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37 results for “Tree breeding”
Efficient genomics based 'end-to-end' selective tree breeding framework
<p>Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingences and concerns. Here, we introduce an "end-to-end" selective tree breeding framework that: 1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, 2) generates unprecedented resolution of genealogical relationships among tested individuals, and 3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals' breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits' correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method's superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.</p>
Fig. 1 in Distribution Pattern, Nest-Tree Features And Breeding Performance Of Population Of The Black Stork, Ciconia Nigra (Ciconiiformes, Ciconiidae), In Northwestern Serbia
Fig. 1. The proportion of tree species picked for nest placement by the Black Stork (Ciconia nigra) in Northwestern Serbia (n = 44).
Fig. 5. Phylogenetic tree depicting inferred genetic relationships among Leucocytozoon mitochondrial DNA cytochrome b in Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska
Fig. 5. Phylogenetic tree depicting inferred genetic relationships among Leucocytozoon mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the Yukon-Kuskokwim Delta, Alaska during 2006–2016 and those previously reported for closely related haemosporidian morphospecies on the National Center for Biotechnology Information GenBank and Malavi databases (accession IDs in parentheses). Bars to the right of tree represent the assignment of sequences to L. simondi clade A (teal), L. simondi clade B (orange), or other Leucocytozoon. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4. Phylogenetic tree depicting inferred genetic relationships among Haemoproteus mitochondrial DNA cytochrome b in Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska
Fig. 4. Phylogenetic tree depicting inferred genetic relationships among Haemoproteus mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the Yukon-Kuskokwim Delta, Alaska during 2006–2016 and those previously reported for closely related haemosporidian morphospecies on the National Center for Biotechnology Information GenBank and Malavi databases (accession IDs in parentheses).
Low-input breeding in stone pine, a multipurpose forest tree with low genome diversity
<p><span>Stone pine (<em>Pinus pinea</em> L.) is an emblematic tree species within the Mediterranean basin, with high ecological and economic relevance due to the production of edible nuts. Breeding programmes to improve pine nut production started decades ago in Southern Europe but have been hindered by the near absence of polymorphisms in the species genome and the lack of suitable genomic tools. In this study, we assessed new stone pine’s genomic resources and their utilisation in breeding and sustainable use, by using a commercial SNP-array (5,671 SNPs). Firstly, we confirmed the accurate clonal identification and identity check of 99 clones from the Spanish breeding programme. Secondly, we successfully estimated genomic relationships in</span><span> clonal collections, an information needed for </span><span>low-input breeding and genomic prediction. Thirdly, we applied this information to genomic prediction for total number of cones unspoiled by pests and their weight measured in three Spanish clonal tests. Genomic prediction accuracy depends on the trait under consideration and possibly on the number of genotypes included in the test. Predictive ability (<em>r</em><sub><span>y</span></sub>) was significant for the mean cone weight measured in the three clonal tests, while solely significant for the number of cones in one clonal test. The combination of a new SNP-array together with the phenotyping of relevant commercial traits into genomic prediction models, proved to be very promising to identify superior clones for cone weight. This approach opens new perspectives for early selection. </span></p>
Figure 3 in Do male tree frogs feed during the breeding season? Stomach flushing of five syntopic hylid species in Rio Grande do Sul, Brazil
Figure 3. Relation between length of the reproductive period and food intake by 50 males per species.
How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote x homozygote relationships in optimal contribution selection in the case study of Populus nigra
<p><span><span><span><span><span><span>In breeding, Optimal Contribution Selection (OCS) is one of the most effective strategies to balance short- and long-term genetic responses, by maximizing genetic gain and minimizing global coancestry. Considering genetic diversity in the selection dynamic – through coancestry – is undoubtedly the reason for the success of OCS, as it avoids intial loss of favorable alleles. Originally formulated with the pedigree relationship matrix, global coancestry can nowadays be assessed with one of the possible formulations of the realized genomic relationship matrix. Most formulations were optimized for genomic evaluation, but few for the management of coancestry. We introduce here an alternative formulation specifically developed for Genomic OCS (GOCS), intended to better control heterozygous loci, and thus better account for Mendelian sampling. We simulated a multi-generation breeding program with mate allocation and under GOCS for twenty generations, solved with quadratic programming. With the case study of </span></span></span><span><i><span>Populus nigra</span></i></span><span><span><span>, we have shown that, although the dynamic was mainly determined by the trade-off between genetic gain and genetic diversity, better formulations of the genomic relationship matrix, especially those fostering individuals carrying multiple heterozygous loci, can lead to better short-term genetic gain and a higher selection plateau. </span></span></span></span></span></span></p>
How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote x homozygote relationships in optimal contribution selection in the case study of Populus nigra
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Efficient genomics based ‘end-to-end’ selective tree breeding framework
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Radar revelations: Insect availability influences parental provisioning in breeding Tree Swallows (Tachycineta bicolor)
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Data from: Forest tree breeding using genomic Markov causal models: A new approach to genomic tree breeding improvement
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Figure 2 in Do male tree frogs feed during the breeding season? Stomach flushing of five syntopic hylid species in Rio Grande do Sul, Brazil
Figure 2. Frequency of animal items ingested by 50 calling male frogs per species.
Figure 1 in Do male tree frogs feed during the breeding season? Stomach flushing of five syntopic hylid species in Rio Grande do Sul, Brazil
Figure 1. Frequency of animal and plant items ingested by 50 calling male frogs per species.
Data from: Exotic tree plantations as alternative breeding habitat for an endemic avian predator
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Rainfall and nest site competition delay Mountain Bluebird and Tree Swallow breeding but do not impact productivity
<p>Optimizing breeding phenology, an important aspect of fitness, is complex for migratory species as they must make key timing decisions early, and remotely, from breeding sites. We examined the role of weather (locally and cross-seasonally), cavity availability, and competitive exclusion in determining among-year variation in breeding phenology over 17 years for two migratory, cavity-nesting birds: Mountain Bluebirds (<em>Sialia currucoides</em>; n = 462 nests) and Tree Swallows (<em>Tachycineta bicolor</em>; n = 572) using natural tree cavities in British Columbia, Canada. We assessed weather effects within the winter and migratory range and at our study sites. We quantified competition as the proportion of cavities occupied by European Starlings (<em>Sturnus vulgaris</em>) (for both species) and Mountain Bluebird (for Tree Swallow only) in each year. For 229 bluebird and 177 swallow nests with known fates, we tested whether late years resulted in reduced productivity. Although the effects were small, heavy rainfall and strong diurnal westerly winds during migration were associated with breeding delays for Mountain Bluebirds. However, cavity availability (earlier breeding with increases) had a 5-8X greater effect on timing than migratory conditions. There was no evidence that starling competition delayed bluebirds. In Tree Swallows, greater local daily rainfall was associated with delayed breeding, as was starling abundance (the effect of starlings was 1.4X times smaller than that of rainfall). Neither bluebird abundance nor cavity availability changed swallow phenology. Neither species showed reduced productivity in late breeding years. In both species, individuals that bred late relative to conspecifics within-year had smaller clutches and greater probability of nest failure. We conclude that breeding ground conditions, particularly cavity limitation and local rainfall (for swallows), are important drivers of breeding phenology for our focal species, but that the productivity cost of late years, at least for Tree Swallows, is minimal. </p>
Data from: Multidimensional environmental influences on timing of breeding in a tree swallow population facing climate change
Most phenological traits are extremely sensitive to current climate change and advances in the timing of important life-history events have been observed in many species. In birds, phenotypic plasticity in response to temperature is thought to be the main mechanism underlying yearly adjustment in the timing of breeding. However, other factors could be important and interact to affect the levels of plastic responses between and/or within-individuals. Here we use long-term individual-based data on Tree swallow (Tachycineta bicolor) to identify the spatial and environmental drivers affecting plasticity in laying date and to assess their importance at both population and individual levels. We found that laying date has advanced by 4.2 days over 10 years, and that it was mainly influenced by latitude and an interaction between spring temperature and breeder density. Analyses of individual plasticity showed that increases in temperature, but not in breeder density, resulted in within-individual advances in laying date. Our results suggest that females can adjust their laying date as a function of temperature, but that this adjustment will be partly constrained in habitats with lower breeder densities. Such potential constraint is especially worrying for the broad array of species already declining as a result of climate change.
FIGURE 3 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 3. (A) Palmar, and (B) plantar views of right hand and foot of the holotype of Osteocephalus castaneicola sp. n. (CBF 6051). Scale bar equals 5 mm.
FIGURE 4 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 4. Schematic map of northern Bolivia showing the known distribution of Osteocephalus castaneicola sp. n. in Bolivia: (1) San Antonio del Matti, (2) San Antonio de Filadelfia (type locality).
FIGURE 1 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 1. The majority rule consensus tree of the Bayesian phylogeny of the frog genus Osteocephalus, using mitochondrial 12S rRNA – tRNA-Val – 16S rRNA data. Nodal support, Bayesian posterior probabilities (BPP) and maximum likelihood (PhyML) bootstrap (1000 pseudoreplicates), are indicated. Collapsed branches were supported <50 % bootstrap and <0.50 BPP. The asterisk denotes the tadpole sample from a water-filled fruit capsule of the Brazil nut tree. Osteocephalus "oophagus" no. AF467267 may represent O. cabrerai according to Fouquet et al. (2007, Supporting Information).
FIGURE 2 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 2. Holotype of Osteocephalus castaneicola sp. n. (CBF 6051) in life, (A) dorsal, and (B) ventral views. (C) Adult female paratype of Osteocephalus castaneicola sp. n. (CBF 6052) in life. (D) Night colouration of adult male paratype of Osteocephalus castaneicola sp. n. (NMP6V 73810/2) under natural conditions. (E) Newly metamorphosed juvenile of Osteocephalus castaneicola sp. n. (F) Adult male of Osteocephalus sp. (B) (NMP6V 73105) from Canadá (Bolivia, Pando) in life.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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