How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote × homozygote relationships in optimal contribution selection in the case study of Populus nigra
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ABSTRACT:
SUBMITTER: Tiret M
PROVIDER: S-EPMC8591327 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The century-old Hardy-Weinberg law remains fundamental to population genetics. Typically Hardy-Weinberg equilibrium is tested in unrelated individuals using a chi(2) goodness-of-fit test that compares expected and observed numbers of heterozygotes and homozygotes. In this report, we propose a likelihood ratio test for Hardy-Weinberg equilibrium that accommodates a mixture of pedigree and random sample data. The underlying statistical model depends on a parameter gamma determining the ratio of heterozygous genotypes to homozygous genotypes among pedigree founders. As our heterozygous-homozygous test accommodates markers with dominant and recessive alleles, it can handle the phase ambiguities encountered in combining several linked single nucleotide polymorphisms into a single supermarker. No prior haplotyping is necessary. Our experience on real and simulated data suggests that the heterozygous-homozygous test has good type-one error and power.
| S-EPMC2986695 | biostudies-literature
Project description:BackgroundThe combination of optimized contribution dynamic selection and various mating schemes was investigated over seven generations for a typical tree breeding scenario. The allocation of mates was optimized using a simulated annealing algorithm for various object functions including random mating (RM), positive assortative mating (PAM) and minimization of pair-wise coancestry between mates (MCM) all combined with minimization of variance in family size and coancestry. The present study considered two levels of heritability (0.05 and 0.25), two restrictions on relatedness (group coancestry; 1 and 2%) and two maximum permissible numbers of crosses in each generation (100 and 400). The infinitesimal genetic model was used to simulate the genetic architecture of the trait that was the subject of selection. A framework of the long term genetic contribution of ancestors was used to examine the impacts of the mating schemes on population parameters.ResultsMCM schemes produced on average, an increased rate of genetic gain in the breeding population, although the difference between schemes was small but significant after seven generations (up to 7.1% more than obtained with RM). In addition, MCM reduced the level of inbreeding by as much as 37% compared with RM, although the rate of inbreeding was similar after three generations of selection. PAM schemes yielded levels of genetic gain similar to those produced by RM, but the increase in the level of inbreeding was substantial (up to 43%).ConclusionThe main reason why MCM schemes yielded higher genetic gains was the improvement in managing the long term genetic contribution of founders in the population; this was achieved by connecting unrelated families. In addition, the accumulation of inbreeding was reduced by MCM schemes since the variance in long term genetic contributions of founders was smaller than in the other schemes. Consequently, by combining an MCM scheme with an algorithm that optimizes contributions of the selected individuals, a higher long term response is obtained while reducing the risk within the breeding program.
| S-EPMC2776599 | biostudies-literature
Project description:BackgroundNAC (NAM, ATAF1–2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses.ResultsIn the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems of Populus simonii×P. nigra among 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150?mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves of Populus simonii × P.nigra among 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86, NAC105, NAC139 and NAC163) and two down-regulated genes (NAC15 and NAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues of Populus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified in Populus simonii×P.nigra.ConclusionsThe study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.
| S-EPMC7336439 | biostudies-literature
Project description:A dwarf mutant (dwf1) was obtained among 15 transgenic lines, when TaLEA (Tamarix androssowii late embryogenesis abundant gene) was introduced into Populus simonii × Populus nigra by Agrobacterium tumefaciens-mediated transformation. Under the same growth conditions, dwf1 height was significantly reduced compared with the wild type and the other transgenic lines. Because only one transgenic line (dwf1) displayed the dwarf phenotype, we considered that T-DNA insertion sites may play a role in the mutant formation. The mechanisms underlying this effect were investigated using TAIL-PCR (thermal asymmetric interlaced PCR) and microarrays methods. According to the TAIL-PCR results, two flanking sequences located on chromosome IV and VIII respectively, were cloned. The results indicated the integration of two independent T-DNA copies. We searched for the potential genes near to the T-DNA insertions. The nearest gene was a putative poplar AP2 transcription factor (GI: 224073210). Expression analysis showed that AP2 was up-regulated in dwf1 compared with the wild type and the other transgenic lines. According to the microarrays results, a total of 537 genes involved in hydrolase, kinase and transcription factor activities, as well as protein and nucleotide binding, showed significant alterations in gene expression. These genes were expressed in more than 60 metabolic pathways, including starch, sucrose, galactose and glycerolipid metabolism and phenylpropanoids and flavonoid biosyntheses. Our transcriptome and T-DNA insertion sites analyses might provide some useful insights into the dwarf mutant formation.
| S-EPMC3317382 | biostudies-literature
Project description:As an important functional organ of plants, leaves alter their shapes in response to a changing environment. The variation of leaf shape has long been an important evolutionary and developmental force in plants. Despite an increasing amount of investigations into the genetic controls of leaf morphology, few have systematically studied the genetic architecture controlling shape differences among distinct altitudes. Altitude denotes a comprehensive complex of environmental factors affecting plant growth in many aspects, e.g., UV-light radiation, temperature, and humidity. To reveal how plants alter ecological adaptation to altitude through genes, we used Populus szechuanica var. tibetica growing on the Qinghai-Tibetan plateau. F ST between the low- and high- altitude population was 0.00748, Q ST for leaf width, length and area were 0.00924, 0.1108, 0.00964 respectively. With the Elliptic Fourier-based morphometric model, association study of leaf shape was allowed, the dissection of the pleiotropic expression of genes mediating altitude-derived leaf shape variation was performed. For high and low altitudes, 130 and 131 significant single-nucleotide polymorphisms (SNPs) were identified. QTLs that affected leaf axis length and leaf width were expressed in both-altitude population, while QTLs regulating "leaf tip" and "leaf base" were expressed in low-altitude population. Pkinase and PRR2 were common significant genes in both types of populations. Auxin-related and differentiation-related genes included PIN1, CDK-like, and CAK1AT at high altitude, whereas they included NAP5, PIN-LIKES, and SCL1 at low altitude. The presence of Stress-antifung gene, CIPK3 and CRPK1 in high-altitude population suggested an interaction between genes and harsh environment in mediating leaf shape, while the senescence repression-related genes (EIN2 and JMJ18) and JMT in jasmonic acid pathway in low-altitude population suggested their crucial roles in ecological adaptability. These data provide new information that strengthens the understanding of genetic control with respect to leaf shape and constitute an entirely novel perspective regarding leaf adaptation and development in plants.
| S-EPMC7267013 | biostudies-literature
Project description:Aspen (Populus tremuloides Michx) is a widespread commercial forest tree of high economic importance in western Canada and has been subject to tree improvement efforts over the past two decades. Such improvement programs rely on accurate estimates of the genetic gain in growth traits and correlated response in adaptive traits that are important for forest health. Here, we estimated genetic parameters in 10 progeny trials containing >30,000 trees with pedigree structures based on a partial factorial mating design that includes 60 half-sibs, 100 full-sib families and 1,400 clonally replicated genotypes. Estimated narrow-sense and broad-sense heritabilities were low for height and diameter (~0.2), but moderate for the dates of budbreak and leaf senescence (~0.4). Furthermore, estimated genetic correlations between growth and phenology were moderate to strong with tall trees being associated with early budbreak (r = -0.3) and late leaf senescence (r = -0.7). Survival was not compromised, but was positively associated with early budbreak or late leaf senescence, indicating that utilizing the growing season was more important for survival and growth than avoiding early fall or late spring frosts. These result suggests that populations are adapted to colder climate conditions and lag behind environmental conditions to which they are optimally adapted due to substantial climate warming observed over the last several decades for the study area.
| S-EPMC7053761 | biostudies-literature
Project description:Background and aimsMorphological and biomechanical alterations occurring in woody roots of many plant species in response to mechanical stresses are well documented; however, little is known about the molecular mechanisms regulating these important alterations. The first forest tree genome to be decoded is that of Populus, thereby providing a tool with which to investigate the mechanisms controlling adaptation of woody roots to changing environments. The aim of this study was to use a proteomic approach to investigate the response of Populus nigra woody taproot to mechanical stress.MethodsTo simulate mechanical perturbations, the taproots of 30 one-year-old seedlings were bent to an angle of 90 ° using a steel net. A spatial and temporal two-dimensional proteome map of the taproot axis was obtained. We compared the events occurring in the above-bending, central bending and below-bending sectors of the taproot.Key resultsThe first poplar woody taproot proteome map is reported here; a total of 207 proteins were identified. Spatial and temporal proteomic analysis revealed that factors involved in plant defence, metabolism, reaction wood formation and lateral root development were differentially expressed in the various sectors of bent vs. control roots, seemingly in relation to the distribution of mechanical forces along the stressed woody taproots. A complex interplay among different signal transduction pathways involving reactive oxygen species appears to modulate these responses.ConclusionsPoplar woody root uses different temporal and spatial mechanisms to respond to mechanical stress. Long-term bending treatment seem to reinforce the defence machinery, thereby enabling the taproot to better overcome winter and to be ready to resume growth earlier than controls.
| S-EPMC3394638 | biostudies-literature
Project description:BackgroundFactor V (FV) deficiency is a rare disease, with a low incidence rate in Asia. Therefore, the F5 mutation in the Taiwanese population is poorly understood.MethodsA Chinese family with FV deficiency was included, and the patient and his family members underwent mutation analysis. Then, patients from Keelung City (Taiwan) were screened for F5 polymorphism; the Chang Gung Human Database was used to determine single-nucleotide variants in the non-FV-deficient patient population.ResultsEight mutation sites on the F5 gene locus, including exon 16 homozygote Met1736Val and seven heterozygous mutations, including Asp68His, were found. Moreover, Met1736Val was found to be the dominant mutation in people living in the Taiwan community, and this result was compared with the records of the Chang Gung Human Database. The above-mentioned polymorphisms may result in a variable incidence of FV deficiency in Keelung City, thereby facilitating carrier diagnosis and prenatal diagnosis in most FV-deficient families.ConclusionThe homozygote Met1736Val and the co-inheritance of the Asp68His F5 gene are unique and worthy of screening in FV-deficient patients.
| S-EPMC9219604 | biostudies-literature
Project description:Hydrogen peroxide (H?O?) is one of the most abundant reactive oxygen species (ROS), which plays dual roles as a toxic byproduct of cell metabolism and a regulatory signal molecule in plant development and stress response. Populus simonii × Populus nigra is an important cultivated forest species with resistance to cold, drought, insect and disease, and also a key model plant for forest genetic engineering. In this study, H?O? response in P. simonii × P. nigra leaves was investigated using physiological and proteomics approaches. The seedlings of 50-day-old P. simonii × P. nigra under H?O? stress exhibited stressful phenotypes, such as increase of in vivo H?O? content, decrease of photosynthetic rate, elevated osmolytes, antioxidant accumulation, as well as increased activities of several ROS scavenging enzymes. Besides, 81 H?O?-responsive proteins were identified in the poplar leaves. The diverse abundant patterns of these proteins highlight the H?O?-responsive pathways in leaves, including 14-3-3 protein and nucleoside diphosphate kinase (NDPK)-mediated signaling, modulation of thylakoid membrane structure, enhancement of various ROS scavenging pathways, decrease of photosynthesis, dynamics of proteins conformation, and changes in carbohydrate and other metabolisms. This study provides valuable information for understanding H?O?-responsive mechanisms in leaves of P. simonii × P. nigra.
| S-EPMC5666767 | biostudies-literature
Project description:Animals are expected to select a breeding habitat using cues that should reflect, directly or not, the fitness outcome of the different habitat options. However, human-induced environmental changes can alter the relationships between habitat characteristics and their fitness consequences, leading to maladaptive habitat choices. The most severe case of such nonideal habitat selection is the ecological trap, which occurs when individuals prefer to settle in poor-quality habitats while better ones are available. Here, we studied the adaptiveness of nest box selection in a tree swallow (Tachycineta bicolor) population breeding over a 10-year period in a network of 400 nest boxes distributed along a gradient of agricultural intensification in southern Québec, Canada. We first examined the effects of multiple environmental and social habitat characteristics on nest box preference to identify potential settlement cues. We then assessed the links between those cues and habitat quality as defined by the reproductive performance of individuals that settled early or late in nest boxes. We found that tree swallows preferred nesting in open habitats with high cover of perennial forage crops, high spring insect biomass, and high density of house sparrows (Passer domesticus), their main competitors for nest sites. They also preferred nesting where the density of breeders and their mean number of fledglings during the previous year were high. However, we detected mismatches between preference and habitat quality for several environmental variables. The density of competitors and conspecific social information showed severe mismatches, as their relationships to preference and breeding success went in opposite direction under certain circumstances. Spring food availability and agricultural landscape context, while related to preferences, were not related to breeding success. Overall, our study emphasizes the complexity of habitat selection behavior and provides evidence that multiple mechanisms may potentially lead to an ecological trap in farmlands.
| S-EPMC8601888 | biostudies-literature