined host. Our phylogenetic inferences suggest reassortment in the tombus-like virus owing to the interaction of different trypanosomatid strains. Two of the new Leishbuviridae members branch early on the phylogenetic tree of this family and display intermediate stages of genomic segment reduction between insect Phenuiviridae and crown Leishbuviridae. CONCLUSIONS: The unprecedented wide range of viruses in one protist species and the simultaneous presence of up to five viral species in a single Leptomonas pyrrhocoris isolate indicate the uniqueness of this flagellate. This is likely determined by the peculiarity of its firebug host, a highly abundant cosmopolitan species with several habits ensuring wide distribution and profuseness of L. pyrrhocoris, as well as its exposure to a wider spectrum of viruses compared to other trypanosomatids combined with a limited ability to transmit these viruses to its relatives. Thus, L. pyrrhocoris represents a suitable model to study the adoption of new viruses and their relationships with a protist host.

• Klíčová slova
• Leishbuviridae, Ostravirus, Pyrrhocoris apterus, Qinviridae, Tombus-like viruses,
• MeSH
• fylogeneze MeSH
• hospodářská zvířata MeSH
• lidé MeSH
• RNA-viry * genetika   MeSH
• Trypanosomatina * genetika   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Lactation is the most energy demanding part of parental care in mammals, so parent-offspring conflict arises over milk provided by the mother. In some species females commonly become pregnant shortly after parturition of previous young. This further intensifies mother-offspring conflict due to concurrent pregnancy and lactation. In equids it has been well established that pregnant females wean their foals earlier than non-pregnant ones. Intensified mother-offspring conflict was presumed to associate with pregnancy also during the period of intensive lactation, i.e., before the weaning process starts. We investigated the effect of pregnancy on suckling behaviour characteristics as indicators of mother-offspring conflict in domestic horses. Contrary to expectation, here we provide evidence of a decreased mother-offspring conflict related to pregnancy in lactating females during first two trimesters of pregnancy. Pregnant mares provided longer suckling bouts and did not reject or terminate suckling of their foals more often than non-pregnant mares. Our results suggest that pregnant mares cope with parallel investment into a nursed foal and a foetus through enhancing nursing behaviour in early stages of pregnancy before the initially low requirements of the foetus increase. They compensate their suckling foal with the perspective of its early weaning due to ongoing pregnancy.

• MeSH
• kojená zvířata fyziologie   MeSH
• koně fyziologie   MeSH
• konflikt (psychologie) * MeSH
• laktace fyziologie   MeSH
• matky * MeSH
• rozmnožování fyziologie   MeSH
• těhotenství u zvířat fyziologie   MeSH
• těhotenství MeSH
• zvířata MeSH
• Check Tag
• těhotenství MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

• MeSH
• délka genomu MeSH
• duplikace genu MeSH
• genetické lokusy MeSH
• genom rostlinný * MeSH
• kontigové mapování metody   MeSH
• kvantitativní znak dědičný * MeSH
• pšenice genetika   MeSH
• regulace genové exprese u rostlin MeSH
• retroelementy MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• škrob biosyntéza   MeSH
• šlechtění rostlin MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zemědělské plodiny genetika   MeSH
• žito genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• retroelementy MeSH
• rostlinné proteiny MeSH
• škrob MeSH

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.

• Klíčová slova
• chromosome sorting, comparative genomics, hexaploid wheat, next-generation sequencing, wild emmer wheat,
• MeSH
• chromozomy rostlin genetika   MeSH
• genetické lokusy genetika   MeSH
• genom rostlinný genetika   MeSH
• konzervovaná sekvence genetika   MeSH
• lipnicovité genetika   MeSH
• mikro RNA genetika   MeSH
• nekódující RNA genetika   MeSH
• polyploidie MeSH
• průtoková cytometrie MeSH
• pšenice genetika   MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• rostlinné geny genetika   MeSH
• tetraploidie MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mikro RNA MeSH
• nekódující RNA MeSH