Half-sib Families Research Articles

Betula pendula Roth. survival and growth in treeline is affected by genotype and environment

Alpine and Arctic treelines are assumed to be shifting toward higher latitudes and altitudes as a consequence of climate warming. Here, we compared the survival and growth of 1264 silver birch (Betula pendula Roth.) trees representing nine half-sib families. The trees were planted in two arboreta situated in distinct altitudinal environments in northern Finland in 1976 and 1977. The arboreta were located 9 km from each other and approximately 60 km north from the species’ most northern natural growth site at that time. They were fenced to prevent vertebrate grazing, which is known to be among the most important factors limiting the expansion and regeneration of forests in European treeline ecotones. Overall, 90% and 81% of the trees were alive five and 40 years after planting in the two arboreta, respectively. Survival of trees varied among the half-sib families, especially in Arboretum 1, situated in a lower altitudinal environment characterized by soils with lower levels of nutrients, a longer growing season, and harsher winter temperatures. Trees were distinctively bigger in Arboretum 2: 50% taller (6.2 m vs. 4.4 m) and 68% thicker (9.5 cm vs. 5.6 cm) compared to trees in Arboretum 1. Furthermore, the performance of half-sib families varied depending on the garden they were grown in. These results demonstrate that the acclimation capacity of B. pendula allows its distribution to expand north from the present range; however, local abiotic environmental conditions (soil fertility and winter temperatures) and other selection pressures (herbivory) are likely to affect the genetic structure and growth of B. pendula populations.

Genomic selection for resistance to one pathogenic strain of Vibrio splendidus in blue mussel Mytilus edulis.

The blue mussel is one of the major aquaculture species worldwide. In France, this species faces a significant threat from infectious disease outbreaks in both mussel farms and the natural environment over the past decade. Diseases caused by various pathogens, particularly Vibrio spp., have posed a significant challenge to the mussel industry. Genetic improvement of disease resistance can be an effective approach to overcoming this issue. In this work, we tested genomic selection in the blue mussel (Mytilus edulis) to understand the genetic basis of resistance to one pathogenic strain of Vibrio splendidus (strain 14/053 2T1) and to predict the accuracy of selection using both pedigree and genomic information. Additionally, we performed a genome-wide association study (GWAS) to identify putative QTLs underlying disease resistance. We conducted an experimental infection involving 2,280 mussels sampled from 24 half-sib families containing each two full-sib families which were injected with V. splendidus. Dead and survivor mussels were all sampled, and among them, 348 dead and 348 surviving mussels were genotyped using a recently published multi-species medium-density 60K SNP array. From potentially 23.5K SNPs for M. edulis present on the array, we identified 3,406 high-quality SNPs, out of which 2,204 SNPs were successfully mapped onto the recently published reference genome. Heritability for resistance to V. splendidus was moderate ranging from 0.22 to 0.31 for a pedigree-based model and from 0.28 to 0.36 for a genomic-based model. GWAS revealed the polygenic architecture of the resistance trait in the blue mussel. The genomic selection models studied showed overall better performance than the pedigree-based model in terms of accuracy of breeding values prediction. This work provides insights into the genetic basis of resistance to V. splendidus and exemplifies the potential of genomic selection in family-based breeding programs in M. edulis.

Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover

Key messageGenomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone.Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from −0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100–120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28–124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.

Rooting for Success: The Role of Microorganisms in Promoting Growth and Resilience in Black Alder Seedlings.

Polycyclic aromatic hydrocarbons (PAHs) pose a global environmental risk, impacting human health. Enhancing phytoremediation with microbial-plant interactions could help mitigate these pollutants. However, tree responses to PAHs are unclear, necessitating controlled studies before field experiments. This study examined how PAH-degrading microbes affect black alder (Alnus glutinosa L.) seedlings grown hydroponically, hypothesizing that specific microbes improve growth and stress tolerance. Two half-sib families (41-65-7 K, 13-99-1 K) were inoculated with Rhodotorula sphaerocarpa (R.s.), Pseudomonas putida (P.p.), and Sphingobium yanoikuyae (S.y.). Results showed family-dependent and microbe-specific effects, with family 41-65-7 K showing enhanced shoot growth (threefold increase by R.s.) and higher carotenoid levels. Antioxidant enzyme activities varied: R.s. elevated superoxide dismutase activity by 4.8-fold in 13-99-1 K, while catalase activity increased but decreased in 41-65-7 K. Principal component analysis revealed distinct phytochemical clustering based on microbial treatment, highlighting genotype-specific modulations. Each microorganism had unique plant growth-promoting traits, with P.p. producing the most phytohormone and S.y. fixing nitrogen. These findings support targeted microbial inoculation for effective remediation of PAH-contaminated environments.

Prediction of genotypic values via REML/BLUP and path analysis in maize half-sib families

Maize has significant relevance to food and economic security. The study aimed to evaluate the genetic gain between maize half-sib families, in the first cycle of recurrent selection, using the REML/BLUP methodology. Path analysis was also performed in order to understand the relationship between the agronomic traits. The experiment was conducted at the Federal Institute of Education, Science and Technology of Triangulo Mineiro – Campus Uberlandia. The agronomic traits evaluated, were: plant height (PH), ear height (EH), stem diameter (SD), ear length (EL), ear diameter (ED) and grain weight (GW). The results indicated significant differences only for the traits EL, GW and ED. A high coefficient of genetic variation (CVg) was observed for the traits EL, GW and ED, with only ED presenting a coefficient of relative variation (CVr) above one. The REML/BLUP methodology demonstrated high accuracy values and the estimates of gains were promising, with values of 24.07%, 21.88% e 18.23% for EL, GW and ED, respectively. Path analysis revealed the possibility of indirect gains in GW through EL.

Climate Response and Radial Growth Dynamics of Pedunculate Oak (Quercus robur L.) Plus Trees and Their Half-Sib Progeny in Periods of Severe Droughts in the Forest-Steppe Zone of Eastern Europe.

The dendrochronological parameters of 97 pedunculate oak (Quercus robur L.) trees including 20 plus trees (142-year-old on average) and four half-sib families for four of them were analyzed considering also specifically years of the most severe droughts that were identified using average monthly air temperature and precipitation data. The tree-ring width (TRW) was mostly affected by air temperature that had the largest cross-dating indices (CDI), up to 78% maximum. However, the 32-year Brückner-Egeson-Lockyer cycle (a climatic cycle of approximately 30-40 years that correlates with sunspot activity) was more reflected in the TRW dynamics in plus trees than precipitation and air temperature. A high-frequency of abnormal TRW was clearly observed during drought periods and in the following 2-3 years. Tree radial-growth reduction due to drought stress varied significantly between families. The resistance to drought based on TRW was higher in the maternal plus oak trees than in progeny. Drought resulted in reduced growth during the subsequent year(s); hence, the minimum growth occurred after the actual climate event. Autumn-winter precipitation and weather conditions were of the greatest importance at the onset of active vegetation in April and May. The influence of air temperature on oak growth was the largest in March (r = 0.39, p < 0.05). The strongest positive correlation between precipitation and growth (with r up to 0.38) was observed in May 2023. Plus trees had a high adaptive potential due to the stability of radial growth during drought with high resistance (Rt = 1.29) and resilience (Rs = 1.09) indexes. The offspring of families 1 (Rt = 0.89, Rs = 0.89) and 2 (Rt = 1.04, Rs = 0.87) had similar resistance and resilience, but the recovery indices (Rc) for offspring in families 1, 2 and 3 exceeded the recovery values for plus trees. For offspring in families 3 and 4, the index values were lower. The revealed responses of wood growth of plus trees to climatic parameters estimated as resistance (Rt), resilience (Rs) and recovery (Rc) indexes and similar responses in their progeny can be used in breeding pedunculate oak for wood growth productivity and drought resistance.

Morphological and Physiological Characteristics Influencing CO2 Assimilation Rate and Growth in Different Half-Sib Families of Quercus acuta and Q. glauca

Climate change alters vegetation patterns, pushing subtropical forests further north. These forests play a crucial role for carbon neutrality efforts due to their significant CO2 assimilation potential. This study investigated CO2 assimilation rate along with growth, morphological, and physiological traits in 23 half-sib families of Quercus acuta and 26 half-sib families of Q. glauca, two prominent East Asian evergreen broadleaf species. Q. acuta exhibited significantly higher growth rates, with diameter at breast height (DBH) and aboveground biomass exceeding those for Q. glauca by 12.1% and 69.9%, respectively (p &lt; 0.001). Leaf traits, including leaf mass pear area (LMA), leaf nitrogen, and chlorophyll content, were also greater in Q. acuta, showing 24.5%, 45.8%, and 15.6% higher values (p &lt; 0.001). While photosynthetic traits were similar, Q. acuta exhibited a 12.7% higher intrinsic water-use efficiency (iWUE) (p &lt; 0.01). Among half-sib families, marginal differences were observed in growth traits (p &lt; 0.1), and significant differences in leaf morphology and physiological traits (p &lt; 0.05) were observed. A positive correlation was found between growth and physiological traits associated with the CO2 assimilation rate in Q. acuta, but not in Q. glauca. These findings highlight the potential of Q. acuta and Q. glauca for supporting future carbon neutrality efforts and provide traits supporting carbon uptake, valuable for selecting tree species with enhanced carbon sequestration potential.

A dominant missense variant within LMBR1 related to equine polydactyly

Polydactyly was recorded before 100 BCE and attracted widespread interest because of its relationship to limb health and ancestral traits in horses. However, the underlying reasons for the development of polydactyly remain unclear. To search for polydactyly-related genes, we utilize a paternal half-sib family and screen for variants that match the mode of inheritance. Through this screening process, 77 variants in 65 genes are filtered. A missense variant (EqCab3.0 chr4: <107353368> A > G) (rs1138485164) in the 3rd exon of LMBR1 is identified as a source of amino acid sequence variation. Gene editing confirms that the variant down-regulates LMBR1expression, increases the proliferative viability of mutant cells, and inhibits apoptosis. This study suggests that LMBR1 might play a role in the development of polydactyly and that the variant detected in this study is related to polydactyly in horses. However, further research is needed to determine whether a direct relationship exists.

Volume-based selection in Pinus pinaster Aiton breeding: evaluating resistance to Bursaphelenchus xylophilus (Steiner & Buhrer) Nickle and wood properties

Key messageGenetic parameter estimates at age 12 years for trunk volume in Pinus pinaster displayed low to moderate heritability for growth and stem form, whereas wood properties showed high heritability. No correlation was detected between resistance to the nematode Bursaphelenchus xylophilus and growth, stem form, or wood properties. However, certain families stood out, showing favorable values across all traits, including resistance to the nematode.ContextThe breeding program for Pinus pinaster should advance towards a second-generation breeding population based on volume, stem form, and resistance to Bursaphelenchus xylophilus, with the challenge of incorporating novel traits of importance.AimsWe focused on assessing the genetic parameters of growth, stem form, wood properties, and resistance to B. xylophilus as well as exploring the relationship between these traits.MethodsWe evaluated 116 half-sib families at three ages (7, 12, and 17 years) in seven progeny trials established in 2005, analyzing growth, stem form, and wood traits. Resistance to B. xylophilus was assessed in 91 of the 116 half-sib families at age 2 by artificial inoculation tests under greenhouse conditions.ResultsAdvancing the selection age to 12 years proved to be feasible for volume selection in Galician P. pinaster. All traits, including resistance to B. xylophilus, showed potential for genetic improvement. Remarkably, resistance to B. xylophilus was not correlated to any other trait.ConclusionExcluding the most susceptible families to B. xylophilus from the Galician P. pinaster breeding program would not result in a significant decrease in volume, stem form, or wood properties.

Among-family variations of wood-color parameters, decay resistance, total phenol, and total flavanol content in the heartwood of the third-generation Acacia mangium in Indonesia

Abstract To evaluate the inheritance of natural durability of Acacia mangium Willd., wood-color parameters (Y [lightness], x [red to green], and y [yellow to blue]), mass loss by a white-rot fungus (Trametes versicolor) and brown-rot fungus (Fomitopsis palustris), and three different extracts (methanol extract, total phenol, and total flavanol content) were measured using the inner and outer heartwood of 10-year-old trees from 20 half-sib families in the third-generation A. mangium in Indonesia. The broad-sense heritability (H 2) values were moderate to high for the wood-color parameters and mass loss by white- and brown-rot fungi (H 2 = 0.210–0.851) and low to moderate for three different extracts (H 2 = 0.000–0.576). Significant negative phenotypic correlations were found between the three different extracts and mass loss by T. versicolor and F. palustris. In addition, negative correlations were found between the wood-color parameters and three different extracts. Similar results were found between the total phenol content and y and between the total flavanol content and Y in genetic correlations. Therefore, A. mangium families with lower Y and y in heartwood could produce progenies with higher total phenol and total flavanol content, leading to higher natural decay resistance.

Drought tolerance to overwatering, periodic underwatering and complete withholding of water in interior Douglas-fir seedlings

Seedlings of 95 greenhouse-grown interior Douglas-fir half-sibling families originating from four breeding zones were subject to overwatering and periodic underwatering and compared to an optimally watered control (15 per family = 1425 seedlings total). Averaged over all trees, annual height was reduced by 4% and 11% compared to controls for overwatering and periodic underwatering, respectively. Family overwatered seedling height was 135–75%, and underwatered height was 100–75% of their respective control heights. Shorter families under stress grew like their control compared to taller families, but this was reversed in taller families when the watering conditions were ideal. A survival analysis indicated that after 30–50 days without water, family survival varied from 25% to 90%, and most trees died after 60 days. The breeding zone had little effect on the tolerance to suboptimal water or survival during complete water withdrawal and did not interact with watering treatments. Family traits for tolerance to overwatering favoured root biomass, traits for underwatering favoured reduced stem biomass, especially in ratio to roots, and traits for survival favoured belowground biomass over aboveground biomass. No tradeoffs between tolerance to over- and underwatering were found. Some families did well in all three conditions and some in one or the other. The study results suggest that variation in family growth and survival to suboptimal watering partly relate to root and stem biomass partitioning in the interior Douglas-fir population of British Columbia.

Chromosomal aberrations and early mortality in a non-mammalian vertebrate: example from pressure-induced triploid Atlantic salmon

In commercial aquaculture, the production of triploid fish is currently the most practical approach to prevent maturation and farm-to-wild introgression following escapes. However, triploids often exhibit poor welfare, and the underlying mechanisms remain unclear. Inheritance issues associated with sub-optimal hydrostatic pressure treatments used to induce triploidy, or the genetic background of parental fish, have been speculated to contribute. We tested this by quantifying the frequency and type of chromosomal aberrations in Atlantic salmon subjected to a gradient of sub-optimal pressure treatments (Experiment 1) and from multiple mothers (Experiment 2). From these experiments, we genotyped a subsample of ~900 eyed eggs and all ~3300 surviving parr across ~20 microsatellites. In contrast to the low frequency of chromosomal aberrations in the diploid (no hydrostatic pressure) and triploid (full 9500 PSI treatment) controls, eyed eggs subjected to sub-optimal pressure treatments (6500–8500 PSI) had a higher incidence of chromosomal aberrations such as aneuploidy and uniparental disomy, corresponding to lower triploidization success and higher egg mortality rates. We also observed maternal effects on triploidization success and incidence of chromosomal aberrations, with certain half-sibling families exhibiting more aberrations than others. Chromosomal aberrations were rare among surviving parr, suggesting a purge of maladapted individuals during early development. This study demonstrates that sub-optimal hydrostatic pressure treatments and maternal effects not only influence the success of triploidization treatments, but may also affect the incidence of chromosomal aberrations and early mortality. The results have important implications for aquaculture breeding programs and their efforts to prevent farm-to-wild introgression.

Seed Treatment with Cold Plasma and Electromagnetic Field: Changes in Antioxidant Capacity of Seedlings in Different Picea abies (L.) H. Karst Half-Sib Families.

In the context of climate change, methods to improve the resistance of coniferous trees to biotic and abiotic stress are in great demand. The common plant response to exposure to vastly different stressors is the generation of reactive oxygen species (ROS) followed by activation of the defensive antioxidant system. We aimed to evaluate whether seed treatment with physical stressors can activate the activity of antioxidant enzymes and radical scavenging activity in young Picea abies (L.) H. Karst seedlings. For this, we applied seed treatment with cold plasma (CP) and electromagnetic field (EMF) and compared the response in ten different half-sib families of Norway spruce. The impact of the treatments with CP (1 min-CP1; 2 min-CP2) and EMF (2 min) on one-year-old and two-year-old P. abies seedlings was determined by the emergence rate, parameters of growth, and spectrophotometric assessment of antioxidant capacity (enzyme activity; DPPH and ABTS scavenging) in needles. The results indicated that the impact of seed treatment is strongly dependent on the genetic family. In the 577 half-sib family, the activity of antioxidant enzymes catalase (CAT), ascorbate peroxidase (APX), peroxidase (POX), and glutathione reductase (GR) increased after EMF-treatment in one-year-old seedlings, while similar effects in 477 half-sib family were induced by CP2 treatment. In two-year-old seedlings, CP1-treatment increased CAT, APX, POX, GR, SOD, DPPH, and ABTS activity in the 457 half-sib family. However, no significant impact of the treatment with CP1 was determined in one-year-old seedlings in this family. The application of novel technologies and the consideration of the combinatory impact of genetic and physical factors could have the potential to improve the accumulation of compounds that play an essential role in the defense mechanisms of P. abies. Nevertheless, for different resistance and responses to stressors of plants, their genetic properties play an essential role. A comprehensive analysis of interactions among the stress factors (CP and EMF), genetic properties, and changes induced in the antioxidant system can be of importance both for the practical application of seed treatment in forestry and for understanding fundamental adaptation mechanisms in conifers.

Vgll3 regulates the timing of puberty in farmed Atlantic salmon, but it does not explain family discordance in male maturation following different smolt production regimes

Atlantic salmon (Salmo salar) farming is moving towards extended periods of land-based production to minimise the time at sea, but this increases the risk of unwanted male sexual maturation. As the timing of puberty is driven by genetics (e.g. vgll3) and the environment, optimising rearing strategies and broodstock management may help alleviate the problem. Subsequently, we used a domesticated strain of vgll3 heterozygous broodstock to produce three all-male half-sibling families using three different production regimes to assess the timing of first puberty. Firstly, “large smolts” were produced in a flow-through system on 13 °C freshwater and constant light from first feeding (day 0) up to 1 kg (day 354). The mean incidence of pubertal males increased from 2% at 30 g, up to 78% at 1 kg. Genetics explained a significant (p < 0.05) amount of the variation, with 93, 71, and 34% of the expected early, intermediate, and late maturing vgll3 genotypes being pubertal on day 354, respectively. In addition, pubertal males in the early vgll3 genotype were found at the first sampling at ≈30 g, while it was not observed in the heterozygous and late genotypes until the fish were ≈90 g and ≈280 g, respectively. Secondly, “post-smolts” were produced by switching half the large smolts to 13 °C seawater at 420 g (day 272) and growing them in tanks to 0.95 kg (day 354). This led to a significant 14% reduction in the total incidence of puberty by day 354 compared to the large smolts. However, the regulation of pubertal timing by vgll3 did not interact with salinity. Thirdly, traditional “under-yearling” smolts were produced using periods of natural or manipulated temperature and photoperiod, followed by transfer to a sea-cage at 150 g in December (day 290) where they stayed for one year until harvest at 4.75 kg (day 648). None of these fish were mature at sea transfer, but 9% were at harvest, with 22, 7, and 2% of the early, intermediate, and late vgll3 genotypes being mature, respectively. When comparing the regimes, family effects outside of vgll3 on the prevalence of sexual maturation were significant for the land-based regimes (family means from 46 to 93% on day 354), but not in sea-cages (family means from 7 to 11% on day 648) and evidence for either vgll3 allele being dominant was mixed. Vgll3 also had minimal effects on body size/growth in any regime/family. In conclusion, i) selecting for the late vgll3 allele is an effective method to delay puberty over a range of production regimes, ii) family effects outside of vgll3 were not consistent across regimes, and iii) using seawater reduced the incidence of precocious puberty during land-based production.

The influence of origin on the quality of pedunculate oak (Quercus robur L.) seedlings

Oak forests are among the most ecologically and economically significant in Europe. Due to the consequences of climate change on the environment, successful restoration of these ecosystems has been reduced in recent times. In order to increase the regeneration of oak forests, the analysis of quality parameters of one hundred and twenty pedunculate oak (Quercus robur L.) seedlings of ten different half-sib families have been carried out in the nursery of the Institute of Forestry in Belgrade (Serbia). This study showed the influence of origin (mother trees) on the morphological characteristics of pedunculate oak seedlings. A high degree of variability has been determined for root collar diameter, height, weight of aboveground part, root weight, Roller’s sturdiness coefficient and seedlings quality index. The largest variability has been determined for the height of seedlings where a large number of transitional half-sib families is noticed between the largest and the smallest values. A small number of half-sib families (33.33%) showed high quality of seedlings, based on the cluster analysis of quality parameters. There was a high degree of correlation between root weight and aboveground part weight, giving the potential for the selection of quality reproductive material with a properly formed habitus. There was a high degree of correlation between root weight and aboveground part weight, which suggests the potential for selecting quality reproductive material with a properly formed habitus. This study facilitates the selection of suitable reproductive material sources for regenerating pedunculate oak forests within this particular region of distribution.

Productivity of hybrid sweetgum (Liquidambar formosana x styraciflua) plantations compared to native sweetgum (L. Styraciflua) in the Western Gulf Region of south-central U.S.

Sweetgum (Liquidambar styraciflua) is an excellent short-rotation woody crop species for producing hardwood pulp and biofuel feedstock on marginal sites. A recent development which may improve growth is the production of hybrid sweetgum (L. formosana x styraciflua) clones. We compared the productivity and attributes, e.g., wood specific gravity and stand growth, of operational plantations of hybrid sweetgum clones to improved native sweetgum half-sib families in 36 stands in Oklahoma, Texas, and Louisiana, U.S. The least square means (LSMean) of wood specific gravity was significantly greater for hybrids clones than the half-sibs (0.49 vs. 0.46 g/cm3), and the hybrid clones had less taper which necessitated developing genotype-specific volume and biomass equations. Despite having less fertilizer inputs on average, the hybrids had greater standing green stem biomass than the half-sibs at an age of 8.5 years (LSMean of 73.3 vs. 51.9 Mg/ha). The hybrids as a group also exhibited greater green biomass growth during the 2022 growing season when compared to the half-sibs at 8.5 years (LSMean of 15.8 vs. 11.4 Mg/ha/y). Therefore, the hybrids provide growth and wood quality advantages that may provide an opportunity to increase productivity and profitability of hardwood SRWC plantings.

Relationships between reproduction, growth, and tolerance to herbivory for the endangered plant clay phacelia (Phacelia argillacea)

The endangered plant clay phacelia (Phacelia argillacea) is endemic to Spanish Fork Canyon, Utah, USA. In addition to habitat loss and abiotic stressors, herbivory is one of clay phacelia's major threats, but negative effects of herbivory have not been quantified. To examine the effects of simulated herbivory by small mammals, we grew 300 clay phacelia plants in a greenhouse (20 replicates of 15 half-sibling families). After six months of growth, half of the plants were randomly assigned to a defoliation treatment that mimicked herbivory from ground squirrels. After providing additional time for growth and natural pollination, we collected seeds and harvested shoots and roots from a subset of the plants. Among the 15 half-sibling families, we found significant genetic variation in shoot mass and a significant correlation between total mass when defoliated and undefoliated, suggesting a strong genetic component to growth. Defoliation significantly reduced seed production, shoot production and root production by 29%, 32%, and 35%, respectively. For these traits, interactions between family (F) and defoliation (D) were not statistically significant, suggesting fixation for tolerance to herbivory. In contrast, for root-to-shoot ratio, there was a statistically significant F × D interaction, revealing genetic variation for tolerance to herbivory. Depending on the type, intensity, and timing of herbivory, clay phacelia may benefit from either increased allocation to shoots or to roots. In fact, tolerance in terms of reproduction was correlated with shoot mass when defoliated, while tolerance in terms of growth was correlated with root mass when defoliated.

Definition of metafounders based on population structure analysis

BackgroundLimitations of the concept of identity by descent in the presence of stratification within a breeding population may lead to an incomplete formulation of the conventional numerator relationship matrix (A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document}). Combining A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document} with the genomic relationship matrix (G\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{G}$$\\end{document}) in a single-step approach for genetic evaluation may cause inconsistencies that can be a source of bias in the resulting predictions. The objective of this study was to identify stratification using genomic data and to transfer this information to matrix A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document}, to improve the compatibility of A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document} and G\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{G}$$\\end{document}.MethodsUsing software to detect population stratification (ADMIXTURE), we developed an iterative approach. First, we identified 2 to 40 strata (k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}) with ADMIXTURE, which we then introduced in a stepwise manner into matrix A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document}, to generate matrix AΓ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathbf{A}}^{{\\varvec{\\Gamma}}}$$\\end{document} using the metafounder methodology. Improvements in consistency between matrix G\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{G}$$\\end{document} and AΓ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathbf{A}}^{{\\varvec{\\Gamma}}}$$\\end{document} were evaluated by regression analysis and through the comparison of the overall mean and mean diagonal values of both matrices. The approach was tested on genotype and pedigree information of European and North American Brown Swiss animals (85,249). Analyses with ADMIXTURE were initially performed on the full set of genotypes (S1). In addition, we used an alternative dataset where we avoided sampling of closely related animals (S2).ResultsResults of the regression analyses of standard A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document} on G\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{G}$$\\end{document} were – 0.489, 0.780 and 0.647 for intercept, slope and fit of the regression. When analysing S1 data results of the regression for AΓ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathbf{A}}^{{\\varvec{\\Gamma}}}$$\\end{document} on G\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{G}$$\\end{document} corresponding values were – 0.028, 1.087 and 0.807 for k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}=7, while there was no clear optimum k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}. Analyses of S2 gave a clear optimal k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document}=24, with − 0.020, 0.998 and 0.817 as results of the regression. For this k\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$k$$\\end{document} differences in mean and mean diagonal values between both matrices were negligible.ConclusionsThe derivation of hidden stratification information based on genotyped animals and its integration into A\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{A}$$\\end{document} improved compatibility of the resulting AΓ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\mathbf{A}}^{{\\varvec{\\Gamma}}}$$\\end{document} and G\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathbf{G}$$\\end{document} considerably compared to the initial situation. In dairy breeding populations with large half-sib families as sub-structures it is necessary to balance the data when applying population structure analysis to obtain meaningful results.

A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle

BackgroundNine male and eight female calves born to a Normande artificial insemination bull named “Ly” were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality.ResultsUsing Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G > A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes.ConclusionsIn conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.

Evaluation of Mechanical Wood Properties of Silver Birch (Betula pendula L. Roth.) of Half-Sib Genetic Families

Silver birch, a widely distributed deciduous tree native to Europe, is valued for its wood applications in construction, furniture making, and paper production. In Lithuania, silver birch ranks as the third most common forest-tree species, comprising 22% of the forested areas, and is an important species for tree breeding due to its potential and adaptability. This study was focused on assessing the mechanical properties of wood (sample and log hardness, wood density, dynamic modulus of elasticity (MOEdyn), static modulus of elasticity (MOE) and bending strength (MOR)) in silver birch (Betula pendula L. Roth.) trees from different half-sibling families. Two experimental plantations of the progenies of Lithuanian populations (half-sib families) of silver birch from different regions were analysed. From these plantations, four genetic families were selected for mechanical properties evaluation. The study findings revealed significant variability in various wood properties among different genetic families, although the static modulus of elasticity did not exhibit significant differences between the chosen genetic families. All measured wood properties decreased from the bottom to the top of the model trees. Wood hardness displayed a moderately negative correlation for wood density and weak correlations for MOE and MOR. Given the weak correlations between wood hardness and other wood mechanical properties, it is suggested that MOEdyn would be a more suitable trait for genetic studies.