scholarly journals Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

2021 ◽  
Author(s):  
Chedly Kastally ◽  
Alina K. Niskanen ◽  
Annika Perry ◽  
Sonja T. Kujala ◽  
Komlan Avia ◽  
...  
Keyword(s):  
Scots Pine ◽  
Genotyping Array

scholarly journals Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

2021 ◽  
Author(s):  
Chedly Kastally ◽  
Alina K. Niskanen ◽  
Annika Perry ◽  
Sonja T. Kujala ◽  
Komlan Avia ◽  
...  
Keyword(s):  
Scots Pine ◽  
Boreal Forests ◽  
Association Studies ◽  
Expression Patterns ◽  
Error Rates ◽  
Specific Expression ◽  
Genotyping Array ◽  
Mendelian Error ◽  
Breeding Populations ◽  
Ecological Importance

Scots pine (Pinus sylvestris) is the most widespread coniferous tree in the boreal forests of Eurasia and has major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies and genomic selection. We present a new 50K SNP genotyping array for Scots pine research, breeding programs, and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array, and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns, and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from breeding populations from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.92%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the amount of Mendelian error was negligible. In addition, array genotypes successfully discriminate Scots pine populations from different geographic origins. The PiSy50k array will be a valuable tool for future genetic studies and forestry applications.

ASSESSMENT OF PINE CROPS GROWTH IN BAIMAK FORESTRY

2020 ◽  
Vol 37 (3) ◽  
pp. 83-90
Author(s):  
T.Z. Mutallapov ◽  
Keyword(s):  
Scots Pine ◽  
Forest Ecosystem ◽  
Distribution Curve ◽  
Comparative Assessment ◽  
Tree Distribution ◽  
Entire Structure ◽  
Structure Changes ◽  
Large Trees ◽  
Different Types ◽  
The Stability

The article presents the results of evaluating the growth of Scots pine in the Baymak forest area. The analysis of forestry and taxation indicators of Scots pine crops on the studied sample areas is carried out, and a comparative assessment of the growth of forest crops growing in different types of forest is given. Increased competition in plantings leads to the natural decline of stunted trees, which is the result of differentiation in the stand. As a result, its structure changes, the number of large trees increases, and, accordingly, the stability of the forest ecosystem increases. In this regard, the appearance of the tree distribution curve by thickness levels also changes. It becomes more "flat", and its competitive load is more evenly distributed over the entire structure of the stand, and competition is weakened.

Baumartenwechsel in den Walliser Waldföhrenwäldern verstärkt nach grossen Störungen

2018 ◽  
Vol 169 (5) ◽  
pp. 260-268 ◽  
Author(s):  
Thomas Wohlgemuth ◽  
Violette Doublet ◽  
Cynthia Nussbaumer ◽  
Linda Feichtinger ◽  
Andreas Rigling
Keyword(s):  
Scots Pine ◽  
Forest Fire ◽  
Tree Regeneration ◽  
Fire Disturbance ◽  
Pine Forests ◽  
The Past ◽  
Vegetation Shift ◽  
Tree Demography ◽  
Scots Pine Forests ◽  
High Share

Vegetation shift in Scots pine forests in the Valais accelerated by large disturbances In the past dozen years, several studies have concluded a vegetation shift from Scots pine to oak (pubescent and sessile) forests in the low elevated zones of the Valais. It is, however, not fully clear in which way such a vegetation shift actually occurs and on which processes such a shift would be based. Two studies, one on the tree demography in the intact Pfynwald and the other on the tree regeneration on the large Leuk forest fire patch, serve to discuss different aspects of the shift from Scots pine to oak. The forest stands of Pfynwald consist of 67% Scots pines and 14% oaks. Regenerating trees are 2–3.5 times more frequent in small gaps than under canopy. In gaps of the Upper Pfynwald, seedlings and saplings of Scots pine are three times more abundant than oaks, while both species regenerate in similar quantities under canopy. In the Lower Pfynwald, young oaks – especially seedlings – are more frequent than Scots pines. A different process is going on at the lower part in the Leuk forest fire patch where Scots pines prevailed before the burn of 2003. While Scots pines regenerate exclusively close to the edge of the intact forest, oaks not only resprout from trunk but also profit from unlimited spreading of their seeds by the Eurasian jay. Regeneration from seeds are hence observed in the whole studied area, independent of the proximity of seed trees. After the large fire disturbance, a mixed forests with a high share of oaks is establishing, which translates to a rapid vegetation shift. The two trajectories are discussed in the light of climate change.

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