Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief ...have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19th century. In order to assess population genetic dynamics of landrace barley (Hordeum vulgare), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange.
Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large ...proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives.
A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl. and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily in S. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.) Roshev, S. ancestrale Zhuk., S. dighoricum (Vav.) Roshev, S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified. These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity.
With the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
ABSTRACT
Barley landraces from Northern Europe form genetically distinct latitudinal groups, suggesting that adaption plays an important role in the geographical distribution of genetic diversity. ...Here, we investigate how Northern European barley landraces relate to landraces from other parts of Europe and whether candidate genes for climate adaption can be identified. For this purpose, 27 barley landraces, available as century‐old seed specimens, were genotyped with a 384 single nucleotide polymorphism (SNP) assay. Landraces from the Nordic countries formed a genetically distinct group relative to landraces from Central and Southern Europe. Polymorphic positions in the flowering time genes HvCO1, HvFT1, Ppd‐H1, and VRN1‐H1 were genotyped. The previously known allele distribution of Ppd‐H1 with the responsive allele present in the South and the nonresponsive allele in the North was confirmed. The other three genes were more variable in Central and Southern Europe compared to the North and neither of the flowering time genes showed any geographically correlated variation within the Nordic countries. Allelic frequencies from the 384 SNP set were correlated with climatic variables. This allowed us to identify five SNPs putatively associated with length of growth season, and two SNPs putatively associated with precipitation. The results show how historical crop specimens can be used to study how genetic variation has been geographically distributed and the genetics of adaption.
Barley, Hordeum vulgare L., has been cultivated in Fennoscandia (Denmark, Norway, Sweden, Finland) since the start of the Neolithic around 4000 years BCE. Genetic studies of extant and 19th century ...barley landraces from the area have previously shown that distinct genetic groups exist with geographic structure according to latitude, suggesting strong local adaptation of cultivated crops. It is, however, not known what time depth these patterns reflect. Here we evaluate different archaeobotanical specimens of barley, extending several centuries in time, for their potential to answer this question by analysis of aDNA. Forty-six charred grains, nineteen waterlogged specimens and nine desiccated grains were evaluated by PCR and KASP genotyping. The charred samples did not contain any detectable endogenous DNA. Some waterlogged samples permitted amplification of endogenous DNA, however not sufficient for subsequent analysis. Desiccated plant materials provided the highest genotyping success rates of the materials analysed here in agreement with previous studies. Five desiccated grains from a grave from 1679 in southern Sweden were genotyped with 100 SNP markers and data compared to genotypes of 19th century landraces from Fennoscandia. The results showed that the genetic composition of barley grown in southern Sweden changed very little from late 17th to late 19th century and farmers stayed true to locally adapted crops in spite of societal and agricultural development.
Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). ...Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h
2
) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h
2
were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.
Celotno besedilo
Dostopno za:
BF, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality ...traits in the species. We performed a functional genome‐wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO‐based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
Significance Statement
Wood provides both structural support and a transport route for water and solutes in trees. Our work provides a framework to dissect the genetic nature of wood formation and adds to our understanding of tree growth and development. With the current research focus on wood cell wall biosynthesis in general, and lignocellulose feedstock for biorefineries, we believe that this contribution will be of wide interest for the plant science community.
Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway ...spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.
The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in ...agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. FST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes.
Barley landraces from Northern Europe formgenetically distinct latitudinal groups, suggestingthat adaption plays an important role inthe geographical distribution of genetic diversity.Here, we ...investigate how Northern Europeanbarley landraces relate to landraces fromother parts of Europe and whether candidategenes for climate adaption can be identified.For this purpose, 27 barley landraces, availableas century-old seed specimens, were genotypedwith a 384 single nucleotide polymorphism(SNP) assay. Landraces from the Nordiccountries formed a genetically distinct grouprelative to landraces from Central and SouthernEurope. Polymorphic positions in the floweringtime genes HvCO1, HvFT1, Ppd-H1, and VRN1-H1 were genotyped. The previously known alleledistribution of Ppd-H1 with the responsive allelepresent in the South and the nonresponsiveallele in the North was confirmed. The otherthree genes were more variable in Central andSouthern Europe compared to the North andneither of the flowering time genes showedany geographically correlated variation withinthe Nordic countries. Allelic frequencies fromthe 384 SNP set were correlated with climaticvariables. This allowed us to identify five SNPsputatively associated with length of growth season,and two SNPs putatively associated withprecipitation. The results show how historicalcrop specimens can be used to study howgenetic variation has been geographically distributedand the genetics of adaption.
Virtualization is a well used technique in the area of internet server systems for managing several (legacy) applications on a single physical machine. These applications do not have strict time ...deadlines, which also reflects how these applications are scheduled. Using virtualization in an embedded real-time systems context is of course attractive, since we want to pack as much software as possible on a, as small as possible, hardware platform. The problem is that this kind of software does not easily cope well together, in the aspect of time related properties. Hence, we need a new mechanism, i.e., a scheduler, that can satisfy the timing requirements of each application. However, scheduler implementations typically require modifications to middleware or kernel and this is not acceptable in the area embedded systems, due to stability and reliability reasons. Hence, in this paper, we propose a framework for scheduling (soft real-time) applications residing in separate operating systems (virtual machines) using hierarchical fixed-priority preemptive scheduling, without the requirement of kernel modifications.
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