Key message Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. AbstractWe investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2762-7) contains supplementary material, which is available to authorized users.

Abstract:Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.Key words: oat, flow cytometry, nucleus, polyploidy.Résumé : La taille du génome est un indicateur de la distance évolutive et constitue un paramètre pour la caractéri-sation des génomes. Ici, les auteurs rapportent des estimés précis de la taille du génome chez 99 accessions appartenant à 26 espèces du genre Avena. Les auteurs montrent que la taille moyenne du génome chez les espèces diploïdes ayant un génome C (2C = 10,26 pg) est 15 % supérieure à celui des espèces ayant un génome A (2C = 8,95 pg), et que cette différence explique vraisemblablement la progression dans la taille des génomes parmi les espèces tétraploïdes, où AB < AC < CC (en moyenne, 2C = 16,76, 18,60 et 21,78 pg, respectivement). Toutes les accessions des trois espèces hexaploïdes ayant une composition génomique ACD présentaient des tailles de génome comparables (en moyenne, 2C = 25,74 pg). La taille du génome était généralement stable au sein d'une espèce, et conforme aux connaissances actuelles en ce qui a trait aux distances évolutives entre elles. Les résultats suggèrent également que la plupart des espèces polyploïdes du genre Avena ont connu une réduction de la taille du génome par rapport aux espèces diploïdes ancestrales. Les mesures de la taille du génome pourraient fournir une source additionnelle de contrôle de qualité lors de l'identification des espèces au sein de collections de ressources génétiques, particulièrement dans les cas où des espèces diploïdes et polyploïdes présentent une morphologie semblable. [Traduit par la Rédaction] Mots-clés : avoine, cytométrie en flux, noyau, polyploïdie.

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It is recognized that human activities, such as fossil fuel burning, land-use change, and forest harvesting at a large scale, have resulted in the increase of greenhouse gases in the atmosphere since the onset of the industrial revolution. The increasing amounts of greenhouse gases, particularly CO2 in the atmosphere, is believed to have induced climate change and global warming. With the ability to remove CO2 from the atmosphere through photosynthesis, forests play a critical role in the carbon cycle and carbon sequestration at both global and local scales. It is necessary to understand the relationship between forest soil carbon dynamics and carbon sequestration capacity, and the impact of forest management practices on soil CO2 efflux for sustainable carbon management in forest ecosystems. This paper reviews a number of current issues related to (1) carbon allocation, (2) soil respiration, and (3) carbon sequestration in the forest ecosystems through forest management strategies. The contribution made by forests and forest management in sequestrating carbon to reduce the CO2 concentration level in the atmosphere is now well recognized. The overall carbon cycle, carbon allocation of the above-and belowground compartments of the forests, soil carbon storage and soil respiration in forest ecosystems and impacts of forest management practices on soil respiration are described. The potential influences of forest soils on the buildup of atmospheric carbon are reviewed.Résumé : On reconnaît que les activités humaines, comme le brûlage d'huiles fossiles, les modifications de l'utilisation du territoire et la récolte des forêts sur de grandes échelles ont conduit à une augmentation de l'effet serre dans l'atmosphère, depuis le début de la révolution industrielle. On croit que l'augmentation des gaz à effet serre dans l'atmosphère, particulièrement le CO 2 , a induit le changement climatique et le réchauffement global. Avec leur capacité à éliminer le CO 2 de l'atmosphère par la photosynthèse, les forêts jouent un rôle critique dans le cycle du carbone et la séquestration du carbone, à la fois à l'échelle globale et à l'échelle locale. On doit comprendre les relations qui existent entre la dynamique du carbone des sols forestiers et leur capacité de séquestration, ainsi que l'impact des pratiques d'aménagement sur l'efflux de CO 2 , dans la perspective de l'aménagement durable des écosystèmes forestiers. Les auteurs présentent une synthèse des problématiques actuelles reliées à (1) l'allocation du carbone (2) la respiration du sol et (3) la séquestration du carbone dans les écosystèmes forestiers par des stratégies d'aménagement forestier. On reconnaît maintenant très bien le rôle des forêts et de l'aménagement forestier dans la séquestration du carbone pour réduire la teneur en CO2 de l'atmosphère. Les auteurs décrivent le cycle global du carbone, l'allocation du carbone aux compartiments épigés et hypogés des forêts, l'accumulation du carbone dans le sol et la respiration des sols des écosystèmes forestiers, ainsi que...

Tibetan semiwild wheat (Triticum aestivum ssp. tibetanum Shao) is a primitive hexaploid wheat resource found in Tibet. It is characterized by tolerance to nutrition deficiency and strong seed dormancy and has potential to be useful in wheat breeding programs. To tap the advantages of Tibetan semiwild wheat in wheat breeding, we investigated nine agronomic traits including heading date (HD), anthesis date (AD), plant height (PHT), tiller number (TN), spike length (SL), spikelet number per spike (SNS), spikelet density (DS), grain weight per spike (GWS), and 1000‐grain weight (TGW) in 186 recombinant inbred lines from a cross between Tibetan semiwild wheat ‘Q1028’ and common wheat ‘Zhengmai 9023’ (ZM 9023) across three growing seasons. Forty‐five qualitative trait loci (QTLs) on 12 chromosomes were detected. The phenotypic variation explained by each of these QTL ranged from 4.7 to 29.7%. Positive alleles for 28 of these QTLs were derived from Q1028. Of these QTLs, 25 (56%) were detected in at least two growing seasons. Fifteen stable QTLs that were significant across all three growing seasons were identified. Novel QTLs derived from Q1028 were identified, such as QSd.sau‐7A for spikelet density, QTgw.sau‐2B for TGW and QSns.sau‐3D for SNS. Eleven QTL clusters were detected, including one on chromosome 5A flanked by the markers wPt‐9094 and wPt‐9513. This cluster consists of QTLs controlling HD, AN, PHT, SL, and spikelet density and explained 6.6 to 12.6% of the phenotypic variation in these traits. The QTLs and molecular markers identified here could be useful in fine mapping and breeding programs.

The development and application of molecular methods in oats has been relatively slow compared with other crops. Results from the previous analyses have left many questions concerning species evolutionary relationships unanswered, especially regarding the origins of the B and D genomes, which are only known to be present in polyploid oat species. To investigate the species and genome relationships in genus Avena, among 13 diploid (A and C genomes), we used the second intron of the nuclear gene FLORICAULA/LEAFY (FL int2) in seven tetraploid (AB and AC genomes), and five hexaploid (ACD genome) species. The Avena FL int2 is rather long, and high levels of variation in length and sequence composition were found. Evidence for more than one copy of the FL int2 sequence was obtained for both the A and C genome groups, and the degree of divergence of the A genome copies was greater than that observed within the C genome sequences. Phylogenetic analysis of the FL int2 sequences resulted in topologies that contained four major groups; these groups reemphasize the major genomic divergence between the A and C genomes, and the close relationship among the A, B, and D genomes. However, the D genome in hexaploids more likely originated from a C genome diploid rather than the generally believed A genome, and the C genome diploid A. clauda may have played an important role in the origination of both the C and D genome in polyploids.

Two uncorrelated nucleotide sequences, chloroplast intergenic spacer psbA-trnH and acetyl CoA carboxylase gene (Acc1), were used to perform phylogenetic analyses in 75 accessions of the genus Avena, representing 13 diploids, seven tetraploid, and four hexaploids by maximum parsimony and Bayesian inference. Phylogenic analyses based on the chloroplast intergenic spacer psbA-trnH confirmed that the A genome diploid might be the maternal donor of species of the genus Avena. Two haplotypes of the Acc1 gene region were obtained from the AB genome tetraploids, indicating an allopolyploid origin for the tetraploid species. Among the AB genome species, both gene trees revealed differences between Avena agadiriana and the other species, suggesting that an AS genome diploid might be the A genome donor and the other genome diploid donor might be the Ac genome diploid Avena canariensis or the Ad genome diploid Avena damascena. Three haplotypes of the Acc1 gene have been detected among the ACD genome hexaploid species. The haplotype that seems to represent the D genome clustered with the tetraploid species Avena murphyi and Avena maroccana, which supported the CD genomic designation instead of AC for A. murphyi and A. maroccana.

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